Nature , IF:49.962 , 2024 Aug , V632 (8023) : P166-173 doi: 10.1038/s41586-024-07707-3
Identification of plant transcriptional activation domains.
Department of Biology, Duke University, Durham, NC, USA.; Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, USA.; Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, USA.; Center for Biomolecular Condensates, Washington University in St. Louis, St. Louis, MO, USA.; Biological Systems Engineering, Virginia Tech, Blacksburg, VA, USA.; Center for Computational Biology, University of California, Berkeley, Berkeley, CA, USA.; Department of Biology, Duke University, Durham, NC, USA. lucia.strader@duke.edu.
Gene expression in Arabidopsis is regulated by more than 1,900 transcription factors (TFs), which have been identified genome-wide by the presence of well-conserved DNA-binding domains. Activator TFs contain activation domains (ADs) that recruit coactivator complexes; however, for nearly all Arabidopsis TFs, we lack knowledge about the presence, location and transcriptional strength of their ADs(1). To address this gap, here we use a yeast library approach to experimentally identify Arabidopsis ADs on a proteome-wide scale, and find that more than half of the Arabidopsis TFs contain an AD. We annotate 1,553 ADs, the vast majority of which are, to our knowledge, previously unknown. Using the dataset generated, we develop a neural network to accurately predict ADs and to identify sequence features that are necessary to recruit coactivator complexes. We uncover six distinct combinations of sequence features that result in activation activity, providing a framework to interrogate the subfunctionalization of ADs. Furthermore, we identify ADs in the ancient AUXIN RESPONSE FACTOR family of TFs, revealing that AD positioning is conserved in distinct clades. Our findings provide a deep resource for understanding transcriptional activation, a framework for examining function in intrinsically disordered regions and a predictive model of ADs.
PMID: 39020176
Mol Plant , IF:13.164 , 2024 Aug doi: 10.1016/j.molp.2024.07.014
A dose-dependent bimodal switch by homologous Aux/IAA transcriptional repressors.
Department of Biological Sciences, Seoul National University, Seoul, Korea. Electronic address: htcho@snu.ac.kr.; Department of Biological Sciences, Seoul National University, Seoul, Korea.; School of Earth and Environmental Sciences, Seoul National University, Seoul, Korea.; School of Earth and Environmental Sciences, Seoul National University, Seoul, Korea; Department of Climate and Energy Systems Engineering, Ewha Womans University, Seoul, Korea.
Combinatorial interactions between different regulators diversify and enrich the chance of transcriptional regulation in eukaryotic cells. However, a dose-dependent functional switch of homologous transcriptional repressors has rarely been reported. Here, we show that SHY2, an auxin/indole-3-acetic acid (Aux/IAA) repressor, exhibits a dose-dependent bimodal role in auxin-sensitive root-hair growth and gene transcription in Arabidopsis, whereas other Aux/IAA homologs consistently repress the auxin responses. The co-repressor (TOPLESS [TPL])-binding affinity of a bimodal Aux/IAA was lower than that of a consistently repressing Aux/IAA. The switch of a single amino acid residue in the TPL-binding motif between the bimodal form and the consistently repressing form switched their TPL-binding affinity and transcriptional and biological roles in auxin responses. Based on these data, we propose a model whereby competition between homologous repressors with different co-repressor-binding affinities could generate a bimodal output at the transcriptional and developmental levels.
PMID: 39095993
Dev Cell , IF:12.27 , 2024 Aug , V59 (16) : P2254-2269.e6 doi: 10.1016/j.devcel.2024.07.001
Soybean symbiotic-nodule zonation and cell differentiation are defined by NIN2 signaling and GH3-dependent auxin homeostasis.
Haixia Institute of Science and Technology, Horticultural Plant Biology and Metabolomics Center, Fujian Agriculture and Forestry University, Fuzhou, China.; Haixia Institute of Science and Technology, Horticultural Plant Biology and Metabolomics Center, Fujian Agriculture and Forestry University, Fuzhou, China; College of Agriculture and Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 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, China.; National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China.; Haixia Institute of Science and Technology, Horticultural Plant Biology and Metabolomics Center, Fujian Agriculture and Forestry University, Fuzhou, China. Electronic address: chenxu@fafu.edu.cn.
Symbiotic nodules comprise two classes, indeterminate and determinate, defined by the presence/absence of apical meristem and developmental zonation. Why meristem and zonation are absent from determinate nodules remains unclear. Here, we define cell types in developing soybean nodules, highlighting the undifferentiated infection zones and differentiated nitrogen-fixation zones. Auxin governs infection zone maintenance. GRETCHEN HAGEN 3 (GH3) enzymes deactivate auxin by conjugation and promote cell differentiation. gh3 mutants increased undifferentiated cells and enlarged infection zones. The central symbiosis-transcription factor NIN2a activates GH3.1 to reduce auxin levels and facilitates cell differentiation. High auxin promotes NIN2a protein accumulation and enhances signaling, further deactivating auxin and depleting infection zones. Our findings shed light on the NIN2a-GH3-auxin module that drives soybean nodule cell differentiation. This study challenges our understanding of determinate nodule development and proposes that the regulation of nodule zonation offers valuable insights into broader mechanisms of cell differentiation across plant species.
PMID: 39053471
Curr Biol , IF:10.834 , 2024 Aug doi: 10.1016/j.cub.2024.07.066
A 3-component module maintains sepal flatness in Arabidopsis.
Key Laboratory of Nuclear Agricultural Sciences of Ministry of Agriculture and Zhejiang Province, Institute of Nuclear Agricultural Sciences, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China.; Laboratoire de Reproduction et Developpement des Plantes, Universite de Lyon, ENS de Lyon, UCBL, CNRS, 46 Allee d'Italie, 69364 Lyon Cedex 07, France; University of Science and Technology of Hanoi, Vietnam Academy of Science and Technology (VAST), 18 Hoang Quoc Viet, Cau Giay, Ha Noi 11355, Vietnam.; Laboratoire de Reproduction et Developpement des Plantes, Universite de Lyon, ENS de Lyon, UCBL, CNRS, 46 Allee d'Italie, 69364 Lyon Cedex 07, France; Cell and Developmental Biology Department, John Innes Centre, Norwich NR4 7UH, UK.; Key Laboratory of Nuclear Agricultural Sciences of Ministry of Agriculture and Zhejiang Province, Institute of Nuclear Agricultural Sciences, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China; The Advanced Seed Institute, National Key Laboratory of Rice Breeding and Biology, Zhejiang Provincial Key Laboratory of Crop Germplasm, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China.; State Key Laboratory of Plant Environmental Resilience, College of Life Sciences, Zhejiang University, Hangzhou 310058, China.; Weill Institute for Cell and Molecular Biology and Section of Plant Biology, School of Integrative Plant Sciences, Cornell University, Ithaca, NY 14853, USA.; Laboratoire de Reproduction et Developpement des Plantes, Universite de Lyon, ENS de Lyon, UCBL, CNRS, 46 Allee d'Italie, 69364 Lyon Cedex 07, France. Electronic address: olivier.hamant@ens-lyon.fr.; Key Laboratory of Nuclear Agricultural Sciences of Ministry of Agriculture and Zhejiang Province, Institute of Nuclear Agricultural Sciences, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China. Electronic address: lilanhong@zju.edu.cn.
As in origami, morphogenesis in living systems heavily relies on tissue curving and folding through the interplay between biochemical and biomechanical cues. By contrast, certain organs maintain their flat posture over several days. Here, we identified a pathway that is required for the maintenance of organ flatness, taking the sepal, the outermost floral organ, in Arabidopsis as a model system. Through genetic, cellular, and mechanical approaches, our results demonstrate that the global gene expression regulator VERNALIZATION INDEPENDENCE 4 (VIP4) fine-tunes the mechanical properties of sepal cell walls and maintains balanced growth on both sides of the sepals, mainly by orchestrating the distribution pattern of AUXIN RESPONSE FACTOR 3 (ARF3). vip4 mutation results in softer cell walls and faster cell growth on the adaxial sepal side, which eventually cause sepals to bend outward. Downstream of VIP4, ARF3 works through modulating auxin to downregulate pectin methylesterase VANGUARD1, resulting in decreased cell wall stiffness. Thus, our work unravels a 3-component module that relates hormonal patterns to organ curvature and actively maintains sepal flatness during its growth.
PMID: 39146940
J Hazard Mater , IF:10.588 , 2024 Sep , V477 : P135423 doi: 10.1016/j.jhazmat.2024.135423
The monokaryotic filamentous fungus Ustilago sp. HFJ311 promotes plant growth and reduces Cd accumulation by enhancing Fe transportation and auxin biosynthesis.
Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou 730000, PR China.; Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou 730000, PR China. Electronic address: naxf@lzu.edu.cn.; Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou 730000, PR China. Electronic address: yrbi@lzu.edu.cn.
Infection with smut fungus like Ustilago maydis decreases crop yield via inducing gall formation. However, the in vitro impact of Ustilago spp. on plant growth and stress tolerance remains elusive. This study investigated the plant growth promotion and cadmium stress mitigation mechanisms of a filamentous fungus discovered on a cultural medium containing 25 muM CdCl(2). ITS sequence alignment revealed 98.7 % similarity with Ustilago bromivora, naming the strain Ustilago sp. HFJ311 (HFJ311). Co-cultivation with HFJ311 significantly enhanced the growth of various plants, including Arabidopsis, tobacco, cabbage, carrot, rice, and maize, and improved Arabidopsis tolerance to abiotic stresses like salt and metal ions. HFJ311 increased chlorophyll and Fe contents in Arabidopsis shoots and enhanced root-to-shoot Fe translocation while decreasing root Fe concentration by approximately 70 %. Concurrently, HFJ311 reduced Cd accumulation in Arabidopsis by about 60 %, indicating its potential for bioremediation in Cd-contaminated soils. Additionally, HFJ311 stimulated IAA concentration by upregulating auxin biosynthesis genes. Overexpression of the Fe transporter IRT1 negated HFJ311's growth-promotion effects under Cd stress. These results suggest that HFJ311 stimulates plant growth and inhibits Cd uptake by enhancing Fe translocation and auxin biosynthesis while disrupting Fe absorption. Our findings offer a promising bioremediation strategy for sustainable agriculture and food security.
PMID: 39106721
J Hazard Mater , IF:10.588 , 2024 Sep , V476 : P135092 doi: 10.1016/j.jhazmat.2024.135092
Methylisothiazolinone pollution inhibited root stem cells and regeneration through auxin transport modification in Arabidopsis thaliana.
Laboratory of Medicinal Plant, Hubei Key Laboratory of Embryonic Stem Cell Research, School of Basic Medicine, Hubei University of Medicine, Shiyan 442000, PR China.; Laboratory of Medicinal Plant, Hubei Key Laboratory of Embryonic Stem Cell Research, School of Basic Medicine, Hubei University of Medicine, Shiyan 442000, PR China; School of Pharmacy, Shaanxi University of Chinese Medicine, Xianyang, Shaanxi, China.; Laboratory of Medicinal Plant, Hubei Key Laboratory of Embryonic Stem Cell Research, School of Basic Medicine, Hubei University of Medicine, Shiyan 442000, PR China; State Key Laboratory for Quality Ensurance and Sustainable Use of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China.; Key Laboratory of Medicinal Resources and Natural Pharmaceutical Chemistry of Ministry of Education, College of Life Sciences, Shaanxi Normal University, Xi'an 710119, China.; State Key Laboratory for Quality Ensurance and Sustainable Use of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China.; Research Center of Environment and Healh of South-to-North Waler Diversion Area, Hubei University of Medicine, Shiyan 442000, China.; College of Ecology, Lishui University, Lishui 323000, China.; Laboratory of Medicinal Plant, Hubei Key Laboratory of Embryonic Stem Cell Research, School of Basic Medicine, Hubei University of Medicine, Shiyan 442000, PR China. Electronic address: lee.childe@qq.com.; State Key Laboratory for Quality Ensurance and Sustainable Use of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China. Electronic address: juanliu126@126.com.
Methylisothiazolinone (MIT) is a widely used preservative and biocide to prevent product degradation, yet its potential impact on plant growth remains poorly understood. In this study, we investigated MIT's toxic effects on Arabidopsis thaliana root growth. Exposure to MIT significantly inhibited Arabidopsis root growth, associated with reduced root meristem size and root meristem cell numbers. We explored the polar auxin transport pathway and stem cell regulation as key factors in root meristem function. Our findings demonstrated that MIT suppressed the expression of the auxin efflux carrier PIN1 and major root stem cell regulators (PLT1, PLT2, SHR, and SCR). Additionally, MIT hindered root regeneration by downregulating the quiescent center (QC) marker WOX5. Transcriptome analysis revealed MIT-induced alterations in gene expression related to oxidative stress, with physiological experiments confirming elevated reactive oxygen species (ROS) levels and increased cell death in root tips at concentrations exceeding 50 muM. In summary, this study provides critical insights into MIT's toxicity on plant root development and regeneration, primarily linked to modifications in polar auxin transport and downregulation of genes associated with root stem cell regulation.
PMID: 38964040
J Adv Res , IF:10.479 , 2024 Sep , V63 : P57-72 doi: 10.1016/j.jare.2023.11.001
Modulation of warm temperature-sensitive growth using a phytochrome B dark reversion variant, phyB[G515E], in Arabidopsis and rice.
Department of Biological Sciences, Chungnam National University, Daejeon 34134, Republic of Korea.; Graduate School of Green-Bio Science and Crop Biotech Institute, Kyung Hee University, Yongin 17104, Republic of Korea.; Department of Applied Biosciences, Kyungpook National University, Daegu 41566, Republic of Korea.; Department of Molecular Biotechnology and Kumho Life Science Laboratory, Chonnam National University, Gwangju 61186, Republic of Korea.; National Institute of Crop Science, Rural Development Administration, Wanju 55365, Republic of Korea.; Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea.; Department of Biological Sciences, Sungkyunkwan University, Suwon 16419, Republic of Korea.; Graduate School of Green-Bio Science and Crop Biotech Institute, Kyung Hee University, Yongin 17104, Republic of Korea. Electronic address: jjeon@khu.ac.kr.; Department of Biological Sciences, Chungnam National University, Daejeon 34134, Republic of Korea. Electronic address: yipark@cnu.ac.kr.
INTRODUCTION: Ambient temperature-induced hypocotyl elongation in Arabidopsis seedlings is sensed by the epidermis-localized phytochrome B (phyB) and transduced into auxin biosynthesis via a basic helix-loop-helix transcription factor, phytochrome-interacting factor 4 (PIF4). Once synthesized, auxin travels down from the cotyledons to the hypocotyl, triggering hypocotyl cell elongation. Thus, the phyB-PIF4 module involved in thermosensing and signal transduction is a potential genetic target for engineering warm temperature-insensitive plants. OBJECTIVES: This study aims to manipulate warm temperature-induced elongation of plants at the post-translational level using phyB variants with dark reversion, the expression of which is subjected to heat stress. METHODS: The thermosensitive growth response of Arabidopsis was manipulated by expressing the single amino acid substitution variant of phyB (phyB[G515E]), which exhibited a lower dark reversion rate than wild-type phyB. Other variants with slow (phyB[G564E]) or rapid (phyB[S584F]) dark reversion or light insensitivity (phyB[G767R]) were also included in this study for comparison. Warming-induced transient expression of phyB variants was achieved using heat shock-inducible promoters. Arabidopsis PHYB[G515E] and PHYB[G564E] were also constitutively expressed in rice in an attempt to manipulate the heat sensitivity of a monocotyledonous plant species. RESULTS: At an elevated temperature, Arabidopsis seedlings transiently expressing PHYB[G515E] under the control of a heat shock-inducible promoter exhibited shorter hypocotyls than those expressing PHYB and other PHYB variant genes. This warm temperature-insensitive growth was related to the lowered PIF4 and auxin responses. In addition, transgenic rice seedlings expressing Arabidopsis PHYB[G515E] and PHYB[G564E] showed warm temperature-insensitive shoot growth. CONCLUSION: Transient expression of phyB variants with altered dark reversion rates could serve as an effective optogenetic technique for manipulating PIF4-auxin-mediated thermomorphogenic responses in plants.
PMID: 37926145
New Phytol , IF:10.151 , 2024 Aug doi: 10.1111/nph.20066
Is auxin the key to improve crop nitrogen use efficiency for greener agriculture?
State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing, 210095, China.; Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095, China.
Strengthening future food security through the application of unsustainable levels of inorganic nitrogen (N) fertilizers to crop fields may exacerbate environmental damage. Coordination of N-use efficiency (NUE) and plant growth is, therefore, crucial for sustainable agriculture. Auxin plays pivotal roles in developmental and signaling responses that affect NUE. Hence, a better understanding of these processes provides great potential to improve crop NUE. This review summarizes the effects of auxin on N-related and root developmental processes that either directly or indirectly affect NUE in the model plant Arabidopsis and major crop species to highlight the potential of fostering sustainable agricultural development in the future through modulating auxin-related processes.
PMID: 39155785
New Phytol , IF:10.151 , 2024 Sep , V243 (5) : P1681-1697 doi: 10.1111/nph.19970
A transcriptional repressor HVA regulates vascular bundle formation through auxin transport in Arabidopsis stem.
Department of Plant Science and Landscape Architecture, University of Connecticut, 1376 Storrs Rd, Storrs, CT, 06269, USA.; Institute for System Genomics, University of Connecticut, Storrs, CT, 06269, USA.
Vascular bundles transport water and photosynthate to all organs, and increased bundle number contributes to crop lodging resistance. However, the regulation of vascular bundle formation is poorly understood in the Arabidopsis stem. We report a novel semi-dominant mutant with high vascular activity, hva-d, showing increased vascular bundle number and enhanced cambium proliferation in the stem. The activation of a C2H2 zinc finger transcription factor, AT5G27880/HVA, is responsible for the hva-d phenotype. Genetic, biochemical, and fluorescent microscopic analyses were used to dissect the functions of HVA. HVA functions as a repressor and interacts with TOPLESS via the conserved Ethylene-responsive element binding factor-associated Amphiphilic Repression motif. In contrast to the HVA activation line, knockout of HVA function with a CRISPR-Cas9 approach or expression of HVA fused with an activation domain VP16 (HVA-VP16) resulted in fewer vascular bundles. Further, HVA directly regulates the expression of the auxin transport efflux facilitator PIN1, as a result affecting auxin accumulation. Genetics analysis demonstrated that PIN1 is epistatic to HVA in controlling bundle number. This research identifies HVA as a positive regulator of vascular initiation through negatively modulating auxin transport and sheds new light on the mechanism of bundle formation in the stem.
PMID: 39014537
New Phytol , IF:10.151 , 2024 Sep , V243 (5) : P1870-1886 doi: 10.1111/nph.19961
ZmSPL10, ZmSPL14 and ZmSPL26 act together to promote stigmatic papilla formation in maize through regulating auxin signaling and ZmWOX3A expression.
State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China.; Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510535, China.; Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
Maize silk is a specialized type of stigma, covered with numerous papillae for pollen grain capture. However, the developmental process of stigmatic papillae and the underlying regulatory mechanisms have remained largely unknown. Here, we combined the cytological, genetic and molecular studies to demonstrate that three homologous genes ZmSPL10, ZmSPL14 and ZmSPL26 play a central role in promoting stigmatic papilla formation in maize. We show that their triple knockout mutants are nearly complete lack of stigmatic papilla, resulting in a severe reduction in kernel setting. Cellular examination reveals that stigmatic papilla is developed from a precursor cell, which is the smaller daughter cell resulting from asymmetric cell division of a silk epidermal cell. In situ hybridization shows that ZmSPL10, ZmSPL14 and their target genes SPI1, ZmPIN1b, ZmARF28 and ZmWOX3A are preferentially expressed in the precursor cells of stigmatic papillae. Moreover, ZmSPL10, ZmSPL14 and ZmSPL26 directly bind to the promoters of SPI1, ZmPIN1b, ZmARF28 and ZmWOX3A and promote their expression. Further, Zmwox3a knockout mutants display severe defects in stigmatic papilla formation and reduced seed setting. Collectively, our results demonstrate that ZmSPL10, ZmSPL14 and ZmSPL26 act together to promote stigmatic papilla development through regulating auxin signaling and ZmWOX3A expression.
PMID: 39010694
New Phytol , IF:10.151 , 2024 Sep , V243 (5) : P1855-1869 doi: 10.1111/nph.19949
The biosynthesis of storage reserves and auxin is coordinated by a hierarchical regulatory network in maize endosperm.
State Key Laboratory of Maize Bio-breeding, Frontiers Science Center for Molecular Design Breeding, Joint International Research Laboratory of Crop Molecular Breeding, National Maize Improvement Center, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China.; State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China.; Shanghai Key Laboratory of Bio-Energy Crops, Plant Science Center, School of Life Sciences, Shanghai University, Shanghai, 200444, China.
Grain filling in maize (Zea mays) is intricately linked to cell development, involving the regulation of genes responsible for the biosynthesis of storage reserves (starch, proteins, and lipids) and phytohormones. However, the regulatory network coordinating these biological functions remains unclear. In this study, we identified 1744 high-confidence target genes co-regulated by the transcription factors (TFs) ZmNAC128 and ZmNAC130 (ZmNAC128/130) through chromatin immunoprecipitation sequencing coupled with RNA-seq analysis in the zmnac128/130 loss-of-function mutants. We further constructed a hierarchical regulatory network using DNA affinity purification sequencing analysis of downstream TFs regulated by ZmNAC128/130. In addition to target genes involved in the biosynthesis of starch and zeins, we discovered novel target genes of ZmNAC128/130 involved in the biosynthesis of lipids and indole-3-acetic acid (IAA). Consistently, the number of oil bodies, as well as the contents of triacylglycerol, and IAA were significantly reduced in zmnac128/130. The hierarchical regulatory network centered by ZmNAC128/130 revealed a significant overlap between the direct target genes of ZmNAC128/130 and their downstream TFs, particularly in regulating the biosynthesis of storage reserves and IAA. Our results indicated that the biosynthesis of storage reserves and IAA is coordinated by a multi-TFs hierarchical regulatory network in maize endosperm.
PMID: 38962989
New Phytol , IF:10.151 , 2024 Aug , V243 (4) : P1299-1300 doi: 10.1111/nph.19879
Dior R. Kelley.
PMID: 38837388
Plant Biotechnol J , IF:9.803 , 2024 Sep , V22 (9) : P2596-2611 doi: 10.1111/pbi.14372
Light control of three-dimensional chromatin organization in soybean.
National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences at Weifang, Shandong, China.; School of Plant Science and Food Security, Tel Aviv University, Tel Aviv, Israel.; School of Advanced Agriculture Sciences and School of Life Sciences, State Key Laboratory of Protein and Plant Gene Research, Peking University, Beijing, China.
Higher-order chromatin structure is critical for regulation of gene expression. In plants, light profoundly affects the morphogenesis of emerging seedlings as well as global gene expression to ensure optimal adaptation to environmental conditions. However, the changes and functional significance of chromatin organization in response to light during seedling development are not well documented. We constructed Hi-C contact maps for the cotyledon, apical hook and hypocotyl of soybean subjected to dark and light conditions. The resulting high-resolution Hi-C contact maps identified chromosome territories, A/B compartments, A/B sub-compartments, TADs (Topologically Associated Domains) and chromatin loops in each organ. We observed increased chromatin compaction under light and we found that domains that switched from B sub-compartments in darkness to A sub-compartments under light contained genes that were activated during photomorphogenesis. At the local scale, we identified a group of TADs constructed by gene clusters consisting of different numbers of Small Auxin-Upregulated RNAs (SAURs), which exhibited strict co-expression in the hook and hypocotyl in response to light stimulation. In the hypocotyl, RNA polymerase II (RNAPII) regulated the transcription of a SAURs cluster under light via TAD condensation. Our results suggest that the 3D genome is involved in the regulation of light-related gene expression in a tissue-specific manner.
PMID: 38762905
Plant Biotechnol J , IF:9.803 , 2024 Sep , V22 (9) : P2578-2592 doi: 10.1111/pbi.14370
Evolutionary relationship of moso bamboo forms and a multihormone regulatory cascade involving culm shape variation.
Key Laboratory of State Forestry and Grassland Administration/Beijing on Bamboo and Rattan Science and Technology, Beijing, China.; Institute of Gene Science and Industrialization for Bamboo and Rattan Resources, International Center for Bamboo and Rattan, Beijing, China.; Sanya Research Base, International Centre for Bamboo and Rattan, Sanya, China.
Moso bamboo (Phyllostachys edulis) known as Mao Zhu (MZ) in Chinese exhibits various forms with distinct morphological characteristics. However, the evolutionary relationship among MZ forms and the mechanisms of culm shape variation are still lacking. Here, the main differences among MZ forms were identified as culm shape variation, which were confirmed by analysing MZ forms (799 bamboo culms) and MZ (458 bamboo culms) populations. To unravel the genetic basis underlying the morphological variations, 20 MZ forms were subjected to whole-genome resequencing. Further analysis yielded 3 230 107 high-quality SNPs and uncovered low genetic diversity and high genotype heterozygosity associated with MZ forms' formation. By integrating the SNP data of 427 MZ individuals representing 15 geographic regions, the origins of eight MZ forms were successfully traced using the phylogenetic tree and the identified common heterozygous loci. Meanwhile, transcriptomic analysis was performed using shoots from MZ and its two forms with culm shape variation. The results, combined with genomic analyses, demonstrated that hormone signalling related genes played crucial roles in culm variation. Co-expression network analysis uncovered genes associated with multiple plant hormone signal transduction, especially auxin and cytokinin were involved in culm shape variation. Furthermore, the regulatory relationships of a specific transcription factor and their target genes associated with auxin and ethylene signalling were validated by yeast one-hybrid, electrophoretic mobility shift assays, and dual-luciferase reporter. Overall, this study provides important insights into the culm shape variation formation in bamboo, which facilitates to breed new varieties with novel culms.
PMID: 38743918
Plant Biotechnol J , IF:9.803 , 2024 Aug , V22 (8) : P2201-2215 doi: 10.1111/pbi.14339
PagARGOS promotes low-lignin wood formation in poplar.
State Key Laboratory of Efficient Production of Forest Resources, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China.; National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, China.; Department of Chemical and Biomolecular Engineering, National University of Singapore, Singapore, Singapore.; Beijing Key Laboratory of Lignocellulosic Chemistry, College of Materials Science and Technology, Beijing Forestry University, Beijing, China.; National Centre for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China.; College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, China.; Shandong Provincial Key Laboratory of Energy Genetics and CAS Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China.
Wood formation, which occurs mainly through secondary xylem development, is important not only for supplying raw material for the 'ligno-chemical' industry but also for driving the storage of carbon. However, the complex mechanisms underlying the promotion of xylem formation remain to be elucidated. Here, we found that overexpression of Auxin-Regulated Gene involved in Organ Size (ARGOS) in hybrid poplar 84 K (Populus alba x Populus tremula var. glandulosa) enlarged organ size. In particular, PagARGOS promoted secondary growth of stems with increased xylem formation. To gain further insight into how PagARGOS regulates xylem development, we further carried out yeast two-hybrid screening and identified that the auxin transporter WALLS ARE THIN1 (WAT1) interacts with PagARGOS. Overexpression of PagARGOS up-regulated WAT1, activating a downstream auxin response promoting cambial cell division and xylem differentiation for wood formation. Moreover, overexpressing PagARGOS caused not only higher wood yield but also lower lignin content compared with wild-type controls. PagARGOS is therefore a potential candidate gene for engineering fast-growing and low-lignin trees with improved biomass production.
PMID: 38492213
Cell Rep , IF:9.423 , 2024 Aug , V43 (8) : P114597 doi: 10.1016/j.celrep.2024.114597
TMK4-mediated FIP37 phosphorylation regulates auxin-triggered N(6)-methyladenosine modification of auxin biosynthetic genes in Arabidopsis.
