Nat Genet , IF:38.33 , 2024 Feb doi: 10.1038/s41588-024-01657-2
Near-gapless and haplotype-resolved apple genomes provide insights into the genetic basis of rootstock-induced dwarfing.
Institute for Horticultural Plants, China Agricultural University, Beijing, China.; Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA. chong_chu@hms.harvard.edu.; Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, China.; The New Zealand Institute for Plant and Food Research Limited (Plant & Food Research), Motueka, New Zealand.; The New Zealand Institute for Plant and Food Research Limited (Plant & Food Research), Palmerston North, New Zealand.; Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Chinese Academy of Agricultural Sciences, Shenzhen, China.; Department of Plant Science and Landscape Architecture, University of Connecticut, Storrs, CT, USA.; College of Horticulture, Shenyang Agricultural University, Shenyang, China.; State Key Laboratory of North China Crop Improvement and Regulation; Key Laboratory of Crop Growth Regulation of Hebei Province, College of Agronomy, Hebei Agricultural University, Baoding, China.; College of Information Science and Technology, Beijing University of Chemical Technology, Beijing, China.; The New Zealand Institute for Plant and Food Research Limited (Plant & Food Research), Auckland, New Zealand. cecilia.deng@plantandfood.co.nz.; Institute for Horticultural Plants, China Agricultural University, Beijing, China. wangyi@cau.edu.cn.; Institute for Horticultural Plants, China Agricultural University, Beijing, China. rschan@cau.edu.cn.
Dwarfing rootstocks have transformed the production of cultivated apples; however, the genetic basis of rootstock-induced dwarfing remains largely unclear. We have assembled chromosome-level, near-gapless and haplotype-resolved genomes for the popular dwarfing rootstock 'M9', the semi-vigorous rootstock 'MM106' and 'Fuji', one of the most commonly grown apple cultivars. The apple orthologue of auxin response factor 3 (MdARF3) is in the Dw1 region of 'M9', the major locus for rootstock-induced dwarfing. Comparing 'M9' and 'MM106' genomes revealed a 9,723-bp allele-specific long terminal repeat retrotransposon/gypsy insertion, DwTE, located upstream of MdARF3. DwTE is cosegregated with the dwarfing trait in two segregating populations, suggesting its prospective utility in future dwarfing rootstock breeding. In addition, our pipeline discovered mobile mRNAs that may contribute to the development of dwarfed scion architecture. Our research provides valuable genomic resources and applicable methodology, which have the potential to accelerate breeding dwarfing rootstocks for apple and other perennial woody fruit trees.
PMID: 38347217
Annu Rev Plant Biol , IF:26.379 , 2024 Feb doi: 10.1146/annurev-arplant-062923-030348
Leaf Vein Patterning.
Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada; email: enrico.scarpella@ualberta.ca.
Leaves form veins whose patterns vary from a single vein running the length of the leaf to networks of staggering complexity where huge numbers of veins connect to other veins at both ends. For the longest time, vein formation was thought to be controlled only by the polar, cell-to-cell transport of the plant hormone auxin; recent evidence suggests that is not so. Instead, it turns out that vein patterning features are best accounted for by a combination of polar auxin transport, facilitated auxin diffusion through plasmodesmata intercellular channels, and auxin signal transduction-though the latter's precise contribution remains unclear. Equally unclear remain the sites of auxin production during leaf development, on which that vein patterning mechanism ought to depend. Finally, whether that vein patterning mechanism can account for the variety of vein arrangements found in nature remains unknown. Addressing those questions will be the exciting challenge of future research. Expected final online publication date for the Annual Review of Plant Biology, Volume 75 is May 2024. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
PMID: 38382907
Nat Plants , IF:15.793 , 2024 Feb , V10 (2) : P300-314 doi: 10.1038/s41477-023-01615-6
D6PK plasma membrane polarity requires a repeated CXX(X)P motif and PDK1-dependent phosphorylation.
Plant Systems Biology, School of Life Sciences, Technical University of Munich, Freising, Germany.; Guangdong Provincial Key Laboratory of Plant Adaptation and Molecular Design, School of Life Sciences, Guangzhou University, Guangzhou, China.; Proteomics and Bioanalytics, School of Life Sciences, Technical University of Munich, Freising, Germany.; Bavarian Center for Biomolecular Mass Spectrometry at Klinikum rechts der Isar, Center for Translational Cancer Research, Munich, Germany.; Helmholtz Zentrum Munchen, German Research Center for Environmental Health, Analytical BioGeoChemistry, Neuherberg, Germany.; Plant Systems Biology, School of Life Sciences, Technical University of Munich, Freising, Germany. claus.schwechheimer@tum.de.
D6 PROTEIN KINASE (D6PK) is a polarly localized plasma-membrane-associated kinase from Arabidopsis thaliana that activates polarly distributed PIN-FORMED auxin transporters. D6PK moves rapidly to and from the plasma membrane, independent of its PIN-FORMED targets. The middle D6PK domain, an insertion between kinase subdomains VII and VIII, is required and sufficient for association and polarity of the D6PK plasma membrane. How D6PK polarity is established and maintained remains to be shown. Here we show that cysteines from repeated middle domain CXX(X)P motifs are S-acylated and required for D6PK membrane association. While D6PK S-acylation is not detectably regulated during intracellular transport, phosphorylation of adjacent serine residues, in part in dependence on the upstream 3-PHOSPHOINOSITIDE-DEPENDENT PROTEIN KINASE, promotes D6PK transport, controls D6PK residence time at the plasma membrane and prevents its lateral diffusion. We thus identify new mechanisms for the regulation of D6PK plasma membrane interaction and polarity.
PMID: 38278951
Nat Commun , IF:14.919 , 2024 Feb , V15 (1) : P1194 doi: 10.1038/s41467-024-45248-5
Phosphorylation of plasma membrane H(+)-ATPase Thr881 participates in light-induced stomatal opening.
Graduate School of Science, Nagoya University, Chikusa, Nagoya, Japan.; Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Chikusa, Nagoya, Japan.; Graduate School of Science, Nagoya University, Chikusa, Nagoya, Japan. kinoshita@bio.nagoya-u.ac.jp.; Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Chikusa, Nagoya, Japan. kinoshita@bio.nagoya-u.ac.jp.
Plasma membrane (PM) H(+)-ATPase is crucial for light-induced stomatal opening and phosphorylation of a penultimate residue, Thr948 (pen-Thr, numbering according to Arabidopsis AHA1) is required for enzyme activation. In this study, a comprehensive phosphoproteomic analysis using guard cell protoplasts from Vicia faba shows that both red and blue light increase the phosphorylation of Thr881, of PM H(+)-ATPase. Light-induced stomatal opening and the blue light-induced increase in stomatal conductance are reduced in transgenic Arabidopsis plants expressing mutant AHA1-T881A in aha1-9, whereas the blue light-induced phosphorylation of pen-Thr is unaffected. Auxin and photosynthetically active radiation induce the phosphorylation of both Thr881 and pen-Thr in etiolated seedlings and leaves, respectively. The dephosphorylation of phosphorylated Thr881 and pen-Thr are mediated by type 2 C protein phosphatase clade D isoforms. Taken together, Thr881 phosphorylation, in addition of the pen-Thr phosphorylation, are important for PM H(+)-ATPase function during physiological responses, such as light-induced stomatal opening in Arabidopsis thaliana.
PMID: 38378616
Nat Commun , IF:14.919 , 2024 Feb , V15 (1) : P1286 doi: 10.1038/s41467-024-45577-5
Chromatin attachment to the nuclear matrix represses hypocotyl elongation in Arabidopsis thaliana.
Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben, 06466, Germany.; Leibniz Institute of Vegetable and Ornamental Crops, Grossbeeren, 14979, Germany.; Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, 9052, Belgium.; VIB Center for Plant Systems Biology, Ghent, 9052, Belgium.; Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben, 06466, Germany. jiangh@ipk-gatersleben.de.
The nuclear matrix is a nuclear compartment that has diverse functions in chromatin regulation and transcription. However, how this structure influences epigenetic modifications and gene expression in plants is largely unknown. In this study, we show that a nuclear matrix binding protein, AHL22, together with the two transcriptional repressors FRS7 and FRS12, regulates hypocotyl elongation by suppressing the expression of a group of genes known as SMALL AUXIN UP RNAs (SAURs) in Arabidopsis thaliana. The transcriptional repression of SAURs depends on their attachment to the nuclear matrix. The AHL22 complex not only brings these SAURs, which contain matrix attachment regions (MARs), to the nuclear matrix, but it also recruits the histone deacetylase HDA15 to the SAUR loci. This leads to the removal of H3 acetylation at the SAUR loci and the suppression of hypocotyl elongation. Taken together, our results indicate that MAR-binding proteins act as a hub for chromatin and epigenetic regulators. Moreover, we present a mechanism by which nuclear matrix attachment to chromatin regulates histone modifications, transcription, and hypocotyl elongation.
PMID: 38346986
Mol Plant , IF:13.164 , 2024 Feb doi: 10.1016/j.molp.2024.02.012
Making connections with cell surface auxin signaling.
PMID: 38368508
Plant Cell , IF:11.277 , 2024 Feb doi: 10.1093/plcell/koae054
An auxin research odyssey: 1989-2023.
Department of Horticultural Science and the Microbial and Plant Genomics Institute, University of Minnesota, Saint Paul, MN 55108, USA.; Department of Biology, Duke University, Durham, NC 27008, USA.
The phytohormone auxin is at times called the master regulator of plant processes and has been shown to be a central player in embryo development, the establishment of the polar axis, early aspects of seedling growth, as well as growth and organ formation during later stages of plant development. The Plant Cell has been key, since the inception of the journal, to developing an understanding of auxin biology. Auxin regulated plant growth control is accomplished by both changes in the levels of active hormones and the sensitivity of plant tissues to these concentration changes. In this historical review, we chart auxin research as it has progressed in key areas and highlighting the role The Plant Cell played in these scientific developments. We focus on understanding auxin-responsive genes, transcription factors, reporter constructs, perception and signal transduction processes. Auxin metabolism is discussed from the development of tryptophan auxotrophic mutants, the molecular biology of conjugate formation and hydrolysis, indole-3-butyric acid metabolism and transport, and key steps in indole-3-acetic acid biosynthesis, catabolism and transport. This progress leads to an expectation of a more comprehensive understanding of the systems biology of auxin and the spatial and temporal regulation of cellular growth and development.
PMID: 38382088
Plant Cell , IF:11.277 , 2024 Feb doi: 10.1093/plcell/koae058
Retain in the membrane: Tinkering with the BRX-PAX-PIP5K auxin efflux machinery affects vascular tissue differentiation.
Assistant Features Editor, The Plant Cell, American Society of Plant Biologists, USA.; Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, Umea Plant Science Centre, Umea, Sweden.
PMID: 38377470
Plant Cell , IF:11.277 , 2024 Feb doi: 10.1093/plcell/koae043
Maternal nitric oxide homeostasis impacts female gametophyte development under optimal and stress conditions.
State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, College of Agronomy, Northwest A&F University, Yangling, Shaanxi 712100, China.; Hainan Yazhou Bay Seed Laboratory, Yazhou, Sanya 572025, China.; Department of Biochemistry & Molecular Biology, University of Massachusetts, Amherst, MA 01003, USA.
In adverse environments, the number of fertilizable female gametophytes (FGs) in plants is reduced, leading to increased survival of remaining offspring. How the maternal plant perceives internal growth cues and external stress conditions to alter FG development remains largely unknown. We report that homeostasis of the stress signaling molecule nitric oxide (NO) plays a key role in controlling FG development under both optimal and stress conditions. NO homeostasis is precisely regulated by S-nitrosoglutathione reductase (GSNOR). Prior to fertilization, GSNOR protein is exclusively accumulated in sporophytic tissues and indirectly controls FG development in Arabidopsis (Arabidopsis thaliana). In GSNOR null mutants, NO species accumulated in the degenerating sporophytic nucellus and auxin efflux into the developing FG was restricted, which inhibited FG development, resulting in reduced fertility. Importantly, restoring GSNOR expression in maternal, but not gametophytic tissues, or increasing auxin efflux substrate significantly increased the proportion of normal FGs and fertility. Furthermore, GSNOR overexpression or added auxin efflux substrate increased fertility under drought and salt stress. These data indicate that NO homeostasis is critical to normal auxin transport and maternal control of FG development, which in turn determine seed yield. Understanding this aspect of fertility control could contribute to mediating yield loss under adverse conditions.
PMID: 38376990
Plant Cell , IF:11.277 , 2024 Feb doi: 10.1093/plcell/koae047
MAC3A and MAC3B mediate degradation of the transcription factor ERF13 and thus promote lateral root emergence.
The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, Shandong, 266237, China.; College of Horticulture, Qingdao Agricultural University, Qingdao, Shandong 266109, China.; School of Life Sciences, Liaocheng University, Liaocheng, Shandong, 252000, China.
Lateral roots (LRs) increase root surface area and allow plants greater access to soil water and nutrients. LR formation is tightly regulated by the phytohormone auxin. Whereas the transcription factor ETHYLENE-RESPONSIVE ELEMENT BINDING FACTOR13 (ERF13) prevents LR emergence in Arabidopsis (Arabidopsis thaliana), auxin activates MITOGEN-ACTIVATED PROTEIN KINASE14 (MPK14), which leads to ERF13 degradation and ultimately promotes LR emergence. In this study, we discovered interactions between ERF13 and the E3 ubiquitin ligases MOS4-ASSOCIATED COMPLEX 3A (MAC3A) and MAC3B. As MAC3A and MAC3B gradually accumulate in the LR primordium, ERF13 levels gradually decrease. We demonstrate that MAC3A and MAC3B ubiquitinate ERF13, leading to its degradation and accelerating the transition of LR primordia from stage IV to stage V. Auxin enhances the MAC3A and MAC3B interaction with ERF13 by facilitating MPK14-mediated ERF13 phosphorylation. In summary, this study reveals the molecular mechanism by which auxin eliminates the inhibitory factor ERF13 through the MPK14-MAC3A and MAC3B signaling module, thus promoting LR emergence.
PMID: 38366565
Plant Cell , IF:11.277 , 2024 Feb doi: 10.1093/plcell/koae041
The Myb73-GDPD2-GA2ox1 transcriptional regulatory module confers phosphate deficiency tolerance in soybean.
Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou 450002, China.; State Key Laboratory of Black Soils Conservation and Utilization, Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin 150081, China.; National Center for Soybean Improvement, National Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China.; State Key Laboratory of Agricultural Microbiology, Center of Integrative Biology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China.; Zhengzhou National Subcenter for Soybean Improvement, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China.; School of Life Sciences, Guangzhou University, Guangzhou 510006, China.
Phosphorus is indispensable in agricultural production. An increasing food supply requires more efficient use of phosphate due to limited phosphate resources. However, how crops regulate phosphate efficiency remains largely unknown. Here, we identified a major quantitative trait locus, qPE19, that controls seven low-phosphate (LP)-related traits in soybean (Glycine max) through linkage mapping and genome-wide association studies. We identified the gene responsible for qPE19 as GLYCEROPHOSPHORYL DIESTER PHOSPHODIESTERASE2 (GmGDPD2), and haplotype 5 represents the optimal allele favoring LP tolerance. Overexpression of GmGDPD2 significantly affects hormone signaling and improves root architecture, phosphate efficiency and yield-related traits; conversely, CRISPR/Cas9-edited plants show decreases in these traits. GmMyb73 negatively regulates GmGDPD2 by directly binding to its promoter, thus GmMyb73 negatively regulates LP tolerance. GmGDPD2 physically interacts with GA 2-oxidase 1 (GmGA2ox1) in the plasma membrane, and overexpressing GmGA2ox1 enhances LP-associated traits, similar to GmGDPD2 overexpression. Analysis of double mutants for GmGDPD2 and GmGA2ox1 demonstrated that GmGDPD2 regulates LP tolerance likely by influencing auxin and gibberellin dose-associated cell division in root. These results reveal a regulatory module that plays a major role in regulating LP tolerance in soybean and is expected to be utilized to develop phosphate-efficient varieties to enhance soybean production, particularly in phosphate-deficient soils.
PMID: 38345432
Plant Cell , IF:11.277 , 2024 Feb , V36 (3) : P493-494 doi: 10.1093/plcell/koad309
An apple a day: MdBPC2 transcription factor keeps the auxin away and causes dwarfing in Malus domestica.
Assistant Features Editor, The Plant Cell, American Society of Plant Biologists.; Natural Resources and the Environment Department, University of New Hampshire, Durham, NH, 03824, USA.
PMID: 38084887
Plant Cell , IF:11.277 , 2024 Feb , V36 (3) : P585-604 doi: 10.1093/plcell/koad297
The transcription factor MdBPC2 alters apple growth and promotes dwarfing by regulating auxin biosynthesis.
State Key Laboratory for Crop Stress Resistance and High-Efficiency Production/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, 712100 Shaanxi, China.
Auxin plays important roles throughout plant growth and development. However, the mechanisms of auxin regulation of plant structure are poorly understood. In this study, we identified a transcription factor (TF) of the BARLEY B RECOMBINANT/BASIC PENTACYSTEINE (BBR/BPC) family in apple (Malus x domestica), MdBPC2. It was highly expressed in dwarfing rootstocks, and it negatively regulated auxin biosynthesis. Overexpression of MdBPC2 in apple decreased plant height, altered leaf morphology, and inhibited root system development. These phenotypes were due to reduced auxin levels and were restored reversed after exogenous indole acetic acid (IAA) treatment. Silencing of MdBPC2 alone had no obvious phenotypic effect, while silencing both Class I and Class II BPCs in apple significantly increased auxin content in plants. Biochemical analysis demonstrated that MdBPC2 directly bound to the GAGA-rich element in the promoters of the auxin synthesis genes MdYUC2a and MdYUC6b, inhibiting their transcription and reducing auxin accumulation in MdBPC2 overexpression lines. Further studies established that MdBPC2 interacted with the polycomb group (PcG) protein LIKE HETEROCHROMATIN PROTEIN 1 (LHP1) to inhibit MdYUC2a and MdYUC6b expression via methylation of histone 3 lysine 27 (H3K27me3). Silencing MdLHP1 reversed the negative effect of MdBPC2 on auxin accumulation. Our results reveal a dwarfing mechanism in perennial woody plants involving control of auxin biosynthesis by a BPC transcription factor, suggesting its use for genetic improvement of apple rootstock.
PMID: 38019898
Curr Biol , IF:10.834 , 2024 Feb , V34 (4) : P825-840.e7 doi: 10.1016/j.cub.2024.01.018
Light-sensitive short hypocotyl genes confer symbiotic nodule identity in the legume Medicago truncatula.
Sainsbury Laboratory, University of Cambridge, 47 Bateman Street, Cambridge CB2 1LR, UK; Crop Science Centre, Department of Plant Sciences, University of Cambridge, 93 Lawrence Weaver Road, Cambridge CB3 0LE, UK.; University of Freiburg, Faculty of Biology, Schanzlestrasse, 79104 Freiburg, Germany.; Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK.; Jodrell Laboratory, Royal Botanic Gardens, Kew, Richmond TW9 3DS, UK.; Sainsbury Laboratory, University of Cambridge, 47 Bateman Street, Cambridge CB2 1LR, UK.; Noble Research Institute, LLC, 2510 Sam Noble Parkway, Ardmore, OK 73401, USA.; University of Freiburg, Faculty of Biology, Schanzlestrasse, 79104 Freiburg, Germany; CIBSS - Centre of Integrative Biological Signalling Studies, University of Freiburg, Schanzlestrasse, 79104 Freiburg, Germany.; Sainsbury Laboratory, University of Cambridge, 47 Bateman Street, Cambridge CB2 1LR, UK; Crop Science Centre, Department of Plant Sciences, University of Cambridge, 93 Lawrence Weaver Road, Cambridge CB3 0LE, UK. Electronic address: gedo2@cam.ac.uk.; Sainsbury Laboratory, University of Cambridge, 47 Bateman Street, Cambridge CB2 1LR, UK. Electronic address: katharina.schiessl@slcu.cam.ac.uk.
Legumes produce specialized root nodules that are distinct from lateral roots in morphology and function, with nodules intracellularly hosting nitrogen-fixing bacteria. We have previously shown that a lateral root program underpins nodule initiation, but there must be additional developmental regulators that confer nodule identity. Here, we show two members of the LIGHT-SENSITIVE SHORT HYPOCOTYL (LSH) transcription factor family, predominantly known to define shoot meristem complexity and organ boundaries, function as regulators of nodule organ identity. In parallel to the root initiation program, LSH1/LSH2 recruit a program into the root cortex that mediates the divergence into nodules, in particular with cell divisions in the mid-cortex. This includes regulation of auxin and cytokinin, promotion of NODULE ROOT1/2 and Nuclear Factor YA1, and suppression of the lateral root program. A principal outcome of LSH1/LSH2 function is the production of cells able to accommodate nitrogen-fixing bacteria, a key feature unique to nodules.
PMID: 38301650
Curr Biol , IF:10.834 , 2024 Feb , V34 (4) : P769-780.e5 doi: 10.1016/j.cub.2024.01.010
Leaf dissection and margin serration are independently regulated by two regulators converging on the CUC2-auxin module in strawberry.
Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742, USA.; Key Laboratory of Quantitative Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China.; Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742, USA. Electronic address: zliu@umd.edu.
The remarkable diversity of leaf forms allows plants to adapt to their living environment. In general, leaf diversity is shaped by leaf complexity (compound or simple) and leaf margin pattern (entire, serrated, or lobed). Prior studies in multiple species have uncovered a conserved module of CUC2-auxin that regulates both leaf complexity and margin serration. How this module is regulated in different species to contribute to the species-specific leaf form is unclear. Furthermore, the mechanistic connection between leaf complexity and leaf serration regulation is not well studied. Strawberry has trifoliate compound leaves with serrations at the margin. In the wild strawberry Fragaria vesca, a mutant named salad was isolated that showed deeper leaf serrations but normal leaf complexity. SALAD encodes a single-Myb domain protein and is expressed at the leaf margin. Genetic analysis showed that cuc2a is epistatic to salad, indicating that SALAD normally limits leaf serration depth by repressing CUC2a expression. When both Arabidopsis homologs of SALAD were knocked out, deeper serrations were observed in Arabidopsis rosette leaves, supporting a conserved function of SALAD in leaf serration regulation. We incorporated the analysis of a third strawberry mutant simple leaf 1 (sl1) with reduced leaf complexity but normal leaf serration. We showed that SL1 and SALAD independently regulate CUC2a at different stages of leaf development to, respectively, regulate leaf complexity and leaf serration. Our results provide a clear and simple mechanism of how leaf complexity and leaf serration are coordinately as well as independently regulated to achieve diverse leaf forms.
PMID: 38272030
Curr Biol , IF:10.834 , 2024 Feb , V34 (4) : P755-768.e4 doi: 10.1016/j.cub.2024.01.004
The mechanism underlying asymmetric bending of lateral petals in Delphinium (Ranunculaceae).
College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China.; State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; China National Botanical Garden, Beijing 100093, China; Department of Computational and Systems Biology, John Innes Centre, Norwich Research Park, Colney Lane, Norwich NR4 7UH, UK.; Institut de Systematique, Evolution, Biodiversite (ISYEB), Museum National d'Histoire naturelle, CNRS, Sorbonne Universite, EPHE, Universite des Antilles, Paris 75005, France.; Office National des Forets, 11 C rue Rene Char, Dijon 21000, France.; State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; China National Botanical Garden, Beijing 100093, China; University of Chinese Academy of Sciences, Beijing 100049, China.; College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China. Electronic address: ruizhang@nwafu.edu.cn.
During the process of flower opening, most petals move downward in the direction of the pedicel (i.e., epinastic movement). In most Delphinium flowers, however, their two lateral petals display a very peculiar movement, the mirrored helical rotation, which requires the twist of the petal stalk. However, in some lineages, their lateral petals also exhibit asymmetric bending that increases the degree of mirrored helical rotation, facilitating the formation of a 3D final shape. Notably, petal asymmetric bending is a novel trait that has not been noticed yet, so its morphological nature, developmental process, and molecular mechanisms remain largely unknown. Here, by using D. anthriscifolium as a model, we determined that petal asymmetric bending was caused by the localized expansion of cell width, accompanied by the specialized array of cell wall nano-structure, on the adaxial epidermis. Digital gene analyses, gene expression, and functional studies revealed that a class I homeodomain-leucine zipper family transcription factor gene, DeanLATE MERISTEM IDENTITY1 (DeanLMI1), contributes to petal asymmetric bending; knockdown of it led to the formation of explanate 2D petals. Specifically, DeanLMI1 promotes cell expansion in width and influences the arrangement of cell wall nano-structure on the localized adaxial epidermis. These results not only provide a comprehensive portrait of petal asymmetric bending for the first time but also shed some new insights into the mechanisms of flower opening and helical movement in plants.
PMID: 38272029
J Hazard Mater , IF:10.588 , 2024 Feb , V468 : P133701 doi: 10.1016/j.jhazmat.2024.133701
Rare earth elements perturb root architecture and ion homeostasis in Arabidopsis thaliana.
Universite de Lorraine, CNRS, LIEC, F-54000 Nancy, France. Electronic address: ngrosjean@lbl.gov.; Universite de Lorraine, CNRS, LIEC, F-54000 Nancy, France.; Universite de Franche-Comte, CNRS, Chrono-Environnement, F-25000 Montbeliard, France; Universite de Lorraine, F-54000 Nancy, France.; Universite de Lorraine, CNRS, LIEC, F-57000 Metz, France.; Universite de Lorraine, CNRS, LIEC, F-57000 Metz, France. Electronic address: marie.lejean@univ-lorraine.fr.
Rare earth elements (REEs) are crucial elements for current high-technology and renewable energy advances. In addition to their increasing usage and their low recyclability leading to their release into the environment, REEs are also used as crop fertilizers. However, little is known regarding the cellular and molecular effects of REEs in plants, which is crucial for better risk assessment, crop safety and phytoremediation. Here, we analysed the ionome and transcriptomic response of Arabidopsis thaliana exposed to a light (lanthanum, La) and a heavy (ytterbium, Yb) REE. At the transcriptome level, we observed the contribution of ROS and auxin redistribution to the modified root architecture following REE exposure. We found indications for the perturbation of Fe homeostasis by REEs in both roots and leaves of Arabidopsis suggesting competition between REEs and Fe. Furthermore, we propose putative ways of entry of REEs inside cells through transporters of microelements. Finally, similar to REE accumulating species, organic acid homeostasis (e.g. malate and citrate) appears critical as a tolerance mechanism in response to REEs. By combining ionomics and transcriptomics, we elucidated essential patterns of REE uptake and toxicity response of Arabidopsis and provide new hypotheses for a better evaluation of the impact of REEs on plant homeostasis.
PMID: 38364576
J Hazard Mater , IF:10.588 , 2024 Mar , V466 : P133639 doi: 10.1016/j.jhazmat.2024.133639
Distinct toxic effects, gene expression profiles, and phytohormone responses of Polygonatum cyrtonema exposed to two different antibiotics.
Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees, Ministry of Education, Central South University of Forestry and Technology, Changsha 410004, China; Key Laboratory of Forest Bio-resources and Integrated Pest Management for Higher Education in Hunan Province, Central South University of Forestry and Technology, Changsha 410004, China.; Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees, Ministry of Education, Central South University of Forestry and Technology, Changsha 410004, China.; Key Laboratory of Research and Utilization of Ethnomedicinal Plant Resources of Hunan Province, College of Biological and Food Engineering, Huaihua University, Huaihua 418099, China.; Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees, Ministry of Education, Central South University of Forestry and Technology, Changsha 410004, China; Key Laboratory of Forest Bio-resources and Integrated Pest Management for Higher Education in Hunan Province, Central South University of Forestry and Technology, Changsha 410004, China. Electronic address: nli@csuft.edu.cn.
The excessive usage of veterinary antibiotics has raised significant concerns regarding their environmental hazard and agricultural impact when entering surface water and soil. Animal waste serves as a primary source of organic fertilizer for intensive large-scale agricultural cultivation, including the widely utilized medicinal and edible plant, Polygonatum cyrtonem. In this study, we employed a novel plant stress tissue culture technology to investigate the toxic effects of tetracycline hydrochloride (TCH) and sulfadiazine (SDZ) on P. cyrtonema. TCH and SDZ exhibited varying degrees of influence on plant growth, photosynthesis, and the reactive oxygen species (ROS) scavenging system. Flavonoid levels increased following exposure to TCH and SDZ. The biosynthesis and signaling pathways of the growth hormones auxin and gibberellic acid were suppressed by both antibiotics, while the salicylic acid-mediated plant stress response was specifically induced in the case of SDZ. Overall, the study unveiled both common and unique responses at physiological, biochemical, and molecular levels in P. cyrtonema following exposure to two distinct types of antibiotics, providing a foundational framework for comprehensively elucidating the precise toxic effects of antibiotics and the versatile adaptive mechanisms in plants.
PMID: 38309169
J Hazard Mater , IF:10.588 , 2024 Mar , V465 : P133077 doi: 10.1016/j.jhazmat.2023.133077
Mechanistic insights into auxin-enhancing polycyclic aromatic hydrocarbon uptake by wheat roots: Evidence from in situ intracellular pH and root-surface H(+) flux.
