Mol Cell , IF:15.584 , 2020 Mar , V77 (5) : P1055-1065.e4 doi: 10.1016/j.molcel.2019.12.015
R-Loop Mediated trans Action of the APOLO Long Noncoding RNA.
Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRA, Universities Paris-Sud, Evry and Paris-Diderot, Sorbonne Paris-Cite, University of Paris-Saclay, Batiment 630, 91405 Orsay, France; Instituto de Agrobiotecnologia del Litoral, CONICET, FBCB, Universidad Nacional del Litoral, Colectora Ruta Nacional 168 km 0, 3000 Santa Fe, Argentina. Electronic address: fariel@santafe-conicet.gov.ar.; Instituto de Agrobiotecnologia del Litoral, CONICET, FBCB, Universidad Nacional del Litoral, Colectora Ruta Nacional 168 km 0, 3000 Santa Fe, Argentina.; Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRA, Universities Paris-Sud, Evry and Paris-Diderot, Sorbonne Paris-Cite, University of Paris-Saclay, Batiment 630, 91405 Orsay, France.; Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal 23955-6900, Kingdom of Saudi Arabia.; Department of General Genetics, Center for Plant Molecular Biology (ZMBP), University of Tubingen, Auf der Morgenstelle 32, 72076 Tubingen, Germany.; Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRA, Universities Paris-Sud, Evry and Paris-Diderot, Sorbonne Paris-Cite, University of Paris-Saclay, Batiment 630, 91405 Orsay, France. Electronic address: martin.crespi@ips2.universite-paris-saclay.fr.
In eukaryotes, three-dimensional genome organization is critical for transcriptional regulation of gene expression. Long noncoding RNAs (lncRNAs) can modulate chromatin conformation of spatially related genomic locations within the nucleus. Here, we show that the lncRNA APOLO (AUXIN-REGULATED PROMOTER LOOP) recognizes multiple distant independent loci in the Arabidopsis thaliana genome. We found that APOLO targets are not spatially associated in the nucleus and that APOLO recognizes its targets by short sequence complementarity and the formation of DNA-RNA duplexes (R-loops). The invasion of APOLO to the target DNA decoys the plant Polycomb Repressive Complex 1 component LHP1, modulating local chromatin 3D conformation. APOLO lncRNA coordinates the expression of distal unrelated auxin-responsive genes during lateral root development in Arabidopsis. Hence, R-loop formation and chromatin protein decoy mediate trans action of lncRNAs on distant loci. VIDEO ABSTRACT.
PMID: 31952990
Proc Natl Acad Sci U S A , IF:9.412 , 2020 Mar , V117 (12) : P6910-6917 doi: 10.1073/pnas.2000172117
IPyA glucosylation mediates light and temperature signaling to regulate auxin-dependent hypocotyl elongation in Arabidopsis.
The Key Laboratory of Plant Development and Environment Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao 266237, People's Republic of China.; Hunan Provincial Key Laboratory of Phytohormones and Growth Development, Hunan Provincial Key Laboratory for Crop Germplasm Innovation and Utilization, Hunan Agricultural University, Changsha 410128, People's Republic of China.; The Key Laboratory of Plant Development and Environment Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao 266237, People's Republic of China; bkhou@sdu.edu.cn.
Auxin is a class of plant hormone that plays a crucial role in the life cycle of plants, particularly in the growth response of plants to ever-changing environments. Since the auxin responses are concentration-dependent and higher auxin concentrations might often be inhibitory, the optimal endogenous auxin level must be closely controlled. However, the underlying mechanism governing auxin homeostasis remains largely unknown. In this study, a UDP-glycosyltransferase (UGT76F1) was identified from Arabidopsis thaliana, which participates in the regulation of auxin homeostasis by glucosylation of indole-3-pyruvic acid (IPyA), a major precursor of the auxin indole-3-acetic acid (IAA) biosynthesis, in the formation of IPyA glucose conjugates (IPyA-Glc). In addition, UGT76F1 was found to mediate hypocotyl growth by modulating active auxin levels in a light- and temperature-dependent manner. Moreover, the transcription of UGT76F1 was demonstrated to be directly and negatively regulated by PIF4, which is a key integrator of both light and temperature signaling pathways. This study sheds a light on the trade-off between IAA biosynthesis and IPyA-Glc formation in controlling auxin levels and reveals a regulatory mechanism for plant growth adaptation to environmental changes through glucosylation of IPyA.