College of Biology, Hunan Key Laboratory of Plant Functional Genomics and Developmental Regulation, Hunan University, Changsha, Hunan 410082, China; State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Hunan Academy of Agricultural Sciences, Changsha, Hunan 410082, China.; College of Biology, Hunan Key Laboratory of Plant Functional Genomics and Developmental Regulation, Hunan University, Changsha, Hunan 410082, China.; School of Pharmacy, Xiangnan University, Chenzhou, Hunan 423000, China.; Temasek Life Sciences Laboratory, National University of Singapore, Singapore 117604, Singapore.; FAFU-Joint Center, Horticulture and Metabolic Biology Center, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China.; College of Biology, Hunan Key Laboratory of Plant Functional Genomics and Developmental Regulation, Hunan University, Changsha, Hunan 410082, China. Electronic address: chongshenghe@outlook.com.
The dynamics of N(6)-methyladenosine (m(6)A) mRNA modification are tightly controlled by the m(6)A methyltransferase complex and demethylases. Here, we find that auxin treatment alters m(6)A modification on auxin-responsive genes. Mechanically, TRANSMEMBRANE KINASE 4 (TMK4), a component of the auxin signaling pathway, interacts with and phosphorylates FKBP12-INTERACTING PROTEIN 37 (FIP37), a core component of the m(6)A methyltransferase complex, in an auxin-dependent manner. Phosphorylation of FIP37 enhances its interaction with RNA, thereby increasing m(6)A modification on its target genes, such as NITRILASE 1 (NIT1), a gene involved in indole-3-acetic acid (IAA) biosynthesis. 1-Naphthalacetic acid (NAA) treatment accelerates the mRNA decay of NIT1, in a TMK4- and FIP37-dependent manner, which leads to inhibition of auxin biosynthesis. Our findings identify a regulatory mechanism by which auxin modulates m(6)A modification through the phosphorylation of FIP37, ultimately affecting mRNA stability and auxin biosynthesis in plants.
PMID: 39106180
Cell Rep , IF:9.423 , 2024 Aug , V43 (8) : P114524 doi: 10.1016/j.celrep.2024.114524
Single-cell RNA sequencing reveals dynamics of gene expression for 2D elongation and 3D growth in Physcomitrium patens.
State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan 430062, China.; CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China.; National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, State Key Laboratory of Crop Stress Adaptation and Improvement, Key Laboratory of Plant Stress Biology, School of Life Sciences, Henan University, 85 Minglun Street, Kaifeng 475001, China.; Mid-Florida Research and Education Center, Department of Environmental Horticulture, University of Florida, 2725 South Binion Road, Apopka, FL 32703, USA.; State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan 430062, China. Electronic address: liuli2020@hubu.edu.cn.
The transition from two-dimensional (2D) to 3D growth likely facilitated plants to colonize land, but its heterogeneity is not well understood. In this study, we utilized single-cell RNA sequencing to analyze the moss Physcomitrium patens, whose morphogenesis involves a transition from 2D to 3D growth. We profiled over 17,000 single cells covering all major vegetative tissues, including 2D filaments (chloronema and caulonema) and 3D structures (bud and gametophore). Pseudotime analyses revealed larger numbers of candidate genes that determine cell fates for 2D tip elongation or 3D bud differentiation. Using weighted gene co-expression network analysis, we identified a module that connects beta-type carbonic anhydrases (betaCAs) with auxin. We further validated the cellular expression patterns of betaCAs and demonstrated their roles in 3D gametophore development. Overall, our study provides insights into cellular heterogeneity in a moss and identifies molecular signatures that underpin the 2D-to-3D growth transition at single-cell resolution.
PMID: 39046878
Environ Sci Technol , IF:9.028 , 2024 Aug , V58 (33) : P14726-14739 doi: 10.1021/acs.est.4c01418
Serendipita indica Drives Sulfur-Related Microbiota in Enhancing Growth of Hyperaccumulator Sedum alfredii and Facilitating Soil Cadmium Remediation.
MOE Key Laboratory of Environment Remediation and Ecological Health, College of Environmental & Resource Science, Zhejiang University, Hangzhou 310058, P. R. China.; Zhejiang Provincial Key Laboratory of Subtropic Soil and Plant Nutrition, Zhejiang University, Hangzhou 310058, P. R. China.; Advanced Photon Source, Argonne National Laboratory, Lemont, Illinois 60439, United States.; Xianghu Laboratory, Biotechnology Institute, Hangzhou 311231, P. R. China.
Endophytic fungus Serendipita indica can bolster plant growth and confer protection against various biotic and abiotic stresses. However, S. indica-reshaped rhizosphere microecology interactions and root-soil interface processes in situ at the submicrometer scale remain poorly understood. We combined amplicon sequencing and high-resolution nano X-ray fluorescence (nano-XRF) imaging of the root-soil interface to reveal cadmium (Cd) rhizosphere processes. S. indica can successfully colonize the roots of Sedum alfredii Hance, which induces a remarkable increase in shoot biomass by 211.32% and Cd accumulation by 235.72%. Nano-XRF images showed that S. indica colonization altered the Cd distribution in the rhizosphere and facilitated the proximity of more Cd and sulfur (S) to enter the roots and transport to the shoot. Furthermore, the rhizosphere-enriched microbiota demonstrated a more stable network structure after the S. indica inoculation. Keystone species were strongly associated with growth promotion and Cd absorption. For example, Comamonadaceae are closely related to the organic acid cycle and S bioavailability, which could facilitate Cd and S accumulation in plants. Meanwhile, Sphingomonadaceae could release auxin and boost plant biomass. In summary, we construct a mutualism system for beneficial fungi and hyperaccumulation plants, which facilitates high-efficient remediation of Cd-contaminated soils by restructuring the rhizosphere microbiota.
PMID: 39116417
Plant Physiol , IF:8.34 , 2024 Aug doi: 10.1093/plphys/kiae453
A lipid synthase maintains metabolic flux for jasmonate synthesis to regulate root growth and phosphate homeostasis.
National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi-110067, India.
Plants require phosphate (Pi) for proper growth and development but often face scarcity of this vital nutrient in the soil. Pi-starvation triggers membrane lipid remodeling to utilize the membrane phospholipid-bound Pi in plants. In this process, phospholipids are replaced by non-Pi-containing galactolipids (MGDG, DGDG) and sulfolipids. The galactolipids ratio (MGDG:DGDG) is suggested to influence jasmonic acid (JA) biosynthesis. However, how the MGDG:DGDG ratio, JA levels, and root growth are coordinated under Pi deficiency in rice (Oryza sativa) remains unknown. Here, we characterized DGDG synthase 1 (OsDGD1) for its role in regulating root development by maintaining metabolic flux for JA biosynthesis. We showed that OsDGD1 is responsive under low Pi and is under the direct control of Phosphate Starvation Response 2 (OsPHR2), the master regulator of low Pi adaptations. Further, OsDGD1 knockout (KO) lines showed marked phenotypic differences compared to the wild type (WT), including a significant reduction in root length and biomass, leading to reduced Pi uptake. Further, lipidome analyses revealed reduced DGDG levels in the KO line, leading to reduced membrane remodeling, thus affecting P utilization efficiency. We also observed an increase in the MGDG: DGDG ratio in KO lines, which enhanced the endogenous JA levels and signaling. This imbalance of JA in KO plants led to changes in auxin levels, causing drastic root growth inhibition. These findings indicate the critical role of OsDGD1 in maintaining optimum levels of JA during Pi deficiency for conducive root growth. Besides acting as signaling molecules and structural components, our study widens the role of lipids as metabolic flux controllers for phytohormone biosynthesis.
PMID: 39190806
Plant Physiol , IF:8.34 , 2024 Aug doi: 10.1093/plphys/kiae417
Temporal and spatial frameworks supporting plant responses to vegetation proximity.
Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Cerdanyola del Valles, 08193-Barcelona, Spain.; Institute for Plant Molecular and Cell Biology (IBMCP), CSIC-UPV, 46022-Valencia, Spain.; Departament de Bioquimica i Biologia Molecular, Universitat Autonoma de Barcelona, Cerdanyola del Valles, 08193-Barcelona, Spain.; Swiss Federal Institute of Technology (ETH) Zurich, CH-8092 Zurich, Switzerland.; Departament de Biologia, Bioquimica i Ciencies Naturals, Universitat Jaume I, 12071 Castello de la Plana, Spain.; Centro Nacional de Analisis Genomico (CNAG) and Universitat de Barcelona, 08028-Barcelona, Spain.
After perception of vegetation proximity by phytochrome photoreceptors, shade-avoider plants initiate a set of responses known as the Shade Avoidance Syndrome (SAS). Shade perception by the phytochrome B (phyB) photoreceptor unleashes the PHYTOCHROME INTERACTING FACTORs (PIFs) and initiates SAS responses. In Arabidopsis (Arabidopsis thaliana) seedlings, shade perception involves rapid and massive changes in gene expression, increases auxin production, and promotes hypocotyl elongation. Other components, such as phyA and ELONGATED HYPOCOTYL 5 (HY5), also participate in the shade regulation of the hypocotyl elongation response by repressing it. However, why and how so many regulators with either positive or negative activities modulate the same response remain unclear. Our physiological, genetic, cellular, and transcriptomic analyses showed that (1) these components are organized into two main branches or modules and (2) the connection between them is dynamic and changes with the time of shade exposure. We propose a model for the regulation of shade-induced hypocotyl elongation in which the temporal and spatial functional importance of the various SAS regulators analyzed here helps to explain the co-existence of differentiated regulatory branches with overlapping activities.
PMID: 39140970
Plant Physiol , IF:8.34 , 2024 Aug doi: 10.1093/plphys/kiae422
A microRNA396b-Growth Regulating Factor module controls castor seed size by mediating auxin synthesis.
State Key Laboratory of Tree Genetics and Breeding, College of Forestry, Northeast Forestry University, Harbin 150040, China.; The Center for Basic Forestry Research, College of Forestry, Northeast Forestry University, Harbin 150040, China.; State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of the State Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, P. R. China.; Tongliao Academy of Agricultural Sciences, Tongliao 028015, China.; College of Life Science, Northeast Forestry University, Harbin 150040, China.
Castor (Ricinus communis L.) is an importance crop cultivated for its oil and economic value. Seed size is a crucial factor that determines crop yield. Gaining insight into the molecular regulatory processes of seed development is essential for the genetic enhancement and molecular breeding of castor. Here, we successfully fine-mapped a major QTL related to seed size, qSS3, to a 180 kb interval on chromosome 03 using F2 populations (DL01xWH11). A 17.6-kb structural variation (SV) was detected through genomic comparison between DL01 and WH11. Analysis of haplotypes showed that the existence of the complete 17.6 kb structural variant may lead to the small seed characteristic in castor. In addition, we found that qSS3 contains the microRNA396b (miR396b) sequence, which is situated within the 17.6 kb SV. The results of our experiment offer additional evidence that miR396-Growth Regulating Factor 4 (GRF4) controls seed size by impacting the growth and multiplication of seed coat and endosperm cells. Furthermore, we found that RcGRF4 activates the expression of YUCCA6 (YUC6), facilitating the production of IAA in seeds and thereby impacting the growth of castor seeds. Our research has discovered a crucial functional module that controls seed size, offering a fresh understanding of the mechanism underlying seed size regulation in castor.
PMID: 39140314
Plant Physiol , IF:8.34 , 2024 Aug doi: 10.1093/plphys/kiae405
Exogenous application of the apocarotenoid retinaldehyde negatively regulates auxin-mediated root growth.
Graduate School of Life Science, Hokkaido University, Sapporo, Japan.; Advanced Instrumental Analysis Center. Teikyo University, Utsunomiya, Japan.; Department of Biosciences, Teikyo University, Utsunomiya, Japan.; Department of Bioscience, Okayama University of Science, Okayama, Japan.; Department of Biology, Graduate School of Science, Kobe University, Kobe, Japan.; Institute of Low Temperature Science, Hokkaido University, Sapporo, Japan.; Division of Biological Sciences, Faculty of Science, Hokkaido University, Sapporo, Japan.
Root development is essential for plant survival. The lack of carotenoid biosynthesis in the phytoene desaturase 3 (pds3) mutant results in short primary roots (PR) and reduced lateral root (LR) formation. In this study, we showed that short-term inhibition of PDS by fluridone suppresses PR growth in WT, but to a lesser extent in auxin mutants of Arabidopsis (Arabidopsis thaliana). Such an inhibition of PDS activity increased endogenous indole-3-acetic acid (IAA) levels, promoted auxin signaling, and partially complemented the PR growth of an auxin deficient mutant, the YUCCA 3 5 7 8 9 quadruple mutant (yucQ). The exogenous application of retinaldehyde (retinal), an apocarotenoid derived from beta-carotene, complemented the fluridone-induced suppression of root growth, as well as the short roots of the pds3 mutant. Retinal also partially complemented the auxin-induced suppression of root growth. These results suggest that retinal may play a role in regulating root growth by modulating endogenous auxin levels.
PMID: 39117340
Sci Total Environ , IF:7.963 , 2024 Oct , V948 : P174663 doi: 10.1016/j.scitotenv.2024.174663
Non-pathogenic microbiome associated to aquatic plants and anthropogenic impacts on this interaction.
Ecotoxicology of Aquatic Microorganisms Laboratory, GRIL, EcotoQ, TOXEN, Department of Biological Sciences, Universite du Quebec a Montreal, Montreal Succ. Centre-Ville, H3C 3P8 Montreal, QC, Canada.; Institut national de la recherche scientifique - Centre Eau Terre Environnement, 490 Couronne St, Quebec City, Quebec G1K 9A9, Canada.; Ecotoxicology of Aquatic Microorganisms Laboratory, GRIL, EcotoQ, TOXEN, Department of Biological Sciences, Universite du Quebec a Montreal, Montreal Succ. Centre-Ville, H3C 3P8 Montreal, QC, Canada. Electronic address: juneau.philippe@uqam.ca.
The microbiota associated with aquatic plants plays a crucial role in promoting plant growth and development. The structure of the plant microbiome is shaped by intricate interactions among hosts, microbes, and environmental factors. Consequently, anthropogenic pressures that disrupt these interactions can indirectly impact the ecosystem services provided by aquatic plants, such as CO(2) fixation, provision of food resources, shelter to animals, nutrient cycling, and water purification. Presently, studies on plant-microbiota interactions primarily focus on terrestrial hosts and overlook aquatic environments with their unique microbiomes. Therefore, there is a pressing need for a comprehensive understanding of plant microbiomes in aquatic ecosystems. This review delves into the overall composition of the microbiota associated with aquatic plant, with a particular emphasis on bacterial communities, which have been more extensively studied. Subsequently, the functions provided by the microbiota to their aquatic plants hosts are explored, including the acquisition and mobilization of nutrients, production of auxin and related compounds, enhancement of photosynthesis, and protection against biotic and abiotic stresses. Additionally, the influence of anthropogenic stressors, such as climate change and aquatic contamination, on the interaction between microbiota and aquatic plants is discussed. Finally, knowledge gaps are highlighted and future directions in this field are suggested.
PMID: 38992379
Sci Total Environ , IF:7.963 , 2024 Oct , V946 : P174198 doi: 10.1016/j.scitotenv.2024.174198
Plant metabolic responses to soil herbicide residues differ under herbivory in two woodland strawberry genotypes.
Biodiversity Unit, University of Turku, 20014 Turku, Finland. Electronic address: Benjamin.fuchs@utu.fi.; Department of Biology, University of Turku, 20014 Turku, Finland.; Biodiversity Unit, University of Turku, 20014 Turku, Finland.; Laboratory of Hormonal Regulations in Plants, Institute of Experimental Botany of the Czech Academy of Sciences, Rozvojova 263, 16502 Prague, Czech Republic.; Department of Environmental and Biological Sciences, University of Eastern Finland, P.O. Box 1627, 70211 Kuopio, Finland.; Natural Chemistry Research Group, Department of Chemistry, FI-20014, University of Turku, Finland.; Biodiversity Unit, University of Turku, 20014 Turku, Finland; Division of Biotechnology and Plant Health, Norwegian Institute of Bioeconomy Research, As, Norway.
The use of glyphosate-based herbicides (GBHs) to control weeds has increased exponentially in recent decades, and their residues and degradation products have been found in soils across the globe. GBH residues in soil have been shown to affect plant physiology and specialised metabolite biosynthesis, which, in turn, may impact plant resistance to biotic stressors. In a greenhouse study, we investigated the interactive effects between soil GBH residues and herbivory on the performance, phytohormone concentrations, phenolic compound concentrations and volatile organic compound (VOC) emissions of two woodland strawberry (Fragaria vesca) genotypes, which were classified as herbivore resistant and herbivore susceptible. Plants were subjected to herbivory by strawberry leaf beetle (Galerucella tenella) larvae, and to GBH residues by growing in soil collected from a field site with GBH treatments twice a year over the past eight years. Soil GBH residues reduced the belowground biomass of the susceptible genotype and the aboveground biomass of both woodland strawberry genotypes. Herbivory increased the belowground biomass of the resistant genotype and the root-shoot ratio of both genotypes. At the metabolite level, herbivory induced the emission of several VOCs. Jasmonic acid, abscisic acid and auxin concentrations were induced by herbivory, in contrast to salicylic acid, which was only induced by herbivory in combination with soil GBH residues in the resistant genotype. The concentrations of phenolic compounds were higher in the resistant genotype compared to the susceptible genotype and were induced by soil GBH residues in the resistant genotype. Our results indicate that soil GBH residues can differentially affect plant performance, phytohormone concentrations and phenolic compound concentrations under herbivore attack, in a genotype-dependent manner. Soil GBH altered plant responses to herbivory, which may impact plant resistance traits and species interactions. With ongoing agrochemical pollution, we need to consider plant cultivars with better resistance to polluted soils while maintaining plant resilience under challenging environmental conditions.
PMID: 38914330
Sci Total Environ , IF:7.963 , 2024 Sep , V942 : P173775 doi: 10.1016/j.scitotenv.2024.173775
High-throughput 16S rRNA gene-based amplicon sequencing reveals the functional divergence of halophilic bacterial communities in the Suaeda salsa root compartments on the eastern coast of China.
Biofuels Institute, School of Environment & Safety Engineering, Jiangsu University, Zhenjiang 212013, China.; Biofuels Institute, School of Environment & Safety Engineering, Jiangsu University, Zhenjiang 212013, China; School of Life Sciences, Jiangsu University, Zhenjiang 212013, China; Department of Zoology & Environmental Biology, University of Nigeria, Nsukka 410001, Nigeria.; Biofuels Institute, School of Environment & Safety Engineering, Jiangsu University, Zhenjiang 212013, China. Electronic address: jxjiang@ujs.edu.cn.
The rhizosphere environment of plants, which harbors halophilic bacterial communities, faces significant challenges in coping with environmental stressors, particularly saline soil properties. This study utilizes a high-throughput 16S rRNA gene-based amplicon sequencing to investigate the variations in bacterial community dynamics in rhizosphere soil (RH), root surface soil (RS), root endophytic bacteria (PE) compartments of Suaeda salsa roots, and adjoining soils (CK) across six locations along the eastern coast of China: Nantong (NT), Yancheng (YC), Dalian (DL), Tianjin (TJ), Dongying (DY), and Qingdao (QD), all characterized by chloride-type saline soil. Variations in the physicochemical properties of the RH compartment were also evaluated. The results revealed significant changes in pH, electrical conductivity, total salt content, and ion concentrations in RH samples from different locations. Notably, the NT location exhibited the highest alkalinity and nitrogen availability. The pH variations were linked to HCO(3)(-) accumulation in S. salsa roots, while salinity stress influenced soil pH through H(+) discharge. Despite salinity stress, enzymatic activities such as catalase and urease were higher in soils from various locations. The diversity and richness of bacterial communities were higher in specific locations, with Proteobacteria dominating PE samples from the DL location. Additionally, Vibrio and Marinobacter were prevalent in RH samples. Significant correlations were found between soil pH, salinity, nutrient content, and the abundance and diversity of bacterial taxa in RH samples. Bioinformatics analysis revealed the prevalence of halophilic bacteria, such as Bacillus, Halomonas, and Streptomyces, with diverse metabolic functions, including amino acid and carbohydrate metabolisms. Essential genes, such as auxin response factor (ARF) and GTPase-encoding genes, were abundant in RH samples, suggesting adaptive strategies for harsh environments. Likewise, proline/betaine transport protein genes were enriched, indicating potential bioremediation mechanisms against high salt stress. These findings provide insight into the metabolic adaptations facilitating resilience in saline ecosystems and contribute to understanding the complex interplay between soil conditions, bacterial communities, and plant adaptation.
PMID: 38844238
BMC Biol , IF:7.431 , 2024 Aug , V22 (1) : P184 doi: 10.1186/s12915-024-01985-z
PmLBD3 links auxin and brassinosteroid signalling pathways on dwarfism in Prunus mume.
Laboratory of Fruit Tree Biotechnology, College of Horticulture, Nanjing Agricultural University, Nanjing, Jiangsu, China.; College of Horticulture, Zhongkai University of Agriculture and Engineering, Guangzhou, Guangdong, China.; Laboratory of Fruit Tree Biotechnology, College of Horticulture, Nanjing Agricultural University, Nanjing, Jiangsu, China. gaozhihong@njau.edu.cn.
BACKGROUND: Grafting with dwarf rootstock is an efficient method to control plant height in fruit production. However, the molecular mechanism remains unclear. Our previous study showed that plants with Prunus mume (mume) rootstock exhibited a considerable reduction in plant height, internode length, and number of nodes compared with Prunus persica (peach) rootstock. The present study aimed to investigate the mechanism behind the regulation of plant height by mume rootstocks through transcriptomic and metabolomic analyses with two grafting combinations, 'Longyan/Mume' and 'Longyan/Peach'. RESULTS: There was a significant decrease in brassinolide levels in plants that were grafted onto mume rootstocks. Plant hormone signal transduction and brassinolide production metabolism gene expression also changed significantly. Flavonoid levels, amino acid and fatty acid metabolites, and energy metabolism in dwarf plants decreased. There was a notable upregulation of PmLBD3 gene expression in plant specimens that were subjected to grafting onto mume rootstocks. Auxin signalling cues promoted PmARF3 transcription, which directly controlled this upregulation. Through its binding to PmBAS1 and PmSAUR36a gene promoters, PmLBD3 promoted endogenous brassinolide inactivation and inhibited cell proliferation. CONCLUSIONS: Auxin signalling and brassinolide levels are linked by PmLBD3. Our findings showed that PmLBD3 is a key transcription factor that regulates the balance of hormones through the auxin and brassinolide signalling pathways and causes dwarf plants in stone fruits.
PMID: 39183294
Free Radic Biol Med , IF:7.376 , 2024 Sep , V222 : P371-385 doi: 10.1016/j.freeradbiomed.2024.06.013
Pulsed high power microwave seeds priming modulates germination, growth, redox homeostasis, and hormonal shifts in barley for improved seedling growth: Unleashing the molecular dynamics.
Plasma Bioscience Research Center (PBRC), Kwangwoon University, Seoul, Republic of Korea; Department of Electrical and Biological Physics, Kwangwoon University, Seoul, Republic of Korea.; Department of Electrical and Biological Physics, Kwangwoon University, Seoul, Republic of Korea; Department of Plasma Bio Display, Kwangwoon University, Seoul, Republic of Korea.; Plasma Bioscience Research Center (PBRC), Kwangwoon University, Seoul, Republic of Korea; Department of Electrical and Biological Physics, Kwangwoon University, Seoul, Republic of Korea; Department of Plasma Bio Display, Kwangwoon University, Seoul, Republic of Korea. Electronic address: ehchoi@kw.ac.kr.
Increasing the seed germination potential and seedling growth rates play a pivotal role in increasing overall crop productivity. Seed germination and early vegetative (seedling) growth are critical developmental stages in plants. High-power microwave (HPM) technology has facilitated both the emergence of novel applications and improvements to existing in agriculture. The implications of pulsed HPM on agriculture remain unexplored. In this study, we have investigated the effects of pulsed HPM exposure on barley germination and seedling growth, elucidating the plausible underlying mechanisms. Barley seeds underwent direct HPM irradiation, with 60 pulses by 2.04 mJ/pulse, across three distinct irradiation settings: dry, submerged in deionized (DI) water, and submerged in DI water one day before exposure. Seed germination significantly increased in all HPM-treated groups, where the HPM-dry group exhibited a notable increase, with a 2.48-fold rise at day 2 and a 1.9-fold increment at day 3. Similarly, all HPM-treated groups displayed significant enhancements in water uptake, and seedling growth (weight and length), as well as elevated levels of chlorophyll, carotenoids, and total soluble protein content. The obtained results indicate that when comparing three irradiation setting, HPM-dry showed the most promising effects. Condition HPM seed treatment increases the level of reactive species within the barley seedlings, thereby modulating plant biochemistry, physiology, and different cellular signaling cascades via induced enzymatic activities. Notably, the markers associated with plant growth are upregulated and growth inhibitory markers are downregulated post-HPM exposure. Under optimal HPM-dry treatment, auxin (IAA) levels increased threefold, while ABA levels decreased by up to 65 %. These molecular findings illuminate the intricate regulatory mechanisms governing phenotypic changes in barley seedlings subjected to HPM treatment. The results of this study might play a key role to understand molecular mechanisms after pulsed-HPM irradiation of seeds, contributing significantly to address the global need of sustainable crop yield.
PMID: 38901500
Plant Cell Environ , IF:7.228 , 2024 Aug doi: 10.1111/pce.15116
Plant growth-promoting abilities of Methylobacterium sp. 2A involve auxin-mediated regulation of the root architecture.
Laboratorio de Transduccion de Senales en Plantas, Instituto de Investigaciones en Ingenieria Genetica y Biologia Molecular (INGEBI), Consejo Nacional de Investigaciones Cientificas y Tecnicas (CONICET), Ciudad Autonoma de Buenos Aires, Argentina.; Institute of Plant Science and Resources, Okayama University, Okayama, Japan.; Departamento de Quimica Biologica, Universidad de Buenos Aires (UBA), Ciudad Autonoma de Buenos Aires, Argentina.
Methylobacterium sp. 2A, a plant growth-promoting rhizobacteria (PGPR) able to produce indole-3-acetic acid (IAA), significantly promoted the growth of Arabidopsis thaliana plants in vitro. We aimed to understand the determinants of Methylobacterium sp. 2A-A. thaliana interaction, the factors underlying plant growth-promotion and the host range. Methylobacterium sp. 2A displayed chemotaxis to methanol and formaldehyde and was able to utilise 1-aminocyclopropane carboxylate as a nitrogen source. Confocal microscopy confirmed that fluorescent protein-labelled Methylobacterium sp. 2A colonises the apoplast of A. thaliana primary root cells and its inoculation increased jasmonic and salicylic acid in A. thaliana, while IAA levels remained constant. However, inoculation increased DR5 promoter activity in root tips of A. thaliana and tomato plants. Inoculation of this PGPR partially restored the agravitropic response in yucQ mutants and lateral root density was enhanced in iaa19, arf7, and arf19 mutant seedlings. Furthermore, Methylobacterium sp. 2A volatile organic compounds (VOCs) had a dose-dependent effect on the growth of A. thaliana. This PGPR is also able to interact with monocots eliciting positive responses upon inoculation. Methylobacterium sp. 2A plant growth-promoting effects can be achieved through the regulation of plant hormone levels and the emission of VOCs that act either locally or at a distance.
PMID: 39189962
Plant Cell Environ , IF:7.228 , 2024 Aug doi: 10.1111/pce.15075
Gbetagamma dimers mediate low K(+) stress-inhibited root growth via modulating auxin redistribution in Arabidopsis.
School of Life Sciences, Shaanxi Normal University, Xi'an, Shaanxi, China.; College of Life and Geographic Sciences, Kashi University, Kashi, Xinjiang, China.; Key Laboratory of Biological Resources and Ecology of Pamirs Plateau in Xinjiang Uygur Autonomous Region, Kashi University, Kashi, Xinjiang, China.