College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, Jiangsu Province 210095, People's Republic of China.; College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, Jiangsu Province 210095, People's Republic of China. Electronic address: xhzhan@njau.edu.cn.
Polycyclic aromatic hydrocarbons (PAHs) are a group of extremely carcinogenic organic pollutants. Our previous findings have demonstrated that plant roots actively take up PAHs through co-transport with H(+) ions. Auxin serves as a pivotal regulator of plant growth and development. However, it remains unclear whether the hormone can enhance the uptake of PAHs by plant roots. Hence, the wheat root exposed to PAHs with/without auxins was set to investigate how the auxin promotes the PAHs uptake by roots. In our study, auxin could significantly enhance the uptake of PAHs after 4 h of exposure. After the addition of auxin, the root tissue cytoplasmic pH value was decreased and the H(+) influx was observed, indicating that the extracellular space was alkalinized in a short time. The increased H(+) influx rate enhanced the uptake of PAHs. In addition, the H(+)-ATPase activity was also increased, suggesting that auxin activated two distinct and antagonistic H(+) flux pathways, and the H(+) influx pathway was dominant. Our findings offer important information for exploring the mechanism underlying auxin regulation of PAHs uptake and the phytoremediation of PAH-contaminated soil and water.
PMID: 38035525
J Adv Res , IF:10.479 , 2024 Feb doi: 10.1016/j.jare.2024.01.026
Cellular and physiological functions of SGR family in gravitropic response in higher plants.
Division of Life Science and Division of Applied Life Science (BK21 Four), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, Gyeongnam, 52828, Republic of Korea.; Division of Life Science and Division of Applied Life Science (BK21 Four), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, Gyeongnam, 52828, Republic of Korea. Electronic address: ukadam@gnu.ac.kr.; Division of Life Science and Division of Applied Life Science (BK21 Four), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, Gyeongnam, 52828, Republic of Korea. Electronic address: jchong@gnu.ac.kr.
BACKGROUND: In plants, gravity directs bidirectional growth; it specifies upward growth of shoots and downward growth of roots. Due to gravity, roots establish robust anchorage and shoot, which enables to photosynthesize. It sets optimum posture and develops plant architecture to efficiently use resources like water, nutrients, CO(2), and gaseous exchange. Hence, gravitropism is crucial for crop productivity as well as for the growth of plants in challenging climate. Some SGR members are known to affect tiller and shoot angle, organ size, and inflorescence stem in plants. AIM OF REVIEW: Although the SHOOT GRAVITROPISM (SGR) family plays a key role in regulating the fate of shoot gravitropism, little is known about its function compared to other proteins involved in gravity response in plant cells and tissues. Moreover, less information on the SGR family's physiological activities and biochemical responses in shoot gravitropism is available. This review scrutinizes and highlights the recent developments in shoot gravitropism and provides an outlook for future crop development, multi-application scenarios, and translational research to improve agricultural productivity. KEY SCIENTIFIC CONCEPTS OF REVIEW: Plants have evolved multiple gene families specialized in gravitropic responses, of which the SGR family is highly significant. The SGR family regulates the plant's gravity response by regulating specific physiological and biochemical processes such as transcription, cell division, amyloplast sedimentation, endodermis development, and vacuole formation. Here, we analyze the latest discoveries in shoot gravitropism with particular attention to SGR proteins in plant cell biology, cellular physiology, and homeostasis. Plant cells detect gravity signals by sedimentation of amyloplast (starch granules) in the direction of gravity, and the signaling cascade begins. Gravity sensing, signaling, and auxin redistribution (organ curvature) are the three components of plant gravitropism. Eventually, we focus on the role of multiple SGR genes in shoot and present a complete update on the participation of SGR family members in gravity.
PMID: 38295878
New Phytol , IF:10.151 , 2024 Feb doi: 10.1111/nph.19623
Cell-layer specific roles for gibberellins in nodulation and root development.
Discipline of Biological Sciences, School of Natural Sciences, University of Tasmania, Private Bag 55, Hobart, TAS, 7001, Australia.
Gibberellins (GA) have a profound influence on the formation of lateral root organs. However, the precise role this hormone plays in the cell-specific events during lateral root formation, rhizobial infection and nodule organogenesis, including interactions with auxin and cytokinin (CK), is not clear. We performed epidermal- and endodermal-specific complementation of the severely GA-deficient na pea (Pisum sativum) mutant with Agrobacterium rhizogenes. Gibberellin mutants were used to examine the spatial expression pattern of CK (TCSn)- and auxin (DR5)-responsive promoters and hormone levels. We found that GA produced in the endodermis promote lateral root and nodule organogenesis and can induce a mobile signal(s) that suppresses rhizobial infection. By contrast, epidermal-derived GA suppress infection but have little influence on root or nodule development. GA suppress the CK-responsive TCSn promoter in the cortex and are required for normal auxin activation during nodule primordia formation. Our findings indicate that GA regulate the checkpoints between infection thread (IT) penetration of the cortex and invasion of nodule primordial cells and promote the subsequent progression of nodule development. It appears that GA limit the progression and branching of IT in the cortex by restricting CK response and activate auxin response to promote nodule primordia development.
PMID: 38396236
New Phytol , IF:10.151 , 2024 Feb doi: 10.1111/nph.19616
In situ seasonal patterns of root auxin concentrations and meristem length in an arctic sedge.
Department of Ecology and Environmental Science, Umea University, 901 87, Umea, Sweden.; Department of Arctic Biology, UNIS - The University Centre in Svalbard, 9171, Longyearbyen, Norway.; Department of Forest Genetics and Plant Physiology, Umea Plant Science Centre, Swedish University of Agricultural Sciences, 901 83, Umea, Sweden.; Laboratory of Growth Regulators, Faculty of Science, Palacky University & Institute of Experimental Botany of the Czech Academy of Sciences, CZ-78371, Olomouc, Czech Republic.
Seasonal dynamics of root growth play an important role in large-scale ecosystem processes; they are largely governed by growth regulatory compounds and influenced by environmental conditions. Yet, our knowledge about physiological drivers of root growth is mostly limited to laboratory-based studies on model plant species. We sampled root tips of Eriophorum vaginatum and analyzed their auxin concentrations and meristem lengths biweekly over a growing season in situ in a subarctic peatland, both in surface soil and at the permafrost thawfront. Auxin concentrations were almost five times higher in surface than in thawfront soils and increased over the season, especially at the thawfront. Surprisingly, meristem length showed an opposite pattern and was almost double in thawfront compared with surface soils. Meristem length increased from peak to late season in the surface soils but decreased at the thawfront. Our study of in situ seasonal dynamics in root physiological parameters illustrates the potential for physiological methods to be applied in ecological studies and emphasizes the importance of in situ measurements. The strong effect of root location and the unexpected opposite patterns of meristem length and auxin concentrations likely show that auxin actively governs root growth to ensure a high potential for nutrient uptake at the thawfront.
PMID: 38375943
New Phytol , IF:10.151 , 2024 Mar , V241 (6) : P2448-2463 doi: 10.1111/nph.19557
Auxin co-receptor IAA17/AXR3 controls cell elongation in Arabidopsis thaliana root solely by modulation of nuclear auxin pathway.
Department of Experimental Plant Biology, Charles University, Prague, 12844, Czech Republic.; Laboratory of Hormonal Regulations in Plants, Institute of Experimental Botany of the Czech Academy of Sciences, Prague, 16502, Czech Republic.; Sainsbury Laboratory, Cambridge University, Cambridge, CB2 1LR, UK.
The nuclear TIR1/AFB-Aux/IAA auxin pathway plays a crucial role in regulating plant growth and development. Specifically, the IAA17/AXR3 protein participates in Arabidopsis thaliana root development, response to auxin and gravitropism. However, the mechanism by which AXR3 regulates cell elongation is not fully understood. We combined genetical and cell biological tools with transcriptomics and determination of auxin levels and employed live cell imaging and image analysis to address how the auxin response pathways influence the dynamics of root growth. We revealed that manipulations of the TIR1/AFB-Aux/IAA pathway rapidly modulate root cell elongation. While inducible overexpression of the AXR3-1 transcriptional inhibitor accelerated growth, overexpression of the dominant activator form of ARF5/MONOPTEROS inhibited growth. In parallel, AXR3-1 expression caused loss of auxin sensitivity, leading to transcriptional reprogramming, phytohormone signaling imbalance and increased levels of auxin. Furthermore, we demonstrated that AXR3-1 specifically perturbs nuclear auxin signaling, while the rapid auxin response remains functional. Our results shed light on the interplay between the nuclear and cytoplasmic auxin pathways in roots, revealing their partial independence but also the dominant role of the nuclear auxin pathway during the gravitropic response of Arabidopsis thaliana roots.
PMID: 38308183
New Phytol , IF:10.151 , 2024 Mar , V241 (5) : P2176-2192 doi: 10.1111/nph.19503
A novel miR160a-GmARF16-GmMYC2 module determines soybean salt tolerance and adaptation.
College of Agronomy, Shandong Agricultural University, Tai'an, Shandong, 271018, China.; Crop Research Institute, Shandong Academy of Agricultural Sciences, Ji'nan, Shandong, 250131, China.; Guangdong Provincial Key Laboratory of Plant Adaptation and Molecular Design, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou, 510006, China.
Salt stress is a major challenge that has a negative impact on soybean growth and productivity. Therefore, it is important to understand the regulatory mechanism of salt response to ensure soybean yield under such conditions. In this study, we identified and characterized a miR160a-GmARF16-GmMYC2 module and its regulation during the salt-stress response in soybean. miR160a promotes salt tolerance by cleaving GmARF16 transcripts, members of the Auxin Response Factor (ARF) family, which negatively regulates salt tolerance. In turn, GmARF16 activates GmMYC2, encoding a bHLH transcription factor that reduces salinity tolerance by down-regulating proline biosynthesis. Genomic analysis among wild and cultivated soybean accessions identified four distinct GmARF16 haplotypes. Among them, the GmARF16(H3) haplotype is preferentially enriched in localities with relatively saline soils, suggesting GmARF16(H3) was artificially selected to improve salt tolerance. Our findings therefore provide insights into the molecular mechanisms underlying salt response in soybean and provide valuable genetic targets for the molecular breeding of salt tolerance.
PMID: 38135657
New Phytol , IF:10.151 , 2024 Feb , V241 (3) : P1177-1192 doi: 10.1111/nph.19391
Auxin homeostasis is maintained by sly-miR167-SlARF8A/B-SlGH3.4 feedback module in the development of locular and placental tissues of tomato fruits.
College of Horticulture, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.; College of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou, 225009, China.; Key Laboratory of Horticultural Plant Biology, Ministry of Education, Huazhong Agricultural University, Wuhan, 430070, China.; Key Laboratory of Plant Hormones and Development Regulation of Chongqing, School of Life Sciences, Chongqing University, Chongqing, 401331, China.
The locular gel, produced by the placenta, is important for fruit flavor and seed development in tomato. However, the mechanism underlying locule and placenta development is not fully understood yet. Here, we show that two SlARF transcription factors, SlARF8B and SlARF8A (SlARF8A/B), promote the development of locular and placenta tissues. The expression of both SlARF8A and SlARF8B is repressed by sly-microRNA167 (sly-miR167), allowing for the activation of auxin downstream genes. In slarf8a, slarf8b, and slarf8a/b mutants, the auxin (IAA) levels are decreased, whereas the levels of inactive IAA conjugates including IAA-Ala, IAA-Asp, and IAA-Glu are increased. We further find that SlARF8B directly inhibits the expression of SlGH3.4, an acyl acid amino synthetase that conjugates the amino acids to IAA. Disruption of such auxin balance by the increased expression of SlGH3.4 or SlGH3.2 results in defective locular and placental tissues. Taken together, our findings reveal an important regulatory module constituted by sly-miR167-SlARF8A/B-SlGH3.4 during the development of locular and placenta tissues of tomato fruits.
PMID: 37985404
New Phytol , IF:10.151 , 2024 Feb , V241 (3) : P1161-1176 doi: 10.1111/nph.19398
Auxin response factors fine-tune lignin biosynthesis in response to mechanical bending in bamboo.
Basic Forestry and Proteomics Center (BFPC), College of Forestry, Haixia Institute for Science and Technology, Fujian Agriculture and Forestry University, 350002, Fujian, China.
Lignin contributes to plant mechanical properties during bending loads. Meanwhile, phytohormone auxin controls various plant biological processes. However, the mechanism of auxin's role in bending-induced lignin biosynthesis was unclear, especially in bamboo, celebrated for its excellent deformation stability. Here, we reported that auxin response factors (ARF) 3 and ARF6 from Moso bamboo (Phyllostachys edulis (Carriere) J. Houz) directly regulate lignin biosynthesis pathway genes, and affect lignin biosynthesis in bamboo. Auxin and lignin exhibited asymmetric distribution patterns, and auxin promoted lignin biosynthesis in response to bending loads in bamboo. Employing transcriptomic and weighted gene co-expression network analysis approach, we discovered that expression patterns of ARF3 and ARF6 strongly correlated with lignin biosynthesis genes. ARF3 and ARF6 directly bind to the promoter regions of 4-coumarate: coenzyme A ligase (4CL3, 4CL7, and 4CL9) or caffeoyl-CoA O-methyltransferase (CCoAOMT2) genes, pivotal to lignin biosynthesis, and activate their expressions. Notably, the efficacy of this binding hinges on auxin levels. Alternation of the expressions of ARF3 and ARF6 substantially altered lignin accumulation in transgenic bamboo. Collectively, our study shed light on bamboo lignification genetics. Auxin signaling could directly modulate lignin biosynthesis genes to impact plant lignin content.
PMID: 37964659
Plant Biotechnol J , IF:9.803 , 2024 Feb doi: 10.1111/pbi.14292
Homoeologous exchanges contribute to branch angle variations in rapeseed: Insights from transcriptome, QTL-seq and gene functional analysis.
Key Laboratory of Cotton and Rapeseed, Ministry of Agriculture and Rural Affairs/Key Laboratory of Jiangsu Province for Agrobiology/Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing, China.; Key Laboratory of Plant Functional Genomics of the Ministry of Education, Yangzhou University, Yangzhou, China.; National Key Laboratory of Crop Genetic Improvement/National Center of Rapeseed Improvement/Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China.
Branch angle (BA) is a critical morphological trait that significantly influences planting density, light interception and ultimately yield in plants. Despite its importance, the regulatory mechanism governing BA in rapeseed remains poorly understood. In this study, we generated 109 transcriptome data sets for 37 rapeseed accessions with divergent BA phenotypes. Relative to adaxial branch segments, abaxial segments accumulated higher levels of auxin and exhibited lower expression of six TCP1 homologues and one GA20ox3. A co-expression network analysis identified two modules highly correlated with BA. The modules contained homologues to known BA control genes, such as FUL, YUCCA6, TCP1 and SGR3. Notably, a homoeologous exchange (HE), occurring at the telomeres of A09, was prevalent in large BA accessions, while an A02-C02 HE was common in small BA accessions. In their corresponding regions, these HEs explained the formation of hub gene hotspots in the two modules. QTL-seq analysis confirmed that the presence of a large A07-C06 HE (~8.1 Mb) was also associated with a small BA phenotype, and BnaA07.WRKY40.b within it was predicted as candidate gene. Overexpressing BnaA07.WRKY40.b in rapeseed increased BA by up to 20 degrees , while RNAi- and CRISPR-mediated mutants (BnaA07.WRKY40.b and BnaC06.WRKY40.b) exhibited decreased BA by up to 11.4 degrees . BnaA07.WRKY40.b was exclusively localized to the nucleus and exhibited strong expression correlations with many genes related to gravitropism and plant architecture. Taken together, our study highlights the influence of HEs on rapeseed plant architecture and confirms the role of WRKY40 homologues as novel regulators of BA.
PMID: 38308663
Cell Rep , IF:9.423 , 2024 Feb , V43 (2) : P113763 doi: 10.1016/j.celrep.2024.113763
Identification of mebendazole as an ethylene signaling activator reveals a role of ethylene signaling in the regulation of lateral root angles.
Plant Molecular and Cellular Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, USA.; Environmental and Complex Analysis Laboratory (ECAL), Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093, USA.; Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA.; Department of Microbiology and Plant Pathology, Center for Plant Cell Biology, University of California, Riverside, Riverside, CA 92521, USA; School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China.; Plant Molecular and Cellular Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, USA; Integrative Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, USA. Electronic address: wbusch@salk.edu.
The lateral root angle or gravitropic set-point angle (GSA) is an important trait for root system architecture (RSA) that determines the radial expansion of the root system. The GSA therefore plays a crucial role for the ability of plants to access nutrients and water in the soil. Only a few regulatory pathways and mechanisms that determine GSA are known. These mostly relate to auxin and cytokinin pathways. Here, we report the identification of a small molecule, mebendazole (MBZ), that modulates GSA in Arabidopsis thaliana roots and acts via the activation of ethylene signaling. MBZ directly acts on the serine/threonine protein kinase CTR1, which is a negative regulator of ethylene signaling. Our study not only shows that the ethylene signaling pathway is essential for GSA regulation but also identifies a small molecular modulator of RSA that acts downstream of ethylene receptors and that directly activates ethylene signaling.
PMID: 38358890
Cell Rep , IF:9.423 , 2024 Feb , V43 (2) : P113747 doi: 10.1016/j.celrep.2024.113747
The single-cell transcriptome program of nodule development cellular lineages in Medicago truncatula.
School of Forest, Fisheries, and Geomatics Sciences, University of Florida, Gainesville, FL 32611, USA.; School of Forest, Fisheries, and Geomatics Sciences, University of Florida, Gainesville, FL 32611, USA; Centro de Biotecnologia y Genomica de Plantas, Universidad Politecnica de Madrid - Instituto Nacional de Investigacion y Tecnologia Agraria y Alimentaria, 28223 Madrid, Spain.; School of Forest, Fisheries, and Geomatics Sciences, University of Florida, Gainesville, FL 32611, USA; PlantLab, Center of Plant Sciences, Sant'Anna School of Advanced Studies, 56010 Pisa, Italy.; School of Forest, Fisheries, and Geomatics Sciences, University of Florida, Gainesville, FL 32611, USA; Horticultural Sciences Department, University of Florida, Gainesville, FL 32611, USA.; Department of Bacteriology, University of Wisconsin - Madison, Madison, WI 53706, USA.; Wisconsin Institute for Discovery, University of Wisconsin, Madison, WI 53715, USA.; Department of Genetics & Biochemistry, Clemson University, Clemson, SC 29634, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.; Department of Genetics & Biochemistry, Clemson University, Clemson, SC 29634, USA; Biomedical Data Science and Informatics Program, Clemson University, Clemson, SC, USA; Clemson Center for Human Genetics, Clemson University, Greenwood, SC 29646, USA.; Wisconsin Institute for Discovery, University of Wisconsin, Madison, WI 53715, USA; Department of Biostatistics and Medical Informatics, University of Wisconsin, Madison, WI 53726, USA; Department of Computer Sciences, University of Wisconsin, Madison, WI 53706, USA.; Department of Genetics & Biochemistry, Clemson University, Clemson, SC 29634, USA.; School of Forest, Fisheries, and Geomatics Sciences, University of Florida, Gainesville, FL 32611, USA. Electronic address: mkirst@ufl.edu.
Legumes establish a symbiotic relationship with nitrogen-fixing rhizobia by developing nodules. Nodules are modified lateral roots that undergo changes in their cellular development in response to bacteria, but the transcriptional reprogramming that occurs in these root cells remains largely uncharacterized. Here, we describe the cell-type-specific transcriptome response of Medicago truncatula roots to rhizobia during early nodule development in the wild-type genotype Jemalong A17, complemented with a hypernodulating mutant (sunn-4) to expand the cell population responding to infection and subsequent biological inferences. The analysis identifies epidermal root hair and stele sub-cell types associated with a symbiotic response to infection and regulation of nodule proliferation. Trajectory inference shows cortex-derived cell lineages differentiating to form the nodule primordia and, posteriorly, its meristem, while modulating the regulation of phytohormone-related genes. Gene regulatory analysis of the cell transcriptomes identifies new regulators of nodulation, including STYLISH 4, for which the function is validated.
PMID: 38329875
Cell Rep , IF:9.423 , 2024 Feb , V43 (2) : P113726 doi: 10.1016/j.celrep.2024.113726
Histone methylation readers MRG1/2 interact with PIF4 to promote thermomorphogenesis in Arabidopsis.
State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, Department of Biochemistry and Biophysics, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai 200438, P.R. China.; Institut de Biologie Moleculaire des Plantes, CNRS, Universite de Strasbourg, 12 rue du General Zimmer, 67084 Strasbourg Cedex, France.; State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, Department of Biochemistry and Biophysics, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai 200438, P.R. China; Department of Energy, Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI 53706, USA. Electronic address: bliu279@wisc.edu.; State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, Department of Biochemistry and Biophysics, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai 200438, P.R. China. Electronic address: aiwudong@fudan.edu.cn.
Warm ambient conditions induce thermomorphogenesis and affect plant growth and development. However, the chromatin regulatory mechanisms involved in thermomorphogenesis remain largely obscure. In this study, we show that the histone methylation readers MORF-related gene 1 and 2 (MRG1/2) are required to promote hypocotyl elongation in response to warm ambient conditions. A transcriptome sequencing analysis indicates that MRG1/2 and phytochrome interacting factor 4 (PIF4) coactivate a number of thermoresponsive genes, including YUCCA8, which encodes a rate-limiting enzyme in the auxin biosynthesis pathway. Additionally, MRG2 physically interacts with PIF4 to bind to thermoresponsive genes and enhances the H4K5 acetylation of the chromatin of target genes in a PIF4-dependent manner. Furthermore, MRG2 competes with phyB for binding to PIF4 and stabilizes PIF4 in planta. Our study indicates that MRG1/2 activate thermoresponsive genes by inducing histone acetylation and stabilizing PIF4 in Arabidopsis.
PMID: 38308844
Plant Physiol , IF:8.34 , 2024 Feb doi: 10.1093/plphys/kiae090
Synthetically derived BiAux modulates auxin co-receptor activity to stimulate lateral root formation.
Centro de Biotecnologia y Genomica de Plantas (UPM-INIA/CSIC). Universidad Politecnica de Madrid (UPM) - Instituto Nacional de Investigacion y Tecnologia Agraria y Alimentaria-CSIC (INIA/CSIC). Campus Montegancedo 28223 Pozuelo de Alarcon (Madrid), Spain.; Departamento de Biotecnologia-Biologia Vegetal, Escuela Tecnica Superior de Ingenieria Agronomica, Alimentaria y de Biosistemas, Universidad Politecnica de Madrid (UPM), 28040 Madrid, Spain.; Universidad Francisco de Vitoria. Facultad de Ciencias Experimentales. Edificio E. 28223. Pozuelo de Alarcon. Madrid. Spain.; Departamento de Quimica en Ciencias Farmaceuticas, Facultad de Farmacia, Universidad Complutense de Madrid, Plaza Ramon y Cajal s/n, 28040, Madrid, Spain.; Centro de Metabolomica y Bioanalisis (CEMBIO), Facultad de Farmacia, Universidad San Pablo-CEU, CEU Universities, Urbanizacion Monteprincipe, 28660 Boadilla del Monte, Madrid. Spain.
The root system plays an essential role in plant growth and adaptation to the surrounding environment. The root clock periodically specifies lateral root prebranch sites (PBS), where a group of pericycle founder cells (FC) is primed to become LR founder cells (LRFCs) and eventually give rise to lateral root primordia (LRP) or lateral roots (LRs). This clock-driven organ formation process is tightly controlled by modulation of auxin content and signaling. Auxin perception entails the physical interaction of TRANSPORT INHIBITOR RESPONSE 1 (TIR1) or AUXIN SIGNALING F-BOX (AFBs) proteins with AUXIN/INDOLE-3-ACETIC ACID (Aux/IAA) repressors to form a co-receptor system. Despite the apparent simplicity, the understanding of how specific auxin co- receptors are assembled remains unclear. We identified the compound bis-methyl auxin conjugated with N-glucoside, or BiAux, in Arabidopsis (Arabidopsis thaliana) that specifically induces the formation of PBS and the emergence of LR, with a slight effect on root elongation. Docking analyses indicated that BiAux binds to F-box proteins, and we showed that BiAux function depends on TIR1 and AFB2 F-box proteins and AUXIN RESPONSE FACTOR 7 (ARF7) activity, which is involved in FC specification and LR formation. Finally, using a yeast (Saccharomyces cerevisiae) heterologous expression system, we showed that BiAux favors the assemblage of specific co-receptors subunits involved in LR formation and enhances AUXIN/INDOLE-3-ACETIC ACID 28 (IAA28) protein degradation. These results indicate that BiAux acts as an allosteric modulator of specific auxin co-receptors. Therefore, BiAux exerts a fine-tune regulation of auxin signaling aimed to the specific formation of LR among the many development processes regulated by auxin.
PMID: 38378170
Plant Physiol , IF:8.34 , 2024 Feb doi: 10.1093/plphys/kiae085
Defying Gravity: WEEP promotes negative gravitropism in peach trees by establishing asymmetric auxin gradients.
Department of Horticulture, Michigan State University, East Lansing, MI 48824.; Department of Biology, Duke University, Durham, NC 27708, USA.; Department of Plant Biology, Michigan State University, East Lansing, MI 48824.
Trees with weeping shoot architectures are valued for their beauty and are a resource for understanding how plants regulate posture control. The peach (Prunus persica) weeping phenotype, which has elliptical downward arching branches, is caused by a homozygous mutation in the WEEP gene. Little is known about the function of WEEP despite its high conservation throughout Plantae. Here, we present the results of anatomical, biochemical, biomechanical, physiological, and molecular experiments that provide insight into WEEP function. Our data suggest that weeping peach trees do not have defects in branch structure. Rather, transcriptomes from the adaxial (upper) and abaxial (lower) sides of standard and weeping branch shoot tips revealed flipped expression patterns for genes associated with early auxin response, tissue patterning, cell elongation, and tension wood development. This suggests that WEEP promotes polar auxin transport toward the lower side during shoot gravitropic response, leading to cell elongation and tension wood development. In addition, weeping peach trees exhibited steeper root systems and faster lateral root gravitropic response. This suggests that WEEP moderates root gravitropism and is essential to establishing the set-point angle of lateral roots from the gravity vector. Additionally, size-exclusion chromatography indicated that WEEP proteins self-oligomerize, like other proteins with sterile alpha motif (SAM) domains. Collectively, our results from weeping peach provide insight into polar auxin transport mechanisms associated with gravitropism and lateral shoot and root orientation.
PMID: 38366651
Plant Physiol , IF:8.34 , 2024 Feb doi: 10.1093/plphys/kiae088
Far-red light-enhanced apical dominance stimulates flower and fruit abortion in sweet pepper.
Horticulture and Product Physiology, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands.; Plant Developmental Genetics, Institute of Biology Leiden, Leiden University, Sylviusweg 72, 2333 BE Leiden, the Netherlands.; Laboratory of Cell and Developmental Biology, Cluster Plant Developmental Biology, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands.
Far-red radiation affects many plant processes, including reproductive organ abortion. Our research aimed to determine the role of apical dominance in far-red light-induced flower and fruit abortion in sweet pepper (Capsicum annuum L.). We conducted several climate room experiments where plants were grown under white or red-rich LED light, with or without additional far-red light. Additional far-red light enhanced apical dominance: it increased auxin levels in the apices of dominant shoots, and caused a greater difference in internode length and apical auxin levels between dominant and subordinate shoots. Additional far-red light stimulated fruit abortion in intact plants but not in decapitated plants, suggesting a crucial role of shoot apices in this effect. However, reducing basipetal auxin transport in the stems with N-1-naphthylphthalamic acid (NPA) did not influence far-red light-stimulated fruit abortion, although auxin levels in the stem were largely reduced. Applying the synthetic auxin 1-naphthaleneacetic acid (NAA) on decapitated apices did not influence fruit abortion. However, applying the auxin biosynthesis inhibitor yucasin to shoot apices reduced fruit abortion regardless of the light conditions, accompanied by slight shoot growth retardation. These findings suggest that the basipetal auxin stream does not mediate far-red light-stimulated fruit abortion. Far-red light-stimulated fruit abortion was associated with reduced sucrose accumulation and lower invertase activities in flowers. We suggest that under additional far-red light conditions, increased auxin levels in shoot apices promote fruit abortion probably through enhanced competition for assimilates between apices and flowers, which limits assimilate import into flowers.
PMID: 38366641
Plant Physiol , IF:8.34 , 2024 Feb doi: 10.1093/plphys/kiae081
Molecular regulatory mechanisms of staminate strobilus development and dehiscence in Torreya grandis.
State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, Zhejiang 311300, China.