In the investigation of heterotrimeric G protein-mediated signal transduction in planta, their roles in the transmittance of low K(+) stimuli remain to be elucidated. Here, we found that the primary root growth of wild-type Arabidopsis was gradually inhibited with the decrease of external K(+) concentrations, while the primary root of the mutants for G protein beta subunit AGB1 and gamma subunits AGG1, AGG2 and AGG3 could still grow under low K(+) conditions (LK). Exogenous NAA application attenuated primary root elongation in agb1 and agg1/2/3 but promoted the growth in wild-type seedlings under LK stress. Using ProDR5:GFP, ProPIN1:PIN1-GFP and ProPIN2:PIN2-GFP reporter lines, a diminishment in auxin concentration at the radicle apex and a reduction in PIN1and PIN2 efflux carrier abundance were observed in wild-type roots under LK, a phenomenon not recorded in the agb1 and agg1/2/3. Further proteolytic and transcriptional assessments revealed an enhanced degradation of PIN1 and a suppressed expression of PIN2 in the wild-type background under LK, contrasting with the stability observed in the agb1 and agg1/2/3 mutants. Our results indicate that the G protein beta and gamma subunits play pivotal roles in suppressing of Arabidopsis root growth under LK by modulating auxin redistribution via alterations in PIN1 degradation and PIN2 biosynthesis.
PMID: 39136400
Plant Cell Environ , IF:7.228 , 2024 Aug , V47 (8) : P3030-3045 doi: 10.1111/pce.14916
Cytosolic ABA Receptor Kinases phosphorylate the D6 PROTEIN KINASE leading to its stabilization which promotes Arabidopsis growth.
Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, State Key Laboratory of Hydraulics and Mountain River Engineering, College of Life Sciences, Sichuan University, Chengdu, China.
The polar auxin transport is required for proper plant growth and development. D6 PROTEIN KINASE (D6PK) is required for the phosphorylation of PIN-FORMED (PIN) auxin efflux carriers to regulate auxin transport, while the regulation of D6PK stabilization is still poorly understood. Here, we found that Cytosolic ABA Receptor Kinases (CARKs) redundantly interact with D6PK, and the interactions are dependent on CARKs' kinase activities. Similarly, CARK3 also could interact with paralogs of D6PK, including D6PKL1, D6PKL2, and D6PKL3. The genetic analysis shows that D6PK acts the downstream of CARKs to regulate Arabidopsis growth, including hypocotyl, leaf area, vein formation, and the length of silique. Loss-of-function of CARK3 in overexpressing GFP-D6PK plants leads to reduce the level of D6PK protein, thereby rescues plant growth. In addition, the cell-free degradation assays indicate that D6PK is degraded through 26 S proteasome pathway, while the phosphorylation by CARK3 represses this process in cells. In summary, D6PK stabilization by the CARK family is required for auxin-mediated plant growth and development.
PMID: 38644762
Plant Cell Environ , IF:7.228 , 2024 Aug , V47 (8) : P2895-2910 doi: 10.1111/pce.14913
The 'Candidatus phytoplasma ziziphi' effectors SJP1 and SJP2 destabilise the bifunctional regulator ZjTCP7 to modulate floral transition and shoot branching.
Anhui Province Key Laboratory of Horticultural Crop Quality Biology, College of Horticulture, Anhui Agricultural University, Hefei, China.; Horticulture Research Institute, Anhui Academy of Agricultural Sciences, Hefei, China.
Phytoplasmic SAP11 effectors alter host plant architecture and flowering time. However, the exact mechanisms have yet to be elucidated. Two SAP11-like effectors, SJP1 and SJP2, from 'Candidatus Phytoplasma ziziphi' induce shoot branching proliferation. Here, the transcription factor ZjTCP7 was identified as a central target of these two effectors to regulate floral transition and shoot branching. Ectopic expression of ZjTCP7 resulted in enhanced bolting and earlier flowering than did the control. Interaction and expression assays demonstrated that ZjTCP7 interacted with the ZjFT-ZjFD module, thereby enhancing the ability of these genes to directly bind to the ZjAP1 promoter. The effectors SJP1 and SJP2 unravelled the florigen activation complex by specifically destabilising ZjTCP7 and ZjFD to delay floral initiation. Moreover, the shoot branching of the ZjTCP7-SRDX transgenic Arabidopsis lines were comparable to those of the SJP1/2 lines, suggesting the involvement of ZjTCP7 in the regulation of shoot branching. ZjTCP7 interacted with the branching repressor ZjBRC1 to enhance suppression of the auxin efflux carrier ZjPIN3 expression. ZjTCP7 also directly bound to and upregulated the auxin biosynthesis gene ZjYUCCA2, thereby promoting auxin accumulation. Our findings confirm that ZjTCP7 serves as a bifunctional regulator destabilised by the effectors SJP1 and SJP2 to modulate plant development.
PMID: 38623040
Microbiol Spectr , IF:7.171 , 2024 Aug : Pe0071224 doi: 10.1128/spectrum.00712-24
Unveiling the multifaceted potential of Pseudomonas khavaziana strain SR9: a promising biocontrol agent for wheat crown rot.
State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Xianyang, Shaanxi, China.; Xinjiang Production and Construction Crops Key Laboratory of Protection and Utilization of Biological Resources in Tarim Basin, College of Life Sciences, Tarim University, Xinjiang, China.; State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, College of Agronomy, Northwest A&F University, Xianyang, Shaanxi, China.
Fusarium pseudograminearum, a soil-borne fungus, is the cause of the devastating wheat disease known as wheat crown rot (WCR). The persistence of this pathogen in the soil and crop residues contributes to the increased occurrence and severity of WCR. Therefore, developing effective strategies to prevent and manage WCR is of great importance. In this study, we isolated a bacterial strain, designated as SR9, from the stem of wheat, that exhibited potent antagonistic effects against F. pseudograminearum, as well as the biocontrol efficacy of SR9 on WCR was quantified at 83.99% +/- 0.11%. We identified SR9 as Pseudomonas khavaziana and demonstrated its potential as a plant probiotic. SR9 displayed broad-spectrum antagonism against other fungal pathogens, including Neurospora dictyophora, Botrytis californica, and Botryosphaeria dothidea. Whole-genome sequencing analysis revealed that SR9 harbored genes encoding various cell wall-degrading enzymes, cellulases, and lipases, along with antifungal metabolites, which are responsible for its antagonistic activity. Gene knockout and quantitative PCR analyses reveal that phenazine is the essential factor for antagonism. SR9 possessed genes related to auxin synthesis, flagellar biosynthesis, biofilm adhesion, and the chemotaxis system, which play pivotal roles in plant colonization and growth promotion; we also evaluated the effects of SR9 on plant growth in wheat and Arabidopsis. Our findings strongly suggest that SR9 holds great promise as a biocontrol agent for WCR in sustainable agriculture.IMPORTANCEThe escalating prevalence of wheat crown rot, primarily attributed to Fusarium pseudograminearum, necessitates the development of cost-effective and eco-friendly biocontrol strategies. While plant endophytes are recognized for their biocontrol potential, reports on effective strains targeting wheat crown rot are sparse. This study introduces the Pseudomonas khavaziana SR9 strain as an efficacious antagonist to the wheat crown rot pathogen Fusarium pseudograminearum. Demonstrating a significant reduction in wheat crown rot incidence and notable plant growth promotion, SR9 emerges as a key contributor to plant health and agricultural sustainability. Our study outlines a biological approach to tackle wheat crown rot, establishing a groundwork for innovative sustainable agricultural practices.
PMID: 39162535
Chemosphere , IF:7.086 , 2024 Aug , V362 : P142604 doi: 10.1016/j.chemosphere.2024.142604
Salicylic acid-mediated alleviation of salt stress: Insights from physiological and transcriptomic analysis in Asarum sieboldii Miq.
School of Pharmacy, Shanghai Jiao Tong University, Shanghai, 200240, China.; School of Pharmacy, Shanghai Jiao Tong University, Shanghai, 200240, China. Electronic address: liuzhong@sjtu.edu.cn.
As global agriculture faces the pressing threat of salt stress, innovative solutions are imperative for sustainable agriculture. The remarkable potential of salicylic acid (SA) in enhancing plant resilience against environmental stressors has recently gained attention. However, the specific molecular mechanisms by which SA mitigates salt stress in Asarum sieboldii Miq., a valuable medicinal plant, remain poorly understood. Here, we evaluated the physiological and transcriptomic regulatory responses of A. sieboldii under salt stress (100 mM NaCl), both in the presence (1 mM SA) and absence of exogenous SA. The results highlighted that SA significantly alleviates salt stress, primarily through enhancing antioxidant activities as evidenced by increased superoxide dismutase, and peroxidase activities. Additionally, we observed an increment in chlorophyll (a and b), proline, total soluble sugar, and plant fresh weight, along with a decrease in malondialdehyde contents. Transcriptome analysis suggested consistency in the regulation of many differentially expressed genes and transcription factors (TFs); however, genes targets (GSTs, TIR1, and NPR1), and TFs (MYB, WRKY, TCP, and bHLH) possessed expressional uniqueness, and majority had significantly up-regulated trends in SA-coupled salt stress treatments. Further, bioinformatics and KEGG enrichment analysis indicated several SA-induced significantly enriched biological pathways. Specifically, plant hormone signal transduction was identified as being populated with key genes distinctive to auxin, cytokinin, ethylene, and salicylic acid signaling, suggesting their important role in salt stress alleviation. Inclusively, this report presents a comprehensive analysis encompassing gene targets, TFs, and biological pathways, and these insights may offer a valuable contribution to our knowledge of SA-mediated regulation and its crucial role in enhancing plant defense against diverse abiotic stressors.
PMID: 38876329
J Integr Plant Biol , IF:7.061 , 2024 Aug doi: 10.1111/jipb.13764
Anchorene, a carotenoid-derived growth regulator, modulates auxin homeostasis by suppressing GH3-mediated auxin conjugation.
National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, State Key Laboratory of Crop Stress Adaptation and Improvement, Henan Joint International Laboratory for Crop Multi-Omics Research, School of Life Sciences, Henan University, Kaifeng, 450046, China.; Sanya Institute of Henan University, Sanya, 572025, China.; State Key Laboratory for Crop Stress Resistance and High-Eficiency Production/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, 712100, China.; Institute of Plant and Food Science, Department of Biology, School of Life Sciences, Southern University of Science and Technology (SUSTech), Shenzhen, 518055, China.; The BioActives Lab, Center for Desert Agriculture, King Abdullah University of Science and Technology, Thuwal, 23955-6900, Kingdom of Saudi Arabia.; Plant Science Program, Biological and Environmental Science and Engineering (BESE) Division, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Kingdom of Saudi Arabia.; Laboratory of Cell Metabolism and Diseases, State Key Laboratory of Conservation and Utilization of Bio-Resources in Yunnan, Center for Life Sciences, School of Life Sciences, Yunnan University, Kunming, 650500, China.
Anchorene, identified as an endogenous bioactive carotenoid-derived dialdehyde and diapocarotenoid, affects root development by modulating auxin homeostasis. However, the precise interaction between anchorene and auxin, as well as the mechanisms by which anchorene modulates auxin levels, remain largely elusive. In this study, we conducted a comparative analysis of anchorene's bioactivities alongside auxin and observed that anchorene induces multifaceted auxin-like effects. Through genetic and pharmacological examinations, we revealed that anchorene's auxin-like activities depend on the indole-3-pyruvate-dependent auxin biosynthesis pathway, as well as the auxin inactivation pathway mediated by Group II Gretchen Hagen 3 (GH3) proteins that mainly facilitate the conjugation of indole-3-acetic acid (IAA) to amino acids, leading to the formation of inactivated storage forms. Our measurements indicated that anchorene treatment elevates IAA levels while reducing the quantities of inactivated IAA-amino acid conjugates and oxIAA. RNA sequencing further revealed that anchorene triggers the expression of numerous auxin-responsive genes in a manner reliant on Group II GH3s. Additionally, our in vitro enzymatic assays and biolayer interferometry (BLI) assay demonstrated anchorene's robust suppression of GH3.17-mediated IAA conjugation with glutamate. Collectively, our findings highlight the significant role of carotenoid-derived metabolite anchorene in modulating auxin homeostasis, primarily through the repression of GH3-mediated IAA conjugation and inactivation pathways, offering novel insights into the regulatory mechanisms of plant bioactive apocarotenoids.
PMID: 39185936
J Integr Plant Biol , IF:7.061 , 2024 Aug doi: 10.1111/jipb.13759
Coordination of miR319-TaPCF8 with TaSPL14 orchestrates auxin signaling and biosynthesis to regulate plant height in common wheat.
College of Life Sciences, Northwest A&F University, Yangling, 712100, China.; State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
Wheat culms, comprising four to six internodes, are critically involved in determining plant height and lodging resistance, essential factors for field performance and regional adaptability. This study revealed the regulatory function of miR319 in common wheat plant height. Repression of tae-miR319 through short tandem target mimics (STTM) caused an increased plant height, while overexpression (OE) of tae-miR319 had the opposite effect. Overexpressing a miR319-resistant target gene TaPCF8 (rTaPCF8), increased plant height. TaPCF8 acted as a transcription repressor of downstream genes TaIAAs, which interact physically with TaSPL14. The significant differences of indole-3-acetic acid (IAA) contents indicate the involvement of auxin pathway in miR319-mediated plant height regulation. Finally, we identified two TaPCF8 haplotypes in global wheat collections. TaPCF8-5A-Hap2, as per association and evolution examinations, was subjected to strong substantial selection throughout wheat breeding. This haplotype, associated with shorter plant height, aligns with global breeding requirements. Consequently, in high-yield wheat breeding, we proposed a potential molecular marker for marker-assisted selection (MAS). Our findings offer fresh perspectives into the molecular mechanisms that underlie the miR319-TaPCF8 module's regulation of plant height by orchestrating auxin signaling and biosynthesis in wheat.
PMID: 39109961
J Integr Plant Biol , IF:7.061 , 2024 Jul doi: 10.1111/jipb.13749
A QTL GN1.1, encoding FT-L1, regulates grain number and yield by modulating polar auxin transport in rice.
National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China.; University of the Chinese Academy of Sciences, Beijing, 100049, China.; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, China.; School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China.
Rice grain number is a crucial agronomic trait impacting yield. In this study, we characterized a quantitative trait locus (QTL), GRAIN NUMBER 1.1 (GN1.1), which encodes a Flowering Locus T-like1 (FT-L1) protein and acts as a negative regulator of grain number in rice. The elite allele GN1.1(B), derived from the Oryza indica variety, BF3-104, exhibits a 14.6% increase in grain yield compared with the O. japonica variety, Nipponbare, based on plot yield tests. We demonstrated that GN1.1 interacted with and enhanced the stability of ADP-ribosylation factor (Arf)-GTPase-activating protein (Gap), OsZAC. Loss of function of OsZAC results in increased grain number. Based on our data, we propose that GN1.1(B) facilitates the elevation of auxin content in young rice panicles by affecting polar auxin transport (PAT) through interaction with OsZAC. Our study unveils the pivotal role of the GN1.1 locus in rice panicle development and presents a novel, promising allele for enhancing rice grain yield through genetic improvement.
PMID: 39083298
J Integr Plant Biol , IF:7.061 , 2024 Aug , V66 (8) : P1675-1687 doi: 10.1111/jipb.13720
MYB2 and MYB108 regulate lateral root development by interacting with LBD29 in Arabidopsis thaliana.
The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, 266237, China.; Advanced Medical Research Institute, Cheeloo College of Medicine, Shandong University, Jinan, 250012, China.
AUXIN RESPONSE FACTOR 7 (ARF7)-mediated auxin signaling plays a key role in lateral root (LR) development by regulating downstream LATERAL ORGAN BOUNDARIES DOMAIN (LBD) transcription factor genes, including LBD16, LBD18, and LBD29. LBD proteins are believed to regulate the transcription of downstream genes as homodimers or heterodimers. However, whether LBD29 forms dimers with other proteins to regulate LR development remains unknown. Here, we determined that the Arabidopsis thaliana (L.) Heynh. MYB transcription factors MYB2 and MYB108 interact with LBD29 and regulate auxin-induced LR development. Both MYB2 and MYB108 were induced by auxin in an ARF7-dependent manner. Disruption of MYB2 by fusion with an SRDX domain severely affected auxin-induced LR formation and the ability of LBD29 to induce LR development. By contrast, overexpression of MYB2 or MYB108 resulted in greater LR numbers, except in the lbd29 mutant background. These findings underscore the interdependence and importance of MYB2, MYB108, and LBD29 in regulating LR development. In addition, MYB2-LBD29 and MYB108-LBD29 complexes promoted the expression of CUTICLE DESTRUCTING FACTOR 1 (CDEF1), a member of the GDSL (Gly-Asp-Ser-Leu) lipase/esterase family involved in LR development. In summary, this study identified MYB2-LBD29 and MYB108-LBD29 regulatory modules that act downstream of ARF7 and intricately control auxin-mediated LR development.
PMID: 38923126
J Exp Bot , IF:6.992 , 2024 Aug doi: 10.1093/jxb/erae340
Local signal from Trichoderma afroharzianum T22 induces host transcriptome and endophytic microbiome leading to growth promotion in sorghum.
School of Sciences, University of Louisiana at Monroe, Monroe, LA 71209, USA.; Scott Research, Extension, and Education Center, School of Plant, Environmental, and Soil Sciences, Louisiana State University, Winnsboro, LA 71295, USA.
Trichoderma, a highly abundant soil fungus, may benefit plants, yet it remains understudied in sorghum (Sorghum bicolor). In this study, sorghum plants were cultivated for five weeks in soil pots with or without the inoculation of T. afroharzianum T22. We found that plants inoculated with T. afroharzianum T22 exhibited significant increases in growth parameters and nutrient levels, demonstrating its beneficial role in sorghum. The split-root assay demonstrated that T. afroharzianum T22 is essential in both compartments of soil pots for promoting plant growth. This suggests that local signals from this fungus drive symbiotic benefits in sorghum. The RNA-seq analysis revealed the induction of genes responsible for mineral transport (such as nitrate and aquaporin transporters), auxin response, sugar assimilation (hexokinase), and disease resistance (thaumatin) in the roots of sorghum inoculated with T. afroharzianum T22. Microbial community analysis further unveiled the positive role of T. afroharzianum T22 in enriching Penicillium (ITS) and Streptomyces (16S) while reducing disease-causing Fusarium in the roots. The microbial consortium, consisting of enriched microbiomes from bacterial and fungal communities, showed disrupted morphological features in plants inoculated with T. afroharzianum T22 in the absence of S. griseus. However, this disruption was not observed in the absence of P. chrysogenum. These results suggest that S. griseus may act as a helper microbe in close association with T. afroharzianum T22 in the sorghum endosphere. This study provides the first comprehensive explanation of how T. afroharzianum T22 modulates host molecular determinants and endophytic helper microbes, thereby collectively promoting sorghum growth. These findings may encourage the formulation of a synthetic inoculum dominated by T. afroharzianum T22 to enhance growth and stress resilience in sorghum and other similar crops.
PMID: 39110656
J Exp Bot , IF:6.992 , 2024 Aug , V75 (15) : P4589-4598 doi: 10.1093/jxb/erae260
Exploring the puzzle of reactive oxygen species acting on root hair cells.
Fundacion Instituto Leloir and IIBBA-CONICET, Av. Patricias Argentinas 435, Buenos Aires CP C1405BWE, Argentina.; Centro de Biotecnologia Vegetal (CBV), Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile.; ANID-Millennium Science Initiative Program-Millennium Nucleus for the Development of Super Adaptable Plants (MN-SAP), Santiago, Chile.; ANID-Millennium Science Initiative Program-Millennium Institute for Integrative Biology (iBio), Santiago, Chile.
Reactive oxygen species (ROS) are essential signaling molecules that enable cells to respond rapidly to a range of stimuli. The ability of plants to recognize various stressors, incorporate a variety of environmental inputs, and initiate stress-response networks depends on ROS. Plants develop resilience and defensive systems as a result of these processes. Root hairs are central components of root biology since they increase the surface area of the root, anchor it in the soil, increase its ability to absorb water and nutrients, and foster interactions between microorganisms. In this review, we specifically focused on root hair cells and we highlighted the identification of ROS receptors, important new regulatory hubs that connect ROS production, transport, and signaling in the context of two hormonal pathways (auxin and ethylene) and under low temperature environmental input related to nutrients. As ROS play a crucial role in regulating cell elongation rates, root hairs are rapidly gaining traction as a very valuable single plant cell model for investigating ROS homeostasis and signaling. These promising findings might soon facilitate the development of plants and roots that are more resilient to environmental stressors.
PMID: 38833316
J Exp Bot , IF:6.992 , 2024 Aug , V75 (16) : P5111-5129 doi: 10.1093/jxb/erae237
ABSCISIC ACID INSENSITIVE 3 promotes auxin signalling by regulating SHY2 expression to control primary root growth in response to dehydration stress.
Department of Biotechnology, St Xavier's College, 30, Mother Teresa Sarani, Kolkata-700016, India.
Plants combat dehydration stress through different strategies including root architectural changes. Here we show that when exposed to varying levels of dehydration stress, primary root growth in Arabidopsis is modulated by regulating root meristem activity. Abscisic acid (ABA) in concert with auxin signalling adjust primary root growth according to stress levels. ABSCISIC ACID INSENSITIVE 3 (ABI3), an ABA-responsive transcription factor, stands at the intersection of ABA and auxin signalling and fine-tunes primary root growth in response to dehydration stress. Under low ABA or dehydration stress, induction of ABI3 expression promotes auxin signalling by decreasing expression of SHY2, a negative regulator of auxin response. This further enhances the expression of auxin transporter gene PIN1 and cell cycle gene CYCB1;1, resulting in an increase in primary root meristem size and root length. Higher levels of dehydration stress or ABA repress ABI3 expression and promote ABSCISIC ACID INSENSITIVE 5 (ABI5) expression. This elevates SHY2 expression, thereby impairing primary root meristem activity and retarding root growth. Notably, ABI5 can promote SHY2 expression only in the absence of ABI3. Such ABA concentration-dependent expression of ABI3 therefore functions as a regulatory sensor of dehydration stress levels and orchestrates primary root growth by coordinating its downstream regulation.
PMID: 38770693
Int J Biol Macromol , IF:6.953 , 2024 Aug , V274 (Pt 2) : P133446 doi: 10.1016/j.ijbiomac.2024.133446
Systematic identification and functional analysis of root meristem growth factors (RGFs) reveals role of PgRGF1 in modulation of root development and ginsenoside production in Panax ginseng.
School of Pharmacy, Shihezi University, Key Laboratory of Xinjiang Phytomedicine Resource and Utilization, Ministry of Education, Xinjiang, Shihezi 832000, China.; State Key Laboratory for Quality Ensurance and Sustainable Use of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China.; Laboratory of Medicinal Plant, Hubei Key Laboratory of Embryonic Stem Cell Research, School of Basic Medicine, Hubei University of Medicine, Shiyan 442000, PR China.; College of Life Sciences, Shaanxi Normal University, Xi'an 710119, China.; School of Pharmacy, Shihezi University, Key Laboratory of Xinjiang Phytomedicine Resource and Utilization, Ministry of Education, Xinjiang, Shihezi 832000, China. Electronic address: 20945549@qq.com.; Laboratory of Medicinal Plant, Hubei Key Laboratory of Embryonic Stem Cell Research, School of Basic Medicine, Hubei University of Medicine, Shiyan 442000, PR China. Electronic address: lee.childe@qq.com.; State Key Laboratory for Quality Ensurance and Sustainable Use of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China. Electronic address: juanliu126@126.com.
Panax ginseng C.A. Mey., known for its medicinal and dietary supplement properties, primarily contains pharmacologically active ginsenosides. However, the regulatory mechanisms linking ginseng root development with ginsenoside biosynthesis are still unclear. Root meristem growth factors (RGFs) are crucial for regulating plant root growth. In our study, we identified five ginseng RGF peptide sequences from the ginseng genome and transcriptome libraries. We treated Arabidopsis and ginseng adventitious roots with exogenous Panax ginseng RGFs (PgRGFs) to assess their activities. Our results demonstrate that PgRGF1 influences gravitropic responses and reduces lateral root formation in Arabidopsis. PgRGF1 has been found to restrict the number and length of ginseng adventitious root branches in ginseng. Given the medicinal properties of ginseng, We determined the ginsenoside content and performed transcriptomic analysis of PgRGF1-treated ginseng adventitious roots. Specifically, the total ginsenoside content in ginseng adventitious roots decreased by 19.98 % and 63.71 % following treatments with 1 muM and 10 muM PgRGF1, respectively, compared to the control. The results revealed that PgRGF1 affects the accumulation of ginsenosides by regulating the expression of genes associated with auxin transportation and ginsenoside biosynthesis. These findings suggest that PgRGF1, as a peptide hormone regulator in ginseng, can modulate adventitious root growth and ginsenoside accumulation.
PMID: 38945337
Am J Respir Cell Mol Biol , IF:6.914 , 2024 Sep , V71 (3) : P307-317 doi: 10.1165/rcmb.2024-0159OC
Indole-3-Acetic Acid Protects Against Lipopolysaccharide-induced Endothelial Cell Dysfunction and Lung Injury through the Activation of USP40.
Department of Physiology and Cell Biology, Dorothy M. Davis Heart and Lung Research Institute, and.; Department of Internal Medicine, The Ohio State University, Columbus, Ohio.
Lung microvascular endothelial cell (EC) dysfunction is the pathological hallmark of acute respiratory distress syndrome. Heat shock protein 90 (HSP90) is a key regulator in control of endothelial barrier disruption and inflammation. Our recent study has demonstrated that ubiquitin-specific peptidase 40 (USP40) preserves endothelial integrity by targeting HSP90beta for its deubiquitination and inactivation. Indole-3-acetic acid (IAA), a plant hormone of the auxin class, can also be catabolized from dietary tryptophan by the intestinal microbiota. Accumulating evidence suggests that IAA reduces oxidative stress and inflammation and promotes intestinal barrier function. However, little is known about the role of IAA in endothelial cells and acute lung injury. In this study, we investigated the role of IAA in lung endothelial cell function in the context of acute lung injury. IAA exhibited EC barrier protection against LPS-induced reduction in transendothelial electrical resistance and inflammatory responses. The underlying mechanism of IAA on EC protective effects was investigated by examining the influence of IAA on degrees of HSP90 ubiquitination and USP40 activity. We identified that IAA, acting as a potential activator of USP40, reduces HSP90 ubiquitination, thereby protecting against LPS-induced inflammation in human lung microvascular endothelial cells as well as alleviating experimental lung injury. Furthermore, the EC protective effects of IAA against LPS-induced EC dysfunction and lung injury were abolished in USP40-deficient human lung microvascular endothelial cell and lungs of USP40 EC-specific knockout (USP40(cdh5-ECKO)) mice. Taken together, this study reveals that IAA protects against LPS-induced EC dysfunction and lung injury through the activation of USP40.
PMID: 38761166
J Environ Manage , IF:6.789 , 2024 Sep , V367 : P121950 doi: 10.1016/j.jenvman.2024.121950
Resource recovery and contaminants of emerging concern mitigation by microalgae treating wastewater.
GEMMA - Group of Environmental Engineering and Microbiology, Department of Civil and Environmental Engineering, Universitat Politecnica de Catalunya - BarcelonaTech, c/ Jordi Girona 1-3, Building D1, E-08034 Barcelona, Spain.; UAL - Chemical Engineering Department, Universidad de Almeria, Carretera Sacramento s/n, E-04120, Almeria, Spain.; Department of Environmental Chemistry, IDAEA-CSIC, c/Jordi Girona, 18-26, E-08034 Barcelona, Spain.; GEMMA - Group of Environmental Engineering and Microbiology, Department of Civil and Environmental Engineering, Universitat Politecnica de Catalunya - BarcelonaTech, c/ Jordi Girona 1-3, Building D1, E-08034 Barcelona, Spain. Electronic address: ivet.ferrer@upc.edu.