Gymnosperms are mostly dioecious, and their staminate strobili undergo a longer developmental period than those of angiosperms. However, the underlying molecular mechanisms remain unclear. This study aimed to identify key genes and pathways involved in staminate strobilus development and dehiscence in Torreya grandis. Through weighted gene co-expression network analysis (WGCNA), we identified fast elongation-related genes enriched in carbon metabolism and auxin signal transduction, whereas dehiscence-related genes were abundant in alpha-linolenic acid metabolism and the phenylpropanoid pathway. Based on WGCNA, we also identified PHYTOCHROME-INTERACTING FACTOR4 (TgPIF4) as a potential regulator for fast elongation of staminate strobilus and two WRKY proteins (TgWRKY3 and TgWRKY31) as potential regulators for staminate strobilus dehiscence. Multiple protein-DNA interaction analyses showed that TgPIF4 directly activates expression of TRANSPORT INHIBITOR RESPONSE2 (TgTIR2) and NADP-MALIC ENZYME (TgNADP-ME). Overexpression of TgPIF4 significantly promoted staminate strobilus elongation by elevating auxin signal transduction and pyruvate content. TgWRKY3 and TgWRKY31 bind to the promoters of the lignin biosynthesis gene PHENYLALANINE AMMONIA-LYASE (TgPAL) and jasmonic acid metabolism gene JASMONATE O-METHYLTRANSFERASE (TgJMT), respectively, and directly activate their transcription. Overexpression of TgWRKY3 and TgWRKY31 in the staminate strobilus led to early dehiscence, accompanied by increased lignin and methyl jasmonate levels respectively. Collectively, our findings offer a perspective for understanding the growth of staminate strobili in gymnosperms.
PMID: 38365225
Plant Physiol , IF:8.34 , 2024 Feb doi: 10.1093/plphys/kiae071
PECTIN ACETYLESTERASE12 regulates shoot branching via acetic acid and auxin accumulation in alfalfa shoots.
School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China.; College of Life Science, Yulin University, Yulin, 719000, China.; State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou 311300, China.; Key Laboratory of Urban Agriculture, Ministry of Agriculture, Shanghai 201101, China.
Shoot branching is an important biological trait affecting alfalfa (Medicago sativa L.) production, but its development is complicated and the mechanism is not fully clear. In the present study, pectin acetylesterase 12 (MsPAE12) and NAM/ATAF/CUC-domain transcription factor gene (MsNAC73) were isolated from alfalfa. MsPAE12 was highly expressed in shoot apexes, and MsNAC73 was found to be a key transcriptional repressor of MsPAE12 by directly binding to SA and JA elements in the MsPAE12 promoter. The biological functions of MsPAE12 and MsNAC73 were studied through overexpression (OE) and down-expression (RNAi) of the two genes in alfalfa. The numbers of shoot branches increased in MsPAE12-OE lines but decreased in MsPAE12-RNAi and MsNAC73-OE plants, which was negatively related to their indole-3-acetic acid (IAA) accumulation in shoot apexes. Furthermore, the contents of acetic acid (AA) in shoot apexes decreased in MsPAE12-OE plants but increased in MsPAE12-RNAi and MsNAC73-OE plants. The changes of AA contents were positively related to the expression of TRYPTOPHAN AMINOTRANSFERASE 1 (MsTAA1), TRYPTOPHAN AMINOTRANSFERASE-RELATED 2 (MsTAR2) and YUCCA flavin monooxygenase (MsYUCC4) and the contents of tryptophan (Trp), indole-3-pyruvic acid (IPA) and IAA in shoot apexes of MsPAE12-OE, MsPAE12-RNAi and MsNAC73-OE plants. Exogenous application of AA to WT and MsPAE12-OE plants increased Trp, IPA and IAA contents and decreased branch number. Exogenous IAA suppressed shoot branching in MsPAE12-OE plants, but exogenous IAA inhibitors increased shoot branching in MsPAE12-RNAi plants. These results indicate that the MsNAC73-MsPAE12 module regulates auxin-modulated shoot branching via affecting acetic acid accumulation in shoot apexes of alfalfa.
PMID: 38365203
Plant Physiol , IF:8.34 , 2024 Jan doi: 10.1093/plphys/kiae050
Molecular Basis and Evolutionary Drivers of Endosperm-based Hybridization Barriers.
Department of Plant Reproductive Biology and Epigenetics, Max Planck Institute of Molecular Plant Physiology, Potsdam, 14476, Germany.; Department of Plant Biology, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Uppsala 75007, Sweden.
The endosperm, a transient seed tissue, plays a pivotal role in supporting embryo growth and germination. This unique feature sets flowering plants apart from gymnosperms, marking an evolutionary innovation in the world of seed-bearing plants. Nevertheless, the importance of the endosperm extends beyond its role in providing nutrients to the developing embryo by acting as a versatile protector, preventing hybridization events between distinct species and between individuals with different ploidy. This phenomenon centers on growth and differentiation of the endosperm and the speed at which both processes unfold. Emerging studies underscore the important role played by type I MADS-box transcription factors, including the paternally expressed gene PHERES1. These factors, along with downstream signaling pathways involving auxin and abscisic acid, are instrumental in regulating endosperm development and, consequently, the establishment of hybridization barriers. Moreover, mutations in various epigenetic regulators mitigate these barriers, unveiling a complex interplay of pathways involved in their formation. In this review, we discuss the molecular underpinnings of endosperm-based hybridization barriers and their evolutionary drivers.
PMID: 38298124
Plant Physiol , IF:8.34 , 2024 Jan , V194 (2) : P884-901 doi: 10.1093/plphys/kiad595
H2 supplied via ammonia borane stimulates lateral root branching via phytomelatonin signaling.
College of Life Sciences, Laboratory Center of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China.; Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing 210014, China.
A reliable and stable hydrogen gas (H2) supply will benefit agricultural laboratory and field trials. Here, we assessed ammonia borane (AB), an efficient hydrogen storage material used in the energy industry, and determined its effect on plant physiology and the corresponding mechanism. Through hydroponics and pot experiments, we discovered that AB increases tomato (Solanum lycopersicum) lateral root (LR) branching and this function depended on the increased endogenous H2 level caused by the sustainable H2 supply. In particular, AB might trigger LR primordia initiation. Transgenic tomato and Arabidopsis (Arabidopsis thaliana) expressing hydrogenase1 (CrHYD1) from Chlamydomonas reinhardtii not only accumulated higher endogenous H2 and phytomelatonin levels but also displayed pronounced LR branching. These endogenous H2 responses achieved by AB or genetic manipulation were sensitive to the pharmacological removal of phytomelatonin, indicating the downstream role of phytomelatonin in endogenous H2 control of LR formation. Consistently, extra H2 supply failed to influence the LR defective phenotypes in phytomelatonin synthetic mutants. Molecular evidence showed that the phytomelatonin-regulated auxin signaling network and cell-cycle regulation were associated with the AB/H2 control of LR branching. Also, AB and melatonin had little effect on LR branching in the presence of auxin synthetic inhibitors. Collectively, our integrated approaches show that supplying H2 via AB increases LR branching via phytomelatonin signaling. This finding might open the way for applying hydrogen storage materials to horticultural production.
PMID: 37944026
Plant Physiol , IF:8.34 , 2024 Jan , V194 (2) : P867-883 doi: 10.1093/plphys/kiad592
Transcription factor CsMYB77 negatively regulates fruit ripening and fruit size in citrus.
National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan 430070, PR China.; Fruit Tree Research Institute, Chongqing Academy of Agricultural Sciences, Chongqing 401329, PR China.
MYB family transcription factors (TFs) play essential roles in various biological processes, yet their involvement in regulating fruit ripening and fruit size in citrus remains poorly understood. In this study, we have established that the R2R3-MYB TF, CsMYB77, exerts a negative regulatory influence on fruit ripening in both citrus and tomato (Solanum lycopersicum), while also playing a role in modulating fruit size in citrus. The overexpression of CsMYB77 in tomato and Hongkong kumquat (Fortunella hindsii) led to notably delayed fruit ripening phenotypes. Moreover, the fruit size of Hongkong kumquat transgenic lines was largely reduced. Based on DNA affinity purification sequencing and verified interaction assays, SEVEN IN ABSENTIA OF ARABIDOPSIS THALIANA4 (SINAT4) and PIN-FORMED PROTEIN5 (PIN5) were identified as downstream target genes of CsMYB77. CsMYB77 inhibited the expression of SINAT4 to modulate abscisic acid (ABA) signaling, which delayed fruit ripening in transgenic tomato and Hongkong kumquat lines. The expression of PIN5 was activated by CsMYB77, which promoted free indole-3-acetic acid decline and modulated auxin signaling in the fruits of transgenic Hongkong kumquat lines. Taken together, our findings revealed a fruit development and ripening regulation module (MYB77-SINAT4/PIN5-ABA/auxin) in citrus, which enriches the understanding of the molecular regulatory network underlying fruit ripening and size.
PMID: 37935634
Plant Physiol , IF:8.34 , 2024 Jan , V194 (2) : P819-831 doi: 10.1093/plphys/kiad548
Age-dependent analysis dissects the stepwise control of auxin-mediated lateral root development in rice.
Bioscience and Biotechnology Center, Nagoya University, Nagoya 464-8601, Japan.; Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya 464-8601, Japan.; School of Agriculture and Environment, The University of Western Australia, Crawley, WA 6009, Australia.; International Center for Research and Education in Agriculture, Nagoya University, Nagoya 464-8601, Japan.
As root elongation rates are different among each individual root, the distance from the root apices does not always reflect the age of root cells. Thus, methods for correcting variations in elongation rates are needed to accurately evaluate the root developmental process. Here, we show that modeling-based age-dependent analysis is effective for dissecting stepwise lateral root (LR) development in rice (Oryza sativa). First, we measured the increases in LR and LR primordium (LRP) numbers, diameters, and lengths in wild type and an auxin-signaling-defective mutant, which has a faster main (crown) root elongation rate caused by the mutation in the gene encoding AUXIN/INDOLE-3-ACETIC ACID protein 13 (IAA13). The longitudinal patterns of these parameters were fitted by the appropriate models and the age-dependent patterns were identified using the root elongation rates. As a result, we found that LR and LRP numbers and lengths were reduced in iaa13. We also found that the duration of the increases in LR and LRP diameters were prolonged in iaa13. Subsequent age-dependent comparisons with gene expression patterns suggest that AUXIN RESPONSE FACTOR11 (ARF11), the homolog of MONOPTEROS (MP)/ARF5 in Arabidopsis (Arabidopsis thaliana), is involved in the initiation and growth of LR(P). Indeed, the arf11 mutant showed a reduction of LR and LRP numbers and lengths. Our results also suggest that PINOID-dependent rootward-to-shootward shift of auxin flux contributes to the increase in LR and LRP diameters. Together, we propose that modeling-based age-dependent analysis is useful for root developmental studies by enabling accurate evaluation of root traits' expression.
PMID: 37831077
Environ Pollut , IF:8.071 , 2024 Feb , V343 : P123112 doi: 10.1016/j.envpol.2023.123112
Exogenous auxin alters the polycyclic aromatic hydrocarbons apoplastic and symplastic uptake by wheat seedling roots.
College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, Jiangsu Province, 210095, People's Republic of China.; College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, Jiangsu Province, 210095, People's Republic of China. Electronic address: xhzhan@njau.edu.cn.
Polycyclic aromatic hydrocarbons (PAHs) are a category of organic pollutants known for their high carcinogenicity. Our previous research has illustrated that plant roots actively absorb PAHs through a co-transport mechanism with H(+) ions. Because auxin can increase the H(+)-ATPase activity, the wheat roots were exposed to PAHs with/without auxins to study whether auxins facilitate the uptake of PAHs by plant roots and to gain insights into the underlying mechanisms of this process. In our study, indole acetic acid (100 muM) and alpha-naphthaleneacetic acid (10 muM) significantly increased the PAHs concentrations in apoplast and symplast, and the treating time and concentrations were positively correlated with PAHs accumulations. The time-dependent kinetics for 36 h followed the Elovich equation, and the concentration-dependent kinetics of apoplastic and symplastic uptake for 4 h could be described with the Freundlich and Michaelis-Menten equations, respectively. The proportion of PAHs accumulated in apoplast could be enhanced by auxins in most treatments. Our findings offer novel insights into the mechanisms of PAH uptake by plant roots under auxin exposure. Additionally, this research aids in refining strategies for ensuring crop safety and improving phytoremediation of PAH-contaminated soil and water.
PMID: 38097155
Sci Total Environ , IF:7.963 , 2024 Feb , V910 : P168522 doi: 10.1016/j.scitotenv.2023.168522
Intergenerational consequences of an auxin-like herbicide on plant sensitivity to a graminicide mediated by a fungal endophyte.
Instituto de Investigacion Interdisciplinaria (I(3)), Universidad de Talca, Talca, Chile; Centro de Ecologia Integrativa, Instituto de Ciencias Biologicas, Universidad de Talca, Talca, Chile. Electronic address: aueno@agro.uba.ar.; IFEVA, CONICET, Facultad de Agronomia, Universidad de Buenos Aires, Buenos Aires, Argentina.; IFEVA, CONICET, Facultad de Agronomia, Universidad de Buenos Aires, Buenos Aires, Argentina; Centro de Ecologia Integrativa, Instituto de Ciencias Biologicas, Universidad de Talca, Talca, Chile.
In agroecosystems, herbicides are the predominant anthropogenic selection pressure for agriculture weed species. While weeds are the primary target, herbicides can have adverse impacts on non-target plant beneficial microorganisms. We aimed to investigate the influence of a foliar endophytic fungus (Epichloe occultans) on the sensitivity of Lolium multiflorum to a graminicide herbicide (diclofop-methyl) during both plant ontogeny and progeny. Susceptible individuals to diclofop-methyl with and without endophyte were pre-exposed to the auxin 2,4-D herbicide. This herbicide is known to stimulate the metabolic detoxification mechanism (CYP-450) of diclofop-methyl. Regardless of the endophyte, 2,4-D pre-treatment increased mother plant survival to nearly 100 % under diclofop treatment but not in the progeny. Furthermore, maternal plant exposure to 2,4-D reduced endophyte transmission to the seeds and from seed-to-seedlings. Our findings suggest that, despite a reduction in diclofop-methyl sensitivity during the ontogeny of mother plants, 2,4-D-mediated induction of likely CYP-450 metabolism is not intergenerationally transmitted and shows detrimental effects on the symbiotic endophyte persistence.
PMID: 37956837
Plant Cell Environ , IF:7.228 , 2024 Feb doi: 10.1111/pce.14853
Phytochrome-interacting factors play shared and distinct roles in regulating shade avoidance responses in Populus trees.
School of Life Sciences, Chongqing Key Laboratory of Plant Resource Conservation and Germplasm Innovation, Integrative Science Center of Germplasm Creation in Western China (Chongqing) Science City, School of Life Sciences, Southwest University, Chongqing, China.; Key Laboratory of Eco-environments of Three Gorges Reservoir Region, Ministry of Education, School of Life Sciences, Southwest University, Chongqing, China.
Plants adjust their growth and development in response to changing light caused by canopy shade. The molecular mechanisms underlying shade avoidance responses have been widely studied in Arabidopsis and annual crop species, yet the shade avoidance signalling in woody perennial trees remains poorly understood. Here, we first showed that PtophyB1/2 photoreceptors serve conserved roles in attenuating the shade avoidance syndrome (SAS) in poplars. Next, we conducted a systematic identification and characterization of eight PtoPIF genes in Populus tomentosa. Knocking out different PtoPIFs led to attenuated shade responses to varying extents, whereas overexpression of PtoPIFs, particularly PtoPIF3.1 and PtoPIF3.2, led to constitutive SAS phenotypes under normal light and enhanced SAS responses under simulated shade. Notably, our results revealed that distinct from Arabidopsis PIF4 and PIF5, which are major regulators of SAS, the Populus homologues PtoPIF4.1 and PtoPIF4.2 seem to play a minor role in controlling shade responses. Moreover, we showed that PtoPIF3.1/3.2 could directly activate the expression of the auxin biosynthetic gene PtoYUC8 in response to shade, suggesting a conserved PIF-YUC-auxin pathway in modulating SAS in tree. Overall, our study provides insights into shared and divergent functions of PtoPIF members in regulating various aspects of the SAS in Populus.
PMID: 38404129
Plant Cell Environ , IF:7.228 , 2024 Feb , V47 (2) : P429-441 doi: 10.1111/pce.14758
Far-red light inhibits lateral bud growth mainly through enhancing apical dominance independently of strigolactone synthesis in tomato.
Department of Horticulture, Zijingang Campus, Zhejiang University, Hangzhou, People's Republic of China.; Hainan Institute, Zhejiang University, Sanya, People's Republic of China.; Agricultural Experiment Station, Zhejiang University, Hangzhou, People's Republic of China.
The ratio of red light to far-red light (R:FR) is perceived by light receptors and consequently regulates plant architecture. Regulation of shoot branching by R:FR ratio involves plant hormones. However, the roles of strigolactone (SL), the key shoot branching hormone and the interplay of different hormones in the light regulation of shoot branching in tomato (Solanum lycopersicum) are elusive. Here, we found that defects in SL synthesis genes CAROTENOID CLEAVAGE DIOXYGENASE 7 (CCD7) and CCD8 in tomato resulted in more lateral bud growth but failed to reverse the FR inhibition of lateral bud growth, which was associated with increased auxin synthesis and decreased synthesis of cytokinin (CK) and brassinosteroid (BR). Treatment of auxin also inhibited shoot branching in ccd mutants. However, CK released the FR inhibition of lateral bud growth in ccd mutants, concomitant with the upregulation of BR synthesis genes. Furthermore, plants that overexpressed BR synthesis gene showed more lateral bud growth and the shoot branching was less sensitive to the low R:FR ratio. The results indicate that SL synthesis is dispensable for light regulation of shoot branching in tomato. Auxin mediates the response to R:FR ratio to regulate shoot branching by suppressing CK and BR synthesis.
PMID: 37916615
Plant Cell Environ , IF:7.228 , 2024 Feb , V47 (2) : P540-556 doi: 10.1111/pce.14746
Natural variation in a K(+) -preferring HKT transporter contributes to wheat shoot K(+) accumulation and salt tolerance.
State Key Laboratory of Crop Stress Biology for Arid Areas and College of Life Science, Northwest A&F University, Yangling, Shaanxi, China.; State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, China.; State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling, Shaanxi, China.; Key Laboratory of Plant Nutrition and Agri-Environment in Northwest China, Ministry of Agriculture and Rural Affairs, College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi, China.; Yangling Seed Industry Innovation Center, Yangling, Shaanxi, China.; State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Shaanxi, China.
Soil salinity can adversely affect crop growth and yield, and an improved understanding of the genetic factors that confer salt tolerance could inform breeding strategies to engineer salt-tolerant crops and improve productivity. Here, a group of K(+) -preferring HKT transporters, TaHKT8, TaHKT9 and TaHKT10, were identified and negatively regulate the wheat shoot K(+) accumulation and salt tolerance. A genome-wide association study (GWAS) and candidate gene association analysis further revealed that TaHKT9-B substantially underlies the natural variation of wheat shoot K(+) accumulation under saline soil conditions. Specifically, an auxin responsive element (ARE) within an 8-bp insertion in the promoter of TaHKT9-B is strongly associated with shoot K(+) content among wheat accessions. This ARE can be directly bound by TaARF4 for transcriptional activation of TaHKT9-B, which subsequently attenuates shoot K(+) accumulation and salt tolerance. Moreover, the tae-miR390/TaTAS3/TaARF4 pathway was identified to regulate the salt-induced root development and salt tolerance in wheat. Taken together, our study describes the genetic basis and accompanying mechanism driving phenotypic variation in wheat shoot K(+) accumulation and salt tolerance. The identified tae-miR390/TaTAS3/TaARF4/TaHKT9-B module is an important regulator in wheat subjected to salt stress, which provides the potentially important genetic resources for breeders to improve wheat salt tolerance.
PMID: 37876337
J Exp Bot , IF:6.992 , 2024 Feb doi: 10.1093/jxb/erae054
Epigenetics and plant hormone dynamics - a functional and methodological perspective.
Mendel Centre for Plant Genomics and Proteomics, CEITEC - Central European Institute of Technology, Masaryk University, Kamenice 753/5, CZ-62500 Brno, Czech Republic.; Department of Cell Biology and Radiobiology, Institute of Biophysics of the Czech Academy of Sciences, Brno, CZ-61265, Czech Republic.; National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 753/5, CZ-62500 Brno, Czech Republic.; Photon Systems Instruments, Prumyslova 470, CZ-664 24 Drasov, Czech Republic.
Plant hormones, pivotal regulators of plant growth, development, and response to environmental cues, have recently emerged as central modulators of epigenetic processes governing gene expression and phenotypic plasticity. This review addresses the complex interplay between plant hormones and epigenetic mechanisms, highlighting the diverse methodologies that have been harnessed to decipher these intricate relationships. We present a comprehensive overview to understand how phytohormones orchestrate epigenetic modifications, shaping plant adaptation and survival strategies. Conversely, we explore how epigenetic regulators ensure hormonal balance and regulate the signalling pathways of key plant hormones. Furthermore, our investigation includes a search for novel genes that are regulated by plant hormones under the control of epigenetic processes. Our review offers a contemporary overview of the epigenetic-plant hormone crosstalk, emphasizing its significance in plant growth, development, and potential agronomical applications.
PMID: 38373206
J Exp Bot , IF:6.992 , 2024 Feb , V75 (5) : P1437-1450 doi: 10.1093/jxb/erad468
AtIAR1 is a Zn transporter that regulates auxin metabolism in Arabidopsis thaliana.
Biochemistry and Metabolism, John Innes Centre, Norwich NR4 7UH, UK.
Root growth in Arabidopsis is inhibited by exogenous auxin-amino acid conjugates, and mutants resistant to one such conjugate [indole-3-acetic acid (IAA)-Ala] map to a gene (AtIAR1) that is a member of a metal transporter family. Here, we test the hypothesis that AtIAR1 controls the hydrolysis of stored conjugated auxin to free auxin through zinc transport. AtIAR1 complements a yeast mutant sensitive to zinc, but not manganese- or iron-sensitive mutants, and the transporter is predicted to be localized to the endoplasmic reticulum/Golgi in plants. A previously identified Atiar1 mutant and a non-expressed T-DNA mutant both exhibit altered auxin metabolism, including decreased IAA-glucose conjugate levels in zinc-deficient conditions and insensitivity to the growth effect of exogenous IAA-Ala conjugates. At a high concentration of zinc, wild-type plants show a novel enhanced response to root growth inhibition by exogenous IAA-Ala which is disrupted in both Atiar1 mutants. Furthermore, both Atiar1 mutants show changes in auxin-related phenotypes, including lateral root density and hypocotyl length. The findings therefore suggest a role for AtIAR1 in controlling zinc release from the secretory system, where zinc homeostasis plays a key role in regulation of auxin metabolism and plant growth regulation.
PMID: 37988591
J Exp Bot , IF:6.992 , 2024 Feb , V75 (3) : P1081-1097 doi: 10.1093/jxb/erad432
Leaf ontogeny modulates epinasty through shifts in hormone dynamics during waterlogging in tomato.
Molecular Plant Hormone Physiology Lab, Division of Crop Biotechnics, Department of Biosystems, KU Leuven, Willem de Croylaan 42, Leuven 3001, Belgium.; Laboratory of Growth Regulators, Centre of the Region Hana for Biotechnological and Agricultural Research, Institute of Experimental Botany, Czech Academy of Sciences, and Faculty of Science, Palacky University, CZ-783 71 Olomouc, Czech Republic.; KU Leuven Plant Institute (LPI), KU Leuven, Arenbergpark 30, 3001 Leuven, Belgium.
Waterlogging leads to hypoxic conditions in the root zone that subsequently cause systemic adaptive responses in the shoot, including leaf epinasty. Waterlogging-induced epinasty in tomato has long been ascribed to the coordinated action of ethylene and auxins. However, other hormonal signals have largely been neglected, despite evidence of their importance in leaf posture control. To cover a large group of growth regulators, we performed a tissue-specific and time-dependent hormonomics analysis. This revealed that multiple hormones are differentially affected throughout a 48 h waterlogging treatment, and that leaf age determines hormone homeostasis and modulates their changes during waterlogging. In addition, we distinguished early hormonal signals that contribute to fast responses to oxygen deprivation from those that potentially sustain the waterlogging response. We found that abscisic acid (ABA) levels peak in petioles within the first 12 h of the treatment, while its precursors only increase much later, suggesting that ABA transport is altered. At the same time, cytokinins (CKs) and their derivatives drastically decline during waterlogging in leaves of all ages. This drop in CKs possibly releases the inhibition of ethylene- and auxin-mediated cell elongation to establish epinastic bending. Auxins themselves rise substantially in the petiole of mature leaves, but mostly after 48 h of root hypoxia. Based on our hormone profiling, we propose that ethylene and ABA might act synergistically as an early signal to induce epinasty, while the balance of indole-3-acetic acid and CKs in the petiole ultimately regulates differential growth.
PMID: 37910663
Int J Biol Macromol , IF:6.953 , 2024 Feb : P130306 doi: 10.1016/j.ijbiomac.2024.130306
Class III plant peroxidases: From classification to physiological functions.
Department of Biochemistry and Molecular Biology, Federal University of Ceara, Campus do Pici, Fortaleza, Ceara CEP 60451-970, Brazil. Electronic address: cleversondiniz@ufc.br.; Department of Biochemistry and Molecular Biology, Federal University of Ceara, Campus do Pici, Fortaleza, Ceara CEP 60451-970, Brazil.; Department of Plant Pathology and Ecology, The Connecticut Agricultural Experiment Station, New Haven 06511, CT, USA.
Peroxidases (EC 1.11.1.7) are involved in a wide range of physiological processes, hence their broad distribution across biological systems. These proteins can be classified as haem or non-haem enzymes. According to the RedOxiBase database, haem peroxidases are approximately 84 % of all known peroxidase enzymes. Class III plant peroxidases are haem-enzymes that share similar three-dimensional structures and a common catalytic mechanism for hydrogen peroxide degradation. They exist as large multigene families and are involved in metabolizing Reactive Oxygen Species (ROS), hormone synthesis and decomposition, fruit growth, defense, and cell wall synthesis and maintenance. As a result, plant peroxidases gained attention in research and became one of the most extensively studied groups of enzymes. This review provides an update on the database, classification, phylogeny, mechanism of action, structure, and physiological functions of class III plant peroxidases.
PMID: 38387641
Int J Biol Macromol , IF:6.953 , 2024 Jan , V262 (Pt 1) : P129721 doi: 10.1016/j.ijbiomac.2024.129721
Stomatal density suppressor PagSDD1 is a "generalist" gene that promotes plant growth and improves water use efficiency.
State Key Laboratory of Tree Genetics and Breeding, National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing 100083, China. Electronic address: xiayufei@bjfu.edu.cn.; Research Institute of Tropical Forestry, Chinese Academy of Forestry, Guangzhou 510520, China. Electronic address: hanqiang1988@caf.ac.cn.; State Key Laboratory of Tree Genetics and Breeding, National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing 100083, China. Electronic address: shujianghai@bjfu.edu.cn.; State Key Laboratory of Tree Genetics and Breeding, National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing 100083, China. Electronic address: jiangsx@bjfu.edu.cn.; State Key Laboratory of Tree Genetics and Breeding, National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing 100083, China. Electronic address: kangxy@bjfu.edu.cn.
The serine protease SDD1 regulates stomatal density, but its potential impact on plant vegetative growth is unclear. Our study reveals a substantial upregulation of SDD1 in triploid poplar apical buds and leaves, suggesting its possible role in their growth regulation. We cloned PagSDD1 from poplar 84 K (Populus alba x P. glandulosa) and found that overexpression in poplar, soybean, and lettuce led to decreased leaf stomatal density. Furthermore, PagSDD1 represses PagEPF1, PagEPF2, PagEPFL9, PagSPCH, PagMUTE, and PagFAMA expression. In contrast, PagSDD1 promotes the expression of its receptors, PagTMM and PagERECTA. PagSDD1-OE poplars showed stronger drought tolerance than wild-type poplars. Simultaneously, PagSDD1-OE poplar, soybean, and lettuce had vegetative growth advantages. RNA sequencing revealed a significant upregulation of genes PagLHCB2.1 and PagGRF5, correlating positively with photosynthetic rate, and PagCYCA3;4 and PagEXPA8 linked to cell division and differentiation in PagSDD1-OE poplars. This increase promoted leaf photosynthesis, boosted auxin and cytokinin accumulation, and enhanced vegetative growth. SDD1 overexpression can increase the biomass of poplar, soybean, and lettuce by approximately 70, 176, and 155 %, respectively, and increase the water use efficiency of poplar leaves by over 52 %, which is of great value for the molecular design and breeding of plants with growth and water-saving target traits.
PMID: 38296132
Hortic Res , IF:6.793 , 2024 Feb , V11 (2) : Puhad275 doi: 10.1093/hr/uhad275
Gibberellins involved in fruit ripening and softening by mediating multiple hormonal signals in tomato.
Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, Sichuan, China.; Life Science and Technology School, Lingnan Normal University, Zhanjiang, 524048, China.; Sichuan Academy of Forestry, Chengdu, 610081, Sichuan, China.; Institute of Vegetable Research, Guangxi Academy of Agricultural Sciences, Nanning, 530007, Guangxi, China.
The phytohormone ethylene is well known for its important role in the ripening of climacteric fruit, such as tomato (Solanum lycopersicum). However, the role and mode of action of other plant hormones in climacteric fruit ripening regulation are not fully understood. Here, we showed that exogenous GA treatment or increasing endogenous gibberellin content by overexpressing the gibberellin synthesis gene SlGA3ox2 specifically in fruit tissues delayed tomato fruit ripening, whereas treatment with the GA biosynthesis inhibitor paclobutrazol (PAC) accelerated fruit ripening. Moreover, exogenous ethylene treatment cannot completely reverse the delayed fruit ripening phenotype. Furthermore, exogenous GA treatment of ethylene signalling mutant Never ripe (Nr) or SlEBF3-overexpressing lines still delayed fruit ripening, suggesting that GA involved in fruit ripening partially depends on ethylene. Transcriptome profiling showed that gibberellin affect the ripening of fruits by modulating the metabolism and signal transduction of multiple plant hormones, such as auxin and abscisic acid, in addition to ethylene. Overall, the results of this study provide new insight into the regulation of gibberellin in fruit ripening through mediating multiple hormone signals.
PMID: 38344652
Plant J , IF:6.417 , 2024 Feb doi: 10.1111/tpj.16683
Hydrotropism mechanisms and their interplay with gravitropism.
Faculty of Life Sciences, School of Plant Sciences and Food Security, Tel Aviv University, Tel Aviv, 69978, Israel.; Cell and Developmental Biology Department, School of Biological Sciences, University of California San Diego, La Jolla, California, 92093-0116, USA.; Faculty of Agriculture, Food and Environment, Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University of Jerusalem, Rehovot, 7610001, Israel.
Plants partly optimize their water recruitment from the growth medium by directing root growth toward a moisture source, a phenomenon termed hydrotropism. The default mechanism of downward growth, termed gravitropism, often functions to counteract hydrotropism when the water-potential gradient deviates from the gravity vector. This review addresses the identity of the root sites in which hydrotropism-regulating factors function to attenuate gravitropism and the interplay between these various factors. In this context, the function of hormones, including auxin, abscisic acid, and cytokinins, as well as secondary messengers, calcium ions, and reactive oxygen species in the conflict between these two opposing tropisms is discussed. We have assembled the available data on the effects of various chemicals and genetic backgrounds on both gravitropism and hydrotropism, to provide an up-to-date perspective on the interactions that dictate the orientation of root tip growth. We specify the relevant open questions for future research. Broadening our understanding of root mechanisms of water recruitment holds great potential for providing advanced approaches and technologies that can improve crop plant performance under less-than-optimal conditions, in light of predicted frequent and prolonged drought periods due to global climate change.
PMID: 38394056
Plant J , IF:6.417 , 2024 Feb doi: 10.1111/tpj.16682
Transient efflux inhibition improves plant regeneration by natural auxins.
Plant Developmental Genetics, Institute of Biology Leiden, Leiden University, Sylviusweg 72, 2333 BE, Leiden, Netherlands.; ENZA Zaden, Haling 1-E, 1602 DB, Enkhuizen, The Netherlands.
Plant genome editing and propagation are important tools in crop breeding and production. Both rely heavily on the development of efficient in vitro plant regeneration systems. Two prominent regeneration systems that are widely employed in crop production are somatic embryogenesis (SE) and de novo shoot regeneration. In many of the protocols for SE or shoot regeneration, explants are treated with the synthetic auxin analog 2,4-dichlorophenoxyacetic acid (2,4-D), since natural auxins, such as indole-3-acetic acid (IAA) or 4-chloroindole-3-acetic acid (4-Cl-IAA), are less effective or even fail to induce regeneration. Based on previous reports that 2,4-D, compared to endogenous auxins, is not effectively exported from plant cells, we investigated whether efflux inhibition of endogenous auxins could convert these auxins into efficient inducers of SE in Arabidopsis immature zygotic embryos (IZEs). We show that natural auxins and synthetic analogs thereof become efficient inducers of SE when their efflux is transiently inhibited by co-application of the auxin transport inhibitor naphthylphthalamic acid (NPA). Moreover, IZEs of auxin efflux mutants pin2 or abcb1 abcb19 show enhanced SE efficiency when treated with IAA or efflux-inhibited IAA, confirming that auxin efflux reduces the efficiency of Arabidopsis SE. Importantly, in contrast to the 2,4-D system, where only 50-60% of the embryos converted to seedlings, all SEs induced by transport-inhibited natural auxins converted to seedlings. Efflux-inhibited IAA, like 2,4-D, also efficiently induced SE from carrot suspension cells, whereas IAA alone could not, and efflux-inhibited 4-Cl-IAA significantly improved de novo shoot regeneration in Brassica napus. Our data provides new insights into the action of 2,4-D as an efficient inducer of plant regeneration but also shows that replacing this synthetic auxin for efflux-inhibited natural auxin significantly improves different types of plant regeneration, leading to a more synchronized and homogenous development of the regenerated plants.
PMID: 38361343
Plant J , IF:6.417 , 2024 Feb doi: 10.1111/tpj.16626
The peptide GOLVEN10 alters root development and noduletaxis in Medicago truncatula.
College of Agriculture, Tennessee State University, Nashville, Tennessee, 37209, USA.; Noble Research Institute, LLC, Ardmore, Oklahoma, 73401, USA.; Institute of Agricultural Biosciences, Oklahoma State University, Ardmore, Oklahoma, 73401, USA.; Sainsbury Laboratory, University of Cambridge, Cambridge, CB2 1LR, UK.; Shanghai Institute of Plant Physiology and Ecology, Shanghai, 200032, China.; University of Queensland, Brisbane, Australia.
The conservation of GOLVEN (GLV)/ROOT MERISTEM GROWTH FACTOR (RGF) peptide encoding genes across plant genomes capable of forming roots or root-like structures underscores their potential significance in the terrestrial adaptation of plants. This study investigates the function and role of GOLVEN peptide-coding genes in Medicago truncatula. Five out of fifteen GLV/RGF genes were notably upregulated during nodule organogenesis and were differentially responsive to nitrogen deficiency and auxin treatment. Specifically, the expression of MtGLV9 and MtGLV10 at nodule initiation sites was contingent upon the NODULE INCEPTION transcription factor. Overexpression of these five nodule-induced GLV genes in hairy roots of M. truncatula and application of their synthetic peptide analogues led to a decrease in nodule count by 25-50%. Uniquely, the GOLVEN10 peptide altered the positioning of the first formed lateral root and nodule on the primary root axis, an observation we term 'noduletaxis'; this decreased the length of the lateral organ formation zone on roots. Histological section of roots treated with synthetic GOLVEN10 peptide revealed an increased cell number within the root cortical cell layers without a corresponding increase in cell length, leading to an elongation of the root likely introducing a spatiotemporal delay in organ formation. At the transcription level, the GOLVEN10 peptide suppressed expression of microtubule-related genes and exerted its effects by changing expression of a large subset of Auxin responsive genes. These findings advance our understanding of the molecular mechanisms by which GOLVEN peptides modulate root morphology, nodule ontogeny, and interactions with key transcriptional pathways.
PMID: 38361340
Commun Biol , IF:6.268 , 2024 Feb , V7 (1) : P161 doi: 10.1038/s42003-024-05848-9
3,4-Dichlorophenylacetic acid acts as an auxin analog and induces beneficial effects in various crops.
Tianjin Key Laboratory of Protein Sciences, Department of Plant Biology and Ecology, College of Life Sciences, Nankai University, 300071, Tianjin, China.; Zhengzhou ZhengShi Chemical Co., Ltd, 450000, Zhengzhou, China.; National Pesticide Engineering Research Center (Tianjin), College of Chemistry, Nankai University, 300071, Tianjin, China. bianqiang@nankai.edu.cn.; Tianjin Key Laboratory of Protein Sciences, Department of Plant Biology and Ecology, College of Life Sciences, Nankai University, 300071, Tianjin, China. shuzhenmen@nankai.edu.cn.
Auxins and their analogs are widely used to promote root growth, flower and fruit development, and yield in crops. The action characteristics and application scope of various auxins are different. To overcome the limitations of existing auxins, expand the scope of applications, and reduce side effects, it is necessary to screen new auxin analogs. Here, we identified 3,4-dichlorophenylacetic acid (Dcaa) as having auxin-like activity and acting through the auxin signaling pathway in plants. At the physiological level, Dcaa promotes the elongation of oat coleoptile segments, the generation of adventitious roots, and the growth of crop roots. At the molecular level, Dcaa induces the expression of auxin-responsive genes and acts through auxin receptors. Molecular docking results showed that Dcaa can bind to auxin receptors, among which TIR1 has the highest binding activity. Application of Dcaa at the root tip of the DR5:GUS auxin-responsive reporter induces GUS expression in the root hair zone, which requires the PIN2 auxin efflux carrier. Dcaa also inhibits the endocytosis of PIN proteins like other auxins. These results provide a basis for the application of Dcaa in agricultural practices.
PMID: 38332111
Int J Mol Sci , IF:5.923 , 2024 Feb , V25 (4) doi: 10.3390/ijms25042260
Genome-Wide Identification of the Paulownia fortunei Aux/IAA Gene Family and Its Response to Witches' Broom Caused by Phytoplasma.
College of Forestry, Henan Agricultural University, Zhengzhou 450002, China.; Institute of Paulownia, Henan Agricultural University, Zhengzhou 450002, China.
The typical symptom of Paulownia witches' broom (PaWB), caused by phytoplasma infection, is excessive branching, which is mainly triggered by auxin metabolism disorder. Aux/IAA is the early auxin-responsive gene that participates in regulating plant morphogenesis such as apical dominance, stem elongation, lateral branch development, and lateral root formation. However, no studies have investigated the response of the Aux/IAA gene family to phytoplasma infection in Paulownia fortunei. In this study, a total of 62 Aux/IAA genes were found in the genome. Phylogenetic analysis showed that PfAux/IAA genes could be divided into eight subgroups, which were formed by tandem duplication and fragment replication. Most of them had a simple gene structure, and several members lacked one or two conserved domains. By combining the expression of PfAux/IAA genes under phytoplasma stress and SA-treated phytoplasma-infected seedlings, we found that PfAux/IAA13/33/45 may play a vital role in the occurrence of PaWB. Functional analysis based on homologous relationships showed a strong correlation between PfAux/IAA45 and branching. Protein-protein interaction prediction showed that PfARF might be the binding partner of PfAux/IAA, and the yeast two-hybrid assay and bimolecular fluorescent complementary assay confirmed the interaction of PfAux/IAA45 and PfARF13. This study provides a theoretical basis for further understanding the function of the PfAux/IAA gene family and exploring the regulatory mechanism of branching symptoms caused by PaWB.
PMID: 38396939
Int J Mol Sci , IF:5.923 , 2024 Feb , V25 (4) doi: 10.3390/ijms25042250
Transcriptome Analysis Reveals the Mechanism by Which Exogenous Melatonin Treatment Delays Leaf Senescence of Postharvest Chinese Kale (Brassica oleracea var. alboglabra).
College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China.
Melatonin, a pleiotropic small molecule, is employed in horticultural crops to delay senescence and preserve postharvest quality. In this study, 100 microM melatonin treatment delayed a decline in the color difference index h* and a*, maintaining the content of chlorophyll and carotenoids, thereby delaying the yellowing and senescence of Chinese kale. Transcriptome analysis unequivocally validates melatonin's efficacy in delaying leaf senescence in postharvest Chinese kale stored at 20 degrees C. Following a three-day storage period, the melatonin treatment group exhibited 1637 differentially expressed genes (DEGs) compared to the control group. DEG analysis elucidated that melatonin-induced antisenescence primarily governs phenylpropanoid biosynthesis, lipid metabolism, plant signal transduction, and calcium signal transduction. Melatonin treatment up-regulated core enzyme genes associated with general phenylpropanoid biosynthesis, flavonoid biosynthesis, and the alpha-linolenic acid biosynthesis pathway. It influenced the redirection of lignin metabolic flux, suppressed jasmonic acid and abscisic acid signal transduction, and concurrently stimulated auxin signal transduction. Additionally, melatonin treatment down-regulated RBOH expression and up-regulated genes encoding CaM, thereby influencing calcium signal transduction. This study underscores melatonin as a promising approach for delaying leaf senescence and provides insights into the mechanism of melatonin-mediated antisenescence in postharvest Chinese kale.
PMID: 38396927
Int J Mol Sci , IF:5.923 , 2024 Feb , V25 (4) doi: 10.3390/ijms25041975
Do DEEPER ROOTING 1 Homologs Regulate the Lateral Root Slope Angle in Cucumber (Cucumis sativus)?
Laboratory of Cellular and Molecular Mechanisms of Plant Development, Komarov Botanical Institute, Russian Academy of Sciences, 197022 Saint Petersburg, Russia.; Department of Ecology, Environment and Plant Sciences, Stockholm University, 10691 Stockholm, Sweden.
The architecture of the root system is fundamental to plant productivity. The rate of root growth, the density of lateral roots, and the spatial structure of lateral and adventitious roots determine the developmental plasticity of the root system in response to changes in environmental conditions. One of the genes involved in the regulation of the slope angle of lateral roots is DEEPER ROOTING 1 (DRO1). Its orthologs and paralogs have been identified in rice, Arabidopsis, and several other species. However, nothing is known about the formation of the slope angle of lateral roots in species with the initiation of lateral root primordia within the parental root meristem. To address this knowledge gap, we identified orthologs and paralogs of the DRO1 gene in cucumber (Cucumis sativus) using a phylogenetic analysis of IGT protein family members. Differences in the transcriptional response of CsDRO1, CsDRO1-LIKE1 (CsDRO1L1), and CsDRO1-LIKE2 (CsDRO1L2) to exogenous auxin were analyzed. The results showed that only CsDRO1L1 is auxin-responsive. An analysis of promoter-reporter fusions demonstrated that the CsDRO1, CsDRO1L1, and CsDRO1L2 genes were expressed in the meristem in cell files of the central cylinder, endodermis, and cortex; the three genes displayed different expression patterns in cucumber roots with only partial overlap. A knockout of individual CsDRO1, CsDRO1L1, and CsDRO1L2 genes was performed via CRISPR/Cas9 gene editing. Our study suggests that the knockout of individual genes does not affect the slope angle formation during lateral root primordia development in the cucumber parental root.
PMID: 38396652
Int J Mol Sci , IF:5.923 , 2024 Feb , V25 (3) doi: 10.3390/ijms25031778
Transcriptome Analysis of White- and Red-Fleshed Apple Fruits Uncovered Novel Genes Related to the Regulation of Anthocyanin Biosynthesis.
The National Institute of Horticultural Research, Konstytucji 3-go Maja, 96-100 Skierniewice, Poland.; Yantai Academy of Agricultural Science, Gangechengxida Street No 26, Fushan District, Yantai 265500, China.; Department of Plant Genetics Breeding and Biotechnology, Warsaw University of Life Sciences, Nowoursynowska 159, 02-776 Warsaw, Poland.
The red flesh coloration of apples is a result of a biochemical pathway involved in the biosynthesis of anthocyanins and anthocyanidins. Based on apple genome analysis, a high number of regulatory genes, mainly transcription factors such as MYB, which are components of regulatory complex MYB-bHLH-WD40, and several structural genes (PAL, 4CL, CHS, CHI, F3H, DFR, ANS, UFGT) involved in anthocyanin biosynthesis, have been identified. In this study, we investigated novel genes related to the red-flesh apple phenotype. These genes could be deemed molecular markers for the early selection of new apple cultivars. Based on a comparative transcriptome analysis of apples with different fruit-flesh coloration, we successfully identified and characterized ten potential genes from the plant hormone transduction pathway of auxin (GH3); cytokinins (B-ARR); gibberellins (DELLA); abscisic acid (SnRK2 and ABF); brassinosteroids (BRI1, BZR1 and TCH4); jasmonic acid (MYC2); and salicylic acid (NPR1). An analysis of expression profiles was performed in immature and ripe fruits of red-fleshed cultivars. We have uncovered genes mediating the regulation of abscisic acid, salicylic acid, cytokinin, and jasmonic acid signaling and described their role in anthocyanin biosynthesis, accumulation, and degradation. The presented results underline the relationship between genes from the hormone signal transduction pathway and UFGT genes, which are directly responsible for anthocyanin color transformation as well as anthocyanin accumulation during apple-fruit ripening.
PMID: 38339057
PLoS Genet , IF:5.917 , 2024 Feb , V20 (2) : Pe1011135 doi: 10.1371/journal.pgen.1011135
ZmARF1 positively regulates low phosphorus stress tolerance via modulating lateral root development in maize.
State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, China.; Maize Research Institute, Sichuan Agricultural University, Wenjiang, Sichuan, China.; Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, China.; Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Sichuan, China.
Phosphorus (P) deficiency is one of the most critical factors for plant growth and productivity, including its inhibition of lateral root initiation. Auxin response factors (ARFs) play crucial roles in root development via auxin signaling mediated by genetic pathways. In this study, we found that the transcription factor ZmARF1 was associated with low inorganic phosphate (Pi) stress-related traits in maize. This superior root morphology and greater phosphate stress tolerance could be ascribed to the overexpression of ZmARF1. The knock out mutant zmarf1 had shorter primary roots, fewer root tip number, and lower root volume and surface area. Transcriptomic data indicate that ZmLBD1, a direct downstream target gene, is involved in lateral root development, which enhances phosphate starvation tolerance. A transcriptional activation assay revealed that ZmARF1 specifically binds to the GC-box motif in the promoter of ZmLBD1 and activates its expression. Moreover, ZmARF1 positively regulates the expression of ZmPHR1, ZmPHT1;2, and ZmPHO2, which are key transporters of Pi in maize. We propose that ZmARF1 promotes the transcription of ZmLBD1 to modulate lateral root development and Pi-starvation induced (PSI) genes to regulate phosphate mobilization and homeostasis under phosphorus starvation. In addition, ZmERF2 specifically binds to the ABRE motif of the promoter of ZmARF1 and represses its expression. Collectively, the findings of this study revealed that ZmARF1 is a pivotal factor that modulates root development and confers low-Pi stress tolerance through the transcriptional regulation of the biological function of ZmLBD1 and the expression of key Pi transport proteins.
PMID: 38315718
J Fungi (Basel) , IF:5.816 , 2024 Feb , V10 (2) doi: 10.3390/jof10020158
A New Biocontrol Agent Bacillus velezensis SF334 against Rubber Tree Fungal Leaf Anthracnose and Its Genome Analysis of Versatile Plant Probiotic Traits.
Shanghai Collaborative Innovation Center of Agri-Seeds, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China.; National Key Laboratory for Tropical Crop Breeding, Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Sanya 572024, China.; School of Agriculture, Yangtze University, Jingzhou 434000, China.; State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai 200240, China.; Sanya Research Institute, Chinese Academy of Tropical Agricultural Sciences, Sanya 572020, China.
Natural rubber is an important national strategic and industrial raw material. The leaf anthracnose of rubber trees caused by the Colletotrichum species is one of the important factors restricting the yields of natural rubber. In this study, we isolated and identified strain Bacillus velezensis SF334, which exhibited significant antagonistic activity against both C. australisinense and C. siamense, the dominant species of Colletotrichum causing rubber tree leaf anthracnose in the Hainan province of China, from a pool of 223 bacterial strains. The cell suspensions of SF334 had a significant prevention effect for the leaf anthracnose of rubber trees, with an efficacy of 79.67% against C. siamense and 71.8% against C. australisinense. We demonstrated that SF334 can lead to the lysis of C. australisinense and C. siamense mycelia by causing mycelial expansion, resulting in mycelial rupture and subsequent death. B. velezensis SF334 also harbors some plant probiotic traits, such as secreting siderophore, protease, cellulase, pectinase, and the auxin of indole-3-acetic acid (IAA), and it has broad-spectrum antifungal activity against some important plant pathogenic fungi. The genome combined with comparative genomic analyses indicated that SF334 possesses most genes of the central metabolic and gene clusters of secondary metabolites in B. velezensis strains. To our knowledge, this is the first time a Bacillus velezensis strain has been reported as a promising biocontrol agent against the leaf anthracnose of rubber trees caused by C. siamense and C. australisinense. The results suggest that B. velezensis could be a potential candidate agent for the leaf anthracnose of rubber trees.
PMID: 38392830
Front Plant Sci , IF:5.753 , 2024 , V15 : P1343928 doi: 10.3389/fpls.2024.1343928
Modulating root system architecture: cross-talk between auxin and phytohormones.
College of Horticulture, South China Agricultural University, Guangzhou, Guangdong, China.; Guangdong Provincial Key Laboratory of Utilization and Conservation of Food and Medicinal Resources in Northern Region, Shaoguan University, Shaoguan, China.; College of Agriculture, South China Agricultural University, Guangzhou, Guangdong, China.; Department of Agronomy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China.; Heyuan Division of Guangdong Laboratory for Lingnan Modern Agricultural Science and Technology, Heyuan, Guangdong, China.
Root architecture is an important agronomic trait that plays an essential role in water uptake, soil compactions, nutrient recycling, plant-microbe interactions, and hormone-mediated signaling pathways. Recently, significant advancements have been made in understanding how the complex interactions of phytohormones regulate the dynamic organization of root architecture in crops. Moreover, phytohormones, particularly auxin, act as internal regulators of root development in soil, starting from the early organogenesis to the formation of root hair (RH) through diverse signaling mechanisms. However, a considerable gap remains in understanding the hormonal cross-talk during various developmental stages of roots. This review examines the dynamic aspects of phytohormone signaling, cross-talk mechanisms, and the activation of transcription factors (TFs) throughout various developmental stages of the root life cycle. Understanding these developmental processes, together with hormonal signaling and molecular engineering in crops, can improve our knowledge of root development under various environmental conditions.
PMID: 38390293
Front Plant Sci , IF:5.753 , 2024 , V15 : P1284125 doi: 10.3389/fpls.2024.1284125
A non-canonical Aux/IAA gene MsIAA32 regulates peltate glandular trichome development in spearmint.
Temasek Life Sciences Laboratory, National University of Singapore, Singapore, Singapore.
Phytohormone auxin controls various aspects of plant growth and development. The typical auxin signalling involves the degradation of canonical Aux/IAA proteins upon auxin perception releasing the auxin response factors (ARF) to activate auxin-regulated gene expression. Extensive research has been pursued in deciphering the role of canonical Aux/IAAs, however, the function of non-canonical Aux/IAA genes remains elusive. Here we identified a non-canonical Aux/IAA gene, MsIAA32 from spearmint (Mentha spicata), which lacks the TIR1-binding domain and shows its involvement in the development of peltate glandular trichomes (PGT), which are the sites for production and storage of commercially important essential oils. Using yeast two-hybrid studies, two canonical Aux/IAAs, MsIAA3, MsIAA4 and an ARF, MsARF3 were identified as the preferred binding partners of MsIAA32. Expression of a R2R3-MYB gene MsMYB36 and a cyclin gene MsCycB2-4 was altered in MsIAA32 suppressed plants indicating that these genes are possible downstream targets of MsIAA32 mediated signalling. Ectopic expression of MsIAA32 in Arabidopsis affected non-glandular trichome formation along with other auxin related developmental traits. Our findings establish the role of non-canonical Aux/IAA mediated auxin signalling in PGT development and reveal species-specific functionalization of Aux/IAAs.
PMID: 38375083
Front Plant Sci , IF:5.753 , 2024 , V15 : P1260140 doi: 10.3389/fpls.2024.1260140
Integrated physiological, transcriptomic, and metabolomic analyses of drought stress alleviation in Ehretia macrophylla Wall. seedlings by SiO(2) NPs (silica nanoparticles).
Pingdingshan University, Henan Province Key Laboratory of Germplasm Innovation and Utilization of Eco-economic Woody Plant, Pingdingshan, China.; College of Agriculture, Henan University of Science and Technology, Luoyang, China.; College of Forestry, Henan Agricultural University, Zhengzhou, Henan, China.
With environmental problems such as climate global warming, drought has become one of the major stress factors, because it severely affects the plant growth and development. Silicon dioxide nanoparticles (SiO(2) NPs) are crucial for mitigating abiotic stresses suffered by plants in unfavorable environmental conditions and further promoting plant growth, such as drought. This study aimed to investigate the effect of different concentrations of SiO(2) NPs on the growth of the Ehretia macrophylla Wall. seedlings under severe drought stress (water content in soil, 30-35%). The treatment was started by starting spraying different concentrations of SiO2 NPs on seedlings of Ehretia macrophyla, which were consistently under normal and severe drought conditions (soil moisture content 30-35%), respectively, at the seedling stage, followed by physiological and biochemical measurements, transcriptomics and metabolomics analyses. SiO(2) NPs (100 mg.L(-1)) treatment reduced malondialdehyde and hydrogen peroxide content and enhanced the activity of antioxidant enzymes under drought stress. Transcriptomic analysis showed that 1451 differentially expressed genes (DEGs) in the leaves of E. macrophylla seedlings were regulated by SiO(2) NPs under drought stress, and these genes mainly participate in auxin signal transduction and mitogen-activated protein kinase signaling pathways. This study also found that the metabolism of fatty acids and alpha-linolenic acids may play a key role in the enhancement of drought tolerance in SiO(2) NP-treated E. macrophylla seedlings. Metabolomics studies indicated that the accumulation level of secondary metabolites related to drought tolerance was higher after SiO(2) NPs treatment. This study revealed insights into the physiological mechanisms induced by SiO(2) NPs for enhancing the drought tolerance of plants.
PMID: 38371410
Microbiol Res , IF:5.415 , 2024 Feb , V282 : P127639 doi: 10.1016/j.micres.2024.127639
Mechanisms on salt tolerant of Paenibacillus polymyxa SC2 and its growth-promoting effects on maize seedlings under saline conditions.
College of Life Sciences, Shandong Engineering Research Center of Plant-Microbia Restoration for Saline-alkali Land, Shandong Key Laboratory of Agricultural Microbiology, National Engineering Research Center for Efficient Utilization of Soil and Fertilizer Resources, Shandong Agricultural University, Tai'an 271018, China. Electronic address: wangcq@sdau.edu.cn.; College of Life Sciences, Shandong Engineering Research Center of Plant-Microbia Restoration for Saline-alkali Land, Shandong Key Laboratory of Agricultural Microbiology, National Engineering Research Center for Efficient Utilization of Soil and Fertilizer Resources, Shandong Agricultural University, Tai'an 271018, China.; Institute of Wetland Agriculture and Ecology, Shandong Academy of Agricultural Sciences, Jinan 250100, China.; Department of Microbiology and Biotechnology, College of Life Sciences, Northeast Agricultural University, Harbin 150030, China. Electronic address: jjqdainty@163.com.; College of Life Sciences, Shandong Engineering Research Center of Plant-Microbia Restoration for Saline-alkali Land, Shandong Key Laboratory of Agricultural Microbiology, National Engineering Research Center for Efficient Utilization of Soil and Fertilizer Resources, Shandong Agricultural University, Tai'an 271018, China; College of Life Sciences, Dezhou University, Dezhou 253023, China. Electronic address: zhaodongying4321@163.com.
Soil salinity negatively affects microbial communities, soil fertility, and agricultural productivity and has become a major agricultural problem worldwide. Plant growth-promoting rhizobacteria (PGPR) with salt tolerance can benefit plant growth under saline conditions and diminish the negative effects of salt stress on plants. In this study, we aimed to understand the salt-tolerance mechanism of Paenibacillus polymyxa at the genetic and metabolic levels and elucidate the mechanism of strain SC2 in promoting maize growth under saline conditions. Under salt stress, we found that strain SC2 promoted maize seedling growth, which was accompanied by a significant upregulation of genes encoding for the biosynthesis of peptidoglycan, polysaccharide, and fatty acid, the metabolism of purine and pyrimidine, and the transport of osmoprotectants such as trehalose, glycine betaine, and K(+) in strain SC2. To further enhance the salt resistance of strain SC2, three mutants (SC2-11, SC2-13, and SC2-14) with higher capacities for salt resistance and exopolysaccharide synthesis were obtained via atmospheric and room-temperature plasma mutagenesis. In saline-alkaline soil, the mutants showed better promoting effect on maize seedlings than wild-type SC2. The fresh weight of maize seedlings was increased by 68.10% after treatment with SC2-11 compared with that of the control group. The transcriptome analysis of maize roots demonstrated that SC2 and SC2-11 could induce the upregulation of genes related to the plant hormone signal transduction, starch and sucrose metabolism, reactive oxygen species scavenging, and auxin and ethylene signaling under saline-alkaline stress. In addition, various transcription factors, such as zinc finger proteins, ethylene-responsive-element-binding protein, WRKY, myeloblastosis proteins, basic helix-loop-helix proteins, and NAC proteins, were up-regulated in response to abiotic stress. Moreover, the microbial community composition of maize rhizosphere soil after inoculating with strain SC2 was varied from the one after inoculating with mutant SC2-11. Our results provide new insights into the various genes involved in the salt resistance of strain SC2 and a theoretical basis for utilizing P. polymyxa in saline-alkaline environments.
PMID: 38354626
Microbiol Res , IF:5.415 , 2024 Apr , V281 : P127630 doi: 10.1016/j.micres.2024.127630
Molecular insights into the mutualism that induces iron deficiency tolerance in sorghum inoculated with Trichoderma harzianum.