This study aimed to investigate the recovery of agricultural biostimulants and biogas from microalgae treating wastewater, in the framework of a circular bioeconomy. To this end, municipal wastewater was treated in demonstrative raceway ponds, and microalgal biomass (Scenedesmus sp.) was then harvested and downstream processed to recover biostimulants and biogas in a biorefinery approach. The effect of microalgal biostimulants on plants was evaluated by means of bioassays, while the biogas produced was quantified in biochemical methane potential (BMP) tests. Furthermore, the fate of contaminants of emerging concern (CECs) over the process was also assessed. Bioassays confirmed the biostimulant effect of microalgae, which showed gibberellin-, auxin- and cytokinin-like activity in watercress seed germination, mung bean rooting, and wheat leaf chlorophyll retention. In addition, the downstream process applied to raw biomass acted as a pre-treatment to enhance anaerobic digestion performance. After biostimulant extraction, the residual biomass represented 91% of the methane yield from the raw biomass (276 mLCH(4).g(-1)VS). The kinetic profile of the residual biomass was 43% higher than that of the unprocessed biomass. Co-digestion with primary sludge further increased biogas production by 24%. Finally, the concentration of CECs in wastewater was reduced by more than 80%, and only 6 out of 22 CECs analyzed were present in the biostimulant obtained. Most importantly, the concentration of those contaminants was lower than in biosolids that are commonly used in agriculture, ensuring environmental safety.
PMID: 39068780
Plant J , IF:6.417 , 2024 Aug doi: 10.1111/tpj.16988
The SCOOP-MIK2 immune pathway modulates Arabidopsis root growth and development by regulating PIN-FORMED abundance and auxin transport.
MOE Key Laboratory for Cellular Dynamics, Center for Advanced Interdisciplinary Science and Biomedicine of IHM, Hefei National Laboratory for Physical Sciences at the Microscale, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230027, China.
Plants synthesize hundreds of small secretory peptides, which are perceived by the receptor-like kinase (RLK) family at the cell surface. Various signaling peptide-RLK pairs ensure plant adaptation to distinct environmental conditions. Here, we report that SERINE RICH ENDOGENOUS PEPTIDE (SCOOP) immune peptides modulate root growth and development by regulating PIN-FORMED (PIN)-regulated polar auxin transport in Arabidopsis. The SCOOP4 and SCOOP12 treatments impaired root gravitropic growth, auxin redistribution in response to gravistimulation, and PIN abundance in the PM. Furthermore, genetic and cell biological analyses revealed that these physiological and cellular effects of SCOOP4 and SCOOP12 peptides are mediated by the receptor MALE DISCOVERER1-INTERACTING RECEPTOR LIKE KINASE2 (MIK2) and the downstream mitogen-activated kinase MPK6. Biochemical evidence indicates that MPK6 directly phosphorylates the cytosolic loop of PIN proteins. Our work established a link between the immune signaling peptide SCOOPs and root growth pathways, providing insights into the molecular mechanisms underlying plant root adaptive growth in the defense response.
PMID: 39162107
Plant J , IF:6.417 , 2024 Aug doi: 10.1111/tpj.16959
An incoherent feed-forward loop involving bHLH transcription factors, Auxin and CYCLIN-Ds regulates style radial symmetry establishment in Arabidopsis.
Department of Crop Genetics, John Innes Centre, Norwich, Norfolk, UK.; Department of Cell and Developmental Biology, John Innes Centre, Norwich, Norfolk, UK.; Department of Computational and Systems Biology, John Innes Centre, Norwich, Norfolk, UK.
The bilateral-to-radial symmetry transition occurring during the development of the Arabidopsis thaliana female reproductive organ (gynoecium) is a crucial biological process linked to plant fertilization and seed production. Despite its significance, the cellular mechanisms governing the establishment and breaking of radial symmetry at the gynoecium apex (style) remain unknown. To fill this gap, we employed quantitative confocal imaging coupled with MorphoGraphX analysis, in vivo and in vitro transcriptional experiments, and genetic analysis encompassing mutants in two bHLH transcription factors necessary and sufficient to promote transition to radial symmetry, SPATULA (SPT) and INDEHISCENT (IND). Here, we show that defects in style morphogenesis correlate with defects in cell-division orientation and rate. We showed that the SPT-mediated accumulation of auxin in the medial-apical cells undergoing symmetry transition is required to maintain cell-division-oriented perpendicular to the direction of organ growth (anticlinal, transversal cell division). In addition, SPT and IND promote the expression of specific core cell-cycle regulators, CYCLIN-D1;1 (CYC-D1;1) and CYC-D3;3, to support progression through the G1 phase of the cell cycle. This transcriptional regulation is repressed by auxin, thus forming an incoherent feed-forward loop mechanism. We propose that this mechanism fine-tunes cell division rate and orientation with the morphogenic signal provided by auxin, during patterning of radial symmetry at the style.
PMID: 39121182
Plant J , IF:6.417 , 2024 Sep , V119 (5) : P2273-2287 doi: 10.1111/tpj.16916
The auxin-responsive CsSPL9-CsGH3.4 module finely regulates auxin levels to suppress the development of adventitious roots in tea (Camellia sinensis).
College of Horticulture, Northwest A&F University, Yangling, Shaanxi, 712100, China.
The cutting technique is extensively used in tea breeding, with key emphasis on promoting the growth of adventitious roots (ARs). Despite its importance in tea cultivation, the mechanisms underlying AR development in tea remain unclear. In this study, we demonstrated the essential role of auxins in the initiation and progression of AR and established that the application of exogenous 1-naphthaleneacetic acid-enhanced AR formation in tissue-cultured seedlings and cuttings. Then, we found that the auxin-responsive transcription factor CsSPL9 acted as a negative regulator of AR development by reducing the levels of free indole-3-acetic acid (IAA) in tea plants. Furthermore, we identified CsGH3.4 as a downstream target of CsSPL9, which was activated by direct binding to its promoter. CsGH3.4 also inhibited AR development and maintained low levels of free IAA. Thus, these results revealed the inhibitory effect of the auxin-responsive CsSPL9-CsGH3.4 module on AR development by reducing free IAA levels in tea. These findings have significant theoretical and practical value for enhancing tea breeding practices.
PMID: 39012276
Plant J , IF:6.417 , 2024 Aug , V119 (3) : P1327-1335 doi: 10.1111/tpj.16851
The additive function of YIGE2 and YIGE1 in regulating maize ear length.
National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China.; Hubei Hongshan Laboratory, Wuhan, 430070, China.; Yazhouwan National Laboratory, Sanya, 572024, China.; Department of Molecular Physiology, Max-Planck-Institute of Molecular Plant Physiology, Potsdam-Golm, 14476, Germany.; Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, 11724, USA.
Ear length (EL) is a key trait that greatly contributes to yield in maize. Although dozens of EL quantitative trait loci have been mapped, very few causal genes have been cloned, and the molecular mechanisms remain largely unknown. Our previous study showed that YIGE1 is involved in sugar and auxin pathways to regulate ear inflorescence meristem (IM) development and thus affects EL in maize. Here, we reveal that YIGE2, the paralog of YIGE1, regulates maize ear development and EL through auxin pathway. Knockout of YIGE2 causes a significant decrease of auxin level, IM length, floret number, EL, and grain yield. yige1 yige2 double mutants had even shorter IM and ears implying that these two genes redundantly regulate IM development and EL. The genes controlling auxin levels are differential expressed in yige1 yige2 double mutants, leading to lower auxin level. These results elucidated the critical role of YIGE2 and the redundancy between YIGE2 and YIGE1 in maize ear development, providing a new genetic resource for maize yield improvement.
PMID: 38804053
Int J Mol Sci , IF:5.923 , 2024 Aug , V25 (16) doi: 10.3390/ijms25168901
Transcriptome Profiles Reveal Key Regulatory Networks during Single and Multifactorial Stresses Coupled with Melatonin Treatment in Pitaya (Selenicereus undatus L.).
Hainan Yazhou-Bay Seed Laboratory, School of Breeding and Multiplication, Hainan University, Sanya 572025, China.; Collaborative Innovation Center of Nanfan and High-Efficiency Tropical Agriculture, School of Tropical Crops and Forestry, Hainan University, Haikou 570228, China.
In response to evolving climatic conditions, plants frequently confront multiple abiotic stresses, necessitating robust adaptive mechanisms. This study focuses on the responses of Selenicereus undatus L. to both individual stresses (cadmium; Cd, salt; S, and drought; D) and their combined applications, with an emphasis on evaluating the mitigating effects of (M) melatonin. Through transcriptome analysis, this study identifies significant gene expression changes and regulatory network activations. The results show that stress decreases pitaya growth rates by 30%, reduces stem and cladode development by 40%, and increases Cd uptake under single and combined stresses by 50% and 70%, respectively. Under stress conditions, enhanced activities of H(2)O(2), POD, CAT, APX, and SOD and elevated proline content indicate strong antioxidant defenses. We identified 141 common DEGs related to stress tolerance, most of which were related to AtCBP, ALA, and CBP pathways. Interestingly, the production of genes related to signal transduction and hormones, including abscisic acid and auxin, was also significantly induced. Several calcium-dependent protein kinase genes were regulated during M and stress treatments. Functional enrichment analysis showed that most of the DEGs were enriched during metabolism, MAPK signaling, and photosynthesis. In addition, weighted gene co-expression network analysis (WGCNA) identified critical transcription factors (WRKYs, MYBs, bZIPs, bHLHs, and NACs) associated with antioxidant activities, particularly within the salmon module. This study provides morpho-physiological and transcriptome insights into pitaya's stress responses and suggests molecular breeding techniques with which to enhance plant resistance.
PMID: 39201587
Int J Mol Sci , IF:5.923 , 2024 Aug , V25 (15) doi: 10.3390/ijms25158385
Genome-Wide Identification, Expression, and Interaction Analysis of the Auxin Response Factor and AUX/IAA Gene Families in Vaccinium bracteatum.
Anhui Provincial Key Laboratory of Molecular Enzymology and Mechanism of Major Metabolic Diseases, College of Life Sciences, Anhui Normal University, Wuhu 241000, China.; Anhui Provincial Engineering Research Centre for Molecular Detection and Diagnostics, College of Life Sciences, Anhui Normal University, Wuhu 241000, China.
BACKGROUND: Auxin, a plant hormone, plays diverse roles in the modulation of plant growth and development. The transport and signal transduction of auxin are regulated by various factors involved in shaping plant morphology and responding to external environmental conditions. The auxin signal transduction is primarily governed by the following two gene families: the auxin response factor (ARF) and auxin/indole-3-acetic acid (AUX/IAA). However, a comprehensive genomic analysis involving the expression profiles, structures, and functional features of the ARF and AUX/IAA gene families in Vaccinium bracteatum has not been carried out to date. RESULTS: Through the acquisition of genomic and expression data, coupled with an analysis using online tools, two gene family members were identified. This groundwork provides a distinguishing characterization of the chosen gene families in terms of expression, interaction, and response in the growth and development of plant fruits. In our genome-wide search of the VaARF and VaIAA genes in Vaccinium bracteatum, we identified 26 VaARF and 17 VaIAA genes. We analyzed the sequence and structural characteristics of these VaARF and VaIAA genes. We found that 26 VaARF and 17 VaIAA genes were divided into six subfamilies. Based on protein interaction predictions, VaIAA1 and VaIAA20 were designated core members of VaIAA gene families. Moreover, an analysis of expression patterns showed that 14 ARF genes and 12 IAA genes exhibited significantly varied expressions during fruit development. CONCLUSION: Two key genes, namely, VaIAA1 and VaIAA20, belonging to a gene family, play a potentially crucial role in fruit development through 26 VaARF-IAAs. This study provides a valuable reference for investigating the molecular mechanism of fruit development and lays the foundation for further research on Vaccinium bracteatum.
PMID: 39125955
Front Plant Sci , IF:5.753 , 2024 , V15 : P1418358 doi: 10.3389/fpls.2024.1418358
Transcriptome analysis unravels key pathways and hub genes related to immature fruit abscission in Camellia oleifera.
Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees of the Ministry of Education, Central South University of Forestry and Technology, Changsha, China.; State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center (HHRRC), Changsha, China.
Immature fruit abscission of Camellia oleifera (C. oleifera) is a common problem limiting yield increases. However, the regulatory mechanisms underlying immature fruit abscission in C. oleifera are unclear. In this study, we systematically investigated changes in the morphological, physiological, and gene expression of fruit abscission zones (FAZs) of soon-to-abscise fruits (M2). We found that fruit abscission before ripening mainly occurs during the August abscission stage of 'Huashuo'. At the beginning of this stage, the FAZs of M2 have a marked dent, and the separation layer structures are preliminarily formed. Phytohormone analysis showed that the contents of indole-3-acetic acid (IAA) and jasmonic acid (JA) in the FAZs of M2 were significantly decreased compared with the non-abscised fruits, while the content of trans-zeatin (TZR) was increased. Transcriptome analysis identified differentially expressed genes (DEGs) mainly involved in phytohormone metabolism, including ethylene, auxin, JA, and the cis-zeatin signal transduction pathway. There were also many DEGs involved in cell wall catabolism. Weighted gene co-expression network analysis (WGCNA) further suggested that the transcription factors NAC100 and ERF114 participate in the immature fruit abscission of C. oleifera. This study provides insights into the fruit abscission mechanism of C. oleifera.
PMID: 39184578
Front Plant Sci , IF:5.753 , 2024 , V15 : P1426647 doi: 10.3389/fpls.2024.1426647
Comparative transcriptome analysis of resistant and susceptible watermelon genotypes reveals the role of RNAi, callose, proteinase, and cell wall in squash vein yellowing virus resistance.
Agricultural Research Service (USDA-ARS), U.S. Vegetable Laboratory (USVL), United States Department of Agriculture, Charleston, SC, United States.; ORISE participant, USVL, USDA-ARS, Charleston, SC, United States.; U.S. Horticultural Research Laboratory, USDA-ARS, Fort Pierce, FL, United States.
Watermelon (Citrullus lanatus) is the third largest fruit crop in the world in term of production. However, it is susceptible to several viruses. Watermelon vine decline (WVD), caused by whitefly-transmitted squash vein yellowing virus (SqVYV), is a disease that has caused over $60 million in losses in the US and continues to occur regularly in southeastern states. Understanding the molecular mechanisms underlying resistance to SqVYV is important for effective disease management. A time-course transcriptomic analysis was conducted on resistant (392291-VDR) and susceptible (Crimson Sweet) watermelon genotypes inoculated with SqVYV. Significantly higher levels of SqVYV were observed over time in the susceptible compared to the resistant genotype. The plasmodesmata callose binding protein (PDCB) gene, which is responsible for increased callose deposition in the plasmodesmata, was more highly expressed in the resistant genotype than in the susceptible genotype before and after inoculation, suggesting the inhibition of cell-to-cell movement of SqVYV. The potential role of the RNA interference (RNAi) pathway was observed in the resistant genotype based on differential expression of eukaryotic initiation factor (eIF), translin, DICER, ribosome inactivating proteins, RNA-dependent RNA polymerase (RDR), and Argonaute (AGO) genes after inoculation. The significant differential expression of hormone-related genes, including those involved in the ethylene, jasmonic acid, auxin, cytokinin, gibberellin, and salicylic acid signaling pathways, was observed, emphasizing their regulatory roles in the defense response. Genes regulating pectin metabolism, cellulose synthesis, cell growth and development, xenobiotic metabolism, and lignin biosynthesis were overexpressed in the susceptible genotype, suggesting that alterations in cell wall integrity and growth processes result in disease symptom development. These findings will be helpful for further functional studies and the development of SqVYV-resistant watermelon cultivars.
PMID: 39157511
Front Plant Sci , IF:5.753 , 2024 , V15 : P1400215 doi: 10.3389/fpls.2024.1400215
Date palm transcriptome analysis provides new insights on changes in response to high salt stress of colonized roots with the endophytic fungus Piriformospora indica.
Department of Integrative Agriculture, College of Agriculture and Veterinary Medicine, United Arab Emirates University, Al Ain, United Arab Emirates.; Department of Vegetable Science, College of Agriculture, Kerala Agricultural University, Vellanikkara, Thrissur, India.; Division of Research, Innovation, and Impact, 106B Bond Life Sciences Center, University of Missouri, Columbia, MO, United States.; Biotechnology and Plant Improvement Laboratory, Centre of Biotechnology of Sfax (CBS)/University of Sfax, Sfax, Tunisia.; College of Plant Science and Technology, Beijing Key Laboratory for Agricultural Application and New Technique, Beijing University of Agriculture, Beijing, China.; King Abdullah University of Science and Technology (KAUST), Biological and Environmental Sciences and Engineering (BESE), Thuwal, Saudi Arabia.
Salinity is a significant threat that causes considerable yield losses in date palm. The root endophytic fungus Piriformospora indica has proven effective in providing salt stress tolerance to host plants. However, the underlying molecular mechanism facilitating the date palm's response to P. indica inoculation, and its involvement in the salt stress tolerance, remains unknown. In this study, the colonization of P. indica on date palm seedlings exposed to saline conditions was observed through confocal microscopy, and its impact on gene expressions was evaluated using the transcriptomic analysis. Our findings show that P. indica colonization reinforced the cortical cells, prevented them from plasmolysis and cell death under salinity. The RNAseq analysis produced clean reads ranging from 62,040,451 to 3,652,095 across the treatment groups, successfully assembling into 30,600 annotated genes. Out of them, the number of differentially expressed genes (DEGs) varied across the treatments: i.e., 2523, 2031, and 1936 DEGs were upregulated, while 2323, 959, and 3546 were downregulated in Salt, Fungi, and Fungi+Salt groups, respectively. Furthermore, principal component analysis based on transcriptome profiles revealed discrete clustering of samples from different treatment groups. KEGG and GO pathways enrichment analysis highlighted variation in the number and types of enriched pathways among the treatments. Our study indicated variations in gene expression related to plant hormone biosynthesis and signal transduction (auxin, abscisic acid, gibberellin, and ethylene), ABC transporters, sodium/hydrogen exchanger, cation HKT transporter, transcription factors such as WRKY and MYBs, and the plant immune system (lipoxygenase and jasmonate) of the date palm seedlings. By characterizing the transcriptome of date palm roots under salt stress and with colonization of P. indica, the present findings provide valuable perspectives on the molecular mechanisms responsible for inducing salinity stress tolerance in plants.
PMID: 39145193
Front Plant Sci , IF:5.753 , 2024 , V15 : P1430639 doi: 10.3389/fpls.2024.1430639
Organ-specific transcriptional regulation by HFR1 and HY5 in response to shade in Arabidopsis.
Temasek Life Sciences Laboratory, National University of Singapore, Singapore, Singapore.; Department of Biological Sciences, National University of Singapore, Singapore, Singapore.
Light is crucial for plants and serves as a signal for modulating their growth. Under shade, where red to far-red light ratio is low, plants exhibit shade avoidance responses (SAR). LONG HYPOCOTYL IN FAR-RED 1 (HFR1) and ELONGATED HYPOCOTYL 5 (HY5) are known to be negative regulators of SAR and physically interact with one another. However, transcriptional regulatory network underlying SAR by these two transcription factors has not been explored. Here, we performed organ-specific transcriptome analyses of Arabidopsis thaliana hfr1-5, hy5-215 and hfr1hy5 to identify genes that are co-regulated by HFR1 and HY5 in hypocotyls and cotyledons. Genes co-regulated by HFR1 and HY5 were enriched in various processes related to cell wall modification and chlorophyll biosynthesis in hypocotyls. Phytohormone (abscisic acid and jasmonic acid) and light responses were significantly regulated by HFR1 and HY5 in both organs, though it is more prominent under shade in cotyledons. HFR1 and HY5 also differentially regulate the expression of the cell wall-related genes for xyloglucan endotransglucosylase/hydrolase, expansin, arabinogalactan protein and class III peroxidase depending on the organs. Furthermore, HFR1 and HY5 cooperatively regulated hypocotyl responsiveness to shade through auxin metabolism. Together, our study illustrates the importance of the HFR1-HY5 module in regulating organ-specific shade responses in Arabidopsis.
PMID: 39145190
Front Microbiol , IF:5.64 , 2024 , V15 : P1431120 doi: 10.3389/fmicb.2024.1431120
The ectomycorrhizal fungus Scleroderma bovista improves growth of hazelnut seedlings and plays a role in auxin signaling and transport.
Jilin Provincial Key Laboratory of Plant Resource Science and Green Production, Jilin Normal University, Siping, China.
INTRODUCTION: Scleroderma bovista can form symbiotic ectomycorrhizal fungi with hazel roots. The mechanism through which S. bovista promotes hazelnut growth remains unclear. METHODS: This study aimed to evaluate the effect of ectomycorrhizal fungus S. bovista on the growth and development of hazel roots and gene expression changes through comparative transcriptome analysis. RESULTS: After inoculation with S. bovista, the fungus symbiotically formed ectomycorrhiza with hazel roots. The fresh weights of the aboveground and underground parts of My treatment (inoculated with S. bovista and formed mycorrhiza) were much higher than those of the control, respectively. The length, project area, surface area, volume, forks, and diameter of the inoculated seedlings root were 1.13 to 2.48 times higher than those of the control. In the paired comparison, 3,265 upregulated and 1,916 downregulated genes were identified. The most significantly enriched Gene Ontology term for the upregulated Differentially Expressed Genes was GO:0005215 (transporter activity). Immunohistochemical analysis suggested that the expression levels of auxin and Auxin Response Factor9 were significantly increased by S. bovista after the formation of mycorrhizal fungi in hazelnut root tips. DISCUSSION: These results indicate that genes related to auxin biosynthesis, transport and signaling, and transport of nutrients may contribute to root development regulation in hazel ectomycorrhiza.
PMID: 39171259
Microbiol Res , IF:5.415 , 2024 Sep , V286 : P127823 doi: 10.1016/j.micres.2024.127823
Aerial signaling by plant-associated Streptomyces setonii WY228 regulates plant growth and enhances salt stress tolerance.
The Key Laboratory of Biotechnology for Medicinal Plant of Jiangsu Province, School of Life Sciences, Jiangsu Normal University, Xuzhou, Jiangsu, PR China.; The Key Laboratory of Biotechnology for Medicinal Plant of Jiangsu Province, School of Life Sciences, Jiangsu Normal University, Xuzhou, Jiangsu, PR China. Electronic address: shengqin@jsnu.edu.cn.
Plant-associated streptomycetes play important roles in plant growth and development. However, knowledge of volatile-mediated crosstalk between Streptomyces spp. and plants remains limited. In this study, we investigated the impact of volatiles from nine endophytic Streptomyces strains on the growth and development of plants. One versatile strain, Streptomyces setonii WY228, was found to significantly promote the growth of Arabidopsis thaliana and tomato seedlings, confer salt tolerance, and induce early flowering and increased fruit yield following volatile treatment. Analysis of plant growth-promoting traits revealed that S. setonii WY228 could produce indole-3-acetic acid, siderophores, ACC deaminase, fix nitrogen, and solubilize inorganic phosphate. These capabilities were further confirmed through genome sequencing and analysis. Volatilome analysis indicated that the volatile organic compounds emitted from ISP-2 medium predominantly comprised sesquiterpenes and 2-ethyl-5-methylpyrazine. Further investigations showed that 2-ethyl-5-methylpyrazine and sesquiterpenoid volatiles were the primary regulators promoting growth, as confirmed by experiments using the terpene synthesis inhibitor phosphomycin, pure compounds, and comparisons of volatile components. Transcriptome analysis, combined with mutant and inhibitor studies, demonstrated that WY228 volatiles promoted root growth by activating Arabidopsis auxin signaling and polar transport, and enhanced root hair development through ethylene signaling activation. Additionally, it was confirmed that volatiles can stimulate plant abscisic acid signaling and activate the MYB75 transcription factor, thereby promoting anthocyanin synthesis and enhancing plant salt stress tolerance. Our findings suggest that aerial signaling-mediated plant growth promotion and abiotic stress tolerance represent potentially overlooked mechanisms of Streptomyces-plant interactions. This study also provides an exciting strategy for the regulation of plant growth and the improvement of horticultural crop yields within sustainable agricultural practices.
PMID: 38959523
Biochem Soc Trans , IF:5.407 , 2024 Aug , V52 (4) : P1873-1883 doi: 10.1042/BST20231558
Amino acids biosynthesis in root hair development: a mini-review.
Departamento de Genomica Funcional de Eucariotas, Centro de Ciencias Genomicas, Universidad Nacional Autonoma de Mexico, Cuernavaca 62210, Mexico.; Departamento de Biologia Molecular de Plantas, Instituto de Biotecnologia, Universidad Nacional Autonoma de Mexico, Cuernavaca 62210, Mexico.
Metabolic factors are essential for developmental biology of an organism. In plants, roots fulfill important functions, in part due to the development of specific epidermal cells, called hair cells that form root hairs (RHs) responsible for water and mineral uptake. RH development consists in (a) patterning processes involved in formation of hair and non-hair cells developed from trichoblasts and atrichoblasts; (b) RH initiation; and (c) apical (tip) growth of the RH. Here we review how these processes depend on pools of different amino acids and what is known about RH phenotypes of mutants disrupted in amino acid biosynthesis. This analysis shows that some amino acids, particularly aromatic ones, are required for RH apical (tip) growth, and that not much is known about the role of amino acids at earlier stages of RH formation. We also address the role of amino acids in rhizosphere, inhibitory and stimulating effects of amino acids on RH growth, amino acids as N source in plant nutrition, and amino acid transporters and their expression in the RHs. Amino acids form conjugates with auxin, a hormone essential for RH growth, and respective genes are overviewed. Finally, we outline missing links and envision some perspectives in the field.
PMID: 38984866
Biochem Soc Trans , IF:5.407 , 2024 Aug , V52 (4) : P1841-1848 doi: 10.1042/BST20231537
AZGs: a new family of cytokinin transporters.
Centre for Organismal Studies (COS), University of Heidelberg, Heidelberg 69120, Germany.; Molecular Plant Physiology, Institute of Cellular Molecular Botany (IZMB), University of Bonn, Kirschallee 1, 53115 Bonn, Germany.
Cytokinins (CKs) are phytohormones structurally similar to purines that play important roles in various aspects of plant physiology and development. The local and long-distance distribution of CKs is very important to control their action throughout the plant body. Over the past decade, several novel CK transporters have been described, many of which have been linked to a physiological function rather than simply their ability to transport the hormone in vitro. Purine permeases, equilibrative nucleotide transporters and ATP-binding cassette transporters are involved in the local and long-range distribution of CK. In addition, members of the Arabidopsis AZA-GUANINE RESISTANT (AZG) protein family, AZG1 and AZG2, have recently been shown to mediate CK uptake at the plasma membrane and endoplasmic reticulum. Despite sharing approximately 50% homology, AZG1 and AZG2 have unique transport mechanisms, tissue-specific expression patterns, and subcellular localizations that underlie their distinct physiological functions. AZG2 is expressed in a small group of cells in the overlying tissue around the lateral root primordia, where its expression is induced by auxins and it is involved in the regulation of lateral root growth. AZG1 is ubiquitously expressed, with high levels in the division zone of the root apical meristem. Here, it binds and stabilises the auxin efflux carrier PIN1, thereby shaping root architecture, particularly under salt stress. This review highlights the latest findings on the protein properties, transport mechanisms and cellular functions of this new family of CK transporters and discusses perspectives for future research in this field.
PMID: 38979638
J Agric Food Chem , IF:5.279 , 2024 Aug doi: 10.1021/acs.jafc.4c06062
Dual-Mediated Roles of H(+)-ATPase in Alleviating the Phytotoxicity of Imazethapyr to Nontarget Wheat.
Key Laboratory of Pollution Exposure and Health Intervention of Zhejiang Province, College of Biological and Environmental Engineering, Zhejiang Shuren University, Hangzhou 310015, China.; MOE Key Laboratory of Environmental Remediation & Ecosystem Health, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China.