School of Sciences, University of Louisiana at Monroe, LA 71209, USA; Department of Genetics, University of Georgia, Athens, GA 30602, USA. Electronic address: kabir@ulm.edu.; Department of Genetics, University of Georgia, Athens, GA 30602, USA. Electronic address: maize@uga.edu.
Iron (Fe) deficiency is a common mineral stress in plants, including sorghum. Although the soil fungus Trichoderma harzianum has been shown to mitigate Fe deficiency in some circumstances, neither the range nor mechanism(s) of this process are well understood. In this study, high pH-induced Fe deficiency in sorghum cultivated in pots with natural field soil exhibited a significant decrease in biomass, photosynthetic rate, transpiration rate, stomatal conductance, water use efficiency, and Fe-uptake in both the root and shoot. However, the establishment of T. harzianum colonization in roots of Fe-deprived sorghum showed significant improvements in morpho-physiological traits, Fe levels, and redox status. Molecular detection of the fungal ThAOX1 (L-aminoacid oxidase) gene showed the highest colonization of T. harzianum in the root tips of Fe-deficient sorghum, a location thus targeted for further analysis. Expression studies by RNA-seq and qPCR in sorghum root tips revealed a significant upregulation of several genes associated with Fe uptake (SbTOM2), auxin synthesis (SbSAURX15), nicotianamine synthase 3 (SbNAS3), and a phytosiderophore transporter (SbYS1). Also induced was the siderophore synthesis gene (ThSIT1) in T. harzianum, a result supported by biochemical evidence for elevated siderophore and IAA (indole acetic acid) levels in roots. Given the high affinity of fungal siderophore to chelate insoluble Fe(3+) ions, it is likely that elevated siderophore released by T. harzianum led to Fe(III)-siderophore complexes in the rhizosphere that were then transported into roots by the induced SbYS1 (yellow-stripe 1) transporter. In addition, the observed induction of several plant peroxidase genes and ABA (abscisic acid) under Fe deficiency after inoculation with T. harzianum may have helped induce tolerance to Fe-deficiency-induced oxidative stress and adaptive responses. This is the first mechanistic explanation for T. harzianum's role in helping alleviate Fe deficiency in sorghum and suggests that biofertilizers using T. harzianum will improve Fe availability to crops in high pH environments.
PMID: 38295681
Microbiol Res , IF:5.415 , 2024 Apr , V281 : P127602 doi: 10.1016/j.micres.2024.127602
Bacterial indole-3-acetic acid: A key regulator for plant growth, plant-microbe interactions, and agricultural adaptive resilience.
Soil Science Department, University of Tehran, Tehran, Iran. Electronic address: hassanetesami@ut.ac.ir.; Department of Biology, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada.
Indole-3-acetic acid (IAA), a fundamental phytohormone categorized under auxins, not only influences plant growth and development but also plays a critical role in plant-microbe interactions. This study reviews the role of IAA in bacteria-plant communication, with a focus on its biosynthesis, regulation, and the subsequent effects on host plants. Bacteria synthesize IAA through multiple pathways, which include the indole-3-acetamide (IAM), indole-3-pyruvic acid (IPyA), and several other routes, whose full mechanisms remain to be fully elucidated. The production of bacterial IAA affects root architecture, nutrient uptake, and resistance to various abiotic stresses such as drought, salinity, and heavy metal toxicity, enhancing plant resilience and thus offering promising routes to sustainable agriculture. Bacterial IAA synthesis is regulated through complex gene networks responsive to environmental cues, impacting plant hormonal balances and symbiotic relationships. Pathogenic bacteria have adapted mechanisms to manipulate the host's IAA dynamics, influencing disease outcomes. On the other hand, beneficial bacteria utilize IAA to promote plant growth and mitigate abiotic stresses, thereby enhancing nutrient use efficiency and reducing dependency on chemical fertilizers. Advancements in analytical methods, such as liquid chromatography-tandem mass spectrometry, have improved the quantification of bacterial IAA, enabling accurate measurement and analysis. Future research focusing on molecular interactions between IAA-producing bacteria and host plants could facilitate the development of biotechnological applications that integrate beneficial bacteria to improve crop performance, which is essential for addressing the challenges posed by climate change and ensuring global food security. This integration of bacterial IAA producers into agricultural practice promises to revolutionize crop management strategies by enhancing growth, fostering resilience, and reducing environmental impact.
PMID: 38228017
Microbiol Res , IF:5.415 , 2024 Apr , V281 : P127594 doi: 10.1016/j.micres.2023.127594
The plant growth promoting rhizobacterium Achromobacter sp. 5B1, rescues Arabidopsis seedlings from alkaline stress by enhancing root organogenesis and hormonal responses.
Instituto de Investigaciones Quimico-Biologicas, Universidad Michoacana de San Nicolas de Hidalgo, Edificio B3, Ciudad Universitaria, C. P., 58030 Morelia, Michoacan, Mexico.; Facultad de Quimico Farmacobiologia, Universidad Michoacana de San Nicolas de Hidalgo, Avenida Tzintzuntzan 173; Col. Matamoros, 58240 Morelia, Michoacan, Mexico.; Catedratico CONACYT-Instituto de Investigaciones Quimico-Biologicas, Universidad Michoacana de San Nicolas de Hidalgo, Edificio B3, Ciudad Universitaria, C. P., 58030 Morelia, Michoacan, Mexico.; Red de Estudios Moleculares Avanzados, Instituto de Ecologia A.C., Carretera Antigua a Coatepec 351, El Haya, C.P. 91070, Xalapa, Ver, Mexico; Departamento de la Conservacion de la Biodiversidad, El Colegio de la Frontera Sur., Carretera Villahermosa-Reforma Km 15.5, Rancheria el Guineo, Seccion II C.P., 86280 Villahermosa, Tabasco, Mexico.; Red de Estudios Moleculares Avanzados, Instituto de Ecologia A.C., Carretera Antigua a Coatepec 351, El Haya, C.P. 91070, Xalapa, Ver, Mexico.; Instituto de Investigaciones Quimico-Biologicas, Universidad Michoacana de San Nicolas de Hidalgo, Edificio B3, Ciudad Universitaria, C. P., 58030 Morelia, Michoacan, Mexico. Electronic address: jbucio@umich.mx.
Soil alkalinity is a critical environmental factor for plant growth and distribution in ecosystems. An alkaline condition (pH > 7) is imposed by the rising concentration of hydroxides and cations, and prevails in semiarid and arid environments, which represent more than 25% of the total arable land of the world. Despite the great pressure exerted by alkalinity for root viability and plant survival, scarce information is available to understand how root microbes contribute to alkaline pH adaptation. Here, we assessed the effects of alkalinity on shoot and root biomass production, chlorophyll content, root growth and branching, lateral root primordia formation, and the expression of CYCB1, TOR kinase, and auxin and cytokinin-inducible trangenes in shoots and roots of Arabidopsis seedlings grown in Petri plates with agar-nutrient medium at pH values of 7.0, 7.5, 8.0, 8.5, and 9.0. The results showed an inverse correlation between the rise of pH and most growth, hormonal and genetic traits analyzed. Noteworthy, root inoculation with Achromobacter sp. 5B1, a beneficial rhizospheric bacterium, with plant growth promoting and salt tolerance features, increased biomass production, restored root growth and branching and enhanced auxin responses in WT seedlings and auxin-related mutants aux1-7 and eir1, indicating that stress adaptation operates independently of canonical auxin transporter proteins. Sequencing of the Achromobacter sp. 5B1 genome unveiled 5244 protein-coding genes, including genes possibly involved in auxin biosynthesis, quorum-sensing regulation and stress adaptation, which may account for its plant growth promotion attributes. These data highlight the critical role of rhizobacteria to increase plant resilience under high soil pH conditions potentially through genes for adaptation to an extreme environment and bacteria-plant communication.
PMID: 38211416
Microbiol Res , IF:5.415 , 2024 Mar , V280 : P127566 doi: 10.1016/j.micres.2023.127566
Phenotypic, genomic and in planta characterization of Bacillus sensu lato for their phosphorus biofertilization and plant growth promotion features in soybean.
Bioinsumos, Area de Recursos Naturales, Produccion y Ambiente, Instituto Nacional de Investigacion Agropecuaria (INIA Uruguay), Uruguay.; Unidad Mixta Pasteur+INIA, Institut Pasteur de Montevideo, Uruguay.; Bioinsumos, Area de Recursos Naturales, Produccion y Ambiente, Instituto Nacional de Investigacion Agropecuaria (INIA Uruguay), Uruguay; Area Mejoramiento Genetico y Biotecnologia Vegetal, Instituto Nacional de Investigacion Agropecuaria (INIA Uruguay), Uruguay.; Bioinsumos, Area de Recursos Naturales, Produccion y Ambiente, Instituto Nacional de Investigacion Agropecuaria (INIA Uruguay), Uruguay. Electronic address: eabreo@inia.org.uy.
Bacillus sensu lato were screened for their capacity to mineralize organic phosphorus (P) and promote plant growth, improving nitrogen (N) and P nutrition of soybean. Isolates were identified through Type Strain Genome Server (TYGS) and Average Nucleotide Identity (ANI). ILBB95, ILBB510 and ILBB592 were identified as Priestia megaterium, ILBB139 as Bacillus wiedmannii, ILBB44 as a member of a sister clade of B. pumilus, ILBB15 as Peribacillus butanolivorans and ILBB64 as Lysinibacillus sp. These strains were evaluated for their capacity to mineralize sodium phytate as organic P and solubilize inorganic P in liquid medium. These assays ranked ILBB15 and ILBB64 with the highest orthophosphate production from phytate. Rhizocompetence and plant growth promotion traits were evaluated in vitro and in silico. Finally, plant bioassays were conducted to assess the effect of the co-inoculation with rhizobial inoculants on nodulation, N and P nutrition. These bioassays showed that B. pumilus, ILBB44 and P. megaterium ILBB95 increased P-uptake in plants on the poor substrate of sand:vermiculite and also on a more fertile mix. Priestia megaterium ILBB592 increased nodulation and N content in plants on the sand:vermiculite:peat mixture. Peribacillus butanolivorans ILBB15 reduced plant growth and nutrition on both substrates. Genomes of ILBB95 and ILBB592 were characterized by genes related with plant growth and biofertilization, whereas ILBB15 was differentiated by genes related to bioremediation. Priestia megaterium ILBB592 is considered as nodule-enhancing rhizobacteria and together with ILBB95, can be envisaged as prospective PGPR with the capacity to exert positive effects on N and P nutrition of soybean plants.
PMID: 38100951
J Agric Food Chem , IF:5.279 , 2024 Feb , V72 (8) : P4476-4492 doi: 10.1021/acs.jafc.3c07768
A Comprehensive Analysis of Transcriptomics and Metabolomics Revealed Key Pathways Involved in Saccharum spontaneum Defense against Sporisorium scitamineum.
National Key Laboratory for Biological Breeding of Tropical Crops, Kunming 650221, China.; Sugarcane Research Institute, Yunnan Academy of Agricultural Sciences/Yunnan Key Laboratory of Sugarcane Genetic Improvement, Kaiyuan 661699, China.; Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs (Yunnan), Kaiyuan 661699, China.; Sugar Crops Research Institute, Agricultural Research Center, Giza 12619, Egypt.
Sugarcane smut, caused by Sporisorium scitamineum, poses a severe threat to sugarcane production. The genetic basis of sugarcane resistance to S. scitamineum remains elusive. A comparative transcriptomic and metabolomic study was conducted on two wild Saccharum species of S. spontaneum with contrast smut resistance. Following infection, the resistant line exhibited greater down-regulation of genes and metabolites compared to the susceptible line, indicating distinct biological processes. Lignan and lignin biosynthesis and SA signal transduction were activated in the resistant line, while flavonoid biosynthesis and auxin signal transduction were enhanced in the susceptible line. TGA2.2 and ARF14 were identified as playing positive and negative roles, respectively, in plant defense. Exogenous auxin application significantly increased the susceptibility of S. spontaneum to S. scitaminum. This study established the significant switching of defense signaling pathways in contrast-resistant S. spontaneum following S. scitamineum infection, offering a hypothetical model and candidate genes for further research into sugarcane smut disease.
PMID: 38373255
Chemistry , IF:5.236 , 2024 Feb : Pe202400066 doi: 10.1002/chem.202400066
Spiropyran-Based Photoisomerizable alpha-Amino Acid for Membrane-Active Peptide Modification.
Karlsruhe Institute of Technology, Institute of Biological Interfaces (IBG-2), POB 3640, 76021, Karlsruhe, GERMANY.; Institute of Organic Synthesis of the Latvian Academy of Sciences, Organic Synthesis Methodology group, Aizkraukles iela 21, 1006, Riga, LATVIA.; Enamine Ltd, R & D, Vul. Winstona Churchilla 78, 02094, Kyiv, UKRAINE.; Enamine Ltd, Organic Synthesis, Vul. Winstona Churchilla 78, 02094, Kyiv, UKRAINE.; Karlsruhe Institute of Technology, Joseph Kolreuter Institute for Plant Sciences, POB 3640, 76021, Karlsruhe, GERMANY.; Taras Shevchenko National University of Kyiv Institute of High Technologies: Kiivs'kij nacional'nij universitet imeni Tarasa Sevcenka Institut visokih tehnologij, Institute of High Technologies, Volodymyrska 60, 1601, Kyiv, UKRAINE.
Photoisomerizable peptides are promising drug candidates in photopharmacology. While azobenzene- and diarylethene-containing photoisomerizable peptides have already demonstrated their potential in this regard, reports on the use of spiropyrans to photoregulate bioactive peptides are still scarce. This work focuses on the design and synthesis of a spiropyran-derived amino acid, (S)-2-amino-3-(6 -methoxy-1 ,3 ,3 -trimethylspiro-[2H-1-benzopyran-2,2 -indolin-6-yl])propanoic acid, which is suitable for the preparation of photoisomerizable peptides. The utility of this amino acid is demonstrated by incorporating it into the backbone of BP100, a known membrane-active peptide, and by examining the photoregulation of the membrane perturbation by the spiropyran-containing peptides. The toxicity of the peptides (against the plant cell line BY-2), their bacteriotoxicity (E. coli), and actin-auxin oscillator modulation ability were shown to be significantly dependent on the photoisomeric state of the spiropyran unit.
PMID: 38366887
Plant Cell Physiol , IF:4.927 , 2024 Feb doi: 10.1093/pcp/pcae014
Recent advances in understanding the regulatory mechanism of plasma membrane H+-ATPase through the brassinosteroid signaling pathway.
Fujian Provincial Key Laboratory of Plant Functional Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China.; School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China.
The polyhydroxylated steroid phytohormone brassinosteroids (BRs) control many aspects of plant growth, development and responses to environmental changes. Plasma membrane (PM) H+-ATPase, the well-known PM proton pump, is a central regulator in plant physiology, which mediates not only plant growth and development, but also adaptation to stresses. Recent studies highlight that PM H+-ATPase is at least partly regulated via the BR signaling. Firstly, the BR cell surface receptor BRASSINOSTEROID-INSENSITIVE 1 (BRI1) and multiple key components of BR signaling directly or indirectly influence PM H+-ATPase activity. Secondly, the SMALL AUXIN UP RNA (SAUR) gene family physically interacts with BRI1 to enhance organ development of Arabidopsis by activating PM H+-ATPase. Thirdly, RNA-sequencing (RNA-seq) assays showed that the expression of some SAUR genes is upregulated under the light or sucrose conditions, which is related to the phosphorylation state of the penultimate residue of PM H+-ATPase in a time-course manner. In this review, we describe the structural and functional features of PM H+-ATPase, and summarize recent progress toward understanding the regulatory mechanism of PM H+-ATPase by BRs, and briefly introduce how PM H+-ATPase activity is modulated by its own biterminal regions and the post-translational modifications.
PMID: 38372617
Pest Manag Sci , IF:4.845 , 2024 Mar , V80 (3) : P1423-1434 doi: 10.1002/ps.7873
Bacillus velezensis WB induces systemic resistance in watermelon against Fusarium wilt.
College of Life Science and Agroforestry, Qiqihar University, Qiqihar, China.; Heilongjiang Provincial Technology Innovation Center of Agromicrobial Preparation Industrialization, Qiqihar, China.; Heilongjiang Provincial Collaborative Innovation Center of Agrobiological Preparation Industrialization, Qiqihar, China.
BACKGROUND: Our previous findings indicated that Bacillus velezensis WB could control Fusarium wilt by changing the structure of the microbial community in the watermelon rhizosphere. However, there are few studies on its mechanism in the pathogen resistance of watermelon. Therefore, in this study, we determined the mechanism of B. velezensis WB-induced systemic resistance in watermelon against Fusarium wilt through glasshouse pot experiments. RESULTS: The results showed that B. velezensis WB significantly reduced the incidence and disease index of Fusarium wilt in watermelon. B. velezensis WB can enhance the basal immunity of watermelon plants by: increasing the activity of phenylalanine ammonia-lyase (PAL), peroxidase (POD), superoxide dismutase (SOD) and beta-1,3-glucanase; accumulating lignin, salicylic acid (SA) and jasmonic acid (JA); reducing malondialdehyde (MDA) concentrations; and inducing callus deposition in watermelon plant cells. RNA-seq analysis showed that 846 watermelon genes were upregulated and 612 watermelon genes were downregulated in the WF treatment. This process led to the activation of watermelon genes associated with auxin, gibberellin, SA, ethylene and JA, and the expression of genes in the phenylalanine biosynthetic pathway was upregulated. In addition, transcription factors involved in plant resistance to pathogens, such as MYB, NAC and WRKY, were induced. Gene correlation analysis showed that Cla97C10G195840 and Cla97C02G049930 in the phenylalanine biosynthetic pathway, and Cla97C02G041360 and Cla97C10G197290 in the plant hormone signal transduction pathway showed strong correlations with other genes. CONCLUSION: Our results indicated that B. velezensis WB is capable of inducing systemic resistance in watermelon against Fusarium wilt. (c) 2023 Society of Chemical Industry.
PMID: 37939121
Pest Manag Sci , IF:4.845 , 2024 Feb , V80 (2) : P637-647 doi: 10.1002/ps.7791
Prevalence, spatial structure and evolution of resistance to acetolactate-synthase (ALS) inhibitors and 2,4-D in the major weed Papaver rhoeas (L.) assessed using a massive, country-wide sampling.
Agroecologie, INRAE, Dijon, France.; Plateforme GeT-Biopuces, TBI, Universite de Toulouse, CNRS, INRAE, INSA, Genotoul, Toulouse, France.
BACKGROUND: Corn poppy (Papaver rhoeas) is the most damaging broadleaf weed in France. Massively parallel amplicon sequencing was used to investigate the prevalence, mode of evolution and spread of resistance-endowing ALS alleles in 422 populations randomly sampled throughout poppy's range in France. Bioassays were used to detect resistance to the synthetic auxin 2,4-D in 43 of these populations. RESULTS: A total of 21 100 plants were analysed and 24 mutant ALS alleles carrying an amino-acid substitution involved or potentially involved in resistance were identified. The vast majority (97.6%) of the substitutions occurred at codon Pro197, where all six possible single-nucleotide non-synonymous substitutions plus four double-nucleotide substitutions were identified. Changes observed in the enzymatic properties of the mutant ALS isoforms could not explain the differences in prevalence among the corresponding alleles. Sequence read analysis showed that mutant ALS alleles had multiple, independent evolutionary origins, and could have evolved several times independently within an area of a few kilometres. Finally, 2,4-D resistance was associated with mutant ALS alleles in individual plants in one third of the populations assayed. CONCLUSION: The intricate geographical mosaic of mutant ALS alleles observed is the likely result of the combination of huge population sizes, multiple independent mutation events and human-mediated spread of resistance. Our work highlights the ability of poppy populations and individual plants to accumulate different ALS alleles and as yet unknown mechanisms conferring resistance to synthetic auxins. This does not bode well for the continued use of chemical herbicides to control poppy. (c) 2023 Society of Chemical Industry.
PMID: 37752099
Plant Sci , IF:4.729 , 2024 Feb : P112050 doi: 10.1016/j.plantsci.2024.112050
Plant-specific environmental and developmental signals regulate the mismatch repair protein MSH6 in Arabidopsis thaliana.
Centro de Estudios Fotosinteticos y Bioquimicos (CEFOBI), Facultad de Ciencias Bioquimicas y Farmaceuticas, Universidad Nacional de Rosario, Suipacha 531, 2000 Rosario, Argentina.; Centro de Estudios Fotosinteticos y Bioquimicos (CEFOBI), Facultad de Ciencias Bioquimicas y Farmaceuticas, Universidad Nacional de Rosario, Suipacha 531, 2000 Rosario, Argentina. Electronic address: spampinato@cefobi-conicet.gov.ar.
The DNA mismatch repair (MMR) is a postreplicative system that guarantees genomic stability by correcting mispaired and unpaired nucleotides. In eukaryotic nuclei, MMR is initiated by the binding of heterodimeric MutS homologue (MSH) complexes to the DNA error or lesion. Among these proteins, MSH2-MSH6 is the most abundant heterodimer. Even though the MMR mechanism and proteins are highly conserved throughout evolution, physiological differences between species can lead to different regulatory features. Here, we investigated how light, sugar, and/or hormones modulate Arabidopsis thaliana MSH6 expression pattern. We first characterized the promoter region of MSH6. Phylogenetic shadowing revealed three highly conserved regions. These regions were analyzed by the generation of deletion constructs of the MSH6 full-length promoter fused to the beta-glucuronidase (GUS) gene. Combined, our in silico and genetic analyses revealed that a 121-bp promoter fragment was necessary for MSH6 expression and contained potential cis-acting elements involved in light- and hormone-responsive gene expression. Accordingly, light exposure or sugar treatment of four-day old A. thaliana seedlings triggered an upregulation of MSH6 in shoot and root apical meristems. Appropriately, MSH6 was also induced by the stem cell inducer WUSCHEL. Further, the stimulatory effect of light was dependent on the presence of phyA. In addition, treatment of seedlings with auxin or cytokinin also caused an upregulation of MSH6 under darkness. Consistent with auxin signals, MSH6 expression was suppressed in the GATA23 RNAi line compared with the wild type. Our results provide evidence that endogenous factors and environmental signals controlling plant growth and development regulate the MSH6 protein in A. thaliana.
PMID: 38401766
Plant Sci , IF:4.729 , 2024 Apr , V341 : P112014 doi: 10.1016/j.plantsci.2024.112014
Overexpression of a BR inactivating enzyme gene GhPAG1 impacts eggplant fruit development and anthocyanin accumulation mainly by altering hormone homeostasis.
School of Agricultural Sciences, Zhengzhou University, Kexue Avenue 100, Zhengzhou, Henan 450001, China.; Henan Engineering Technology Research Center of New Germplasm Creation and Utilization for Solanaceous Vegetable Crops, Zhumadian Academy of Agricultural Sciences, Fuqiang Road 51, Zhumadian 463000, China.; Henan Youmei Agricultural Technology Co., Ltd, Zhoukou 466100, China.; Henan Engineering Technology Research Center of New Germplasm Creation and Utilization for Solanaceous Vegetable Crops, Zhumadian Academy of Agricultural Sciences, Fuqiang Road 51, Zhumadian 463000, China. Electronic address: jiangjun2251@163.com.; School of Agricultural Sciences, Zhengzhou University, Kexue Avenue 100, Zhengzhou, Henan 450001, China. Electronic address: zhangyanjie@zzu.edu.cn.
Brassinosteroids (BRs) function importantly in plant growth and development, but the roles in regulating fruit development and anthocyanin pigmentation remain unclear. Eggplant (Solanum melongena L.) is an important Solanaceae vegetable crop rich in anthocyanins. The fruit size and coloration are important agronomic traits for eggplant breeding. In this study, transgenic eggplant exhibiting endogenous BRs deficiency was created by overexpressing a heterologous BRs-inactivating enzyme gene GhPAG1 driven by CaMV 35 S promoter. 35 S::GhPAG1 eggplant exhibited severe dwarfism, reduced fruit size, and less anthocyanin accumulation. Microscopic observation showed that the cell size of 35 S::GhPAG1 eggplant was significantly reduced compared to WT. Furthermore, the levels of IAA, ME-IAA, and active JAs (JA, JA-ILE, and H2JA) all decreased in 35 S::GhPAG1 eggplant fruit. RNA-Seq analyses showed a decrease in the expression of genes involved in cell elongation, auxin signaling, and JA signaling. Besides, overexpression of GhPAG1 significantly downregulated anthocyanin biosynthetic genes and associated transcription regulators. Altogether, these results strongly suggest that endogenous brassinosteroid deficiency arising from GhPAG1 overexpression impacts eggplant fruit development and anthocyanin coloration mainly by altering hormone homeostasis.
PMID: 38309473
Plant Sci , IF:4.729 , 2024 Apr , V341 : P112008 doi: 10.1016/j.plantsci.2024.112008
The Mh-miR393a-TIR1 module regulates Alternaria alternata resistance of Malus hupehensis mainly by modulating the auxin signaling.
College of Horticulture, Nanjing Agricultural University, Nanjing, Jiangsu 210095, PR China.; College of Horticulture, Nanjing Agricultural University, Nanjing, Jiangsu 210095, PR China; Xuzhou Institute of Agricultural Sciences in Jiangsu Xuhuai District, Xuzhou, Jiangsu 221131, PR China.; Institute of Fruit Science, Guizhou Academy of Agricultural Science, Guiyang, Guizhou 550006, PR China. Electronic address: 376258195@qq.com.; College of Horticulture, Nanjing Agricultural University, Nanjing, Jiangsu 210095, PR China. Electronic address: qscnj@njau.edu.cn.
miRNAs govern gene expression and regulate plant defense. Alternaria alternata is a destructive fungal pathogen that damages apple. The wild apple germplasm Malus hupehensis is highly resistant to leaf spot disease caused by this fungus. Herein, we elucidated the regulatory and functional role of miR393a in apple resistance against A. alternata by targeting Transport Inhibitor Response 1. Mature miR393 accumulation in infected M. hupehensis increased owing to the transcriptional activation of MIR393a, determined to be a positive regulator of A. alternata resistance to either 'Orin' calli or 'Gala' leaves. 5' RLM-RACE and co-transformation assays showed that the target of miR393a was MhTIR1, a gene encoding a putative F-box auxin receptor that compromised apple immunity. RNA-seq analysis of transgenic calli revealed that MhTIR1 upregulated auxin signaling gene transcript levels and influenced phytohormone pathways and plant-pathogen interactions. miR393a compromised the sensitivity of several auxin-signaling genes to A. alternata infection, whereas MhTIR1 had the opposite effect. Using exogenous indole-3-acetic acid or the auxin synthesis inhibitor L-AOPP, we clarified that auxin enhances apple susceptibility to this pathogen. miR393a promotes SA biosynthesis and impedes pathogen-triggered ROS bursts by repressing TIR1-mediated auxin signaling. We uncovered the mechanism underlying the miR393a-TIR1 module, which interferes with apple defense against A. alternata by modulating the auxin signaling pathway.
PMID: 38307352
Plant Sci , IF:4.729 , 2024 Apr , V341 : P111998 doi: 10.1016/j.plantsci.2024.111998
Arabidopsis HAPLESS13/AP-1micro is critical for pollen sac formation and tapetal function.
Frontiers Science Center for Cell Responses, College of Life Sciences, Nankai University, Tianjin 300071, China.; College of Life Sciences, Shandong Agricultural University, Tai'an 271018, China.; College of Life Sciences, Shandong Agricultural University, Tai'an 271018, China. Electronic address: shali@sdau.edu.cn.; Frontiers Science Center for Cell Responses, College of Life Sciences, Nankai University, Tianjin 300071, China. Electronic address: yzhang2020@nankai.edu.cn.
The production of excess and viable pollen grains is critical for reproductive success of flowering plants. Pollen grains are produced within anthers, the male reproductive organ whose development involves precisely controlled cell differentiation, division, and intercellular communication. In Arabidopsis thaliana, specification of an archesporial cell (AC) at four corners of a developing anther, followed by programmed cell divisions, generates four pollen sacs, walled by four cell layers among which the tapetum is in close contact with developing microspores. Tapetum secretes callose-dissolving enzymes to release microspores at early stages and undergoes programmed cell death (PCD) to deliver nutrients and signals for microspore development at later stages. Except for transcription factors, plasma membrane (PM)-associated and secretory peptides have also been demonstrated to mediate anther development. Adaptor protein complexes (AP) recruit both cargos and coat proteins during vesicle trafficking. Arabidopsis AP-1micro/HAPLESS13 (HAP13) is a core component of AP-1 for protein sorting at the trans-Golgi network/early endosomes (TGN/EE). We report here that Arabidopsis HAP13 is critical for pollen sac formation and for sporophytic control of pollen production. Functional loss of HAP13 causes a reduction in pollen sac number. It also results in the dysfunction of tapetum such that secretory function of tapetum at early stages and PCD of tapetum at later stages are both compromised. We further show that the expression of SPL, the polar distribution of auxin maximum, as well as the asymmetric distribution of PIN1 are interfered in hap13 anthers, which in combination may lead to male sterility in hap13.