The regulation solutions and mechanisms of reducing pesticide phytotoxicity to nontarget plants are not well-defined and detailed. Here, we have proposed a new detoxification strategy to control the toxic effects of herbicide imazethapyr (IM) induced in wheat seedlings from the perspective of the plasma membrane (PM) H(+)-ATPase. We found that the changes in PM H(+)-ATPase activity have a regulatory effect on the phytotoxic effects induced by IM in plants. Treatment with PM H(+)-ATPase activators restored the reduced auxin content and photosynthetic efficiency caused by IM, thereby promoting plant growth. Application of a PM H(+)-ATPase inhibitor further reduced phosphorus content and significantly increased 2,4-dihydroxy-7-methoxy-2H,1,4-benzoxazin-3(4H)one (DIMBOA) and jasmonic acid levels. These effects indicate that auxin and DIMBOA may regulate plant growth trends and detoxification effects mediated by PM H(+)-ATPase. This work opens a new strategy for regulating herbicide toxicity to nontarget plants from the PM H(+)-ATPase.
PMID: 39183467
J Agric Food Chem , IF:5.279 , 2024 Aug , V72 (34) : P19028-19039 doi: 10.1021/acs.jafc.4c05082
Molecular Mechanism of ARF5-AHL15-Mediated Auxin-Induced Embryogenic Cell Formation in Apples.
College of Landscape Architecture and Art, Northwest A&F University, Yangling 712100, Shaanxi, China.
The somatic embryo (SE) has bipolar characteristics, which is an ideal material for large-scale microproduction of woody plants represented by apples, and the somatic embryo is also an excellent receptor for genetic transformation. The formation of embryogenic cells is a prerequisite for somatic embryogenesis to occur. The embryogenic cells of apples cannot be obtained without induction of exogenous auxin, but how the auxin pathway regulates this process remains unknown. In this study, via RNA sequencing, MdARF5 and MdAHL15 were identified as differentially expressed genes involved in this process. Overexpression of MdARF5 and MdAHL15 induced the formation and proliferation of embryogenic cells and thus substantially shortened the induction cycle and improved the somatic embryo proliferation efficiency. A yeast one-hybrid assay showed that MdARF5 can directly bind to the promoter of MdAHL15. beta-Glucuronidase (GUS) and dual-luciferase reporter assays revealed that MdARF5 activation of MdAHL15 transcription was substantial. In conclusion, our results suggest that MdAHL15 is induced by auxin and promotes the formation of embryogenic cells in early somatic embryogenesis via the positive regulation of MdARF5 in apples. The results will provide a theoretical basis for somatic embryogenesis-based development, reproduction, and transgenic breeding in apples.
PMID: 39150252
J Agric Food Chem , IF:5.279 , 2024 Aug , V72 (34) : P19219-19231 doi: 10.1021/acs.jafc.4c02650
Global Characterization of DNA Methylation during Rice Leaf Angle Development.
Key Laboratory of Three Gorges Regional Plant Genetics and Germplasm Enhancement (CTGU)/Biotechnology Research Center, College of Biological and Pharmaceutical Sciences, China Three Gorges University, Yichang 443002, China.
During plant development and growth, genomic DNA accumulates chemical markers that determine the levels of gene expression. DNA methylation is an important epigenetic marker involved in plant developmental events. However, the characterization of the role of DNA methylation in rice leaf angle development has lagged behind. Herein, we performed bisulfite sequencing to characterize DNA methylation sites and performed transcriptome and small RNA sequencing during leaf angle development. The results revealed a global reduction in CG methylation during leaf angle establishment. A reduction in gene body CG methylation appears to play a vital role in leaf angle development. The hypomethylated and weakly expressed genes were functionally enriched in the brassinosteroid and auxin signaling pathways. Additionally, the main DNA methyltransferases were inactive. The addition of exogenous DNA methylation inhibitor 5-azacytidine increased the leaf angle, which confirmed that DNA methylation is crucial for leaf angle development. This study revealed a gradual decrease in 24-nucleotide siRNA levels during leaf angle development, particularly in relation to the enrichment of 24-nucleotide siRNAs at different hypomethylated regions that induce leaf angle inclination. Our results indicate crucial roles for DNA methylation in the rice leaf angle developmental stages.
PMID: 39146245
ACS Synth Biol , IF:5.11 , 2024 Aug doi: 10.1021/acssynbio.4c00186
Genetically Encoded, Noise-Tolerant, Auxin Biosensors in Yeast.
Department of Biological Systems Engineering, Virginia Tech, Blacksburg, Virginia 24061, United States.; Fralin Life Sciences Institute, Virginia Tech, Blacksburg, Virginia 24061, United States.; Department of Biochemistry, Virginia Tech, Blacksburg, Virginia 24061, United States.; The Translational Plant Sciences Center (TPSC), Virginia Tech, Blacksburg, Virginia 24061, United States.
Auxins are crucial signaling molecules that regulate the growth, metabolism, and behavior of various organisms, most notably plants but also bacteria, fungi, and animals. Many microbes synthesize and perceive auxins, primarily indole-3-acetic acid (IAA, referred to as auxin herein), the most prevalent natural auxin, which influences their ability to colonize plants and animals. Understanding auxin biosynthesis and signaling in fungi may allow us to better control interkingdom relationships and microbiomes from agricultural soils to the human gut. Despite this importance, a biological tool for measuring auxin with high spatial and temporal resolution has not been engineered in fungi. In this study, we present a suite of genetically encoded, ratiometric, protein-based auxin biosensors designed for the model yeast Saccharomyces cerevisiae. Inspired by auxin signaling in plants, the ratiometric nature of these biosensors enhances the precision of auxin concentration measurements by minimizing clonal and growth phase variation. We used these biosensors to measure auxin production across diverse growth conditions and phases in yeast cultures and calibrated their responses to physiologically relevant levels of auxin. Future work will aim to improve the fold change and reversibility of these biosensors. These genetically encoded auxin biosensors are valuable tools for investigating auxin biosynthesis and signaling in S. cerevisiae and potentially other yeast and fungi and will also advance quantitative functional studies of the plant auxin perception machinery, from which they are built.
PMID: 39197086
Biology (Basel) , IF:5.079 , 2024 Aug , V13 (8) doi: 10.3390/biology13080622
The Mechanism of the Development and Maintenance of Sexual Dimorphism in the Dioecious Mulberry Plant (Morus alba).
Jiangsu Key Laboratory of Sericulture Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang 212100, China.; Key Laboratory of Silkworm and Mulberry Genetic Improvement, Ministry of Agriculture and Rural Affairs, The Sericultural Research Institute, Chinese Academy of Agricultural Sciences, Zhenjiang 212100, China.; Institute of Plant Nutrition and Soil Science, Kiel University, Hermann-Rodewald-Strasse 2, 24118 Kiel, Germany.; Department of Materials Science and Engineering, Suzhou University of Science and Technology, Suzhou 215011, China.; Department of Crop Science, School of Agriculture, College of Agriculture and Natural Sciences, University of Cape Coast, Cape Coast P.O. Box 5007, Ghana.
Intersexual differentiation is crucial for the speciation and maintenance of dioecious plants, but the underlying mechanisms, including the genes involved, are still poorly understood. Here, we focused on a typical dioicous plant Morus alba, to explore the molecular footprints relevant to sex evolution by revealing the differentially expressed genes (DEGs) between two sexes and the testing signals of selection for these DEGs. From the results, we found a total of 1543 DEGs. Interestingly, 333 and 66 genes expression were detected only in male and female inflorescences, respectively. Using comparative transcriptomics, the expression of 841 genes were found to be significantly higher in male than in female inflorescences and were mainly enriched in defense-related pathways including the biosynthesis of phenylpropanoids, cutin, suberine and waxes. Meanwhile, the expression of 702 genes was female-biased and largely enriched in pathways related to growth and development, such as carbohydrate metabolism, auxin signaling and cellular responses. In addition, 16.7% and 17.6% signals of selection were significantly detected in female- and male-biased genes, respectively, suggesting their non-negligible role in evolution. Our findings expanded the understanding of the molecular basis of intersexual differentiation and contribute to further research on sex evolution in dioecious plants.
PMID: 39194560
Mol Cells , IF:5.034 , 2024 Aug , V47 (8) : P100093 doi: 10.1016/j.mocell.2024.100093
OsMYB14, an R2R3-MYB transcription factor, regulates plant height through the control of hormone metabolism in rice.
Department of Biosciences and Bioinformatics, Myongji University, Yongin, Gyeonggi-do 17058, Republic of Korea.; Genomics Genetics Institute, GreenGene Biotech Inc, Yongin, Gyeonggi-do 17058, Republic of Korea.; Graduate School of Green-Bio Science and Crop Biotech Institute, Kyung Hee University, Yongin, Gyeonggi-do 17104, Republic of Korea.; Department of Agricultural Biotechnology, National Institute of Agricultural Sciences, Jeonju, Jeollabuk-do 54875, Republic of Korea.; Department of Biosciences and Bioinformatics, Myongji University, Yongin, Gyeonggi-do 17058, Republic of Korea. Electronic address: kim750a11@mju.ac.kr.
Plant growth must be regulated throughout the plant life cycle. The myeloblastosis (MYB) transcription factor (TF) family is one of the largest TF families and is involved in metabolism, lignin biosynthesis, and developmental processes. Here, we showed that OsMYB14, a rice R2R3-MYB TF, was expressed in leaves and roots, especially in rice culm and panicles, and that it localized to the nucleus. Overexpression of OsMYB14 (OsMYB14-ox) in rice resulted in a 30% reduction in plant height compared to that of the wild type (WT), while the height of the osmyb14-knockout (osmyb14-ko) mutant generated using the CRISPR/Cas9 system was not significantly different. Microscopic observations of the first internode revealed that the cell size did not differ significantly among the lines. RNA sequencing analysis revealed that genes associated with plant development, regulation, lipid metabolism, carbohydrate metabolism, and gibberellin (GA) and auxin metabolic processes were downregulated in the OsMYB14-ox line. Hormone quantitation revealed that inactive GA19 accumulated in OsMYB14-ox but not in the WT or knockout plants, suggesting that GA20 generation was repressed. Indole-3-acetic acid (IAA) and IAA-aspartate accumulated in OsMYB14-ox and osmyb14-ko, respectively. Indeed, real-time PCR analysis revealed that the expression of OsGA20ox1, encoding GA20 oxidase 1, and OsGH3-2, encoding IAA-amido synthetase, was downregulated in OsMYB14-ox and upregulated in osmyb14-ko. A protein-binding microarray revealed the presence of a consensus DNA-binding sequence, the ACCTACC-like motif, in the promoters of the OsGA20ox1 and GA20ox2 genes. These results suggest that OsMYB14 may act as a negative regulator of biological processes affecting plant height in rice by regulating GA biosynthesis and auxin metabolism.
PMID: 39004308
Plant Cell Physiol , IF:4.927 , 2024 Aug doi: 10.1093/pcp/pcae090
Natural variation in sexual traits and gene expression between selfing and outcrossing Arabidopsis lyrata suggests sexual selection at work.
Department of Botany, Faculty of Science, Charles University, Benatska 2, CZ-128 01 Prague, Czech Republic.; Institute of Botany of the Czech Academy of Sciences, Zamek 1, CZ-252 43 Pruhonice, Czech Republic.
Flowering plants show significant diversity in sexual strategies, profoundly impacting the evolution of sexual traits and associated genes. Sexual selection is one of the primary evolutionary forces driving sexual trait variation, particularly evident during pollen-pistil interactions, where pollen grains compete for fertilization and females select mating partners. Multiple mating may intensify competition among pollen donors for siring, while in contrast, self-fertilization reduces sire-sire competition, relaxing the sexual selection pressure. Traits involved in male-male competition and female choice are well described, and molecular mechanisms underlying pollen development and pollen-pistil interactions have been extensively studied in the model species Arabidopsis thaliana. However, whether these molecular mechanisms are involved in sexual selection in nature remains unclear. To address this gap, we measured intrinsic pollen performance and its interaction with female choice, and investigated the associated gene expression patterns in a selfing and an outcrossing population of Arabidopsis lyrata. We found that pollen germination and pollen tube growth were significantly higher in outcrossers than selfers, and this difference was accompanied by changes in expression of genes involved in vesicle transport and cytoskeleton. Outcrosser mother plants showed a negative impact on pollen tube growth compared to selfer mother plants, together with a difference of expression for genes involved in auxin and stress response, suggesting a potential mechanism for female choice through molecular crosstalk at the post-pollination stage. Our study provides insight on the impact of sexual selection on the evolution of sexual gene expression in plants.
PMID: 39126152
Pest Manag Sci , IF:4.845 , 2024 Aug doi: 10.1002/ps.8373
Metabolism of 2,4-D in plants: comparative analysis of metabolic detoxification pathways in tolerant crops and resistant weeds.
Department of Agricultural and Forest Sciences and Engineering, University of Lleida - Agrotecnio CERCA Center, Lleida, Spain.; Departmento de Agronomia, Universidade Federal de Vicosa, Vicosa, Brazil.; Department of Agricultural Biology, Colorado State University, Fort Collins, CO, USA.; Department of Agronomy, Kansas State University, Manhattan, KS, USA.; Department of Crop Science, Federal University of Rio Grande do Sul, Porto Alegre, Brazil.; Departamento de Parasitologia Agricola, Universidad Autonoma Chapingo, Texcoco, Mexico.; Department of Agricultural Chemistry and Soil Science, University of Cordoba, Cordoba, Spain.; Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
The commercialization of 2,4-D (2,4-dichlorophenoxyacetic acid) latifolicide in 1945 marked the beginning of the selective herbicide market, with this active ingredient playing a pivotal role among commercial herbicides due to the natural tolerance of monocots compared with dicots. Due to its intricate mode of action, involving interactions within endogenous auxin signaling networks, 2,4-D was initially considered a low-risk herbicide to evolve weed resistance. However, the intensification of 2,4-D use has contributed to the emergence of 2,4-D-resistant broadleaf weeds, challenging earlier beliefs. This review explores 2,4-D tolerance in crops and evolved resistance in weeds, emphasizing an in-depth understanding of 2,4-D metabolic detoxification. Nine confirmed 2,4-D-resistant weed species, driven by rapid metabolism, highlight cytochrome P450 monooxygenases in Phase I and glycosyltransferases in Phase II as key enzymes. Resistance to 2,4-D may also involve impaired translocation associated with mutations in auxin/indole-3-acetic acid (Aux/IAA) co-receptor genes. Moreover, temperature variations affect 2,4-D efficacy, with high temperatures increasing herbicide metabolism rates and reducing weed control, while drought stress did not affect 2,4-D efficacy. Research on 2,4-D resistance has primarily focused on non-target-site resistance (NTSR) mechanisms, including 2,4-D metabolic detoxification, with limited exploration of the inheritance and genetic basis underlying these traits. Resistance to 2,4-D in weeds is typically governed by a single gene, either dominant or incompletely dominant, raising questions about gain-of-function or loss-of-function mutations that confer resistance. Future research should unravel the physiological and molecular-genetic basis of 2,4-D NTSR, exploring potential cross-resistance patterns and assessing fitness costs that may affect future evolution of auxin-resistant weeds. (c) 2024 Society of Chemical Industry.
PMID: 39132883
Plant Sci , IF:4.729 , 2024 Oct , V347 : P112204 doi: 10.1016/j.plantsci.2024.112204
PoARRO-1 regulates adventitious rooting through interaction with PoIAA27b in Paeonia ostii.
College of Landscape Architecture and Art, Henan Agricultural University, Zhengzhou 450002, China.; College of Horticulture, Henan Agricultural University, Zhengzhou 450002, China.; School of Horticulture Landscape Architecture, Henan Institute of Science and Technology, Xinxiang 453003, China.; College of Landscape Architecture, Central South University of Forestry and Technology, Changsha 410004, China.; College of Landscape Architecture and Art, Henan Agricultural University, Zhengzhou 450002, China. Electronic address: wenqianshang@henau.edu.cn.; College of Landscape Architecture and Art, Henan Agricultural University, Zhengzhou 450002, China. Electronic address: hsl213@yeah.net.; College of Landscape Architecture and Art, Henan Agricultural University, Zhengzhou 450002, China. Electronic address: wzhengt@163.com.
Adventitious root (AR) formation is a limiting factor in the vegetative propagation of tree peony (Paeonia suffruticosa Andr.). PoARRO-1, which encodes an auxin oxidase involved in AR formation, plays a role in the root development of P. ostii, but its associated molecular regulatory mechanisms are not yet understood. In this study, we examined the role of PoARRO-1 in AR formation in P. ostii. The overexpression of PoARRO-1 in P. ostii test-tube plantlets led to a notable enhancement in both the rooting rate and the average number of ARs in vitro, as well as increased activities of peroxidase (POD), superoxide dismutase (SOD), and indoleacetic acid oxidase (IAAO). PoARRO-1 was involved in the conversion of IAA-Asp and IAA-Glu to OxIAA and promoted IAA oxidation. RNA sequencing analysis revealed that PoARRO-1 overexpression led to upregulation of enzyme activity, auxin metabolism related genes. Further analyses showed that PoARRO-1 interacted with the 1-175 aa position of PoIAA27b to regulate the formation of ARs. We therefore propose that PoARRO-1 interacts with PoIAA27b to promote AR formation, and it may be useful targets for enhancing the in vitro propagation of P. ostii.
PMID: 39059631
Plant Sci , IF:4.729 , 2024 Sep , V346 : P112177 doi: 10.1016/j.plantsci.2024.112177
The mutation of CsSUN, an IQD family protein, is responsible for the short and fat fruit (sff) in cucumber (Cucumis sativus L.).
College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China.; College of Forestry, Northwest A&F University, Yangling, Shaanxi 712100, China.; College of Horticulture, Gansu Agricultural University, Lanzhou, Gansu 730070, China.; College of Horticulture, Shanxi Agricultural University, Taigu, Shanxi 030801, China.; Vegetable Research Institute, Gansu Academy of Agricultural Sciences, Lanzhou, Gansu 730070, China.; USDA-ARS Vegetable Crops Research Unit, University of Wisconsin, Madison, WI 53706, USA.; College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China. Electronic address: liyuhong73@nwsuaf.edu.cn.; College of Life Science, Northwest A&F University, Yangling, Shaanxi 712100, China. Electronic address: pengchen@nwsuaf.edu.cn.
The fruit shape of cucumber is an important agronomic trait, and mining regulatory genes, especially dominant ones, is vital for cucumber breeding. In this study, we identified a short and fat fruit mutant, named sff, from an EMS mutagenized population. Compared to the CCMC (WT), sff (MT) exhibited reduced fruit length and increased dimeter. Segregation analysis revealed that the sff phenotype is controlled by a semi-dominant single gene with dosage effects. Through map-based cloning, the SFF locus was narrowed down to a 52.6 kb interval with two SNPs (G651A and C1072T) in the second and third exons of CsaV3_1G039870, which encodes an IQD family protein, CsSUN. The G651A within the IQ domain of CsSUN was identified as the unique SNP among 114 cucumber accessions, and it was the primary cause of the functional alteration in CsSUN. By generating CsSUN knockout lines in cucumber, we confirmed that CsSUN was responsible for sff mutant phenotype. The CsSUN is localized to the plasma membrane. CsSUN exhibited the highest expression in the fruit with lower expression in sff compared to WT. Histological observations suggest that the sff mutant phenotype is due to increased transverse cell division and inhibited longitudinal cell division. Transcriptome analysis revealed that CsSUN significantly affected the expression of genes related to cell division, expansion, and auxin signal transduction. This study unveils CsSUN's crucial role in shaping cucumber fruit and offers novel insights for cucumber breeding.
PMID: 38964612
Plant Sci , IF:4.729 , 2024 Sep , V346 : P112160 doi: 10.1016/j.plantsci.2024.112160
Integrating histology and phytohormone/metabolite profiling to understand rooting in yellow camellia cuttings.
Department of Biochemistry and Genetics, Clemson University, Clemson, SC 29634, United States.; D.W. Daniel High School, Central, SC 29630, United States.; Department of Biochemistry and Genetics, Clemson University, Clemson, SC 29634, United States. Electronic address: hliang@clemson.edu.
Vegetative propagation through cutting is a widely used clonal approach for maintaining desired genotypes. However, some woody species have difficulty forming adventitious roots (ARs) with this approach, including yellow camellia (YC) C. nitidissima. Yellow camellias, prized for their ornamental value and potential health benefits in tea, remain difficult to propagate clonally due to this rooting recalcitrance. As part of the efforts to understand YC cuttings' recalcitrance, we conducted a detailed investigation into AR formation in yellow camellia cuttings via histology and endogenous phytohormone dynamics during this process. We also compared YC endogenous phytohormone and metabolite phytohormone profiles with those of easy-to-root poplar and willow cuttings. Our results indicate that the induction of ARs in YC cuttings is achievable through auxin treatment, and YC ARs are initiated from cambial derivatives and develop a vascular system connected with that of the stem. During AR induction, endogenous hormones showed a dynamic profile, with IAA continuing to increase starting 9 days after auxin induction. JA, JA-Ile, and OPDA showed a similar trend as IAA but decreased by the 45th day. Cytokinin first decreased to its lowest level by the 18th day and then increased. SA largely exhibited an increasing trend with a drop on the 36th day, while ABA first increased to its peak level by the 18th day and then decreased. Compared to poplar, YC cuttings had a low level of IAA, IAA-Asp, and OPDA, and a high level of cytokinin and SA. Metabolite profiling highlighted significant down-accumulation of compounds associated with AR formation in yellow camellias, such as citric and ascorbic acid, fructose, sucrose, flavonoids, and phenolic acid derivatives. Our study reveals the unfavorable endogenous hormone and metabolite profiles underlying the rooting recalcitrance of YC cuttings, providing valuable knowledge for addressing this challenge in clonal propagation.
PMID: 38908800
Plant Sci , IF:4.729 , 2024 Sep , V346 : P112133 doi: 10.1016/j.plantsci.2024.112133
WUSCHEL RELATED HOMEOBOX5 and 7 maintain callus development by promoting cell division in Arabidopsis.
State Key Laboratory of Hybrid Rice, Institute for Advanced Studies (IAS), Wuhan University, Wuhan, Hubei 430072, China.; National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai 200032, China. Electronic address: zhaining@cemps.ac.cn.; State Key Laboratory of Hybrid Rice, Institute for Advanced Studies (IAS), Wuhan University, Wuhan, Hubei 430072, China. Electronic address: limin.pi@whu.edu.cn.
In tissue culture, a high concentration of auxin in the callus induction medium (CIM) stimulates cell division and subsequent callus formation, which acquires root primordium-like characteristics necessary for cell pluripotency. In Arabidopsis, WUSCHEL-RELATED HOMEOBOX5 (WOX5) and its closest homolog WOX7, which are abundant in the middle cell layer of mature callus, play a crucial role in maintaining pluripotency by promoting auxin accumulation and enhancing cytokinin sensitivity. However, the mechanism by which WOX5/7 regulate callus formation remains unclear. In this study, we found that mutations in WOX5/7 resulted in a significant down-regulation of genes involved in the G2M and S phases during callus induction. Loss-of-function mutants of WOX5/7 exhibited reduced callus formation, which was correlated with decreased expression of CYCB1;1 compared to the wild-type. Furthermore, we provided evidence that WOX5 physically interacts with PHYTOCHROME A SIGNAL TRANSDUCTION1 (PAT1), which spatio-temporally co-expresses with WOX5 in early-induced callus, and up-regulates a subset of cycle-regulating genes targeted by PAT1. Collectively, our findings suggest a critical role for the WOX5-PAT1 protein complex in regulating cell cycle progression, thereby promoting the continuous growth capacity of pluripotent callus.
PMID: 38795752
Analyst , IF:4.616 , 2024 Aug , V149 (17) : P4436-4442 doi: 10.1039/d4an00682h
Phenotyping of single plant cells on a microfluidic cytometry platform with fluorescent, mechanical, and electrical modules.
State Key Laboratory of Precision Measuring Technology and Instruments, College of Precision Instruments and Optoelectronics Engineering, Tianjin University, Weijin Rd. 92, Tianjin 300072, China. xduan@tju.edu.cn.; School of Environmental Science and Engineering, Tianjin University, Weijin Rd. 92, Tianjin 300072, China. jiehuawang@tju.edu.cn.
Compared to animal cells, phenotypic characterization of single plant cells on microfluidic platforms is still rare. In this work, we collated population statistics on the morphological, biochemical, physical and electrical properties of Arabidopsis protoplasts under different external and internal conditions, using progressively improved microfluidic platforms. First, we analyzed the different effects of three phytohormones (auxin, cytokinin and gibberellin) on the primary cell wall (PCW) regeneration process using a microfluidic flow cytometry platform equipped with a single-channel fluorescence sensor. Second, we correlated the intracellular reactive oxygen species (ROS) level induced by heavy metal stress with the concurrent PCW regeneration process by using a dual-channel fluorescence sensor. Third, by integrating contraction channels, we were able to effectively discriminate variations in cell size while monitoring the intensity of intracellular ROS signaling. Fourth, by combining an electrical impedance electrode with the contraction channel, we analyzed the differences in electrical and mechanical properties of wild-type and mutant plant cells before and after primary cell wall regeneration. Overall, our work demonstrates the feasibility and sensitivity of microfluidic flow cytometry in high-throughput phenotyping of plant cells and provides a reference for assessing metabolic and physiological indicators of individual plant cells in multiple dimensions.
PMID: 39015957
Front Genet , IF:4.599 , 2024 , V15 : P1419399 doi: 10.3389/fgene.2024.1419399
Transcriptomic analysis for the gamma-ray-induced sweetpotato mutants with altered stem growth pattern.
Department of Agriculture, Forestry and Bioresources and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea.; Bioenergy Crop Research Institute, National Institute of Crop Science, Rural Development Administration, Muan, Republic of Korea.; Department of Forest Resources, College of Forest and Environmental Sciences, Kangwon National University, Chuncheon, Republic of Korea.; Bioinformatics Institute, Macrogen Inc., Seoul, Republic of Korea.; Plant Genomics and Breeding Institute, Seoul National University, Seoul, Republic of Korea.
INTRODUCTION: Sweetpotato faces breeding challenges due to physiological and genomic issues. Gamma radiation is a novel approach for inducing genetic variation in crops. We analyzed the transcriptomic changes in gamma ray-induced sweetpotato mutants with altered stem development compared with those in the wild-type 'Tongchaeru' cultivar. METHODS: RNA sequencing analyses were performed to identify changes in the expression of genes related to stem development. RESULTS: Transcriptomic analysis identified 8,931 upregulated and 6,901 downregulated genes, including the upregulation of the auxin-responsive SMALL AUXIN UP RNA (SAUR) and three PHYTOCHROME INTERACTING FACTOR 4 (PIF4) genes. PIF4 is crucial for regulating the expression of early auxin-responsive SAUR genes and stem growth in Arabidopsis thaliana. In the mutant, several genes related to stem elongation, including PIF4 and those involved in various signaling pathways such as auxin and gibberellin, were upregulated. DISCUSSION: Our results suggest that gamma ray-induced mutations influence auxin-dependent stem development by modulating a complex regulatory network involving the expression of PIF4 and SAUR genes, and other signaling pathways such as gibberellin and ethylene signaling genes. This study enhances our understanding of the regulatory mechanisms underlying stem growth in sweetpotato, providing valuable insights for genomics-assisted breeding efforts.
PMID: 39144719
Plant Cell Rep , IF:4.57 , 2024 Aug , V43 (9) : P212 doi: 10.1007/s00299-024-03293-w
Auxin responsive factor MdARF17 promotes ethylene synthesis in apple fruits by activating MdERF003 expression.
College of Horticulture Sciences, Shandong Agricultural University, No. 61 Daizong Road, Tai'an, 271018, Shandong, China.; College of Horticulture, Northwest A&F University, Yangling, 712100, Shanxi, China.; Jiushan Town Agricultural Comprehensive Service Center, Weifang, 262608, Shandong, China.; College of Horticulture Sciences, Shandong Agricultural University, No. 61 Daizong Road, Tai'an, 271018, Shandong, China. zongyingzhang@sdau.edu.cn.; College of Horticulture Sciences, Shandong Agricultural University, No. 61 Daizong Road, Tai'an, 271018, Shandong, China. chenxs@sdau.edu.cn.
Auxin (AUX) promotion of apple fruit ripening is ethylene-dependent, and AUX-MdARF17-MdERF003 plays a role in AUX-promoted ethylene synthesis in apple. Phytohormones play important roles in plant growth and fleshy fruit ripening, and the phytohormone auxin (AUX) can either promote or inhibit the ripening of fleshy fruits. Although AUX can influence ethylene (ETH) synthesis in apple (Malus domestica) fruits by affecting ETH system II, this mechanism remains to be explored. Here, we identified an ETH response factor (ERF) family transcription factor, MdERF003, whose expression could be activated by naphthalene acetic acid. The transient silencing of MdERF003 inhibited ETH synthesis in fruits, and MdERF003 could bind to the MdACS1 promoter. To explore the upstream target genes of MdERF003, we screened the MdARF family members by yeast one-hybrid assays of the MdERF003 promoter, and found that the transcription factor MdARF17, which showed AUX-promoted expression, could bind to the MdERF003 promoter and promote its expression. Finally, we silenced MdERF003 in apple fruits overexpressing MdARF17 and found that MdERF003 plays a role in MdARF17-promoted ETH synthesis in apple. Thus, AUX-MdARF17-MdERF003 promotes ETH synthesis in apple fruits.
PMID: 39127969
Plant Physiol Biochem , IF:4.27 , 2024 Aug , V215 : P109055 doi: 10.1016/j.plaphy.2024.109055
Target of rapamycin coordinates auxin are involved in exogenous melatonin regulated low temperature tolerance in cucumber seedlings.
College of Life Sciences, Northwest Normal University, Lanzhou, 730070, China.; College of Life Sciences, Northwest Normal University, Lanzhou, 730070, China. Electronic address: zhangtengguo@163.com.
Low temperature (LT) is an important environmental factor affecting the growth and yield of plants. Melatonin (MT) can effectively enhance the LT tolerance of cucumber. This study found that LT stress induced the expression of Comt1 (caffeic acid O-methyltransferase 1), with the highest expression being about 2-times that of the control. Meanwhile, the content of MT was found to be roughly 63.16% of that in the control samples. Compared with LT treatment alone, exogenous MT pretreatment upregulated the expression levels of TOR (Target of rapamycin), PIN1 (Pin-formed 1), and YUC4 (YUCCA 4), with maximum upregulations reaching approximately 66.67%, 79.32%, and 42.86%, respectively. These results suggest that MT may modulate the tolerance of cucumber seedlings to LT stress by regulating the expression of TOR, PIN1, and YUC4. In addition, co-treatment with AZD-8055 (a TOR inhibitor) or NPA (N-1-naphthylphthalamic acid, an auxin polar transport inhibitor) and MT attenuated MT-induced resistance to LT stress, leading to higher levels of reactive oxygen species (ROS), reduced antioxidant defense capacity, and increased damage to the membrane system in cucumber seedlings. Concurrently, the content of osmoregulatory substances and the photosynthesis decreased. These results demonstrate that both TOR and auxin were required for MT to alleviate LT-induced damage in cucumber. In summary, the present study demonstrates that TOR and auxin signaling synergistically contribute to alleviating LT damage in cucumber seedlings by exogenous MT. These findings help us understand the function of MT and provide insights into the regulatory network of MT that regulates the LT tolerance of plants.
PMID: 39182426
Plant Physiol Biochem , IF:4.27 , 2024 Aug , V215 : P109027 doi: 10.1016/j.plaphy.2024.109027
Genome-wide analysis of Citrus medica ABC transporters reveals the regulation of fruit development by CmABCB19 and CmABCC10.
State Key Laboratory for Quality Ensurance and Sustainable Use of Dao-di Herbs, Experimental Research Center, Chinese Academy of Chinese Medical Sciences (CACMS), Beijing, China; National Resource Center for Chinese Materia Medica, Chinese Academy of Chinese Medical Sciences (CACMS), Beijing, China. Electronic address: adazbd@163.com.; State Key Laboratory for Quality Ensurance and Sustainable Use of Dao-di Herbs, Experimental Research Center, Chinese Academy of Chinese Medical Sciences (CACMS), Beijing, China; National Resource Center for Chinese Materia Medica, Chinese Academy of Chinese Medical Sciences (CACMS), Beijing, China.; Co-construction Collaborative Innovation Center for Chinese Medicine Resources Industrialization by Shaanxi & Education Ministry, Shaanxi University of Chinese Medicine, Xianyang, China. Electronic address: jhh211411@163.com.; State Key Laboratory for Quality Ensurance and Sustainable Use of Dao-di Herbs, Experimental Research Center, Chinese Academy of Chinese Medical Sciences (CACMS), Beijing, China.; State Key Laboratory for Quality Ensurance and Sustainable Use of Dao-di Herbs, Experimental Research Center, Chinese Academy of Chinese Medical Sciences (CACMS), Beijing, China; National Resource Center for Chinese Materia Medica, Chinese Academy of Chinese Medical Sciences (CACMS), Beijing, China. Electronic address: y_yuan0732@163.com.
ATP-binding cassette (ABC) transporters are vital for plant growth and development as they facilitate the transport of essential molecules. Despite the family's significance, limited information exists about its functional distinctions in Citrus medica. Our study identified 119 genes encoding ABC transporter proteins in the C. medica genome. Through an evolutionary tree and qPCR analysis, two ABC genes, CmABCB19 and CmABCC10, were implicated in C. medica fruit development, showing upregulation in normal fruits compared to malformed fruits. CmABCB19 was found to localize to the plasma membrane of Nicotiana tabacum, exhibiting indole-3-acetic acid (IAA) efflux activity in the yeast mutant strain yap1. CmABCC10, a tonoplast-localized transporter, exhibited efflux of diosmin, nobiletin, and naringin, with rutin influx in strain ycf1. Transgenic expression of CmABCB19 and CmABCC10 in Arabidopsis thaliana induced alterations in auxin and flavonoid content, impacting silique and seed size. This effect was attributed to the modulation of structural genes in the auxin biosynthesis (YUC5/9, CYP79B2, CYP83B1, SUR1) and flavonoid biosynthesis (4CL2/3, CHS, CHI, FLS1/3) pathways. In summary, the functional characterization of CmABCB19 and CmABCC10 illuminates auxin and flavonoid transport, offering insights into their interplay with biosynthetic pathways and providing a foundation for understanding the transporter's role in fruit development.
PMID: 39154422
Plant Physiol Biochem , IF:4.27 , 2024 Aug , V215 : P109031 doi: 10.1016/j.plaphy.2024.109031
PGPR isolated from hot spring imparts resilience to drought stress in wheat (Triticum aestivum L.).
CSIR- Institute of Himalayan Bioresource Technology, Palampur, 176061, HP, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India.; CSIR- Institute of Himalayan Bioresource Technology, Palampur, 176061, HP, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India. Electronic address: aparna@ihbt.res.in.
Drought is a major abiotic stress that occurs frequently due to climate change, severely hampers agricultural production, and threatens food security. In this study, the effect of drought-tolerant PGPRs, i.e., PGPR-FS2 and PGPR-VHH4, was assessed on wheat by withholding water. The results indicate that drought-stressed wheat seedlings treated with PGPRs-FS2 and PGPR-VHH4 had a significantly higher shoot and root length, number of roots, higher chlorophyll, and antioxidant enzymatic activities of guaiacol peroxidase (GPX) compared to without PGPR treatment. The expression study of wheat genes related to tryptophan auxin-responsive (TaTAR), drought-responsive (TaWRKY10, TaWRKY51, TaDREB3, and TaDREB4) and auxin-regulated gene organ size (TaARGOS-A, TaARGOS-B, and TaARGOS-D) exhibited significantly higher expression in the PGPR-FS2 and PGPR-VHH4 treated wheat under drought as compared to without PGPR treatment. The results of this study illustrate that PGPR-FS2 and PGPR-VHH4 mitigate the drought stress in wheat and pave the way for imparting drought in wheat under water deficit conditions. Among the two PGPRs, PGPR-VHH4 more efficiently altered the root architecture to withstand drought stress.
PMID: 39137684
Plant Physiol Biochem , IF:4.27 , 2024 Sep , V214 : P108972 doi: 10.1016/j.plaphy.2024.108972
Overexpression of EgrZFP6 from Eucalyptus grandis increases ROS levels by downregulating photosynthesis in plants.
State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, Zhejiang, 311300, China. Electronic address: ljcheng@zju.edu.cn.; State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, Zhejiang, 311300, China.; State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, Zhejiang, 311300, China. Electronic address: xfwang@zafu.edu.cn.
In plants, abiotic stressors are frequently encountered during growth and development. To counteract these challenges, zinc finger proteins play a critical role as transcriptional regulators. The EgrZFP6 gene, which codes for a zinc finger protein of the C2H2 type, was shown to be considerably elevated in the leaves of Eucalyptus grandis seedlings in the current study when they were subjected to a variety of abiotic stimuli, including heat, salinity, cold, and drought. Analysis conducted later showed that in EgrZFP6 transgenic Arabidopsis thaliana, EgrZFP6 was essential for causing hyponastic leaves and controlling the stress response. Furthermore, the transgenic plants showed elevated levels of reactive oxygen species (ROS), such as superoxide and hydrogen peroxide (H(2)O(2)). Additionally, in EgrZFP6-overexpressing plants, transcriptome sequencing analysis demonstrated a considerable downregulation of many genes involved in photosynthesis, decreasing electron transport efficiency and perhaps promoting the buildup of ROS. Auxin levels were higher and auxin signal transduction was compromised in the transgenic plants. Stress-related genes were also upregulated in Arabidopsis as a result of EgrZFP6 overexpression. It is hypothesized that EgrZFP6 can downregulate photosynthesis, which would cause the production of ROS in chloroplasts. As a result, this protein may alter plant stress responses and leaf morphology via a retrograde mechanism driven by ROS. These results highlight the significance of zinc finger proteins in this sophisticated process and advance our understanding of the complex link between gene regulation, ROS signaling, and plant stress responses.
PMID: 39067106
Plant Physiol Biochem , IF:4.27 , 2024 Sep , V214 : P108930 doi: 10.1016/j.plaphy.2024.108930
Selenite improves growth by modulating phytohormone pathways and reprogramming primary and secondary metabolism in tomato plants.
College of Horticulture, Shanxi Agricultural University, Taigu, 030801, China; Shanxi Key Laboratory of Germplasm Resources Innovation and Utilization of Vegetable and Flower, Taiyuan, 030031, China.; College of Horticulture, Shanxi Agricultural University, Taigu, 030801, China; Shanxi Key Laboratory of Germplasm Resources Innovation and Utilization of Vegetable and Flower, Taiyuan, 030031, China. Electronic address: xujin@sxau.edu.cn.
Selenium (Se) is an essential micronutrient in organisms that has a significant impact on physiological activity and gene expression in plants, thereby affecting growth and development. Humans and animals acquire Se from plants. Tomato (Solanum lycopersicum L.) is an important vegetable crop worldwide. Improving the Se nutrient level not only is beneficial for growth, development and stress resistance in tomato plants but also contributes to improving human health. However, the molecular basis of Se-mediated tomato plant growth has not been fully elucidated. In this study, using physiological and transcriptomic analyses, we investigated the effects of a low dosage of selenite [Se(â…£)] on tomato seedling growth. Se(IV) enhanced the photosynthetic efficiency and increased the accumulation of soluble sugars, dry matter and organic matter, thereby promoting tomato plant growth. Transcriptome analysis revealed that Se(IV) reprogrammed primary and secondary metabolic pathways, thus modulating plant growth. Se(IV) also increased the concentrations of auxin, jasmonic acid and salicylic acid in leaves and the concentration of cytokinin in roots, thus altering phytohormone signaling pathways and affecting plant growth and stress resistance in tomato plants. Furthermore, exogenous Se(IV) alters the expression of genes involved in flavonoid biosynthesis, thereby modulating plant growth and development in tomato plants. Taken together, these findings provide important insights into the regulatory mechanisms of low-dose Se(IV) on tomato growth and contribute to the breeding of Se-accumulating tomato cultivars.
PMID: 39013356
Plant Physiol Biochem , IF:4.27 , 2024 Aug , V213 : P108720 doi: 10.1016/j.plaphy.2024.108720
Synergy of plant growth promoting rhizobacteria and silicon in regulation of AgNPs induced stress of rice seedlings.
Department of Biotechnology, Motilal Nehru National Institute of Technology Allahabad, Prayagraj, 211004, UP, India.; Crop Nanobiology and Molecular Stress Physiology Lab, Amity Institute of Organic Agriculture, Amity University Uttar Pradesh, Sector-125, Noida, 201313, India.; Department of Biotechnology, Motilal Nehru National Institute of Technology Allahabad, Prayagraj, 211004, UP, India. Electronic address: shiveshs@mnnit.ac.in.
Silver Nanoparticles (AgNPs), as an emerging pollutant, have been receiving significant attention as they deepen the concern regarding the issue of food security. Silicon (Si) and plant growth-promoting rhizobacteria (PGPR) are likely to serve as a sustainable approach to ameliorating abiotic stress and improving plant growth through various mechanisms. The present study aims to evaluate the synergistic effect of Si and PGPRs on growth, physiological, and molecular response in rice seedlings (Oryza sativa) under AgNPs stress. Data suggested that under AgNPs exposure, the root and shoot growth, photosynthetic pigments, antioxidant enzymes (CAT and APX), expression of antioxidant genes (OsAPX and OsGR), silicon transporter (OsLsi2), and auxin hormone-related genes (OsPIN10 and OsYUCCA1) were significantly decreased which accompanied with the overproduction of reactive oxygen species (ROS), nitric oxide (NO) and might be due to higher accumulation of Ag in plant cells. Interestingly, the addition of Si along with the AgNPs enhances the level of ROS generation, thus oxidative stress, which causes severe damage in all the above-tested parameters. On the other hand, application of PGPR alone and along with Si reduced the toxic effect of AgNPs through the improvement of growth, biochemical, and gene regulation (OsAPX and OsGR, OsPIN10 and OsYUCCA1). However, the addition of L-NAME along with PGPR and silicon drastically lowered the AgNPs induced toxicity through lowering the oxidative stress and maintained the overall growth of rice seedlings, which suggests the role of endogenous NO in Si and PGPRs mediated management of AgNPs toxicity in rice seedlings.
PMID: 38901227
Plant Physiol Biochem , IF:4.27 , 2024 Aug , V213 : P108827 doi: 10.1016/j.plaphy.2024.108827
Genomic analysis of PIN-FORMED genes reveals the roles of SmPIN3 in root architecture development in Salvia miltiorrhiza.
College of Bioscience and Biotechnology, Yangzhou University, Yangzhou, Jiangsu, 225009, China.; College of Bioscience and Biotechnology, Yangzhou University, Yangzhou, Jiangsu, 225009, China; Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China.; Key Laboratory of Plant Secondary Metabolism and Regulation of Zhejiang Province, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, Zhejiang, 310018, China.; College of Bioscience and Biotechnology, Yangzhou University, Yangzhou, Jiangsu, 225009, China. Electronic address: zhangsc@yzu.edu.cn.
Salvia miltiorrhiza is a widely utilized medicinal herb in China. Its roots serve as crucial raw materials for multiple drugs. The root morphology is essential for the quality of this herb, but little is known about the molecular mechanism underlying the root development in S. miltiorrhiza. Previous study reveals that the polar auxin transport is critical for lateral root development in S. miltiorrhiza. Whether the auxin efflux carriers PIN-FORMEDs (PINs) are involved in this process is worthy investigation. In this study, we identified nine SmPIN genes in S. miltiorrhiza, and their chromosome localization, physico-chemical properties, and phylogenetic relationship were analyzed. SmPINs were unevenly distributed across four chromosomes, and a variety of hormone responsive elements were detected in their promoter regions. The SmPIN proteins were divided into three branches according to the phylogenetic relationship. SmPINs with close evolutionary distance showed similar conserved motif features. The nine SmPINs showed distinct tissue-specific expression patterns and most of them were auxin-inducible genes. We generated SmPIN3 overexpression S. miltiorrhiza seedlings to investigate the function of SmPIN3 in the root development in this species. The results demonstrated that SmPIN3 regulated the root morphogenesis of S. miltiorrhiza by simultaneously affecting the lateral root development and the root anatomical structure. The root morphology, patterns of root xylem and phloem as well as the expressions of genes in the auxin signaling pathway all altered in the SmPIN3 overexpression lines. Our findings provide new insights for elucidating the regulatory roles of SmPINs in the auxin-mediated root development in S. miltiorrhiza.
PMID: 38875779
Plant Physiol Biochem , IF:4.27 , 2024 Aug , V213 : P108813 doi: 10.1016/j.plaphy.2024.108813
Plastid dynamism integrates development and environment.
Department of Environmental Biology, Sapienza University of Rome, Italy. Electronic address: mariamaddalena.altamura@uniroma1.it.; Department of Environmental Biology, Sapienza University of Rome, Italy.
In land plants plastid type differentiation occurs concomitantly with cellular differentiation and the transition from one type to another is under developmental and environmental control. Plastid dynamism is based on a bilateral communication between plastids and nucleus through anterograde and retrograde signaling. Signaling occurs through the interaction with specific phytohormones (abscisic acid, strigolactones, jasmonates, gibberellins, brassinosteroids, ethylene, salicylic acid, cytokinin and auxin). The review is focused on the modulation of plastid capabilities at both transcriptional and post-translational levels at the crossroad between development and stress, with a particular attention to the chloroplast, because the most studied plastid type. The role of plastid-encoded and nuclear-encoded proteins for plastid development and stress responses, and the changes of plastid fate through the activity of stromules and plastoglobules, are discussed. Examples of plastid dynamism in response to soil stress agents (salinity, lead, cadmium, arsenic, and chromium) are described. Albinism and root greening are described based on the modulation activities of auxin and cytokinin. The physiological and functional responses of the sensory epidermal and vascular plastids to abiotic and biotic stresses along with their specific roles in stress sensing are described together with their potential modulation of retrograde signaling pathways. Future research perspectives include an in-depth study of sensory plastids to explore their potential for establishing a transgenerational memory to stress. Suggestions about anterograde and retrograde pathways acting at interspecific level and on the lipids of plastoglobules as a novel class of plastid morphogenic agents are provided.
PMID: 38861821
BMC Plant Biol , IF:4.215 , 2024 Aug , V24 (1) : P762 doi: 10.1186/s12870-024-05461-2
Genome-wide identification of Ankyrin (ANK) repeat gene families in three Dendrobium species and the expression of ANK genes in D. officinale under gibberellin and abscisic acid treatments.
College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China.; Jiangsu Provincial Engineering Research Center for Technical Industrialization of Dendrobiums, Nanjing, China.; College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China. dingxynj@263.net.; Jiangsu Provincial Engineering Research Center for Technical Industrialization of Dendrobiums, Nanjing, China. dingxynj@263.net.
BACKGROUND: Dendrobium Sw. represents one of the most expansive genera within the Orchidaceae family, renowned for its species' high medicinal and ornamental value. In higher plants, the ankyrin (ANK) repeat protein family is characterized by a unique ANK repeat domain, integral to a plethora of biological functions and biochemical activities. The ANK gene family plays a pivotal role in various plant physiological processes, including stress responses, hormone signaling, and growth. Hence, investigating the ANK gene family and identifying disease-resistance genes in Dendrobium is of paramount importance. RESULTS: This research identified 78 ANK genes in Dendrobium officinale Kimura et Migo, 77 in Dendrobium nobile Lindl., and 58 in Dendrobium chrysotoxum Lindl. Subsequently, we conducted comprehensive bioinformatics analyses on these ANK gene families, encompassing gene classification, chromosomal localization, phylogenetic relationships, gene structure and motif characterization, cis-acting regulatory element identification, collinearity assessment, protein-protein interaction network construction, and gene expression profiling. Concurrently, three DoANK genes (DoANK14, DoANK19, and DoANK47) in D. officinale were discerned to indirectly activate the NPR1 transcription factor in the ETI system via SA, thereby modulating the expression of the antibacterial PR gene. Hormonal treatments with GA(3) and ABA revealed that 17 and 8 genes were significantly up-regulated, while 4 and 8 genes were significantly down-regulated, respectively. DoANK32 was found to localize to the ArfGAP gene in the endocytosis pathway, impacting vesicle transport and the polar movement of auxin. CONCLUSION: Our findings provide a robust framework for the taxonomic classification, evolutionary analysis, and functional prediction of Dendrobium ANK genes. The three highlighted ANK genes (DoANK14, DoANK19, and DoANK47) from D. officinale may prove valuable in disease resistance and stress response research. DoANK32 is implicated in the morphogenesis and development of D. officinale through its role in vesicular transport and auxin polarity, with subcellular localization studies confirming its presence in the nucleus and cell membrane. ANK genes displaying significant expression changes in response to hormonal treatments could play a crucial role in the hormonal response of D. officinale, potentially inhibiting its growth and development through the modulation of plant hormones such as GA(3) and ABA.
PMID: 39123107
BMC Plant Biol , IF:4.215 , 2024 Aug , V24 (1) : P758 doi: 10.1186/s12870-024-05474-x
Ultrasonic treatment can improve maize seed germination and abiotic stress resistance.
Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Zhongguancun South Street No. 12, Haidian District, Beijing, 100081, China.; National Agro-tech Extension and Service Center, Beijing, 100125, China.; Guangzhou Jindao Agricultural Technology Co., Ltd, Guangzhou, 510940, China.; Shandong Agri-tech Extension Center, Jiefang Road No. 15, Lixia District, Jinan, 250013, China. whan01@163.com.; Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Zhongguancun South Street No. 12, Haidian District, Beijing, 100081, China. lvguohua@caas.cn.; Institute of Dongying Shengli Salt Alkali Agriculture Industrialization and Technology Research, Dongying, 257000, China. lvguohua@caas.cn.
Constant-frequency ultrasonic treatment helped to improve seed germination. However, variable-frequency ultrasonic treatment on maize seed germination were rarely reported. In this study, maize seeds were exposed to 20-40 kHz ultrasonic for 40 s. The germination percentage and radicle length of maize seeds increased by 10.4% and 230.5%. Ultrasonic treatment also significantly increased the acid protease, alpha-amylase, and beta-amylase contents by 96.4%, 73.8%, and 49.1%, respectively. Transcriptome analysis showed that 11,475 differentially expressed genes (DEGs) were found in the ultrasonic treatment and control groups, including 5,695 upregulated and 5,780 downregulated. Metabolic pathways and transcription factors (TFs) were significantly enriched among DEGs after ultrasonic treatment. This included metabolism and genetic information processing, that is, ribosome, proteasome, and pyruvate metabolism, sesquiterpenoid, triterpenoid, and phenylpropanoid biosynthesis, and oxidative phosphorylation, as well as transcription factors in the NAC, MYB, bHLH, WRKY, AP2, bZIP, and ARF families. Variable-frequency ultrasonic treatment increased auxin, gibberellin, and salicylic acid by 5.5%, 37.3%, and 28.9%, respectively. Abscisic acid significantly decreased by 33.2%. The related DEGs were upregulated and downregulated to varying degrees. Seed germination under the abiotic stress conditions of salt stress (NaCl solution), drought (PEG solution), and waterlogging (water-saturated sand bed) under ultrasonic treatment were promoted, radicle length was significantly increased by 30.2%, 30.5%, and 27.3%, respectively; and germination percentage by 14.8%, 20.1%, and 21.6%, respectively. These findings provide new insight into the mechanisms through ultrasonic to promote maize seed germination.
PMID: 39112960
BMC Plant Biol , IF:4.215 , 2024 Aug , V24 (1) : P734 doi: 10.1186/s12870-024-05442-5
Overexpression of MtIPT gene enhanced drought tolerance and delayed leaf senescence of creeping bentgrass (Agrostis stolonifera L.).
School of Grassland Science of Beijing Forestry University, Beijing, China.; Engineering and Technology Research Center for Sports Field and Slope Protection Turf, National Forestry and Grassland Administration, Beijing, China.; UWA School of Agriculture and Environment, The UWA Institute of Agriculture, The University of Western Australia, Perth, WA, Australia.; Shenzhen Tidyfield System Biotechnology Co., Ltd, Shenzhen, China.; College of Agronomy, State Key Laboratory of North China Crop Improvement and Regulation/Key Laboratory of Crop Growth Regulation of Hebei Province, Hebei Agricultural University, Baoding, China.; School of Grassland Science of Beijing Forestry University, Beijing, China. hanliebao@163.com.; Engineering and Technology Research Center for Sports Field and Slope Protection Turf, National Forestry and Grassland Administration, Beijing, China. hanliebao@163.com.; School of Grassland Science of Beijing Forestry University, Beijing, China. chaoyuehui@bjfu.edu.cn.; Engineering and Technology Research Center for Sports Field and Slope Protection Turf, National Forestry and Grassland Administration, Beijing, China. chaoyuehui@bjfu.edu.cn.
BACKGROUND: Isopentenyltransferases (IPT) serve as crucial rate-limiting enzyme in cytokinin synthesis, playing a vital role in plant growth, development, and resistance to abiotic stress. RESULTS: Compared to the wild type, transgenic creeping bentgrass exhibited a slower growth rate, heightened drought tolerance, and improved shade tolerance attributed to delayed leaf senescence. Additionally, transgenic plants showed significant increases in antioxidant enzyme levels, chlorophyll content, and soluble sugars. Importantly, this study uncovered that overexpression of the MtIPT gene not only significantly enhanced cytokinin and auxin content but also influenced brassinosteroid level. RNA-seq analysis revealed that differentially expressed genes (DEGs) between transgenic and wild type plants were closely associated with plant hormone signal transduction, steroid biosynthesis, photosynthesis, flavonoid biosynthesis, carotenoid biosynthesis, anthocyanin biosynthesis, oxidation-reduction process, cytokinin metabolism, and wax biosynthesis. And numerous DEGs related to growth, development, and stress tolerance were identified, including cytokinin signal transduction genes (CRE1, B-ARR), antioxidase-related genes (APX2, PEX11, PER1), Photosynthesis-related genes (ATPF1A, PSBQ, PETF), flavonoid synthesis genes (F3H, C12RT1, DFR), wax synthesis gene (MAH1), senescence-associated gene (SAG20), among others. CONCLUSION: These findings suggest that the MtIPT gene acts as a negative regulator of plant growth and development, while also playing a crucial role in the plant's response to abiotic stress.
PMID: 39085786
FEBS Lett , IF:4.124 , 2024 Aug , V598 (15) : P1855-1863 doi: 10.1002/1873-3468.14908
l-2-Aminopimelic acid acts as an auxin mimic to induce lateral root formation across diverse plant species.
RIKEN Center for Sustainable Resource Science, Yokohama, Japan.; Department of Applied Biosciences, Graduate School of Bioagricultural Science, Nagoya University, Japan.
The identification of chemicals that modulate plant development and adaptive responses to stresses has attracted increasing attention for agricultural applications. Recent basic studies have identified functional amino acids that are essential for plant organogenesis, indicating that amino acids can regulate plant growth. In this study, we newly identified 2-aminopimelic acid (2APA), a nonproteinogenic amino acid, as a novel bioactive compound involved in root morphogenesis. This biological effect was confirmed in several plant species. Our phenotypic analysis revealed that the bioactive 2APA is an l-form stereoisomer. Overall, our study identified a promising root growth regulator and provided insight into the intricate metabolism related to root morphology.