PMID: 38307351
Plant Sci , IF:4.729 , 2024 Apr , V341 : P111997 doi: 10.1016/j.plantsci.2024.111997
Scaffold protein BTB/TAZ domain-containing genes (CmBTs) play a negative role in root development of chrysanthemum.
College of Horticulture Science and Engineering, Shandong Agricultural University, Tai-An, Shandong 271018, China.; Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, Department of Ornamental Horticulture, China Agricultural University, Beijing, China.; Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, Department of Ornamental Horticulture, China Agricultural University, Beijing, China; College of Horticulture Science and Engineering, Shandong Agricultural University, Tai-An, Shandong 271018, China. Electronic address: suncuihui@163.com.
Scaffold proteins, which are known as hubs controlling information flow in cells, can function in a diverse array of biological processes in plants. The BTB/TAZ domain-containing scaffold proteins are associated with multiple signaling pathways in plants. However, there have been few studies of the roles of BT scaffold proteins in chrysanthemum to date. In this study, four CmBT genes named as CmBT1, CmBT1-LIKE1 (CmBT1L1), CmBT1-LIKE2 (CmBT1L2), and CmBT5 were cloned based our previous RNA-seq database. The four CmBT genes showed distinctive expression patterns both in different tissues and in response to different stimuli, such as light, sugar, nitrate and auxin. Knockdown of the four CmBTs facilitated the development of adventitious roots and root hair in chrysanthemum. Transcriptome sequencing analysis revealed thousands of differentially expressed genes after knockdown of the four CmBT genes. Moreover, functional annotation suggested that CmBTs play a tethering role as scaffold proteins. Our findings reveal that CmBTs can negatively regulate root development of chrysanthemum by mediating nitrate assimilation, amino acid biosynthesis, and auxin and jasmonic acid (JA) signaling pathways. This study provides new insights into the role of CmBTs in root development of chrysanthemum.
PMID: 38280641
Plant Sci , IF:4.729 , 2024 Feb , V339 : P111936 doi: 10.1016/j.plantsci.2023.111936
Differential influence of Bacillus subtilis strains on Arabidopsis root architecture through common and distinct plant hormonal pathways.
Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, Denmark; Plant Health Innovation, Chr-Hansen A/S, Taastrup, Denmark.; Bacterial Interactions and Evolution Group, DTU Bioengineering, Technical University of Denmark, Kgs. Lyngby, Denmark.; Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, Denmark.; Plant Health Innovation, Chr-Hansen A/S, Taastrup, Denmark.; Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, Denmark. Electronic address: als@plen.ku.dk.
Plant growth-promoting microbes (PGPM) can enhance crop yield and health, but knowledge of their mode-of-action is limited. We studied the influence of two Bacillus subtilis strains, the natural isolate ALC_02 and the domesticated 168 Go, on Arabidopsis and hypothesized that they modify the root architecture by modulating hormone transport or signaling. Both bacteria promoted increase of shoot and root surface area in vitro, but through different root anatomical traits. Mutant plants deficient in auxin transport or signaling responded less to the bacterial strains than the wild-type, and application of the auxin transport inhibitor NPA strongly reduced the influence of the strains. Both bacteria produced auxin and enhanced shoot auxin levels in DR5::GUS reporter plants. Accordingly, most of the beneficial effects of the strains were dependent on functional auxin transport and signaling, while only 168 Go depended on functional ethylene signaling. As expected, only ALC_02 stimulated plant growth in soil, unlike 168 Go that was previously reported to have reduced biofilms. Collectively, the results highlight that B. subtilis strains can have strikingly different plant growth-promoting properties, dependent on what experimental setup they are tested in, and the importance of choosing the right PGPM for a desired root phenotype.
PMID: 38042415
Plant Cell Rep , IF:4.57 , 2024 Feb , V43 (2) : P47 doi: 10.1007/s00299-023-03108-4
Unveiling the defensive role of Snakin-3, a member of the subfamily III of Snakin/GASA peptides in potatoes.
Instituto de Agrobiotecnologia y Biologia Molecular (IABIMO), CICVyA, Instituto Nacional de Tecnologia Agropecuaria (INTA), Consejo Nacional de Investigaciones Cientificas y Tecnologicas (CONICET), Los Reseros y Nicolas Repetto, Hurlingham, Argentina.; Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina.; Instituto de Agrobiotecnologia y Biologia Molecular (IABIMO), CICVyA, Instituto Nacional de Tecnologia Agropecuaria (INTA), Consejo Nacional de Investigaciones Cientificas y Tecnologicas (CONICET), Los Reseros y Nicolas Repetto, Hurlingham, Argentina. vazquez.cecilia@inta.gob.ar.
The first in-depth characterization of a subfamily III Snakin/GASA member was performed providing experimental evidence on promoter activity and subcellular localization and unveiling a role of potato Snakin-3 in defense Snakin/GASA proteins share 12 cysteines in conserved positions in the C-terminal region. Most of them were involved in different aspects of plant growth and development, while a small number of these peptides were reported to have antimicrobial activity or participate in abiotic stress tolerance. In potato, 18 Snakin/GASA genes were identified and classified into three groups based on phylogenetic analysis. Snakin-1 and Snakin-2 are members of subfamilies I and II, respectively, and were reported to be implicated not only in defense against pathogens but also in plant development. In this work, we present the first in-depth characterization of Snakin-3, a member of the subfamily III within the Snakin/GASA gene family of potato. Transient co-expression of Snakin-3 fused to the green fluorescent protein and organelle markers revealed that it is located in the endoplasmic reticulum. Furthermore, expression analyses via pSnakin-3::GUS transgenic plants showed GUS staining mainly in roots and vascular tissues of the stem. Moreover, GUS expression levels were increased after inoculation with Pseudomonas syringae pv. tabaci or Pectobacterium carotovorum subsp. carotovorum and also after auxin treatment mainly in roots and stems. To gain further insights into the function of Snakin-3 in planta, potato overexpressing lines were challenged against P. carotovorum subsp. carotovorum showing enhanced tolerance to this bacterial pathogen. In sum, here we report the first functional characterization of a Snakin/GASA gene from subfamily III in Solanaceae. Our findings provide experimental evidence on promoter activity and subcellular localization and reveal a role of potato Snakin-3 in plant defense.
PMID: 38302779
Plant Cell Rep , IF:4.57 , 2024 Feb , V43 (2) : P49 doi: 10.1007/s00299-023-03133-3
Paenibacillus lentimorbus alleviates nutrient deficiency-induced stress in Zea mays by modulating root system architecture, auxin signaling, and metabolic pathways.
CSIR-National Botanical Research Institute (CSIR-NBRI), Rana Pratap Marg, Lucknow, 226001, India.; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India.; CSIR-National Botanical Research Institute (CSIR-NBRI), Rana Pratap Marg, Lucknow, 226001, India. puneet@nbri.res.in.; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India. puneet@nbri.res.in.
Paenibacillus lentimorbus reprograms auxin signaling and metabolic pathways for modulating root system architecture to mitigate nutrient deficiency in maize crops. The arable land across the world is having deficiency and disproportionate nutrients, limiting crop productivity. In this study, the potential of plant growth-promoting rhizobacteria (PGPR) viz., Pseudomonas putida, Paenibacillus lentimorbus, and their consortium was explored for growth promotion in maize (Zea mays) under nutrient-deficient conditions. PGPR inoculation improved the overall health of plants under nutrient-deficient conditions. The PGPR inoculation significantly improved the root system architecture and also induced changes in root cortical aerenchyma. Based on plant growth and physiological parameters inoculation with P. lentimorbus performed better as compared to P. putida, consortium, and uninoculated control. Furthermore, expression of auxin signaling (rum1, rul1, lrp1, rtcs, rtcl) and root hair development (rth)-related genes modulated the root development process to improve nutrient acquisition and tolerance to nutrient-deficient conditions in P. lentimorbus inoculated maize plants. Further, GC-MS analysis indicated the involvement of metabolites including carbohydrates and organic acids due to the interaction between maize roots and P. lentimorbus under nutrient-deficient conditions. These findings affirm that P. lentimorbus enhance overall plant growth by modulating the root system of maize to provide better tolerance to nutrient-deficient condition.
PMID: 38302760
Sci Rep , IF:4.379 , 2024 Feb , V14 (1) : P3106 doi: 10.1038/s41598-024-53242-6
Genome-wide identification of AAAP gene family and expression analysis in response to saline-alkali stress in foxtail millet (Setaria italica L.).
College of Agronomy and Biotechnology/Hebei Key Laboratory of Crop Stress Biology, Hebei Normal University of Science and Technology, Qinhuangdao, 066000, China.; Research Center of Rural Vitalization, Hebei Normal University of Science and Technology, Qinhuangdao, 066000, China.; College of Agronomy and Biotechnology/Hebei Key Laboratory of Crop Stress Biology, Hebei Normal University of Science and Technology, Qinhuangdao, 066000, China. yucuihan84@163.com.; College of Agronomy and Biotechnology/Hebei Key Laboratory of Crop Stress Biology, Hebei Normal University of Science and Technology, Qinhuangdao, 066000, China. xiaohulin2008@163.com.
Amino acid/auxin permease (AAAP) genes encode a large family of protein transporters that play important roles in various aspects of plant growth and development. Here, we performed genome-wide identification of members in the foxtail millet (Setaria italica L.) AAAP family (SiAAAP) and their saline-alkali stress-induced expression patterns, resulting in the identification of 65 SiAAAP genes, which could be divided into eight subfamilies. Except for SiAAAP65, the remaining 64 genes were located on nine chromosomes of foxtail millet. Gene structure and conserved motif analyses indicated that the members in the same subfamily are highly conserved. Gene duplication event analysis suggested that tandem duplication may be the main factor driving the expansion of this gene family, and Ka/Ks analysis indicated that all the duplicated genes have undergone purifying selection. Transcriptome analysis showed differential expression of SiAAAPs in roots, stems, leaves, and tassel inflorescence. Analysis of cis-acting elements in the promoter indicated that SiAAAPs contain stress-responsive cis-acting elements. Under saline-alkali stress, qRT-PCR analysis showed that SiAAP3, SiLHT2, and SiAAP16 were differentially expressed between salt-alkali tolerant millet variety JK3 and salt-alkali sensitive millet variety B175. These results suggest that these genes may be involved in or regulate the response to saline-alkali stress, providing a theoretical basis for further studying the function of SiAAAPs.
PMID: 38326447
Plant Physiol Biochem , IF:4.27 , 2024 Feb , V207 : P108429 doi: 10.1016/j.plaphy.2024.108429
Lateral root primordium: Formation, influencing factors and regulation.
School of Life Sciences, Jiangsu University, Zhenjiang, 212013, Jiangsu, China.; School of Life Sciences, Jiangsu University, Zhenjiang, 212013, Jiangsu, China. Electronic address: cjinfor@163.com.
Roots are the primary determinants of water and nutrient uptake by plants. The structure of roots is largely determined by the repeated formation of new lateral roots (LR). A new lateral root primordium (LRP) is formed between the beginning and appearance of LR, which defines the organization and function of LR. Therefore, proper LRP morphogenesis is a crucial process for lateral root formation. The development of LRP is regulated by multiple factors, including hormone and environmental signals. Roots integrate signals and regulate growth and development. At the molecular level, many genes regulate the growth and development of root organs to ensure stable development plans, while also being influenced by various environmental factors. To gain a better understanding of the LRP formation and its influencing factors, this study summarizes previous research. The cell cycle involved in LRP formation, as well as the roles of ROS, auxin, other auxin-related plant hormones, and genetic regulation, are discussed in detail. Additionally, the effects of gravity, mechanical stress, and cell death on LRP formation are explored. Throughout the text unanswered or poorly understood questions are identified to guide future research in this area.
PMID: 38359556
Environ Sci Pollut Res Int , IF:4.223 , 2024 Mar , V31 (11) : P16972-16985 doi: 10.1007/s11356-024-32327-9
Role of calcium signaling in cadmium stress mitigation by indol-3-acetic acid and gibberellin in chickpea seedlings.
University of Carthage, Faculty of Sciences of Bizerte, LR18ES38 Plant Toxicology and Environmental Microbiology, 7021, Bizerte, Tunisia. lamiasakouhi@hotmail.com.; Department of Botany, Faculty of Life Sciences, Government College University, Faisalabad, 38000, Pakistan.; Graduate School of Environmental, Life, Natural Science and Technology, Okayama University, Okayama, 700-8530, Japan.; University of Carthage, Faculty of Sciences of Bizerte, LR18ES38 Plant Toxicology and Environmental Microbiology, 7021, Bizerte, Tunisia.
Given the adverse impacts of heavy metals on plant development and physiological processes, the present research investigated the protective role of indole-3-acetic acid (IAA) and gibberellic acid (GA3) against cadmium (Cd)-induced injury in chickpea seedlings. Therefore, seeds germinated for 6 days in a medium containing 200 muM Cd alone or combined with 10 muM GA3 or 10 muM IAA. Both GA3 and IAA mitigated Cd-imposed growth delays in roots and shoots (80% and 50% increase in root and shoot length, respectively). This beneficial effect was accompanied by a significant reduction in Cd(2+) accumulation in both roots (74% for IAA and 38% for GA3) and shoots (68% and 35%, respectively). Furthermore, these phytohormones restored the cellular redox state by reducing the activity of NADPH oxidase and downregulating the transcription level of RbohF and RbohD genes. Likewise, hydrogen peroxide contents were reduced by GA3 and IAA supply. Additionally, GA3 and IAA countered the Cd-induced reduction in total phenols, flavonoids, and reducing sugars in both roots and shoots. The exogenous effectors enhanced the activities of catalase, ascorbate peroxidase, and thioredoxin, as well as the corresponding gene expressions. Interestingly, adding GA3 and IAA to the Cd-contaminated germination media corrected the level of calcium (Ca(2+)) ion within seedling tissues. This effect coincided with the upregulation of key genes associated with stress sensing and signal transduction, including auxin-binding protein (ABP19a), mitogen-activated protein kinase (MAPK2), calcium-dependent protein kinase (CDPK1), and calmodulin (CaM). Overall, the current results suggest that GA3 and IAA sustain the Ca(2+) signaling pathway, resulting in metal phytotoxicity relief. Amendment of agricultural soils contaminated with heavy metals with GA3 or IAA could represent an effective practice to improve crop yield.
PMID: 38329668
BMC Plant Biol , IF:4.215 , 2024 Feb , V24 (1) : P123 doi: 10.1186/s12870-024-04797-z
Identification of genetics and hormonal factors involved in Quercus robur root growth regulation in different cultivation system.
Department of Ecology, Institute of Dendrology, Polish Academy of Sciences, 62-035, Kornik, Poland. pkoscielniak@man.poznan.pl.; Department of Plant Physiology and Biotechnology, Faculty of Biological and Veterinary Sciences, Nicolaus Copernicus University, 87-100, Torun, Poland.; Department of Ecology, Institute of Dendrology, Polish Academy of Sciences, 62-035, Kornik, Poland.; Faculty of Forestry and Wood Technology, Poznan University of Life Sciences, Wojska Polskiego 71a, 60-625, Poznan, Poland.
Understanding the molecular processes and hormonal signals that govern root growth is of paramount importance for effective forest management. While Arabidopsis studies have shed light on the role of the primary root in root system development, the structure of root systems in trees is considerably more intricate, posing challenges to comprehend taproot growth in acorn-sown and nursery-cultivated seedlings. In this study, we investigated Quercus robur seedlings using rhizotrons, containers, and transplanted containers to rhizotrons, aiming to unravel the impact of forest nursery practices on processes governing taproot growth and root system development. Root samples were subjected to RNA-seq analysis to identify gene expression patterns and perform differential gene expression and phytohormone analysis. Among studied cultivation systems, differentially expressed genes (DEGs) exhibited significant diversity, where the number of co-occurring DEGs among cultivation systems was significantly smaller than the number of unique DEGs in different cultivation systems. Moreover, the results imply that container cultivation triggers the activation of several genes associated with linolenic acid and peptide synthesis in root growth. Upon transplantation from containers to rhizotrons, rapid enhancement in gene expression occurs, followed by gradual reduction as root growth progresses, ultimately reaching a similar expression pattern as observed in the taproot of rhizotron-cultivated seedlings. Phytohormone analysis revealed that taproot growth patterns under different cultivation systems are regulated by the interplay between auxin and cytokinin concentrations. Moreover, the diversification of hormone levels within the root zone and cultivation systems allows for taproot growth inhibition and prompt recovery in transplanted seedlings. Our study highlights the crucial role of hormone interactions during the early stages of taproot elongation, influencing root system formation across.
PMID: 38373900
BMC Plant Biol , IF:4.215 , 2024 Feb , V24 (1) : P120 doi: 10.1186/s12870-024-04806-1
Contrasting plant transcriptome responses between a pierce-sucking and a chewing herbivore go beyond the infestation site.
Centro de Biotecnologia y Genomica de Plantas, Universidad Politecnica de Madrid (UPM) - Instituto Nacional de Investigacion y Tecnologia Agraria y Alimentaria (INIA/CSIC) Campus de Montegancedo, Pozuelo de Alarcon, 28223, Madrid, Spain.; Universidad de Zaragoza, Calle Pedro Cerbuna, 12, Zaragoza, 50009, Spain.; Departamento de Biotecnologia-Biologia Vegetal, Escuela Tecnica Superior de Ingenieria Agronomica, Alimentaria y de Biosistemas, Universidad Politecnica de Madrid, Madrid, Spain.; Departamento de Quimica, Facultad de Ciencias, Universidad de Burgos, Plaza de Misael Banuelos s/n, Burgos, 09001, Spain.; Centro de Biotecnologia y Genomica de Plantas, Universidad Politecnica de Madrid (UPM) - Instituto Nacional de Investigacion y Tecnologia Agraria y Alimentaria (INIA/CSIC) Campus de Montegancedo, Pozuelo de Alarcon, 28223, Madrid, Spain. me.santamaria@upm.es.; Departamento de Biotecnologia-Biologia Vegetal, Escuela Tecnica Superior de Ingenieria Agronomica, Alimentaria y de Biosistemas, Universidad Politecnica de Madrid, Madrid, Spain. me.santamaria@upm.es.
BACKGROUND: Plants have acquired a repertoire of mechanisms to combat biotic stressors, which may vary depending on the feeding strategies of herbivores and the plant species. Hormonal regulation crucially modulates this malleable defense response. Jasmonic acid (JA) and salicylic acid (SA) stand out as pivotal regulators of defense, while other hormones like abscisic acid (ABA), ethylene (ET), gibberellic acid (GA) or auxin also play a role in modulating plant-pest interactions. The plant defense response has been described to elicit effects in distal tissues, whereby aboveground herbivory can influence belowground response, and vice versa. This impact on distal tissues may be contingent upon the feeding guild, even affecting both the recovery of infested tissues and those that have not suffered active infestation. RESULTS: To study how phytophagous with distinct feeding strategies may differently trigger the plant defense response during and after infestation in both infested and distal tissues, Arabidopsis thaliana L. rosettes were infested separately with the chewing herbivore Pieris brassicae L. and the piercing-sucker Tetranychus urticae Koch. Moderate infestation conditions were selected for both pests, though no quantitative control of damage levels was carried out. Feeding mode did distinctly influence the transcriptomic response of the plant under these conditions. Though overall affected processes were similar under either infestation, their magnitude differed significantly. Plants infested with P. brassicae exhibited a short-term response, involving stress-related genes, JA and ABA regulation and suppressing growth-related genes. In contrast, T. urticae elicited a longer transcriptomic response in plants, albeit with a lower degree of differential expression, in particular influencing SA regulation. These distinct defense responses transcended beyond infestation and through the roots, where hormonal response, flavonoid regulation or cell wall reorganization were differentially affected. CONCLUSION: These outcomes confirm that the existent divergent transcriptomic responses elicited by herbivores employing distinct feeding strategies possess the capacity to extend beyond infestation and even affect tissues that have not been directly infested. This remarks the importance of considering the entire plant's response to localized biotic stresses.
PMID: 38369495
BMC Plant Biol , IF:4.215 , 2024 Feb , V24 (1) : P94 doi: 10.1186/s12870-024-04765-7
Genomic survey and expression analysis of LcARFs reveal multiple functions to somatic embryogenesis in Liriodendron.
Key Laboratory of Forest Genetics and Biotechnology, Ministry of Education of China, Co-Innovation Center for the Sustainable Forestry in Southern China, Nanjing Forestry University, No.159 Longpan Road, Nanjing, 210037, China.; Key Laboratory of Forest Genetics and Biotechnology, Ministry of Education of China, Co-Innovation Center for the Sustainable Forestry in Southern China, Nanjing Forestry University, No.159 Longpan Road, Nanjing, 210037, China. jshi@njfu.edu.cn.; Key Laboratory of Forest Genetics and Biotechnology, Ministry of Education of China, Co-Innovation Center for the Sustainable Forestry in Southern China, Nanjing Forestry University, No.159 Longpan Road, Nanjing, 210037, China. chenjh@njfu.edu.cn.
BACKGROUND: Auxin response factors (ARFs) are critical transcription factors that mediate the auxin signaling pathway and are essential for regulating plant growth. However, there is a lack of understanding regarding the ARF gene family in Liriodendron chinense, a vital species in landscaping and economics. Thus, further research is needed to explore the roles of ARFs in L. chinense and their potential applications in plant development. RESULT: In this study, we have identified 20 LcARF genes that belong to three subfamilies in the genome of L. chinense. The analysis of their conserved domains, gene structure, and phylogeny suggests that LcARFs may be evolutionarily conserved and functionally similar to other plant ARFs. The expression of LcARFs varies in different tissues. Additionally, they are also involved in different developmental stages of somatic embryogenesis. Overexpression of LcARF1, LcARF2a, and LcARF5 led to increased activity within callus. Additionally, our promoter-GFP fusion study indicated that LcARF1 may play a role in embryogenesis. Overall, this study provides insights into the functions of LcARFs in plant development and embryogenesis, which could facilitate the improvement of somatic embryogenesis in L. chinense. CONCLUSION: The research findings presented in this study shed light on the regulatory roles of LcARFs in somatic embryogenesis in L. chinense and may aid in accelerating the breeding process of this tree species. By identifying the specific LcARFs involved in different stages of somatic embryogenesis, this study provides a basis for developing targeted breeding strategies aimed at optimizing somatic embryogenesis in L. chinense, which holds great potential for improving the growth and productivity of this economically important species.
PMID: 38326748
BMC Plant Biol , IF:4.215 , 2024 Feb , V24 (1) : P81 doi: 10.1186/s12870-023-04717-7
Evolution and function analysis of auxin response factors reveal the molecular basis of the developed root system of Zygophyllum xanthoxylum.
State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems; Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730000, People's Republic of China.; State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems; Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730000, People's Republic of China. yinhj@lzu.edu.cn.
BACKGROUND: As a xerophytic shrub, forming developed root system dominated with lateral roots is one of the effective strategies for Zygophyllum xanthoxylum to adapt to desert habitat. However, the molecular mechanism of lateral root formation in Z. xanthoxylum is still unclear. Auxin response factors (ARFs) are a master family of transcription factors (TFs) in auxin-mediated biological processes including root growth and development. RESULTS: Here, to determine the relationship between ARFs and root system formation in Z. xanthoxylum, a total of 30 potential ZxARF genes were first identified, and their classifications, evolutionary relationships, duplication events and conserved domains were characterized. 107 ARF protein sequences from alga to higher plant species including Z. xanthoxylum are split into A, B, and C 3 Clades, consisting with previous studies. The comparative analysis of ARFs between xerophytes and mesophytes showed that A-ARFs of xerophytes expanded considerably more than that of mesophytes. Furthermore, in this Clade, ZxARF5b and ZxARF8b have lost the important B3 DNA-binding domain partly and completely, suggesting both two proteins may be more functional in activating transcription by dimerization with AUX/IAA repressors. qRT-PCR results showed that all A-ZxARFs are high expressed in the roots of Z. xanthoxylum, and they were significantly induced by drought stress. Among these A-ZxARFs, the over-expression assay showed that ZxARF7c and ZxARF7d play positive roles in lateral root formation. CONCLUSION: This study provided the first comprehensive overview of ZxARFs and highlighted the importance of A-ZxARFs in the lateral root development.
PMID: 38302884
Mol Plant Microbe Interact , IF:4.171 , 2024 Feb : PMPMI10230170R doi: 10.1094/MPMI-10-23-0170-R
AefR, a TetR Family Transcriptional Repressor, Regulates Several Auxin Responses in Pseudomonas syringae Strain PtoDC3000.
Department of Biology, Washington University in St. Louis, St. Louis, MO 63130, U.S.A.
The plant hormone indole-3-acetic acid (IAA), also known as auxin, plays important roles in plant growth and development, as well as in several plant-microbe interactions. IAA also acts as a microbial signal and in many bacteria regulates metabolism, stress responses, and virulence. In the bacterial plant pathogen Pseudomonas syringae pv. tomato strain DC3000 (PtoDC3000), exposure to IAA results in large-scale transcriptional reprogramming, including the differential expression of several known virulence genes. However, how PtoDC3000 senses and responds to IAA and what aspects of its biology are regulated by IAA is not understood. To investigate the mechanisms involved in perceiving and responding to IAA, we carried out a genetic screen for mutants with altered responses to IAA. One group of mutants of particular interest carried disruptions in the aefR gene encoding a TetR family transcriptional regulator. Gene expression analysis confirmed that the aefR mutants have altered responses to IAA. Thus, AefR is the first demonstrated auxin response regulator in PtoDC3000. We also investigated several aspects of PtoDC3000 biology that are regulated by both AefR and IAA, including antibiotic resistance, motility, and virulence. The observation that the aefR mutant has altered virulence on Arabidopsis, suggests that the sector of the IAA response regulated by aefR is important during pathogenesis. Our findings also provide evidence that AefR plays a role in coordinating changes in gene expression during the transition from early to late stages of infection. [Formula: see text] Copyright (c) 2024 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.
PMID: 38079389
Planta , IF:4.116 , 2024 Feb , V259 (3) : P71 doi: 10.1007/s00425-024-04335-z
In vitro regeneration, photomorphogenesis and light signaling gene expression in Hydrangea quercifolia cv. 'Harmony' under different LED environments.
The Center for Ion Beam Bioengineering & Green Agriculture, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, 230031, Anhui, People's Republic of China.; School of Life Science, University of Science and Technology of China, Hefei, 230026, Anhui, People's Republic of China.; The Center for Ion Beam Bioengineering & Green Agriculture, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, 230031, Anhui, People's Republic of China. jyhou@ipp.ac.cn.; The Center for Ion Beam Bioengineering & Green Agriculture, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, 230031, Anhui, People's Republic of China. lfwu@ipp.ac.cn.; School of Life Science, University of Science and Technology of China, Hefei, 230026, Anhui, People's Republic of China. lfwu@ipp.ac.cn.; Zhongke Taihe Experimental Station, Taihe, 236626, Anhui, China. lfwu@ipp.ac.cn.
Plant growth regulators, sucrose concentration, and light quality significantly impact in vitro regeneration of 'Harmony'. Blue light promotes photomorphogenesis by enhancing light energy utilization, adjusting transcription of light signal genes, and altering hormone levels. Hydrangea quercifolia cv. 'Harmony', celebrated for lush green foliage and clusters of white flowers, has been extensively researched for its regenerative properties. Regeneration in stem segments, leaves, and petioles is facilitated by exogenous auxin and cytokinins (CTKs), with the concentration of sucrose (SC) being a key determinant for shoot regeneration from leaves. The study also highlights the significant impact of light conditions on photomorphogenesis. With an increase in the proportion of red (R) light, there is an inhibitory effect, leading to a reduction in leaf area, a decrease in the quantum yield of PSII (PhiPSII), and an increase in non-photochemical quenching (PhiNPQ) and non-regulated energy dissipation in PSII (PhiNO). Conversely, blue (B) light enhances growth, characterized by an increase in leaf area, elevated PhiPSII, and stable PhiNPQ and PhiNO levels. Additionally, B light induces the upregulation of HqCRYs, HqHY5-like, HqXTH27-like, and HqPHYs genes, along with an increase in endogenous CTKs levels, which positively influence photomorphogenesis independent of HqHY5-like regulation. This light condition also suppresses the synthesis of endogenous gibberellins (GA) and brassinosteroids (BR), further facilitating photomorphogenesis. In essence, B light is fundamental in expediting photomorphogenesis in 'Harmony', demonstrating the vital role in plant growth and development.
PMID: 38353793
Planta , IF:4.116 , 2024 Feb , V259 (3) : P70 doi: 10.1007/s00425-024-04347-9
Transcriptome analysis in Aegilops tauschii unravels further insights into genetic control of stripe rust resistance.
Department of Plant Production and Genetics, School of Agriculture, Shiraz University, Shiraz, 71441-65186, Iran.; Department of Plant Production and Genetics, School of Agriculture, Shiraz University, Shiraz, 71441-65186, Iran. dadkhodaie@shirazu.ac.ir.; Institute of Biotechnology, School of Agriculture, Shiraz University, Shiraz, Iran.; Seed and Plant Improvement Research Department, Fars Agricultural and Natural Resources Research and Education Center, AREEO, Shiraz, Iran.