PMID: 38782630
Planta , IF:4.116 , 2024 Aug , V260 (3) : P74 doi: 10.1007/s00425-024-04507-x
Phenotypic and transcriptomics characterization uncovers genes underlying tuber yield traits and gene expression marker development in potato under aeroponics.
Indian Council of Agricultural Research-Central Potato Research Institute, Shimla, Himachal Pradesh, India.; School of Bioengineering and Biosciences, Lovely Professional University, Phagwara, Punjab, India.; Indian Council of Agricultural Research-Central Potato Research Institute, Shimla, Himachal Pradesh, India. jagesh.kumar@icar.gov.in.; Indian Council of Agricultural Research- Indian Institute of Vegetable Research, Varanasi, Uttar Pradesh, India. jagesh.kumar@icar.gov.in.; Indian Council of Agricultural Research- Indian Institute of Vegetable Research, Varanasi, Uttar Pradesh, India.
Transcriptome analysis in potato varieties revealed genes associated with tuber yield-related traits and developed gene expression markers. This study aimed to identify genes involved in high tuber yield and its component traits in test potato varieties (Kufri Frysona, Kufri Khyati, and Kufri Mohan) compared to control (Kufri Sutlej). The aeroponic evaluation showed significant differences in yield-related traits in the varieties. Total RNA sequencing was performed using tuber and leaf tissues on the Illumina platform. The high-quality reads (QV > 25) mapping with the reference potato genomes revealed statistically significant (P < 0.05) differentially expressed genes (DEGs) into two categories: up-regulated (> 2 Log(2) fold change) and down-regulated (< -2 Log(2) fold change). DEGs were characterized by Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. Collectively, we identified genes participating in sugar metabolism, stress response, transcription factors, phytohormones, kinase proteins, and other genes greatly affecting tuber yield and its related traits. A few selected genes were UDP-glucose glucosyltransferase, glutathion S-transferase, GDSL esterase/lipase, transcription factors (MYB, WRKY, bHLH63, and BURP), phytohormones (auxin-induced protein X10A, and GA20 oxidase), kinase proteins (Kunitz-type tuber invertase inhibitor, BRASSINOSTEROID INSENSITIVE 1-associated receptor kinase 1) and laccase. Based on the selected 17 peptide sequences representing 13 genes, a phylogeny tree and motifs were analyzed. Real time-quantitative polymerase chain reaction (RT-qPCR) analysis was used to validate the RNA-seq results. RT-qPCR based gene expression markers were developed for the genes such as 101 kDa heat shock protein, catechol oxidase B chloroplastic, cysteine protease inhibitor 1, Kunitz-type tuber invertase inhibitor, and laccase to identify high yielding potato genotypes. Thus, our study paved the path for potential genes associated with tuber yield traits in potato under aeroponics.
PMID: 39153022
Genes (Basel) , IF:4.096 , 2024 Aug , V15 (8) doi: 10.3390/genes15081042
Molecular Manipulation of the miR160/AUXIN RESPONSE FACTOR Expression Module Impacts Root Development in Arabidopsis thaliana.
Centre for Plant Science, School of Environmental and Life Sciences, College of Engineering, Science and Environment University of Newcastle, Callaghan, NSW 2308, Australia.; Research School of Biology, Australian National University, Canberra, ACT 2601, Australia.; CSIRO Agriculture and Food, Canberra, ACT 2601, Australia.; School of Agriculture and Food Sustainability, The University of Queensland, St Lucia, QLD 4072, Australia.; Seaweed Research Group, School of Health, University of the Sunshine Coast, Maroochydore, QLD 4558, Australia.
In Arabidopsis thaliana (Arabidopsis), microRNA160 (miR160) regulates the expression of AUXIN RESPONSE FACTOR10 (ARF10), ARF16 and ARF17 throughout development, including the development of the root system. We have previously shown that in addition to DOUBLE-STRANDED RNA BINDING1 (DRB1), DRB2 is also involved in controlling the rate of production of specific miRNA cohorts in the tissues where DRB2 is expressed in wild-type Arabidopsis plants. In this study, a miR160 overexpression transgene (MIR160B) and miR160-resistant transgene versions of ARF10 and ARF16 (mARF10 and mARF16) were introduced into wild-type Arabidopsis plants and the drb1 and drb2 single mutants to determine the degree of requirement of DRB2 to regulate the miR160 expression module as part of root development. Via this molecular modification approach, we show that in addition to DRB1, DRB2 is required to regulate the level of miR160 production from its precursor transcripts in Arabidopsis roots. Furthermore, we go on to correlate the altered abundance of miR160 or its ARF10, ARF16 and ARF17 target genes in the generated series of transformant lines with the enhanced development of the root system displayed by these plant lines. More specifically, promotion of primary root elongation likely stemmed from enhancement of miR160-directed ARF17 expression repression, while the promotion of lateral and adventitious root formation was the result of an elevated degree of miR160-directed regulation of ARF17 expression, and to a lesser degree, ARF10 and ARF16 expression. Taken together, the results presented in this study identify the requirement of the functional interplay between DRB1 and DRB2 to tightly control the rate of miR160 production, to in turn ensure the appropriate degree of miR160-directed ARF10, ARF16 and ARF17 gene expression regulation as part of normal root system development in Arabidopsis.
PMID: 39202402
Plant Genome , IF:4.089 , 2024 Aug : Pe20504 doi: 10.1002/tpg2.20504
Genome-wide analysis of HD-Zip genes in Sophora alopecuroides and their role in salt stress response.
College of Biological and Agricultural Engineering, Jilin University, Changchun, China.; College of Plant Science, Jilin University, Changchun, China.
We aimed to identify HD-Zip (homologous domain leucine zipper) family genes based on the complete Sophora alopecuroides genome sequence. Eighty-six Sophora alopecuroides HD-Zip family (SaHDZ) genes were identified and categorized into four subclasses using phylogenetic analysis. Chromosome localization analysis revealed that these genes were distributed across 18 chromosomes. Gene structure and conserved motif analysis showed high similarity among members of the SaHDZ genes. Prediction analysis revealed 71 cis-acting elements in SaHDZ genes. Transcriptome and quantitative real-time polymerase chain reaction analyses showed that under salt stress, SaHDZ responded positively in S. alopecuroides, and that SaHDZ22 was significantly upregulated afterward. Functional verification experiments revealed that SaHDZ22 overexpression increased the tolerance of Arabidopsis to salt and osmotic stress. Combined with cis-acting element prediction and expression level analysis, HD-Zip family transcription factors may be involved in regulating the balance between plant growth and stress resistance under salt stress by modulating the expression of auxin and abscisic acid signaling pathway genes. The Sophora alopecuroides adenylate kinase protein (SaAKI) and S. alopecuroides tetrapeptide-like repeat protein (SaTPR; pCAMBIA1300-SaTPR-cLUC) expression levels were consistent with those of SaHDZ22, indicating that SaHDZ22 may coordinate with SaAKI and SaTPR to regulate plant salt tolerance. These results lay a foundation in understanding the salt stress response mechanisms of S. alopecuroides and provide a reference for future studies oriented toward exploring plant stress resistance.
PMID: 39198230
Plant Mol Biol , IF:4.076 , 2024 Aug , V114 (5) : P89 doi: 10.1007/s11103-024-01482-5
Transcriptome analysis of Sesuvium portulacastrum L. uncovers key genes and pathways involved in root formation in response to low-temperature stress.
Key Laboratory for Green Mariculture of Ministry of Agriculture and Rural Affairs, School of Marine Sciences, Ningbo University, 818 Fenghua Road, Ningbo, Zhejiang Province, 315832, PR China.; Xiangshan Laifa Aquaculture Hatchery Facility, Ningbo, 315704, PR China.; Key Laboratory for Green Mariculture of Ministry of Agriculture and Rural Affairs, School of Marine Sciences, Ningbo University, 818 Fenghua Road, Ningbo, Zhejiang Province, 315832, PR China. jiangmaowang@nbu.edu.cn.
Sesuvium portulacastrum L., a perennial facultative halophyte, is extensively distributed across tropical and subtropical coastal regions. Its limited cold tolerance significantly impacts both the productivity and the geographical distribution of this species in higher-latitude areas. In this study, we employed RNA-Seq technology to delineate the transcriptomic alterations in Sesuvium plants exposed to low temperatures, thus advancing our comprehension of the molecular underpinnings of this physiological adaptation and root formation. Our findings demonstrated differential expression of 10,805, 16,389, and 10,503 genes in the low versus moderate temperature (LT vs. MT), moderate versus high temperature (MT vs. HT), and low versus high temperature (LT vs. HT) comparative analyses, respectively. Notably, the gene categories "structural molecule activity", "ribosome biogenesis", and "ribosome" were particularly enriched among the LT vs. HT-specific differentially expressed genes (DEGs). When synthesizing the insights from these three comparative studies, the principal pathways associated with the cold response mechanism were identified as "carbon fixation in photosynthetic organisms", "starch and sucrose metabolism", "plant hormone signal transduction", "glycolysis/gluconeogenesis", and "photosynthesis". In addition, we elucidated the involvement of auxin signaling pathways, adventitious root formation (ARF), lateral root formation (LRF), and novel genes associated with shoot system development in root formation. Subsequently, we constructed a network diagram to investigate the interplay between hormone levels and pivotal genes, thereby clarifying the regulatory pathways of plant root formation under low-temperature stress and isolating key genes instrumental in root development. This study has provided critical insights into the molecular mechanisms that facilitate the adaptation to cold stress and root formation in S. portulacastrum.
PMID: 39168922
J Proteomics , IF:4.044 , 2024 Aug , V307 : P105288 doi: 10.1016/j.jprot.2024.105288
Proteomic insights into adventitious root formation in Larix kaempferi.
State Key Laboratory of Tree Genetics and Breeding, College of Biological Sciences and Technology, Beijing Forestry University, 100083 Beijing, China; The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of Chinese Forestry Administration, 100083 Beijing, China.; State Key Laboratory of Tree Genetics and Breeding, College of Biological Sciences and Technology, Beijing Forestry University, 100083 Beijing, China; The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of Chinese Forestry Administration, 100083 Beijing, China. Electronic address: gaiying@bjfu.edu.cn.
The adventitious root formaton (ARF) in excised plant parts is essential for the survival of isolated plant fragments. In this study, we explored the complex mechanisms of ARF in Larix kaempferi by conducting a comprehensive proteomic analysis across three distinct stages: the induction of adventitious root primordia (C1, 0-25 d), the formation of adventitious root primordia (C2, 25-35 d), and the elongation of adventitious roots (C3, 35-45 d). We identified 1976 proteins, with 263 and 156 proteins exhibiting increased abundance in the C2/C1 and C3/C2 transitions, respectively. In contrast, a decrease in the abundance of 106 and 132 proteins suggests a significant demand for metabolic processes during the C2/C1 phase. The abundance of IAA-amino acid hydrolase and S-adenosylmethionine synthase were increased in the C2/C1 phase, underscoring the role of auxin in adventitious root induction. The decrease in abundance of photosynthesis-related proteins during the C2/C1 phase highlights the significance of initial light conditions in adventitious root induction. Moreover, variation in cell wall synthesis and metabolic proteins in the C2/C1 and C3/C2 stages suggests that cell wall metabolism is integral to adventitious root regeneration. Gene Ontology enrichment analysis revealed pathways related to protein modification enzymes, including deubiquitinases and kinases, which are crucial for modulating protein modifications to promote ARF. Furthermore, the increased abundance of antioxidant enzymes, such as peroxidases and glutathione peroxidases, indicates a potential approach for enhancing ARF by supplementing the culture medium with antioxidants. Our study provides insights into metabolic changes during ARF in L. kaempferi, offering strategies to enhance adventitious root regeneration. These findings have the potential to refine plant propagation techniques and expedite breeding processes. SIGNFICANCE: The main challenge in the asexual reproduction technology of Larix kaempferi lies in adventitious root formation (ARF). While numerous studies have concentrated on the efficiency of ARF, proteomic data are currently scarce. In this study, we collected samples from three stages of ARF in L. kaempferi and subsequently performed proteomic analysis. The data generated not only reveal changes in protein abundance but also elucidate key metabolic processes involved in ARF. These insights offer a novel perspective on addressing the challenge of adventurous root regeneration.
PMID: 39173904
BMC Genomics , IF:3.969 , 2024 Aug , V25 (1) : P788 doi: 10.1186/s12864-024-10623-5
Transcriptomic profiling reveals histone acetylation-regulated genes involved in somatic embryogenesis in Arabidopsis thaliana.
Faculty of Natural Sciences, Institute of Biology, Biotechnology and Environmental Protection, University of Silesia in Katowice, Katowice, Poland. barbara.wojcikowska@us.edu.pl.; Centre for Bioinformatics and Data Analysis, Medical University of Bialystok, Bialystok, Poland.; Faculty of Natural Sciences, Institute of Biology, Biotechnology and Environmental Protection, University of Silesia in Katowice, Katowice, Poland.; Universite Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), Versailles, 78000, France.
BACKGROUND: Somatic embryogenesis (SE) exemplifies the unique developmental plasticity of plant cells. The regulatory processes, including epigenetic modifications controlling embryogenic reprogramming of cell transcriptome, have just started to be revealed. RESULTS: To identify the genes of histone acetylation-regulated expression in SE, we analyzed global transcriptomes of Arabidopsis explants undergoing embryogenic induction in response to treatment with histone deacetylase inhibitor, trichostatin A (TSA). The TSA-induced and auxin (2,4-dichlorophenoxyacetic acid; 2,4-D)-induced transcriptomes were compared. RNA-seq results revealed the similarities of the TSA- and auxin-induced transcriptomic responses that involve extensive deregulation, mostly repression, of the majority of genes. Within the differentially expressed genes (DEGs), we identified the master regulators (transcription factors - TFs) of SE, genes involved in biosynthesis, signaling, and polar transport of auxin and NITRILASE-encoding genes of the function in indole-3-acetic acid (IAA) biosynthesis. TSA-upregulated TF genes of essential functions in auxin-induced SE, included LEC1/LEC2, FUS3, AGL15, MYB118, PHB, PHV, PLTs, and WUS/WOXs. The TSA-induced transcriptome revealed also extensive upregulation of stress-related genes, including those related to stress hormone biosynthesis. In line with transcriptomic data, TSA-induced explants accumulated salicylic acid (SA) and abscisic acid (ABA), suggesting the role of histone acetylation (Hac) in regulating stress hormone-related responses during SE induction. Since mostly the adaxial side of cotyledon explant contributes to SE induction, we also identified organ polarity-related genes responding to TSA treatment, including AIL7/PLT7, RGE1, LBD18, 40, HB32, CBF1, and ULT2. Analysis of the relevant mutants supported the role of polarity-related genes in SE induction. CONCLUSION: The study results provide a step forward in deciphering the epigenetic network controlling embryogenic transition in somatic cells of plants.
PMID: 39148037
Plants (Basel) , IF:3.935 , 2024 Aug , V13 (16) doi: 10.3390/plants13162266
First Peek into the Transcriptomic Response in Heat-Stressed Tomato Inoculated with Septoglomus constrictum.
Department of Microbiology and Applied Biotechnology, Institute of Genetics and Biotechnology, Hungarian University of Agriculture and Life Sciences, 2100 Godollo, Hungary.; Agribiotechnology and Precision Breeding for Food Security National Laboratory, Institute of Genetics and Biotechnology, Hungarian University of Agriculture and Life Sciences, 2100 Godollo, Hungary.; Institute of One Health, University of Debrecen, 4032 Debrecen, Hungary.; Research Institute for Medicinal Plants and Herbs Ltd., 2011 Budakalasz, Hungary.; Department of Information Technology and Its Applications, Faculty of Information Technology, University of Pannonia, 8900 Zalaegerszeg, Hungary.
In this study, we report the interaction between an arbuscular mycorrhizal fungus, Septoglomus constrictum, and tomato plants under heat stress. For the first time, this interaction was studied by Illumina RNA-seq, followed by a comprehensive bioinformatic analysis that investigated root and leaf tissue samples. The genome-wide transcriptional profiling displayed fewer transcriptomic changes in the root under heat-stress conditions caused by S. constrictum. The top 50 DEGs suggested significant changes in the expression of genes encoding heat-shock proteins, transporter proteins, and genes of phytohormone metabolism involving jasmonic acid signalling. S. constrictum induced the upregulation of genes associated with pathways such as 'drought-responsive' and the 'development of root hair' in the root, as well as 'glycolipid desaturation', 'intracellular auxin transport', and 'ethylene biosynthesis' in the leaf. The pathways 'biotin biosynthesis' and 'threonine degradation' were found in both investigated tissue types. Expression analysis of transcription factors showed 2 and 11 upregulated transcription factors in heat-stressed root and leaf tissues, respectively. However, we did not find shared transcription factors. Heat-stressed arbuscular mycorrhizal plants suffered less oxidative stress when exposed to high temperatures. Colorimetric tests demonstrated less accumulation of H(2)O(2) and MDA in heat-stressed mycorrhizal plants. This phenomenon was accompanied by the higher expression of six stress genes that encode peroxidases, glutathione S-transferase and ubiquitin carboxyl-terminal hydrolase in roots and leaves. Our findings provide a new perspective on elucidating the functional metabolic processes of tomato plants under mycorrhizal-heat stressed conditions.
PMID: 39204702
Plants (Basel) , IF:3.935 , 2024 Aug , V13 (16) doi: 10.3390/plants13162247
Allele-Specific Hormone Dynamics in Highly Transgressive F2 Biomass Segregants in Sugarcane (Saccharum spp.).
Center for Genomics, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou 350002, China.; Department of Biological Sciences, Lehman College, City University of New York, 250 Bedford Park Boulevard West, Bronx, NY 10468, USA.
Sugarcane holds global promise as a biofuel feedstock, necessitating a deep understanding of factors that influence biomass yield. This study unravels the intricate dynamics of plant hormones that govern growth and development in sugarcane. Transcriptome analysis of F2 introgression hybrids, derived from the cross of Saccharum officinarum "LA Purple" and wild Saccharum robustum "MOL5829", was conducted, utilizing the recently sequenced allele-specific genome of "LA Purple" as a reference. A total of 8059 differentially expressed genes were categorized into gene models (21.5%), alleles (68%), paralogs (10%), and tandemly duplicated genes (0.14%). KEGG analysis highlighted enrichment in auxin (IAA), jasmonic acid (JA), and abscisic acid (ABA) pathways, revealing regulatory roles of hormone repressor gene families (Aux/IAA, PP2C, and JAZ). Signaling pathways indicated that downregulation of AUX/IAA and PP2C and upregulation of JAZ repressor genes in high biomass segregants act as key players in influencing downstream growth regulatory genes. Endogenous hormone levels revealed higher concentrations of IAA and ABA in high biomass, which contrasted with lower levels of JA. Weighted co-expression network analysis demonstrated strong connectivity between hormone-related key genes and cell wall structural genes in high biomass genotypes. Expression analysis confirmed the upregulation of genes involved in the synthesis of structural carbohydrates and the downregulation of inflorescence and senescence-related genes in high biomass, which suggested an extended vegetative growth phase. The study underscores the importance of cumulative gene expression, including gene models, dominant alleles, paralogs, and tandemly duplicated genes and activators and repressors of disparate hormone (IAA, JA, and ABA) signaling pathways are the points of hormone crosstalk in contrasting biomass F2 segregants and could be applied for engineering high biomass acquiring varieties.
PMID: 39204683
Plants (Basel) , IF:3.935 , 2024 Aug , V13 (16) doi: 10.3390/plants13162241
Transcriptomic and Physiological Analyses for the Role of Hormones and Sugar in Axillary Bud Development of Wild Strawberry Stolon.
School of Agriculture, Yunnan University, Kunming 650091, China.; College of Horticulture and Landscape, Yunnan Agricultural University, Kunming 650201, China.; Key Laboratory of Phytochemistry and Natural Medicines, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China.
Strawberries are mainly propagated by stolons, which can be divided into monopodial and sympodial types. Monopodial stolons consistently produce ramets at each node following the initial single dormant bud, whereas sympodial stolons develop a dormant bud before each ramet. Sympodial stolon encompasses both dormant buds and ramet buds, making it suitable for studying the formation mechanism of different stolon types. In this study, we utilized sympodial stolons from Fragaria nilgerrensis as materials and explored the mechanisms underlying sympodial stolon development through transcriptomic and phytohormonal analyses. The transcriptome results unveiled that auxin, cytokinin, and sugars likely act as main regulators. Endogenous hormone analysis revealed that the inactivation of auxin could influence bud dormancy. Exogenous cytokinin application primarily induced dormant buds to develop into secondary stolons, with the proportion of ramet formation being very low, less than 10%. Furthermore, weighted gene co-expression network analysis identified key genes involved in ramet formation, including auxin transport and response genes, the cytokinin activation gene LOG1, and glucose transport genes SWEET1 and SFP2. Consistently, in vitro cultivation experiments confirmed that glucose enhances the transition of dormant buds into ramets within two days. Collectively, cytokinin and glucose act as dormant breakers, with cytokinin mainly driving secondary stolon formation and glucose promoting ramet generation. This study improved our understanding of stolon patterning and bud development in the sympodial stolon of strawberries.
PMID: 39204677
Gene , IF:3.688 , 2024 Oct , V926 : P148623 doi: 10.1016/j.gene.2024.148623
Transcriptome analysis reveals the key network of axillary bud outgrowth modulated by topping in citrus.
National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops / College of Horticulture & Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, PR China.; National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops / College of Horticulture & Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, PR China. Electronic address: liuyongzhong@mail.hzau.edu.cn.
Topping, an important tree shaping and pruning technique, can promote the outgrowth of citrus axillary buds. However, the underlying molecular mechanism is still unclear. In this study, spring shoots of Citrus reticulata 'Huagan No.2' were topped and transcriptome was compared between axillary buds of topped and untopped shoots at 6 and 11 days after topping (DAT). 1944 and 2394 differentially expressed genes (DEGs) were found at 6 and 11 DAT, respectively. KEGG analysis revealed that many DEGs were related to starch and sucrose metabolism, signal transduction of auxin, cytokinin and abscisic acid. Specially, transcript levels of auxin synthesis, transport, and signaling-related genes (SAURs and ARF5), cytokinin signal transduction related genes (CRE1, AHP and Type-A ARRs), ABA signal responsive genes (PYL and ABF) were up-regulated by topping; while transcript levels of auxin receptor TIR1, auxin responsive genes AUX/IAAs, ABA signal transduction related gene PP2Cs and synthesis related genes NCED3 were down-regulated. On the other hand, the contents of sucrose and fructose in axillary buds of topped shoots were significantly higher than those in untopped shoots; transcript levels of 16 genes related to sucrose synthase, hexokinase, sucrose phosphate synthase, endoglucanase and glucosidase, were up-regulated in axillary buds after topping. In addition, transcript levels of genes related to trehalose 6-phosphate metabolism and glycolysis/tricarboxylic acid (TCA) cycle, as well to some transcription factors including Pkinase, Pkinase_Tyr, Kinesin, AP2/ERF, P450, MYB, NAC and Cyclin_c, significantly responded to topping. Taken together, the present results suggested that topping promoted citrus axillary bud outgrowth through comprehensively regulating plant hormone and carbohydrate metabolism, as well as signal transduction. These results deepened our understanding of citrus axillary bud outgrowth by topping and laid a foundation for further research on the molecular mechanisms of citrus axillary bud outgrowth.
PMID: 38821328
Gene , IF:3.688 , 2024 Aug , V921 : P148532 doi: 10.1016/j.gene.2024.148532
Identification of cotton PIP5K genes and role of GhPIP5K9a in primary root development.
National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research of Chinese Academy of Agricultural Sciences (CAAS), Anyang 455000, China; Western Agricultural Research Center, Chinese Academy of Agricultural Sciences, Changji 831100, China.; Anyang Academy of Agricultural Sciences, Anyang 455000, China.; National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research of Chinese Academy of Agricultural Sciences (CAAS), Anyang 455000, China.; National Nanfan Research Institute (Sanya), Chinese Academy of Agricultural Sciences, Sanya 572024, China; National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research of Chinese Academy of Agricultural Sciences (CAAS), Anyang 455000, China.; National Nanfan Research Institute (Sanya), Chinese Academy of Agricultural Sciences, Sanya 572024, China; National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research of Chinese Academy of Agricultural Sciences (CAAS), Anyang 455000, China; Western Agricultural Research Center, Chinese Academy of Agricultural Sciences, Changji 831100, China. Electronic address: fsl427@126.com.; National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research of Chinese Academy of Agricultural Sciences (CAAS), Anyang 455000, China; Western Agricultural Research Center, Chinese Academy of Agricultural Sciences, Changji 831100, China. Electronic address: 13837240176@163.com.
Phosphatidylinositol 4 phosphate 5-kinase (PIP5K) is crucial for the phosphatidylinositol (PI) signaling pathway. It plays a significant role in plant growth and development, as well as stress response. However, its effects on cotton are unknown. This study identified PIP5K genes from four cotton species and conducted bioinformatic analyses, with a particular emphasis on the functions of GhPIP5K9a in primary roots. The results showed that cotton PIP5Ks were classified into four subgroups. Analysis of gene structure and motif composition showed obvious conservation within each subgroup. Synteny analysis suggested that the PIP5K gene family experienced significant expansion due to both whole-genome duplication (WGD) and segmental duplication. Transcriptomic data analysis revealed that the majority of GhPIP5K genes had the either low or undetectable levels of expression. Moreover, GhPIP5K9a is highly expressed in the root and was located in plasmalemma. Suppression of GhPIP5K9a transcripts resulted in longer primary roots, longer primary root cells and increased auxin polar transport-related genes expression, and decreased abscisic acid (ABA) content, indicating that GhPIP5K9a negatively regulates cotton primary root growth. This study lays the foundation for further exploration of the role of the PIP5K genes in cotton.
PMID: 38705423
J Plant Physiol , IF:3.549 , 2024 Oct , V301 : P154313 doi: 10.1016/j.jplph.2024.154313
miRNAs: Primary modulators of plant drought tolerance.
State Key Laboratory of Tree Genetics and Breeding, National Engineering Research Center of Tree Breeding and Ecological Restoration, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, 100083, China.; State Key Laboratory of Tree Genetics and Breeding, National Engineering Research Center of Tree Breeding and Ecological Restoration, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, 100083, China. Electronic address: ywwang@bjfu.edu.cn.
Drought is a principal environmental factor that affects the growth and development of plants. Accordingly, plants have evolved adaptive mechanisms to cope with adverse environmental conditions. One of the mechanisms is gene regulation mediated by microRNAs (miRNAs). miRNAs are regarded as primary modulators of gene expression at the post-transcriptional level and have been shown to participate in drought stress response, including ABA response, auxin signaling, antioxidant defense, and osmotic regulation through downregulating the corresponding targets. miRNA-based genetic reconstructions have the potential to improve the tolerance of plants to drought. However, there are few precise classification and discussion of miRNAs in specific response behaviors to drought stress and their applications. This review summarized and discussed the specific response behaviors of miRNAs under drought stress and the role of miRNAs as regulators in the response of plants to drought and highlighted that the modification of miRNAs might effectively improve the tolerance of plants to drought.
PMID: 38991233
Protoplasma , IF:3.356 , 2024 Sep , V261 (5) : P937-950 doi: 10.1007/s00709-024-01945-y
Plant regeneration capacity in seeds of three species of Miconia (Melastomataceae) may be related to endogenous polyamine profiles.
Programa de Pos-Graduacao em Biologia Vegetal, Campinas, Universidade Estadual de Campinas, Sao Paulo, 13083-862, Brazil. juliana.ziemmer@gmail.com.; Laboratorio de Biologia Celular e Tecidual, Centro de Biociencias e Biotecnologia, Universidade Estadual do Norte Fluminense Darcy Ribeiro, Campos dos Goytacazes, Rio de Janeiro, 28013-602, Brazil.; Departamento de Botanica, Universidade Federal do Parana, Curitiba, Parana, 81531-970, Brazil.