The Aegilops tauschii resistant accession prevented the pathogen colonization by controlling the sugar flow and triggering the hypersensitive reaction. This study suggested that NBS-LRRs probably induce resistance through bHLH by controlling JA- and SA-dependent pathways. Stripe rust, caused by Puccinia striiformis f. sp. tritici (Pst) is one of wheat's most destructive fungal diseases that causes a severe yield reduction worldwide. The most effective and economically-friendly strategy to manage this disease is genetic resistance which can be achieved through deploying new and effective resistance genes. Aegilops tauschii, due to its small genome and co-evolution with Pst, can provide detailed information about underlying resistance mechanisms. Hence, we used RNA-sequencing approach to identify the transcriptome variations of two contrasting resistant and susceptible Ae. tauschii accessions in interaction with Pst and differentially expressed genes (DEGs) for resistance to stripe rust. Gene ontology, pathway analysis, and search for functional domains, transcription regulators, resistance genes, and protein-protein interactions were used to interpret the results. The genes encoding NBS-LRR, CC-NBS-kinase, and phenylalanine ammonia-lyase, basic helix-loop-helix (bHLH)-, basic-leucine zipper (bZIP)-, APETALA2 (AP2)-, auxin response factor (ARF)-, GATA-, and LSD-like transcription factors were up-regulated exclusively in the resistant accession. The key genes involved in response to salicylic acid, amino sugar and nucleotide sugar metabolism, and hypersensitive response contributed to plant defense against stripe rust. The activation of jasmonic acid biosynthesis and starch and sucrose metabolism pathways under Pst infection in the susceptible accession explained the colonization of the host. Overall, this study can fill the gaps in the literature on host-pathogen interaction and enrich the Ae. tauschii transcriptome sequence information. It also suggests candidate genes that could guide future breeding programs attempting to develop rust-resistant cultivars.
PMID: 38345645
Planta , IF:4.116 , 2024 Feb , V259 (3) : P66 doi: 10.1007/s00425-024-04341-1
Temporal profiling of physiological, histological, and transcriptomic dissection during auxin-induced adventitious root formation in tetraploid Robinia pseudoacacia micro-cuttings.
State Key Laboratory of Tree Genetics and Breeding, Engineering Technology Research Center of Black Locust of National Forestry and Grassland Administration, National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, People's Republic of China.; College of Horticulture and Landscape Architecture, Southwest University, Chongqing, 400716, China.; School of Environment and Energy, Shenzhen Graduate School, Peking University, Shenzhen, 518055, China.; Instituto de Bioingenieria, Universidad Miguel Hernandez de Elche, Alicante, Spain.; Department of Horticulture, College of Horticulture and Plant Protection, Yangzhou University, Yangzhou, 225009, China.; Department of Botany and Plant Sciences, University of California Riverside, Riverside, CA, 22963, USA.; Department of Plant Breeding, Swedish University of Agricultural Sciences, Alnarp, Sweden.; Crop Sciences Institute, National Agricultural Research Centre, Islamabad, 44000, Pakistan.; State Key Laboratory of Tree Genetics and Breeding, Engineering Technology Research Center of Black Locust of National Forestry and Grassland Administration, National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, People's Republic of China. syh831008@163.com.; State Key Laboratory of Tree Genetics and Breeding, Engineering Technology Research Center of Black Locust of National Forestry and Grassland Administration, National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, People's Republic of China. yunli@bjfu.edu.cn.
Optimal levels of indole-3-butyric acid (IBA) applied at the stem base promote adventitious root (AR) initiation and primordia formation, thus promoting the rooting of leafy micro-cuttings of tetraploid Robinia pseudoacacia. Tetraploid Robinia pseudoacacia L. is a widely cultivated tree in most regions of China that has a hard-rooting capability, propagated by stem cuttings. This study utilizes histological, physiological, and transcriptomic approaches to explore how root primordia are induced after indole butyric acid (IBA) treatment of micro-cuttings. IBA application promoted cell divisions in some cells within the vasculature, showing subcellular features associated with adventitious root (AR) founder cells. The anatomical structure explicitly showed that AR initiated from the cambium layer and instigate the inducible development of AR primordia. Meanwhile, the hormone data showed that similar to that of indole-3-acetic acid, the contents of trans-zeatin and abscisic acid peaked at early stages of AR formation and increased gradually in primordia formation across the subsequent stages, suggesting their indispensable roles in AR induction. On the contrary, 24-epibrassinolide roughly maintained at extremely high levels during primordium initiation thoroughly, indicating its presence was involved in cell-specific reorganization during AR development. Furthermore, antioxidant activities transiently increased in the basal region of micro-cuttings and may serve as biochemical indicators for distinct rooting phases, potentially aiding in AR formation. Transcriptomic analysis during the early stages of root formation shows significant downregulation of the abscisic acid and jasmonate signaling pathways, while ethylene and cytokinin signaling seems upregulated. Network analysis of genes involved in carbon metabolism and photosynthesis indicates that the basal region of the micro-cuttings undergoes rapid reprogramming, which results in the breakdown of sugars into pyruvate. This pyruvate is then utilized to fuel the tricarboxylic acid cycle, thereby sustaining growth through aerobic respiration. Collectively, our findings provide a time-course morphophysiological dissection and also suggest the regulatory role of a conserved auxin module in AR development in these species.
PMID: 38332379
Planta , IF:4.116 , 2024 Feb , V259 (3) : P55 doi: 10.1007/s00425-023-04325-7
A GARP transcription factor SlGCC positively regulates lateral root development in tomato via auxin-ethylene interplay.
Molecular Biology and Biotechnology, CSIR-National Botanical Research Institute, Lucknow, 226001, India.; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India.; CSIR-Institute of Himalayan Bioresource Technology, Palampur, 176061, India.; Molecular Biology and Biotechnology, CSIR-National Botanical Research Institute, Lucknow, 226001, India. va.sane@nbri.res.in.; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India. va.sane@nbri.res.in.
SlGCC, a GARP transcription factor, functions as a root-related transcriptional repressor. SlGCC synchronizes auxin and ethylene signaling involving SlPIN3 and SlIAA3 as intermediate targets sketching a molecular map for lateral root development in tomato. The root system is crucial for growth and development of plants as it performs basic functions such as providing mechanical support, nutrients and water uptake, pathogen resistance and responds to various stresses. SlGCC, a GARP family transcription factor (TF), exhibited predominant expression in age-dependent (initial to mature stages) tomato root. SlGCC is a transcriptional repressor and is regulated at a transcriptional and translational level by auxin and ethylene. Auxin and ethylene mediated SlGCC protein stability is governed via proteasome degradation pathway during lateral root (LR) growth development. SlGCC over-expressor (OE) and under-expressed (UE) tomato transgenic lines demonstrate its role in LR development. This study is an attempt to unravel the vital role of SlGCC in regulating tomato LR architecture.
PMID: 38300324
Planta , IF:4.116 , 2024 Jan , V259 (3) : P53 doi: 10.1007/s00425-023-04326-6
A biostimulant yeast, Hanseniaspora opuntiae, modifies Arabidopsis thaliana root architecture and improves the plant defense response against Botrytis cinerea.
Centro de Ciencias Genomicas, Universidad Nacional Autonoma de Mexico, Cuernavaca, Morelos, Mexico.; Center for Desert Agriculture, Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia.; Instituto de Biotecnologia, Universidad Nacional Autonoma de Mexico, Cuernavaca, Morelos, Mexico.; Laboratorio de Biologia Molecular de Hongos y Plantas, Division de Biologia Molecular, Instituto Potosino de Investigacion Cientifca y Tecnologica AC, San Luis Potosi, Mexico.; Facultad de Ciencias, Universidad Autonoma de San Luis Potosi (UASLP), Av. Chapultepec 1570, Priv. del Pedregal, 78295, San Luis Potosi, Mexico.; Departamento de Agronomia, Universidade Estadual de Maringa, Maringa, 87020, Brazil.; Centro de Ciencias Genomicas, Universidad Nacional Autonoma de Mexico, Cuernavaca, Morelos, Mexico. serrano@ccg.unam.mx.
The biostimulant Hanseniaspora opuntiae regulates Arabidopsis thaliana root development and resistance to Botrytis cinerea. Beneficial microbes can increase plant nutrient accessibility and uptake, promote abiotic stress tolerance, and enhance disease resistance, while pathogenic microorganisms cause plant disease, affecting cellular homeostasis and leading to cell death in the most critical cases. Commonly, plants use specialized pattern recognition receptors to perceive beneficial or pathogen microorganisms. Although bacteria have been the most studied plant-associated beneficial microbes, the analysis of yeasts is receiving less attention. This study assessed the role of Hanseniaspora opuntiae, a fermentative yeast isolated from cacao musts, during Arabidopsis thaliana growth, development, and defense response to fungal pathogens. We evaluated the A. thaliana-H. opuntiae interaction using direct and indirect in vitro systems. Arabidopsis growth was significantly increased seven days post-inoculation with H. opuntiae during indirect interaction. Moreover, we observed that H. opuntiae cells had a strong auxin-like effect in A. thaliana root development during in vitro interaction. We show that 3-methyl-1-butanol and ethanol are the main volatile compounds produced by H. opuntiae. Subsequently, it was determined that A. thaliana plants inoculated with H. opuntiae have a long-lasting and systemic effect against Botrytis cinerea infection, but independently of auxin, ethylene, salicylic acid, or jasmonic acid pathways. Our results demonstrate that H. opuntiae is an important biostimulant that acts by regulating plant development and pathogen resistance through different hormone-related responses.
PMID: 38294549
Planta , IF:4.116 , 2024 Jan , V259 (2) : P46 doi: 10.1007/s00425-023-04327-5
Auxin synthesis promotes N metabolism and optimizes root structure enhancing N acquirement in maize (Zea mays L.).
College of Resources, Hunan Agricultural University, Changsha, 410128, People's Republic of China.; Yiyang City Academy of Agricultural Sciences, Yiyang, 413046, People's Republic of China.; Changde Cigarette Factory, Changde, 415200, People's Republic of China.; College of Resources, Hunan Agricultural University, Changsha, 410128, People's Republic of China. helloyanglan@163.com.
Foliar NAA increases photosynthate supplied by enhancing photosynthesis, to strengthen root activity and provide a large sink for root carbohydrate accumulation, which is beneficial to acquire more nitrogen. The improvement of grain yield is an effective component in the food security. Auxin acts as a well-known plant hormone, plays an important role in maize growth and nutrient uptake. In this study, with maize variety Zhengdan 958 (ZD958) as material, the effects of auxin on nitrogen (N) uptake and assimilation of seedling maize were studied by hydroponic experiments. With water as the control, naphthalene acetic acid (NAA, 0.1 mmol/L) and aminoethoxyvinylglycine (AVG, 0.1 mmol/L, an auxin synthesis inhibitor) were used for foliar spraying. The results showed that NAA significantly improved photosynthetic rate and plant biomass by 58.6% and 91.7%, respectively, while the effect of AVG was opposite to that of NAA. At the same time, key enzymes activities related N assimilation in NAA leaves were significantly increased, and the activities of nitrate reductase (NR), glutamine synthetase (GS) and glutamate synthase (GOGAT) were increased by 32.3%, 22.9%, and 16.2% in new leaves. Furthermore, NAA treatment promoted underground growth. When compared with control, total root length, root surface area, root tip number, branch number and root activity were significantly increased by 37.8%, 22.2%, 35.1%, 28.8% and 21.2%. Root growth is beneficial to N capture in maize. Ultimately, the total N accumulation of NAA treatment was significantly increased by 74.5%, as compared to the control. In conclusion, NAA foliar spraying increased endogenous IAA content, and enhanced the activity of N assimilation-related enzymes and photosynthesis rate, in order to build a large sink for carbohydrate accumulation. In addition, NAA strengthened root activity and regulated root morphology and architecture, which facilitated further N uptake and plant growth.
PMID: 38285079
Plant Genome , IF:4.089 , 2024 Feb : Pe20432 doi: 10.1002/tpg2.20432
Genome-wide analysis of PvMADS in common bean and functional characterization of PvMADS31 in Arabidopsis thaliana as a player in abiotic stress responses.
Department of Agricultural Biotechnology, Faculty of Agriculture, Ondokuz Mayis University, Samsun, Turkey.; The Central Laboratory for Date Palm Research and Development, Agricultural Research Center (ARC), Giza, Egypt.
Changing climatic conditions with rising temperatures and altered precipitation patterns pose significant challenges to agricultural productivity, particularly for common bean crops. Transcription factors (TFs) are crucial regulators that can mitigate the impact of biotic and abiotic stresses on crop production. The MADS-box TFs family has been implicated in various plant physiological processes, including stress-responsive mechanisms. However, their role in common bean and their response to stressful conditions remain poorly understood. Here, we identified 35 MADS-box gene family members in common bean, with conserved MADS-box domains and other functional domains. Gene duplication events were observed, suggesting the significance of duplication in the evolutionary development of gene families. The analysis of promoter regions revealed diverse elements, including stress-responsive elements, indicating their potential involvement in stress responses. Notably, PvMADS31, a member of the PvMADS-box gene family, demonstrated rapid upregulation under various abiotic stress conditions, including NaCl, polyethylene glycol, drought, and abscisic acid (ABA) treatments. Transgenic plants overexpressing PvMADS31 displayed enhanced lateral root development, root elongation, and seed germination under stress conditions. Furthermore, PvMADS31 overexpression in Arabidopsis resulted in improved drought tolerance, likely attributed to the enhanced scavenging of ROS and increased proline accumulation. These findings suggest that PvMADS31 might play a crucial role in modulating seed germination, root development, and stress responses, potentially through its involvement in auxin and ABA signaling pathways. Overall, this study provides valuable insights into the potential roles of PvMADS-box genes in abiotic stress responses in common bean, offering prospects for crop improvement strategies to enhance resilience under changing environmental conditions.
PMID: 38327143
BMC Genomics , IF:3.969 , 2024 Feb , V25 (1) : P207 doi: 10.1186/s12864-024-10119-2
Integrated metabolomics and transcriptomics analysis highlight key pathways involved in the somatic embryogenesis of Darjeeling tea.
Department of Biological Sciences, Bose Institute, EN80, Sector V, Salt Lake, Kolkata, 700091, India.; School of Agriculture and Food Science, University College Dublin, Dublin, Ireland.; Department of Biological Sciences, Bose Institute, EN80, Sector V, Salt Lake, Kolkata, 700091, India. gaurabgangopadhyay@gmail.com.
BACKGROUND: Darjeeling tea is a globally renowned beverage, which faces numerous obstacles in sexual reproduction, such as self-incompatibility, poor seed germination, and viability, as well as issues with vegetative propagation. Somatic embryogenesis (SE) is a valuable method for rapid clonal propagation of Darjeeling tea. However, the metabolic regulatory mechanisms underlying SE in Darjeeling tea remain largely unknown. To address this, we conducted an integrated metabolomics and transcriptomics analysis of embryogenic callus (EC), globular embryo (GE), and heart-shaped embryo (HE). RESULTS: The integrated analyses showed that various genes and metabolites involved in the phenylpropanoid pathway, auxin biosynthesis pathway, gibberellin, brassinosteroid and amino acids biosynthesis pathways were differentially enriched in EC, GE, and HE. Our results revealed that despite highly up-regulated auxin biosynthesis genes YUC1, TAR1 and AAO1 in EC, endogenous indole-3-acetic acid (IAA) was significantly lower in EC than GE and HE. However, bioactive Gibberellin A4 displayed higher accumulation in EC. We also found higher BABY BOOM (BBM) and Leafy cotyledon1 (LEC1) gene expression in GE along with high accumulation of castasterone, a brassinosteroid. Total flavonoids and phenolics levels were elevated in GE and HE compared to EC, especially the phenolic compound chlorogenic acid was highly accumulated in GE. CONCLUSIONS: Integrated metabolome and transcriptome analysis revealed enriched metabolic pathways, including auxin biosynthesis and signal transduction, brassinosteroid, gibberellin, phenylpropanoid biosynthesis, amino acids metabolism, and transcription factors (TFs) during SE in Darjeeling tea. Notably, EC displayed lower endogenous IAA levels, conducive to maintaining differentiation, while higher IAA concentration in GE and HE was crucial for preserving embryo identity. Additionally, a negative correlation between bioactive gibberellin A4 (GA4) and IAA was observed, impacting callus growth in EC. The high accumulation of chlorogenic acid, a phenolic compound, might contribute to the low success rate in GE and HE formation in Darjeeling tea. TFs such as BBM1, LEC1, FUS3, LEA, WOX3, and WOX11 appeared to regulate gene expression, influencing SE in Darjeeling tea.
PMID: 38395740
Plants (Basel) , IF:3.935 , 2024 Jan , V13 (3) doi: 10.3390/plants13030416
Somatic Embryogenesis and Agrobacterium-Mediated Gene Transfer Procedures in Chilean Temperate Japonica Rice Varieties for Precision Breeding.
Natural Sciences, Mathematics, and Environment Faculty, Metropolitan Technological University, Santiago 8330526, Chile.; Biotechnology Laboratory, La Platina Research Station, INIA-Chile, Santiago 8831314, Chile.; Rice Breeding Program, Quilamapu Research Station, INIA-Chile, Chillan 3780000, Chile.
Rice (Oryza sativa) varieties are generated through breeding programs focused on local requirements. In Chile, the southernmost rice producer, rice productivity relies on the use and generation of temperate japonica germplasms, which need to be adapted to the intensifying effects of climate change. Advanced biotechnological tools can contribute to these breeding programs; new technologies associated with precision breeding, including gene editing, rely on procedures such as regeneration and gene transfer. In this study, the local rice varieties Platino, Cuarzo, Esmeralda, and Zafiro were evaluated for somatic embryogenesis potential using a process that involved the combined use of auxins and cytokinins. An auxin-based (2,4-D) general medium (2N6) allowed for the induction of embryogenic masses in all the genotypes. After induction, masses required culturing either in N6R (kinetin; Platino) or N6RN (BAP, kinetin, IBA, and 2,4-D; Cuarzo, Esmeralda, and Zafiro) to yield whole plants using regeneration medium (N6F, no hormone). The sprouting rates indicated Platino as the most responsive genotype; for this reason, this variety was evaluated for gene transfer. Fifteen-day-old embryo masses were assayed for Agrobacterium-mediated transformation using the bacterial strain EHA105 harboring pFLC-Myb/HPT/GFP, a modified T-DNA vector harboring a geminivirus-derived replicon. The vector included the green fluorescent protein reporter gene, allowing for continuous traceability. Reporter mRNA was produced as early as 3 d after agroinfiltration, and stable expression of the protein was observed along the complete process. These achievements enable further biotechnological steps in these and other genotypes from our breeding program.
PMID: 38337949
Plants (Basel) , IF:3.935 , 2024 Jan , V13 (3) doi: 10.3390/plants13030408
Unveiling Molecular Signatures in Light-Induced Seed Germination: Insights from PIN3, PIN7, and AUX1 in Arabidopsis thaliana.
Instituto de Investigaciones Fisiologicas y Ecologicas Vinculadas a la Agricultura (IFEVA), Consejo Nacional de Investigaciones Cientificas y Tecnicas (CONICET), Facultad de Agronomia, Universidad de Buenos Aires (UBA), Buenos Aires C1417DSE, Argentina.; Departamento de Fisiologia, Biologia, Molecular, y Celular, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires C1428EGA, Argentina.; Instituto de Fisiologia, Biologia Molecular y Neurociencias (IFIBYNE), Consejo Nacional de Investigaciones Cientificas y Tecnicas (CONICET), Universidad de Buenos Aires, Buenos Aires C1428EHA, Argentina.; Umea Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, SE-901 83 Umea, Sweden.
Light provides seeds with information that is essential for the adjustment of their germination to the conditions that are most favorable for the successful establishment of the future seedling. The promotion of germination depends mainly on environmental factors, like temperature and light, as well as internal factors associated with the hormonal balance between gibberellins (GA) and abscisic acid (ABA), although other hormones such as auxins may act secondarily. While transcriptomic studies of light-germinating Arabidopsis thaliana seeds suggest that auxins and auxin transporters are necessary, there are still no functional studies connecting the activity of the auxin transporters in light-induced seed germination. In this study, we investigated the roles of two auxin efflux carrier (PIN3 and PIN7) proteins and one auxin influx (AUX1) carrier protein during Arabidopsis thaliana seed germination. By using next-generation sequencing (RNAseq), gene expression analyses, hormonal sensitivity assays, and the quantification of indole-3-acetic acid (IAA) levels, we assessed the functional roles of PIN3, PIN7, and AUX1 during light-induced seed germination. We showed that auxin levels are increased 24 h after a red-pulse (Rp). Additionally, we evaluated the germination responses of pin3, pin7, and aux1 mutant seeds and showed that PIN3, PIN7, and AUX1 auxin carriers are important players in the regulation of seed germination. By using gene expression analysis in water, fluridone (F), and ABA+F treated seeds, we confirmed that Rp-induced seed germination is associated with auxin transport, and ABA controls the function of PIN3, PIN7, and AUX1 during this process. Overall, our results highlight the relevant and positive role of auxin transporters in germinating the seeds of Arabidopsis thaliana.
PMID: 38337941
Plants (Basel) , IF:3.935 , 2024 Jan , V13 (3) doi: 10.3390/plants13030402
Pseudomonas taetrolens ULE-PH5 and Pseudomonas sp. ULE-PH6 Isolated from the Hop Rhizosphere Increase Phosphate Assimilation by the Plant.
Instituto de Investigacion de la Vina y el Vino, Escuela de Ingenieria Agraria, Universidad de Leon, 24009 Leon, Spain.
Most of the phosphorus incorporated into agricultural soils through the use of fertilizers precipitates in the form of insoluble salts that are incapable of being used by plants. This insoluble phosphorus present in large quantities in soil forms the well-known "phosphorus legacy". The solubilization of this "phosphorus legacy" has become a goal of great agronomic importance, and the use of phosphate-solubilizing bacteria would be a useful tool for this purpose. In this work, we have isolated and characterized phosphate-solubilizing bacteria from the rhizosphere of hop plants. Two particular strains, Pseudomonas taetrolens ULE-PH5 and Pseudomonas sp. ULE-PH6, were selected as plant growth-promoting rhizobacteria due to their high phosphate solubilization capability in both plate and liquid culture assays and other interesting traits, including auxin and siderophore production, phytate degradation, and acidic and alkaline phosphatase production. These strains were able to significantly increase phosphate uptake and accumulation of phosphorus in the aerial part (stems, petioles, and leaves) of hop plants, as determined by greenhouse trials. These strains are promising candidates to produce biofertilizers specifically to increase phosphate adsorption by hop plants.
PMID: 38337935
Gene , IF:3.688 , 2024 Mar , V898 : P148080 doi: 10.1016/j.gene.2023.148080
Transcriptomic changes in soybean underlying growth promotion and defense against cyst nematode after Bacillus simplex Sneb545 treatment.
College of Environment, Shenyang University, Shenyang 110044, PR China.; College of plant protection, Shenyang Agricultural University, Shenyang 110866, PR China.; Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang 110016, PR China. Electronic address: piaolei9411@163.com.
Bacillus simplex Sneb45 is a plant-growth-promoting rhizobacterium that promotes soybean growth and systemic resistance to cyst nematode. To investigate transcriptional changes in soybean roots in response to B. simplex Sneb45 treatment, transcriptome analysis and quantitative real-time PCR were conducted to detect and validate the differentially expressed genes (DEGs). In total, 19,109 DEGs were obtained. After B. simplex Sneb545 treatment, 970 and 1265 genes were up- and down-regulated at 5 days post-inoculation (dpi), respectively, and 142 and 47 genes were up- and down-regulated at 10 dpi, respectively, compared with untreated soybean roots. Functional annotation of DEGs indicated that B. simplex Sneb545 regulated soybean growth and defense against cyst nematode possibly through genes related to auxin, gibberellin, and NB-LRR protein. In addition, GO and KEGG enrichment analyses indicated that the DEGs were enriched in metabolism, signal transduction, and plant-pathogen interaction pathways. Moreover, the auxin and gibberellin contents were lower in B. simplex Sneb545-treated soybean roots than in untreated roots at 5 dpi. B. simplex Sneb545 possibly altered the expression of wound-induced protein and NAC transcription factor to regulate soybean growth and defense against cyst nematode. Our study provided deep insights into the alterations in soybean transcriptome after exposure to B. simplex Sneb45 and a theoretical basis for further exploring molecular functions underlying the biological control activity of B. simplex Sneb545.
PMID: 38101712
Biochem Biophys Res Commun , IF:3.575 , 2024 Feb , V696 : P149507 doi: 10.1016/j.bbrc.2024.149507
Arabidopsis plasma membrane H(+)-ATPase interacts with auxin to regulate Danger-Associated Peptide Pep1-induced root growth inhibition.
School of Integrated Chinese and Western Medicine, Anhui University of Chinese Medicine, Hefei, 230012, China.; School of Integrated Chinese and Western Medicine, Anhui University of Chinese Medicine, Hefei, 230012, China. Electronic address: yjsbxk2009@163.com.
Plant elicitor peptide 1 (Pep1) is one of plant-derived damage-associated molecular patterns (DAMPs) involved in the regulation of multiple biological processes, including immune response and root growth. The exogenous application of Pep1 was shown to inhibit root growth by affecting the auxin content and extracellular pH level in the transition zone (TZ). However, the signaling relationship between extracellular pH and auxin in Pep1-regulated root growth inhibition has not been explored. Our study here suggested that both pH signaling and auxin signaling were responsible for Pep1-regulated root growth inhibition, and the Pep1-induced auxin accumulation in TZ depended on apoplastic acidification. To increase the apoplastic pH in TZ, we mutated the AHA2 and found that the mutants of aha2-4 and pin2aha2-4 both reduced Pep1-induced auxin content in TZ, thereby alleviating root growth inhibition. Thus, our results reveal a new auxin-pH signaling crosstalk mechanism in regulating root growth, and provide new insights into the function of Pep1 in regulating root growth in Arabidopsis.
PMID: 38237234
J Plant Physiol , IF:3.549 , 2024 Feb , V293 : P154168 doi: 10.1016/j.jplph.2023.154168
Auxin resistant 1 gene (AUX1) mediates auxin effect on Arabidopsis thaliana callus growth by regulating its content and distribution pattern.
Plant Physiology and Biotechnology Department, Nicolaus Copernicus University in Torun, Lwowska 1, 87-100 Torun, Poland; Centre for Modern Interdisciplinary Technologies, Nicolaus Copernicus University in Torun, Wilenska 4, 87-100 Torun, Poland.; Plant Physiology and Biotechnology Department, Nicolaus Copernicus University in Torun, Lwowska 1, 87-100 Torun, Poland.; Plant Physiology and Biotechnology Department, Nicolaus Copernicus University in Torun, Lwowska 1, 87-100 Torun, Poland; Centre for Modern Interdisciplinary Technologies, Nicolaus Copernicus University in Torun, Wilenska 4, 87-100 Torun, Poland. Electronic address: tybr@umk.pl.
Callus sustained growth relies heavily on auxin, which is supplied to the culture medium. Surprisingly, there is a noticeable absence of information regarding the involvement of carrier-mediated auxin polar transport gene in callus growth regulation. Here, we delve into the role of the AUXIN RESISTANT 1 (AUX1) influx transporter in the regulation of callus growth, comparing the effects under conditions of light versus darkness. It was observed that callus growth was significantly enhanced under light illumination. This growth-stimulatory effect was accompanied by a decrease in the levels of free auxin within the callus cells when compared to conditions of darkness. In the aux1-22 mutant callus, which lacks functional AUX1, there was a substantial reduction in IAA levels. Nonetheless, the mutant callus exhibited markedly higher growth rates compared to the wild type. This suggests that the reduction in exogenous auxin uptake through the AUX1-dependent pathway may prevent the overaccumulation of growth-restricting hormone concentrations. The growth-stimulatory effect of AUX1 deficiency was counteracted by nonspecific auxin influx transport inhibitors. This finding shows that other auxin influx carriers likely play a role in facilitating the diffusion of auxin from the culture medium to sustain high growth rates. AUX1 was primarily localized in the plasma membranes of the two outermost cell layers of the callus clump and the parenchyma cells adjacent to tracheary elements. Significantly, these locations coincided with the regions of maximal auxin concentration. Consequently, it can be inferred that AUX1 mediates the auxin distribution within the callus.
PMID: 38176282
Phytochem Anal , IF:3.373 , 2024 Feb doi: 10.1002/pca.3340
A rapid and robust colorimetric method for measuring relative abundance of auxins in plant tissues.
National Institute of Plant Genome Research, New Delhi, India.
INTRODUCTION: Auxin estimation in plant tissues is a crucial component of auxin signaling studies. Despite the availability of various high-throughput auxin quantification methods like LC-MS, GC-MS, HPLC, biosensors, and DR5-gus/gfp-based assays, auxin quantification remains troublesome because these techniques are very expensive and technology intensive and they mostly involve elaborate sample preparation or require the development of transgenic plants. OBJECTIVES: To find a solution to these problems, we made use of an old auxin detection system to quantify microbe derived auxins and modified it to effectively measure auxin levels in rice plants. MATERIALS AND METHODS: Auxins from different tissues of rice plants, including root samples of seedlings exposed to IAA/TIBA or subjected to different abiotic stresses, were extracted in ethanol. The total auxin level was measured by the presently described colorimetric assay and counterchecked by other auxin estimation methods like LC-MS or gus staining of DR5-gus overexpressing lines. RESULTS: The presented colorimetric method could measure (1) the auxin levels in different tissues of rice plants, thus identifying the regions of higher auxin abundance, (2) the differential accumulation of auxins in rice roots when auxin or its transport inhibitor was supplied exogenously, and (3) the levels of auxin in roots of rice seedlings subjected to various abiotic stresses. The thus obtained auxin levels correlated well with the auxin levels determined by other methods like LC-MS or gus staining and the expression pattern of auxin biosynthesis pathway genes. CONCLUSIONS: The auxin estimation method described here is simple, rapid, cost-effective, and sensitive and allows for the efficient detection of relative auxin abundances in plant tissues.
PMID: 38419380
World J Microbiol Biotechnol , IF:3.312 , 2024 Feb , V40 (4) : P107 doi: 10.1007/s11274-024-03920-4
Synthesis of nanoparticles using Trichoderma Harzianum, characterization, antifungal activity and impact on Plant Growth promoting Bacteria.
Department of Soil Sciecne, Faculty of Agriculture, Shahid Chamran University of Ahvaz, Ahvaz, Iran.; Department of Soil Sciecne, Faculty of Agriculture, Shahid Chamran University of Ahvaz, Ahvaz, Iran. n.enayatzamir@scu.ac.ir.; State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou, China.; Department of Plant Protection, Khuzestan Agricultural and Natural Resource Research and Education Center, Agricultural Research, Education and Extension Organization (AREEO), Ahvaz, Iran.
Globally cultivated cereals are frequently threatened by various plant pathogenic agents such as Fusarium fungi. To combat these pathogens, researchers have made nanoparticles as potential agricultural pesticides. In this study, selenium and titanium dioxide NPs were synthesized using Trichoderma harzianum metabolites. Characterization of the NPs indicated varying size and shapes of both NPs and functional groups existence to constitute both NPs. The evaluation of antifungal activity of NPs against plant pathogenic fungi, Fusarium culmorum, indicated both NPs maximum antifungal activity at concentration of 100 mg/L. The impacts of nanoparticles on some beneficial plant growth promoting bacteria (PGPB) were evaluated and showed their inhibition effect on optical density of PGPB at a concentration of 100 mg/L but they did not have any impact on nitrogen fixation by bacteria. Existence of TiO(2)NPs reduced the intensity of color change to pink compared to the control indicating auxin production. Both NPs demonstrated different impact on phosphate solubilization index. This study suggests that the synthesized nanoparticles have the potential to serve as antifungal compounds at special concentration against plant diseases without significantly reducing the potential of PGPB at low concentrations.
PMID: 38396217
J Biotechnol , IF:3.307 , 2024 Feb , V381 : P27-35 doi: 10.1016/j.jbiotec.2024.01.002
Comparison of plant biostimulating properties of Chlorella sorokiniana biomass produced in batch and semi-continuous systems supplemented with pig manure or acetate.
Research Centre for Plant Growth and Development, School of Life Sciences, University of KwaZulu-Natal, Pietermaritzburg, P/Bag X01, Scottsville 3209, South Africa. Electronic address: stirk@ukzn.ac.za.; Department of Plant Sciences, Albert Kazmer Mosonmagyarovar Faculty, Szechenyi Istvan University, Var Square 2, Mosonmagyarovar H-9200, Hungary.; Laboratory of Growth Regulators, Faculty of Science, Palacky University and Institute of Experimental Botany ASCR, Slechtitelu 27, Olomouc 78371, Czech Republic.; Institute of Environmental Protection and Nature Conservation, Faculty of Forestry, University of Sopron, Bajcsy-Zsilinszky str., Sopron 4H-9400, Hungary.; Institute of Agronomy, Kaposvar Campus, Hungarian University of Agriculture and Life Sciences, Guba Sandor Str. 40, Kaposvar H-7400, Hungary.; Department of Water and Environmental Sciences, Albert Kazmer Mosonmagyarovar Faculty, Szechenyi Istvan University, Var Square 2, Mosonmagyarovar H-9200, Hungary.; Institute of Plant Biology, HUN-REN Biological Research Centre, Szeged 6726, Hungary; Faculty of Water Sciences, University of Public Service, Baja 6500, Hungary.; Research Centre for Plant Growth and Development, School of Life Sciences, University of KwaZulu-Natal, Pietermaritzburg, P/Bag X01, Scottsville 3209, South Africa.; Research Centre for Plant Growth and Development, School of Life Sciences, University of KwaZulu-Natal, Pietermaritzburg, P/Bag X01, Scottsville 3209, South Africa; Department of Plant Sciences, Albert Kazmer Mosonmagyarovar Faculty, Szechenyi Istvan University, Var Square 2, Mosonmagyarovar H-9200, Hungary.
Microalgae-derived biostimulants provide an eco-friendly biotechnology for improving crop productivity. The strategy of circular economy includes reducing biomass production costs of new and robust microalgae strains grown in nutrient-rich wastewater and mixotrophic culture where media is enriched with organic carbon. In this study, Chlorella sorokiniana was grown in 100 l bioreactors under sub-optimal conditions in a greenhouse. A combination of batch and semi-continuous cultivation was used to investigate the growth, plant hormone and biostimulating effect of biomass grown in diluted pig manure and in nutrient medium supplemented with Na-acetate. C. sorokiniana tolerated the low light (sum of PAR 0.99 +/- 0.18 mol/photons/(m(2)/day)) and temperature (3.7-23.7 degrees C) conditions to maintain a positive growth rate and daily biomass productivity (up to 149 mg/l/day and 69 mg/l/day dry matter production in pig manure and Na-acetate supplemented cultures respectively). The protein and lipid content was significantly higher in the biomass generated in batch culture and dilute pig manure (1.4x higher protein and 2x higher lipid) compared to the Na-acetate enriched culture. Auxins indole-3-acetic acid (IAA) and 2-oxindole-3-acetic acid (oxIAA) and salicylic acid (SA) were present in the biomass with significantly higher auxin content in the biomass generated using pig manure (> 350 pmol/g DW IAA and > 84 pmol/g DW oxIAA) compared to cultures enriched with Na-acetate and batch cultures (< 200 pmol/g DW IAA and < 27 pmol/g DW oxIAA). No abscisic acid and jasmonates were detected. All samples had plant biostimulating activity measured in the mungbean rooting bioassay with the Na-acetate supplemented biomass eliciting higher rooting activity (equivalent to 1-2 mg/l IBA) compared to the pig manure (equivalent to 0.5-1 mg/l IBA) and batch culture (equivalent to water control) generated biomass. Thus C. sorokiniana MACC-728 is a robust new strain for biotechnology, tolerating low light and temperature conditions. The strain can adapt to alternative nutrient (pig manure) and carbon (acetate) sources with the generated biomass having a high auxin concentration and plant biostimulating activity detected with the mungbean rooting bioassay.
PMID: 38190851
Mol Genet Genomics , IF:3.291 , 2024 Feb , V299 (1) : P10 doi: 10.1007/s00438-024-02106-9
miRNAs are involved in regulating the formation of recovery tissues in virus infected Nicotiana tabacum.
Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, Sichuan, China.; Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education), College of Life Science, China West Normal University, Nanchong, 637009, China.; Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, Sichuan, China. xidh@scu.edu.cn.
MiRNAs play an important role in regulating plant growth and immune response. Mosaic diseases are recognized as the most important plant diseases in the world, and mosaic symptoms are recovery tissues formed by plants against virus infection. However, the mechanism of the formation of mosaic symptoms remains elusive. In this study, two typical mosaic systems consisting of Nicotiana tabacum-cucumber mosaic virus (CMV) and N. tabacum-tobacco mosaic virus (TMV) were used to investigate the relevance of miRNAs to the appearance of mosaic symptoms. The results of miRNA-seq showed that there were significant differences in miRNA abundance between dark green tissues and chlorotic tissues in mosaic leaves caused by the infection of CMV or TMV. Compared with healthy tissues, miRNA expression was significantly increased in chlorotic tissues, but slightly increased in dark green tissues. Three miRNAs, namely miR1919, miR390a, and miR6157, were identified to be strongly up-regulated in chlorotic tissues of both mosaic systems. Results of overexpressing or silencing of the three miRNAs proved that they were related to chlorophyll synthesis, auxin response, and small GTPase-mediated immunity pathway, which were corresponding to the phenotype, physiological parameters and susceptibility of the chlorotic tissues in mosaic leaves. Besides, the newly identified novel-miRNA48, novel-miRNA96 and novel-miRNA103 may also be involved in this formation of mosaic symptoms. Taken together, our results demonstrated that miR1919, miR390a and miR6157 are involved in the formation of mosaic symptoms and plant antiviral responses, providing new insight into the role of miRNAs in the formation of recovery tissue and plant immunity.
PMID: 38376608
PLoS One , IF:3.24 , 2024 , V19 (2) : Pe0296675 doi: 10.1371/journal.pone.0296675
QTL analysis of femaleness in monoecious spinach and fine mapping of a major QTL using an updated version of chromosome-scale pseudomolecules.
Graduate School of Agriculture, Hokkaido University, Sapporo, Japan.; School of Agriculture, Hokkaido University, Sapporo, Japan.; Department of International Agricultural Development, Faculty of International Agriculture and Food Studies, Tokyo University of Agriculture, Setagaya-ku, Tokyo, Japan.; NODAI Genome Research Center, Tokyo University of Agriculture, Setagaya-ku, Tokyo, Japan.; Department of Informatics, Tokyo University of Information Sciences, Chiba, Japan.; Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Japan.; Department of Genomics and Evolutionary Biology, National Institute of Genetics, Mishima, Japan.; The Department of Technology Development, Kazusa DNA Research Institute, Kisarazu, Japan.; The Research Faculty of Agriculture, Hokkaido University, Sapporo, Japan.
Although spinach is predominantly dioecious, monoecious plants with varying proportions of female and male flowers are also present. Recently, monoecious inbred lines with highly female and male conditions have been preferentially used as parents for F1-hybrids, rather than dioecious lines. Accordingly, identifying the loci for monoecism is an important issue for spinach breeding. We here used long-read sequencing and Hi-C technology to construct SOL_r2.0_pseudomolecule, a set of six pseudomolecules of spinach chromosomes (total length: 879.2 Mb; BUSCO complete 97.0%) that are longer and more genetically complete than our previous version of pseudomolecules (688.0 Mb; 81.5%). Three QTLs, qFem2.1, qFem3.1, and qFem6.1, responsible for monoecism were mapped to SOL_r2.0_pseudomolecule. qFem3.1 had the highest LOD score and corresponded to the M locus, which was previously identified as a determinant of monoecious expression, by genetic analysis of progeny from female and monoecious plants. The other QTLs were shown to modulate the ratio of female to male flowers in monoecious plants harboring a dominant allele of the M gene. Our findings will enable breeders to efficiently produce highly female- and male-monoecious parental lines for F1-hybrids by pyramiding the three QTLs. Through fine-mapping, we narrowed the candidate region for the M locus to a 19.5 kb interval containing three protein-coding genes and one long non-coding RNA gene. Among them, only RADIALIS-like-2a showed a higher expression in the reproductive organs, suggesting that it might play a role in reproductive organogenesis. However, there is no evidence that it is involved in the regulation of stamen and pistil initiation, which are directly related to the floral sex differentiation system in spinach. Given that auxin is involved in reproductive organ formation in many plant species, genes related to auxin transport/response, in addition to floral organ formation, were identified as candidates for regulators of floral sex-differentiation from qFem2.1 and qFem6.1.
PMID: 38394294
J Appl Genet , IF:3.24 , 2024 Feb , V65 (1) : P13-30 doi: 10.1007/s13353-023-00800-9
The improvement of the in vitro plant regeneration in barley with the epigenetic modifier of histone acetylation, trichostatin A.
Faculty of Natural Sciences, Institute of Biology, Biotechnology and Environmental Protection, University of Silesia, 40-007, Katowice, Poland. katarzyna.nowak@us.edu.pl.; Faculty of Natural Sciences, Institute of Biology, Biotechnology and Environmental Protection, University of Silesia, 40-007, Katowice, Poland.; Toxicology Research Group, Lukasiewicz Research Network, Institute of Industrial Organic Chemistry Branch Pszczyna, Doswiadczalna 27, 43-200, Pszczyna, Poland.; Institut Jean-Pierre Bourgin (IJPB), INRAE, AgroParisTech, Universite Paris-Saclay, 78000, Versailles, France.
Genotype-limited plant regeneration is one of the main obstacles to the broader use of genetic transformation in barley breeding. Thus, developing new approaches that might improve responses of in vitro recalcitrant genotypes remains at the center of barley biotechnology. Here, we analyzed different barley genotypes, including "Golden Promise," a genotype commonly used in the genetic transformation, and four malting barley cultivars of poor regenerative potential. The expression of hormone-related transcription factor (TF) genes with documented roles in plant regeneration was analyzed in genotypes with various plant-regenerating capacities. The results indicated differential expression of auxin-related TF genes between the barley genotypes in both the explants and the derived cultures. In support of the role of auxin in barley regeneration, distinct differences in the accumulation of free and oxidized auxin were observed in explants and explant-derived callus cultures of barley genotypes. Following the assumption that modifying gene expression might improve plant regeneration in barley, we treated the barley explants with trichostatin A (TSA), which affects histone acetylation. The effects of TSA were genotype-dependent as TSA treatment improved plant regeneration in two barley cultivars. TSA-induced changes in plant regeneration were associated with the increased expression of auxin biosynthesis-involved TFs. The study demonstrated that explant treatment with chromatin modifiers such as TSA might provide a new and effective epigenetic approach to improving plant regeneration in recalcitrant barley genotypes.
PMID: 37962803
G3 (Bethesda) , IF:3.154 , 2024 Feb doi: 10.1093/g3journal/jkae026
GWAS supported by computer vision identifies large numbers of candidate regulators of in planta regeneration in Populus trichocarpa.
Department of Forest Ecosystems and Society, Oregon State University, 321 Richardson Hall, Corvallis, OR, 97311, United States.; Department of Electrical Engineering and Computer Science, Oregon State University, 1148 Kelley Engineering Center, Corvallis, OR, 97331, United States.; Statistics Department, Oregon State University, 239 Weniger Hall, Corvallis, OR, 97331, United States.; Biosciences Division, Oak Ridge National Laboratory, P.O. Box 2008, Oak Ridge, TN, 37831, United States.; Center for Bioenergy Innovation, Oak Ridge National Laboratory, P.O. Box 2008, Oak Ridge, TN, 37831, United States.; Bredesen Center for Interdisciplinary Research, University of Tennessee-Knoxville, 310 Ferris Hall 1508 Middle Dr, Knoxville, TN, 37996, United States.
Plant regeneration is an important dimension of plant propagation and a key step in the production of transgenic plants. However, regeneration capacity varies widely among genotypes and species, the molecular basis of which is largely unknown. While association mapping methods such as genome-wide association studies (GWAS) have long demonstrated abilities to help uncover the genetic basis of trait variation in plants, the abilities of these methods depend on the accuracy and scale of phenotyping. To enable a largescale GWAS of in planta regeneration in the model tree Populus, we developed a phenomics workflow involving semantic segmentation to quantify regenerating plant tissues (callus and shoot) over time. We found the resulting statistics are of highly non-normal distributions, and employed transformations or permutations to avoid violating assumptions of linear models used in GWAS. We report over 200 statistically supported quantitative trait loci (QTLs), with genes encompassing or near to top QTLs including regulators of cell adhesion, stress signaling, and hormone signaling pathways, as well as other diverse functions. Our results encourage models of hormonal signaling during plant regeneration to consider keystone roles of stress-related signaling (e.g., involving jasmonates and salicylic acid) in addition to the auxin and cytokinin pathways commonly considered. The putative regulatory genes and biological processes we identified provide new insights into the biological complexity of plant regeneration, and may serve as new reagents for improving regeneration and transformation of recalcitrant genotypes and species.
PMID: 38325329
Funct Plant Biol , IF:3.101 , 2024 Feb doi: 10.1071/FP23248
Melatonin as a master regulatory hormone for genetic responses to biotic and abiotic stresses in model plant Arabidopsis thaliana: a comprehensive review.
Melatonin is a naturally occurring biologically active amine produced by plants, animals and microbes. This review explores the biosynthesis of melatonin in plants, with a particular focus on its diverse roles in Arabidopsis thaliana, a model species. Melatonin affects abiotic and biotic stress resistance in A. thaliana. Exogenous and endogenous melatonin is addressed in association with various conditions, including cold stress, high light stress, intense heat and infection with Botrytis cinerea or Pseudomonas, as well as in seed germination and lateral root formation. Furthermore, melatonin confers stress resistance in Arabidopsis by initiating the antioxidant system, remedying photosynthesis suppression, regulating transcription factors involved with stress resistance (CBF, DREB, ZAT, CAMTA, WRKY33, MYC2, TGA) and other stress-related hormones (abscisic acid, auxin, ethylene, jasmonic acid and salicylic acid). This article additionally addresses other precursors, metabolic components, expression of genes (COR, CBF, SNAT, ASMT, PIN, PR1, PDF1.2 and HSFA) and proteins (JAZ, NPR1) associated with melatonin and reducing both biological and environmental stressors. Furthermore, the future perspective of melatonin rich agri-crops is explored to enhance plant tolerance to abiotic and biotic stresses, maximise crop productivity and enhance nutritional worth, which may help improve food security.
PMID: 38310885
PeerJ , IF:2.984 , 2024 , V12 : Pe16873 doi: 10.7717/peerj.16873
Above and belowground phenotypic response to exogenous auxin across Arabidopsis thaliana mutants and natural accessions varies from seedling to reproductive maturity.
Department of Biology, College of Charleston, Charleston, SC, United States.; Department of Plant Science, The Pennsylvania State University, University Park, PA, United States.
BACKGROUND: Plant hormones influence phenology, development, and function of above and belowground plant structures. In seedlings, auxin influences the initiation and development of lateral roots and root systems. How auxin-related genes influence root initiation at early life stages has been investigated from numerous perspectives. There is a gap in our understanding of how these genes influence root size through the life cycle and in mature plants. Across development, the influence of a particular gene on plant phenotypes is partly regulated by the addition of a poly-A tail to mRNA transcripts via alternative polyadenylation (APA). Auxin related genes have documented variation in APA, with auxin itself contributing to APA site switches. Studies of the influence of exogenous auxin on natural plant accessions and mutants of auxin pathway gene families exhibiting variation in APA are required for a more complete understanding of genotype by development by hormone interactions in whole plant and fitness traits. METHODS: We studied Arabidopsis thaliana homozygous mutant lines with inserts in auxin-related genes previously identified to exhibit variation in number of APA sites. Our growth chamber experiment included wildtype Col-0 controls, mutant lines, and natural accession phytometers. We applied exogenous auxin through the life cycle. We quantified belowground and aboveground phenotypes in 14 day old, 21 day old seedlings and plants at reproductive maturity. We contrasted root, rosette and flowering phenotypes across wildtype, auxin mutant, and natural accession lines, APA groups, hormone treatments, and life stages using general linear models. RESULTS: The root systems and rosettes of mutant lines in auxin related genes varied in response to auxin applications across life stages and varied between genotypes within life stages. In seedlings, exposure to auxin decreased size, but increased lateral root density, whereas at reproductive maturity, plants displayed greater aboveground mass and total root length. These differences may in part be due to a shift which delayed the reproductive stage when plants were treated with auxin. Root traits of auxin related mutants depended on the number of APA sites of mutant genes and the plant's developmental stage. Mutants with inserts in genes with many APA sites exhibited lower early seedling belowground biomass than those with few APA sites but only when exposed to exogenous auxin. As we observed different responses to exogenous auxin across the life cycle, we advocate for further studies of belowground traits and hormones at reproductive maturity. Studying phenotypic variation of genotypes across life stages and hormone environments will uncover additional shared patterns across traits, assisting efforts to potentially reach breeding targets and enhance our understanding of variation of genotypes in natural systems.
PMID: 38348101
Plant Signal Behav , IF:2.247 , 2024 Dec , V19 (1) : P2305030 doi: 10.1080/15592324.2024.2305030
Cytokinin signaling is involved in root hair elongation in response to phosphate starvation.
School of Biological Science and Technology, College of Science and Engineering, Kanazawa University, Kanazawa, Ishikawa, Japan.; Graduate School of Science and Technology, Nara Institute of Science and Technology, Takayama, Ikoma, Nara, Japan.
Root hair, single-celled tubular structures originating from the epidermis, plays a vital role in the uptake of nutrients from the soil by increasing the root surface area. Therefore, optimizing root hair growth is crucial for plants to survive in fluctuating environments. Root hair length is determined by the action of various plant hormones, among which the roles of auxin and ethylene have been extensively studied. However, evidence for the involvement of cytokinins has remained elusive. We recently reported that the cytokinin-activated B-type response regulators, ARABIDOPSIS RESPONSE REGULATOR 1 (ARR1) and ARR12 directly upregulate the expression of ROOT HAIR DEFECTIVE 6-LIKE 4 (RSL4), which encodes a key transcription factor that controls root hair elongation. However, depending on the nutrient availability, it is unknown whether the ARR1/12-RSL4 pathway controls root hair elongation. This study shows that phosphate deficiency induced the expression of RSL4 and increased the root hair length through ARR1/12, though the transcript and protein levels of ARR1/12 did not change. These results indicate that cytokinins, together with other hormones, regulate root hair growth under phosphate starvation conditions.
PMID: 38267225
Anal Methods , 2024 Feb , V16 (9) : P1347-1356 doi: 10.1039/d4ay00067f
A rapid and sensitive ultra-performance liquid chromatography-tandem mass spectrometry method for determination of phytohormones in the medicinal plant saffron.
TCM Key Laboratory Cultivation Base of Zhejiang Province for the Development and Clinical Transformation of Immunomodulatory Drugs, Huzhou Central Hospital, Affiliated Central Hospital HuZhou University, Huzhou Hospital, Zhejiang University, Huzhou, China. liliqin@hzhospital.com.; Department of Chinese Medicine, Zhejiang University of Traditional Chinese Medicine, Hangzhou, China.
Saffron (Crocus sativus L.) is a valuable Chinese herb with high medicinal value. Saffron pistils are used as medicine, so increasing the number of flowers can increase the yield. Plant hormones have essential roles in the growth and development of saffron, as well as the response to biotic and abiotic stresses (especially in floral initiation), which may directly affect the number of flowers. Quantitative analysis of plant hormones provides a basis for more efficient research on their synthesis, transportation, metabolism, and action. However, starch (which interferes with extraction) is present in high levels, and hormone levels are extremely low, in saffron corms, thereby hampering accurate determination of plant-hormone levels in saffron. Herein, we screened an efficient and convenient pre-treatment method for plant materials containing abundant amounts of starch. Also, we proposed an ultra-performance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS) method for the quantification of abscisic acid (ABA) and auxin (IAA). Then, the method was applied for the detection of hormone-content differences between flowering and non-flowering top buds, as well as between lateral and top buds. Our method showed high sensitivity, reproducibility, and reliability. Specifically, good linearity in the range 2-100 ng ml(-1) was achieved in the determination of ABA and IAA, and the correlation coefficient (R(2)) was >0.9982. The relative standard deviation was 2.956-14.51% (intraday) and 9.57-18.99% (interday), and the recovery range was 89.04-101.1% (n = 9). The matrix effect was 80.38-90.50% (n = 3). The method was thoroughly assessed employing various "green" chemistry evaluation tools: Blue Applicability Grade Index (BAGI), Complementary Green Analytical Procedure Index (Complex GAPI) and Red Green Blue 12 Algorithm (RGB12). These tools revealed the good greenness, analytical performance, applicability, and overall sustainability alignment of our method. Quantitative results showed that, compared with saffron with a flowering phenotype cultivated at 25 degrees C, the contents of IAA and ABA in the terminal buds of saffron cultivated at 16 degrees C decreased significantly. When cultivated at 25 degrees C, the IAA and ABA contents in the terminal buds of saffron were 1.54- and 4.84-times higher than those in the lateral buds, respectively. A simple, rapid, and accurate UPLC-MS/MS method was established to determine IAA and ABA contents. Using this method, a connection between the contents of IAA and ABA and the flowering phenotype was observed in the quantification results. Our data lay a foundation for studying the flowering mechanism of saffron.
PMID: 38334707
Mol Breed , 2024 Feb , V44 (2) : P13 doi: 10.1007/s11032-024-01452-1
Generation of parthenocarpic tomato plants in multiple elite cultivars using the CRISPR/Cas9 system.
Division of Applied Life Science (BK21 Four Program), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, Korea. ROR: https://ror.org/00saywf64. GRID: grid.256681.e. ISNI: 0000 0001 0661 1492; Faculty of Biotechnology, Vietnam National University of Agriculture, Hanoi, Vietnam. ROR: https://ror.org/01abaah21. GRID: grid.444964.f. ISNI: 0000 0000 9825 317X; Institute of Environmental Technology, Vietnam Academy of Science and Technology, Hanoi, Vietnam. ROR: https://ror.org/02wsd5p50. GRID: grid.267849.6. ISNI: 0000 0001 2105 6888; Agricultural Genetics Institute, Hanoi, Vietnam. ROR: https://ror.org/05sswkg52. GRID: grid.499672.7; Division of Applied Life Science (BK21+) and Research Institute of Life Science, Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, Korea. ROR: https://ror.org/00saywf64. GRID: grid.256681.e. ISNI: 0000 0001 0661 1492
Tomato (Solanum lycopersicum L.) is one of the most important crops in the world for its fruit production. Advances in cutting-edge techniques have enabled the development of numerous critical traits related to the quality and quantity of tomatoes. Genetic engineering techniques, such as gene transformation and gene editing, have emerged as powerful tools for generating new plant varieties with superior traits. In this study, we induced parthenocarpic traits in a population of elite tomato (ET) lines. At first, the adaptability of ET lines to genetic transformation was evaluated to identify the best-performing lines by transforming the SlANT1 gene overexpression cassette and then later used to produce the SlIAA9 knockout lines using the CRISPR/Cas9 system. ET5 and ET8 emerged as excellent materials for these techniques and showed higher efficiency. Typical phenotypes of knockout sliaa9 were clearly visible in G0 and G1 plants, in which simple leaves and parthenocarpic fruits were observed. The high efficiency of the CRISPR/Cas9 system in developing new tomato varieties with desired traits in a short period was demonstrated by generating T-DNA-free homozygous sliaa9 knockout plants in the G1 generation. Additionally, a simple artificial fertilization method was successfully applied to recover seed production from parthenocarpic plants, securing the use of these varieties as breeding materials. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s11032-024-01452-1.
PMID: 38317771
Plant Commun , 2024 Feb , V5 (2) : P100791 doi: 10.1016/j.xplc.2023.100791
A graph-based pan-genome of Brassica oleracea provides new insights into its domestication and morphotype diversification.
State Key Laboratory of Vegetable Biobreeding, National Engineering Research Center for Vegetables, Beijing Key Laboratory of Vegetable Germplasm Improvement, Key Laboratory of Biology and Genetics Improvement of Horticultural Crops (North China), Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Science, Beijing 100097, China.; Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Vegetable Research Institute, Jiangsu Academy of Agricultural Science, Nanjing, Jiangsu, China.; Smartgenomics Technology Institute, Tianjin 301700, China.; Smartgenomics Technology Institute, Tianjin 301700, China. Electronic address: chenliyang@smartgenomics.cn.; Boyce Thompson Institute, Ithaca, NY, USA. Electronic address: zf25@cornell.edu.; Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Vegetable Research Institute, Jiangsu Academy of Agricultural Science, Nanjing, Jiangsu, China. Electronic address: jbli@jaas.ac.cn.; State Key Laboratory of Vegetable Biobreeding, National Engineering Research Center for Vegetables, Beijing Key Laboratory of Vegetable Germplasm Improvement, Key Laboratory of Biology and Genetics Improvement of Horticultural Crops (North China), Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Science, Beijing 100097, China. Electronic address: liufan@nercv.org.
The domestication of Brassica oleracea has resulted in diverse morphological types with distinct patterns of organ development. Here we report a graph-based pan-genome of B. oleracea constructed from high-quality genome assemblies of different morphotypes. The pan-genome harbors over 200 structural variant hotspot regions enriched in auxin- and flowering-related genes. Population genomic analyses revealed that early domestication of B. oleracea focused on leaf or stem development. Gene flows resulting from agricultural practices and variety improvement were detected among different morphotypes. Selective-sweep and pan-genome analyses identified an auxin-responsive small auxin up-regulated RNA gene and a CLAVATA3/ESR-RELATED family gene as crucial players in leaf-stem differentiation during the early stage of B. oleracea domestication and the BoKAN1 gene as instrumental in shaping the leafy heads of cabbage and Brussels sprouts. Our pan-genome and functional analyses further revealed that variations in the BoFLC2 gene play key roles in the divergence of vernalization and flowering characteristics among different morphotypes, and variations in the first intron of BoFLC3 are involved in fine-tuning the flowering process in cauliflower. This study provides a comprehensive understanding of the pan-genome of B. oleracea and sheds light on the domestication and differential organ development of this globally important crop species.
PMID: 38168637