In plant tissue culture, differences in endogenous levels of species-specific plant growth regulators (PGRs) may explain differences in regenerative capacity. In the case of polyamines (PAs), their dynamics and distribution may vary between species, genotypes, tissues, and developmental pathways, such as sexual reproduction and apomixis. In this study, for the first time, we aimed to assess the impact of varying endogenous PAs levels in seeds from distinct reproductive modes in Miconia spp. (Melastomataceae), on their in vitro regenerative capacity. We quantified the free PAs endogenous content in seeds of Miconia australis (obligate apomictic), Miconia hyemalis (facultative apomictic), and Miconia sellowiana (sexual) and evaluated their in vitro regenerative potential in WPM culture medium supplemented with a combination of 2,4-dichlorophenoxyacetic acid (2,4-D) and 6-benzylaminopurine (BAP). The morphogenic responses were characterized by light microscopy and scanning electron microscopy and discussed regarding the endogenous PAs profiles found. Seeds of M. sellowiana presented approximately eight times more putrescine than M. australis, which was associated with a higher percentage of regenerated calluses (76.67%) than M. australis (5.56%). On the other hand, spermine levels were significantly higher in M. australis. Spermine is indicated as an inhibitor of auxin-carrying gene expression, which may have contributed to its lower regenerative capacity under the tested conditions. These findings provide important insights into in vitro morphogenesis mechanisms in Miconia and highlight the significance of endogenous PA levels in plant regeneration. These discoveries can potentially optimize future regeneration protocols in Miconia, a plant group still underexplored in this area.
PMID: 38530427
J Biotechnol , IF:3.307 , 2024 Aug , V394 : P34-47 doi: 10.1016/j.jbiotec.2024.07.023
System-wide analysis of groundnut's salinity resilience: Integrating plant-cell interactions with environmental stress dynamics through cutting-edge transcriptomics.
Department of Biotechnology, Faculty of Agriculture, Junagadh Agricultural University, Junagadh, India.; Krishi Vigyan Kendra, Targhadia, Rajkot (Gujarat), Junagadh Agricultural University, Junagadh, India.; Department of Biotechnology, Faculty of Science, Kerala Agricultural University, Kerala, India.; Department of Biotechnology, Faculty of Agriculture, Junagadh Agricultural University, Junagadh, India. Electronic address: ashishvala@jau.in.
Salinity stress is a major concern in regions where irrigation relies on saline water. This study aimed to investigate the relative water content (RWC), electrolytic leakage (EL), total chlorophyll content, free amino acid content, and total soluble sugar content were analyzed in different groundnut species subjected to various salinity treatments. The results showed that salinity stress significantly reduced the RWC in groundnut leaves, with A. duranensis (wild type) exhibiting higher RWC values compared to the Arachis hypogaea species. RNA sequencing was performed to identify differentially expressed genes (DEGs) during salt stress. A total of 9079 DEGs were identified, with 1372 genes upregulated and 2509 genes downregulated. Genes belonging to transcription factor families, such as WRKY, MYB, bHLH, E2F, and Auxin efflux carrier proteins, were induced under salt stress in the tolerant genotype. Conversely, genes encoding NADH dehydrogenase, glutathione S-transferase, protein kinases, UDP-glycosyltransferase, and peroxidase were downregulated. Gene ontology and pathway analyses revealed several enriched categories and metabolic pathways associated with salt stress response, including catalytic activity, response to salt stress, ATP-dependent activity, and oxidative phosphorylation. The findings of this study provide insights into the physiological and molecular responses of groundnut to salinity stress. A. duranensis exhibited better salinity tolerance than Arachis hypogaea, as indicated by higher RWC values, lower electrolytic leakage, and differential gene expression patterns. These results contribute to our understanding of the mechanisms underlying salt stress tolerance in groundnut and may guide future efforts to develop salinity-tolerant groundnut species, ultimately improving crop yield in saline-affected regions.
PMID: 39128505
Environ Technol , IF:3.247 , 2024 Aug , V45 (20) : P4003-4016 doi: 10.1080/09593330.2023.2238928
Isolation of bacteria with plant growth-promoting properties from microalgae-bacterial flocs produced in high-rate oxidation ponds.
Institute for Environmental Biotechnology, Rhodes University (EBRU), Makhanda, South Africa.
Exploring plant growth-promoting (PGP) bacterial activity of microbial components aggregated by wastewater treatment can reduce dependence on fossil fuel-derived fertilisers. This study describes the isolation and identification of bacteria from microalgae-bacteria flocs (MaB-flocs) generated in high-rate algal oxidation ponds (HRAOP) of an integrated algal pond system (IAPS) remediating municipal wastewater. Amplified 16S rRNA gene sequence analysis determined the molecular identity of the individual strains. Genetic relatedness to known PGP rhizobacteria in the NCBI GenBank database was by metagenomics. Isolated strains were screened for the production of indoles (measured as indole-3-acetic acid; IAA) and an ability to mineralise NH4+, PO43-, and K (+) . Of the twelve bacterial strains isolated from HRAOP MaB-flocs, four produced indoles, nine mineralised NH4+, seven solubilised P, and one K. Potential of isolated strains for PGP activity according to one-way ANOVA on ranks was: ECCN 7b > ECCN 4b > ECCN 6b > ECCN 3b = ECCN 10b > ECCN 1b = ECCN 5b > ECCN 8b > ECCN 2b > ECCN 12b > ECCN 9b = ECCN 11b. Further study revealed that cell-free filtrate from indole-producing cultures of Aeromonas strain ECCN 4b, Enterobacter strain ECCN 7b, and Arthrobacter strain ECCN 6b promoted mung bean adventitious root formation suggestive of the presence of auxin-like biological activity.
PMID: 37469005
PLoS One , IF:3.24 , 2024 , V19 (8) : Pe0307368 doi: 10.1371/journal.pone.0307368
Foliar application of melatonin improve the number of secondary branches and secondary branch grains quality of rice.
School of Life Sciences and Food Engineering, Huaiyin Institute of Technology, Huai'an, Jiangsu, China.; Seed Science and Technology Research Center, Huaiyin Agricultural Institute of Xuhuai Prefecture, Huai'an, Jiangsu, China.; Crop Breeding Research Office, Jiangsu Tianfeng Seed Industry Company Limited, Huai'an, Jiangsu, China.
Melatonin plays an important role in plant growth and development. However, little information is available about melatonin regulating rice panicle structure and yield. This study explored the regulatory effects and mechanisms of melatonin spraying before the panicle differentiation stage on rice panicle structure and grain quality. The results showed that spraying melatonin before panicle differentiation increased rice yield, which was mainly reflected in the increase in spikelets per panicle and the percentage of filled grains. In addition, melatonin treatment significantly increased the panicle length. The results of panicle structure analysis showed that the increase in spikelets per panicle caused by melatonin was attributed to the significant increase in the number of secondary branches, total number of secondary branch spikelets, and number of spikelets per secondary branch. The results showed that melatonin can increase the content of zeatin, auxin, and gibberellin, and reduce the content of abscisic acid. These results showed that melatonin affected panicle structure by regulating hormone content, thereby improving yield. In addition, melatonin improves the processing quality, appearance quality, and nutritional quality of secondary branch grains. The above results indicate that application of melatonin improves the number of secondary branches and the quality of grainss on secondary branches.
PMID: 39163308
Lett Appl Microbiol , IF:2.858 , 2024 Aug doi: 10.1093/lambio/ovae075
The potential of plant growth-promoting bacteria isolated from arid heavy metal contaminated environments in alleviating salt and water stresses in alfalfa.
AgroBiosciences Program, College for Sustainable Agriculture and Environmental Sciences, University Mohammed VI Polytechnic (UM6P), Lot 660, Hay Moulay Rachid, 43150 Benguerir, Morocco.; Laboratory of Microbial Biotechnologies, Agrosciences, and Environment (BioMagE), Labeled Research Unit-CNRST N degrees 4, Faculty of Sciences Semlalia, Cadi Ayyad University, PO Box 2390 Marrakesh, Morocco.; Laboratory of Agro-Food, Biotechnologies, and Valorization of Plant Bioresources (Agrobioval), Center of Agrobiotechnology and Bioengineering, Research Unit labeled CNRST (Centre AgroBiotech-URL-CNRST-05), "Physiology of Abiotic Stresses" Team, Cadi Ayyad University, PO Box 2390 Marrakesh, Morocco.; Department of Biology, Nador Multidisciplinary Faculty, Mohamed First University, Nador, Morocco.; Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Seville, 41012 Seville, SPAIN.
Co-evolution of plant beneficial microbes in contaminated environments enhances plant growth and mitigates abiotic stress. However, few studies on heavy metal (HM) tolerant plant growth-promoting bacteria (PGPB) promoting crop growth in Morocco's farming areas affected by drought and salinity are available. Plant associated bacteria tolerant to HM and able to produce indole acetic acid and siderophores, display ACC-deaminase activity and solubilize phosphate, were isolated from long-term metal exposed environments. Tolerance to HM and biofilms formation in the absence or presence of HM were assessed. A consortium including two Ensifer meliloti strains (RhOL6 and RhOL8), one Pseudomonas sp. strain (DSP17), and one Proteus sp. strain (DSP1), was used to inoculate alfalfa (Medicago sativa) seedlings under various conditions, namely, salt stress (85 mM) and water stress (30% water holding capacity). Shoot and root dry weights of alfalfa were measured 60 days after sowing. In the presence of HM, DSP17 showed the greatest auxin production, whereas RhOL8 had the highest ACC-deaminase activity and DSP17 formed the densest biofilm. Root dry weight increased 138% and 195% in salt and water stressed plants, respectively, regarding non-inoculated controls. Our results confirm the improvement of alfalfa growth and mitigation of salt and drought stress upon inoculation.
PMID: 39191534
Biol Open , IF:2.422 , 2024 Aug doi: 10.1242/bio.060531
An atlas of Brachypodium distachyon lateral root development.
Laboratory of Molecular and Cell Biology, Institute of Biology, University of Neuchatel, Switzerland.; IPSiM, University of Montpellier, CNRS, INRAE, Institut Agro, Montpellier, France.; Department of Plant Molecular Biology, University of Lausanne, Lausanne, Switzerland.; Sainsbury Lab, University of Cambridge, Cambridge, UK.
The root system of plants is a vital part for successful development and adaptation to different soil types and environments. A major determinant of the shape of a plant root system is the formation of lateral roots, allowing for expansion of the root system. Arabidopsis thaliana, with its simple root anatomy, has been extensively studied to reveal the genetic program underlying root branching. However, to get a more general understanding of lateral root development, comparative studies in species with a more complex root anatomy are required. Here, by combining optimized clearing methods and histology, we describe an atlas of lateral root development in Brachypodium distachyon, a wild, temperate grass species. We show that lateral roots initiate from enlarged phloem pole pericycle cells and that the overlying endodermis reactivates its cell cycle and eventually forms the root cap. In addition, auxin signaling reported by the DR5 reporter was not detected in the phloem pole pericycle cells or young primordia. In contrast, auxin signaling was activated in the overlying cortical cell layers, including the exodermis. Thus, Brachypodium is a valuable model to investigate how signaling pathways and cellular responses have been repurposed to facilitate lateral root organogenesis.
PMID: 39158386
Physiol Mol Biol Plants , IF:2.391 , 2024 Aug , V30 (8) : P1253-1263 doi: 10.1007/s12298-024-01493-y
A point mutation in the IAA14 promoter enhances callus formation and regeneration.
Key Laboratory of Organic Dry Farming for Special Crops in Datong City, College of Agriculture and Life Science, Shanxi Datong University, Datong, 037009 Shanxi Province China. ROR: https://ror.org/03s8xc553. GRID: grid.440639.c. ISNI: 0000 0004 1757 5302; Engineering Research Center of Coal-based Ecological Carbon Sequestration Technology of the Ministry of Education, Key Laboratory of National Forest and Grass Administration for the Application of Graphene in Forestry, Shanxi Datong University, Datong, 037009 Shanxi Province China. ROR: https://ror.org/03s8xc553. GRID: grid.440639.c. ISNI: 0000 0004 1757 5302
Callus formation induced by auxin accumulation is considered the first step of in vitro plant regeneration. In Arabidopsis, degradation of the Aux/IAA protein, IAA14, in response to auxin signaling, which activates the AUXIN RESPONSE FACTOR 7 (ARF7) and ARF19 along with a series of downstream transcription factors, also plays a critical role in this process. However, the specific mechanism by which auxin regulates callus formation remains unclear. By screening mutant library in the solitary root 1 (iaa14/slr) Arabidopsis background we obtained the callus formation related 2 (cfr2) mutant. The cfr2 mutant exhibited a stronger capacity for callus formation, as well as lateral root and adventitious root regeneration from leaf explants than wild type (WT) seedlings, but did not recover gravitropism capability. The auxin signal in cfr2 was significantly enhanced, and the expression of some downstream transcription factors was increased. Map-based cloning, whole genome resequencing, and phenotypic complementation experiments showed that the phenotypes observed in the cfr2 mutant were caused by a point mutation in the IAA14 promoter region. This mutation, which is predicted to disrupt the binding of LBD16, LBD19, and LBD30 to the IAA14 promoter, changed the expression pattern of IAA14 in cfr2. Taken together, our results identified a new mutation in the IAA14 promoter region, which affects the expression pattern of IAA14 and in turn its ability to control plant regeneration. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s12298-024-01493-y.
PMID: 39184564
Plant Signal Behav , IF:2.247 , 2024 Dec , V19 (1) : P2391658 doi: 10.1080/15592324.2024.2391658
Genome-wide identification and expression analysis of SMALL AUXIN UP RNA (SAUR) genes in rice (Oryza sativa).
Tianjin Key Laboratory of Intelligent Breeding of Major Crops, College of Agronomy & Resources and Environment, Tianjin Agricultural University, Tianjin, China.; College of Basic Sciences, Tianjin Agricultural University, Tianjin, China.
SMALL AUXIN UP RNAs (SAURs), the largest family of early auxin response genes, plays crucial roles in multiple processes, including cell expansion, leaf growth and senescence, auxin transport, tropic growth and so on. Although the rice SAUR gene family was identified in 2006, it is necessary to identify the rice SAUR gene due to the imperfection of its analysis methods. In this study, a total of 60 OsSAURs (including two pseudogenes) distributed on 10 chromosomes were identified in rice (Oryza sativa). Bioinformatics tools were used to systematically analyze the physicochemical properties, subcellular localization, motif compositions, chromosomal location, gene duplication, evolutionary relationships, auxin-responsive cis-elements of the OsSAURs. In addition, the expression profiles obtained from microarray data analysis showed that OsSAUR genes had different expression patterns in different tissues and responded to auxin treatment, indicating functional differences among members of OsSAUR gene family. In a word, this study provides basic information for SAUR gene family of rice and lays a foundation for further study on the role of SAUR in rice growth and development.
PMID: 39148317
Plant Signal Behav , IF:2.247 , 2024 Dec , V19 (1) : P2383822 doi: 10.1080/15592324.2024.2383822
Highly efficient CRISPR/Cas9-RNP mediated CaPAD1 editing in protoplasts of three pepper (Capsicum annuum L.) cultivars.
Department of Biological Sciences, Kangwon National University, Chuncheon, Republic of Korea.; Interdisciplinary Program of Genomic Data Science, Pusan National University, Busan, Republic of Korea.; Graduate School of Medical AI, Pusan National University, Busan, Republic of Korea.; Interdisciplinary Graduate Program in BIT Medical Convergence, Kangwon National University, Chuncheon, Republic of Korea.
Parthenocarpy, characterized by seedless fruit development without pollination or fertilization, offers the advantage of consistent fruit formation, even under challenging conditions such as high temperatures. It can be induced by regulating auxin homeostasis; PAD1 (PARENTAL ADVICE-1) is an inducer of parthenocarpy in Solanaceae plants. However, precise editing of PAD1 is not well studied in peppers. Here, we report a highly efficient clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 (Cas9) ribonucleoprotein (RNP) for CaPAD1 editing in three valuable cultivars of pepper (Capsicum annuum L.): Dempsey, a gene-editable bell pepper; C15, a transformable commercial inbred line; and Younggo 4, a Korean landrace. To achieve the seedless pepper trait under high temperatures caused by unstable climate change, we designed five single guide RNAs (sgRNAs) targeting the CaPAD1 gene. We evaluated the in vitro on-target activity of the RNP complexes in three cultivars. Subsequently, we introduced five CRISPR/Cas9-RNP complexes into protoplasts isolated from three pepper leaves and compared indel frequencies and patterns through targeted deep sequencing analyses. We selected two sgRNAs, sgRNA2 and sgRNA5, which had high in vivo target efficiencies for the CaPAD1 gene across the three cultivars and were validated as potential off-targets in their genomes. These findings are expected to be valuable tools for developing new seedless pepper cultivars through precise molecular breeding of recalcitrant crops in response to climate change.
PMID: 39052485
Plant Signal Behav , IF:2.247 , 2024 Dec , V19 (1) : P2348917 doi: 10.1080/15592324.2024.2348917
Investigation of Arabidopsis root skototropism with different distance settings.
Institute of Cellular and Molecular Botany, University of Bonn, Bonn, Germany.
Plants can activate protective and defense mechanisms under biotic and abiotic stresses. Their roots naturally grow in the soil, but when they encounter sunlight in the top-soil layers, they may move away from the light source to seek darkness. Here we investigate the skototropic behavior of roots, which promotes their fitness and survival. Glutamate-like receptors (GLRs) of plants play roles in sensing and responding to signals, but their role in root skototropism is not yet understood. Light-induced tropisms are known to be affected by auxin distribution, mainly determined by auxin efflux proteins (PIN proteins) at the root tip. However, the role of PIN proteins in root skototropism has not been investigated yet. To better understand root skototropism and its connection to the distance between roots and light, we established five distance settings between seedlings and darkness to investigate the variations in root bending tendencies. We compared differences in root skototropic behavior across different expression lines of Arabidopsis thaliana seedlings (atglr3.7 ko, AtGLR3.7 OE, and pin2 knockout) to comprehend their functions. Our research shows that as the distance between roots and darkness increases, the root's positive skototropism noticeably weakens. Our findings highlight the involvement of GLR3.7 and PIN2 in root skototropism.
PMID: 38704856
Plant Signal Behav , IF:2.247 , 2024 Dec , V19 (1) : P2341506 doi: 10.1080/15592324.2024.2341506
Complex genetic interaction between glucose sensor HXK1 and E3 SUMO ligase SIZ1 in regulating plant morphogenesis.
National Institute of Plant Genome Research, New Delhi, India.
Sugar signaling forms the basis of metabolic activities crucial for an organism to perform essential life activities. In plants, sugars like glucose, mediate a wide range of physiological responses ranging from seed germination to cell senescence. This has led to the elucidation of cell signaling pathways involving glucose and its counterparts and the mechanism of how these sugars take control over major hormonal pathways such as auxin, ethylene, abscisic acid and cytokinin in Arabidopsis. Plants use HXK1(Hexokinase) as a glucose sensor to modulate changes in photosynthetic gene expression in response to high glucose levels. Other proteins such as SIZ1, a major SUMO E3 ligase have recently been implicated in controlling sugar responses via transcriptional and translational regulation of a wide array of sugar metabolic genes. Here, we show that these two genes work antagonistically and are epistatic in controlling responsiveness toward high glucose conditions.
PMID: 38607960
Plant Signal Behav , IF:2.247 , 2024 Dec , V19 (1) : P2331358 doi: 10.1080/15592324.2024.2331358
Plant hormone profiling of scion and rootstock incision sites and intra- and inter-family graft junctions in Nicotiana benthamiana.
Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan.; RIKEN Center for Sustainable Resource Science, Plant Productivity Systems Research Group, Yokohama, Japan.
Many previous studies have suggested that various plant hormones play essential roles in the grafting process. In this study, to understand the plant hormones that accumulate in the graft junctions, whether these are supplied from the scion or rootstock, and how these hormones play a role in the grafting process, we performed a hormonome analysis that accumulated in the incision site of the upper plants from the incision as "ungrafted scion" and lower plants from the incision as "ungrafted rootstock" in Nicotiana benthamiana. The results revealed that indole-3-acetic acid (IAA) and gibberellic acid (GA), which regulate cell division; abscisic acid (ABA) and jasmonic acid (JA), which regulate xylem formation; cytokinin (CK), which regulates callus formation, show different accumulation patterns in the incision sites of the ungrafted scion and rootstock. In addition, to try discussing the differences in the degree and speed of each event during the grafting process between intra- and inter-family grafting by determining the concentration and accumulation timing of plant hormones in the graft junctions, we performed hormonome analysis of graft junctions of intra-family grafted plants with N. benthamiana as scion and Solanum lycopersicum as rootstock (Nb/Sl) and inter-family grafted plants with N. benthamiana as scion and Arabidopsis thaliana as rootstock (Nb/At), using the ability of Nicotiana species to graft with many plant species. The results revealed that ABA and CK showed different accumulation timings; IAA, JA, and salicylic acid (SA) showed similar accumulation timings, while different accumulated concentrations in the graft junctions of Nb/Sl and Nb/At. This information is important for understanding the molecular mechanisms of plant hormones in the grafting process and the differences in molecular mechanisms between intra- and inter-family grafting.
PMID: 38513064
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
Curr Microbiol , IF:2.188 , 2024 Aug , V81 (10) : P327 doi: 10.1007/s00284-024-03851-1
Actinobacteria Isolated from Soils of Arid Saharan Regions Display Simultaneous Antifungal and Plant Growth Promoting Activities.
Department of Natural Sciences and Life, University of Oum El Bouaghi, 04000, Oum El Bouaghi, Algeria. boukelloul.inas@univ-oeb.dz.; Department of Natural Sciences and Life, Laboratory of Biomolecules and Plant Breeding, University of Oum El Bouaghi, 04000, Oum El Bouaghi, Algeria. boukelloul.inas@univ-oeb.dz.; Department of Natural Sciences and Life, Laboratory of Biomolecules and Plant Breeding, University of Oum El Bouaghi, 04000, Oum El Bouaghi, Algeria.; Biotechnology Research Center-CRBT, Constantine-Algeria, 25000, Constantine, Algeria.; Interdisciplinary Centre of Marine and Environmental Research, Terminal de Cruzeiros Do Porto de Leixoes, University of Porto, Av. General Norton de Matos S/N, 4450-208, Matosinhos, Portugal.; ICBAS - School of Medicine and Biomedical Sciences, University of Porto, Rua Jorge de Viterbo Ferreira 228, 4050-313, Porto, Portugal.; Centre for Functional Ecology, Associate Laboratory TERRA, Department of Life Sciences, University of Coimbra, Calcada Martim de Freitas, 3000-456, Coimbra, Portugal.; Unit for the Valorization of Natural Resources, Faculty of Exact Sciences, Department of Chemistry, Bioactive Molecules and Physico-Chemical and Biological Analyzes, Mentouri University of Constantine 1, Algeria Route de Ain El Bey, 25000, Constantine, Algeria.; Department of Food Technology, Food Science and Nutrition, Faculty of Veterinary Sciences, University of Murcia, Regional Campus of International Excellence "Campus Mare Nostrum", 30071, Murcia, Espinardo, Spain.; Department of Biochemistry and Cellular and Molecular Biology, Laboratory of Microbiological Engineering and Applications, Mentouri University of Constantine 1, Algeria Route de Ain El Bey, 25000, Constantine, Algeria.
Application of actinobacteria has grown exponentially in recent years in sustainable agricultural. Most actinobacterial inoculants are tailored to function as either biocontrol agents or biofertilizers. Hence, there is the need to obtain and include multifunctional actinobacterial strains in inocula formulations. In this research, 90 actinobacterial isolates were isolated from rhizospheric and non-rhizospheric soils of Algerian Saharan arid regions and were screened for their activity against the phytopathogenic fungi Alternaria alternata, Aspergillus flavus, Botrytis cinerea, Fusarium oxysporum, and Fusarium solani. Five isolates that inhibited at least three of these fungi were characterized according to morphological, environmental and biochemical parameters, and were preliminarily identified as Streptomyces enissocaesilis A1, Streptomyces olivoverticillatus A5, Streptomyces erumpens A6, Streptomyces cavourensis A8, and Streptomyces microflavus A20. These strains were then screened for plant growth promoting activities. All strains produced siderophores, hydrocyanic acid, ammonia and the auxin indole-3-acetic acid (IAA) and were capable of solubilizing phosphate. The highest producer of siderophores (69.19 percent siderophore units), ammonia (70.56 mug mL(-1)) and IAA (148.76 mug mL(-1)) was strain A8, A20, and A5, respectively. These findings showed that the five actinobacteria are multipurpose strains with simultaneous antifungal and plant growth promoting activities and have the potential to be used for sustainable agricultural practices, particularly in arid regions.
PMID: 39181975
Biosci Biotechnol Biochem , IF:2.043 , 2024 Aug , V88 (9) : P1007-1018 doi: 10.1093/bbb/zbae080
A mature liquid fertilizer derived from cattle urine promotes Arabidopsis thaliana growth via hormone-like responses.
Kankyo Daizen Co., Ltd, Hokkaido, Japan.; Cold Regions, Environmental and Energy Engineering Course, Graduate School of Engineering, Kitami Institute of Technology, Hokkaido, Japan.; Department of Applied Chemistry, Kitami Institute of Technology, Hokkaido, Japan.
To understand the fertilization effects of liquid fertilizer (LF) produced by aerobic microbial processing of cattle urine, we investigated the influence of LF on growth and shoot genetic responses of the model plant Arabidopsis thaliana. LF significantly enhanced both shoot and root growth under aseptic conditions. Although filtrate from ultrafiltration (molecular weight cutoff: 10 000) also promoted shoot growth and root elongation, the concentrate only promoted root growth. Multiple growth-promoting factors were therefore associated with the growth promotion. Transcriptome analysis of shoots following LF addition identified 353 upregulated and 512 downregulated genes. According to gene ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analyses, signal transduction of a phytohormone cytokinin was influenced by LF addition. Cytochrome P450 induction triggered the related signal transitions, and would introduce the growth promotion for shoot. Primary auxin responses and abscisic acid signaling responses were also observed in the presence of LF. Ethylene signaling seemed to be insensitive.
PMID: 38849314
Plant Commun , 2024 Aug , V5 (8) : P100978 doi: 10.1016/j.xplc.2024.100978
Single-cell network analysis reveals gene expression programs for Arabidopsis root development and metabolism.
MOE Key Laboratory for Cellular Dynamics, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Innovation Academy for Seed Design, Chinese Academy of Sciences, Hefei 230027, China.; MOE Key Laboratory for Cellular Dynamics, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Innovation Academy for Seed Design, Chinese Academy of Sciences, Hefei 230027, China; School of Data Science, University of Science and Technology of China, Hefei 230027, China. Electronic address: sma@ustc.edu.cn.
Single-cell RNA-sequencing datasets of Arabidopsis roots have been generated, but related comprehensive gene co-expression network analyses are lacking. We conducted a single-cell gene co-expression network analysis with publicly available scRNA-seq datasets of Arabidopsis roots using a SingleCellGGM algorithm. The analysis identified 149 gene co-expression modules, which we considered to be gene expression programs (GEPs). By examining their spatiotemporal expression, we identified GEPs specifically expressed in major root cell types along their developmental trajectories. These GEPs define gene programs regulating root cell development at different stages and are enriched with relevant developmental regulators. As examples, a GEP specific for the quiescent center (QC) contains 20 genes regulating QC and stem cell niche homeostasis, and four GEPs are expressed in sieve elements (SEs) from early to late developmental stages, with the early-stage GEP containing 17 known SE developmental regulators. We also identified GEPs for metabolic pathways with cell-type-specific expression, suggesting the existence of cell-type-specific metabolism in roots. Using the GEPs, we discovered and verified a columella-specific gene, NRL27, as a regulator of the auxin-related root gravitropism response. Our analysis thus systematically reveals GEPs that regulate Arabidopsis root development and metabolism and provides ample resources for root biology studies.
PMID: 38783601