PMID: 32152121
J Hazard Mater , IF:9.038 , 2020 Mar , V386 : P121437 doi: 10.1016/j.jhazmat.2019.121437
A metabolomic, transcriptomic profiling, and mineral nutrient metabolism study of the phytotoxicity mechanism of uranium.
College of Environment and Resources, Southwest University of Science and Technology, Mianyang, 621010, China; Engineering Research Center of Biomass Materials, Ministry of Education, Southwest University of Science and Technology, Mianyang, 621010, China. Electronic address: laijinlongshust@aliyun.com.; School of Life Science and Engineering, Southwest University of Science and Technology, Mianyang, 621010, China. Electronic address: 2501731662@qq.com.; School of Life Science and Engineering, Southwest University of Science and Technology, Mianyang, 621010, China; Engineering Research Center of Biomass Materials, Ministry of Education, Southwest University of Science and Technology, Mianyang, 621010, China. Electronic address: lxg@swust.edu.cn.
Uranium (U) is a nonessential element that is readily adsorbed and retained in plant roots, causing root damage plants, rather than being translocated to other parts of the plant. The phytotoxicity mechanism of U is poorly understood. In this study, Vicia faba, a model plant for toxicological research, was selected as experimental material to investigate the phytotoxicity mechanism of U. In this study, the effects of U on the growth and development, methonome, transcriptome and mineral nutrient metabolism of V. faba were studied under different U treatments (0-25muM) by integrating metabolomics, transcriptomic, and mineral nutrient metabolism analysis techniques. The results showed that U accumulation in roots and aboveground parts reached 164.34-927.90mug/pot, and 0.028-0.119mug/pot, respectively. U was mainly accumulated in the cell wall of roots, which damaged the root microstructure and inhibited root growth and development. In terms of mineral nutrient metabolism, U treatment (0-25muM) led to changes in mineral metabolic profiles of seedlings. In total, 612 different metabolites were identified in nontargeted metabolomics, including 309 significantly upregulated metabolites and 303 significantly downregulated metabolites. Using RNA-seq, 4974 differentially expressed genes (DEGs) were identified under the high-concentration U treatment (25muM), including 1654 genes significantly upregulated genes and 3320 genes significantly downregulated genes. Metabolic pathway analysis showed that a high concentration of U led to an imbalance of mineral nutrient metabolism in plants and changes in the metabolism and transcriptome pathway of plants, including alterations in the function of plasmodesmata and auxin signal transduction pathway. The latter finding may potentially explain the toxic effect of U on plant roots.
PMID: 31899027
New Phytol , IF:8.512 , 2020 Mar , V225 (6) : P2513-2525 doi: 10.1111/nph.16315
How grass keeps growing: an integrated analysis of hormonal crosstalk in the maize leaf growth zone.
Laboratory for Integrated Plant Physiology Research (IMPRES), Department of Biology, University of Antwerp, 2020, Antwerp, Belgium.; Modeling Of Systems And Internet Communication (MOSAIC), Department of Mathematics and Informatics, University of Antwerp, 2020, Antwerp, Belgium.; Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052, Ghent, Belgium.; VIB Center for Plant Systems Biology, 9052, Ghent, Belgium.; Department of Botany and Microbiology, Faculty of Science, Beni-Suef University, Beni-Suef, 62511, Egypt.
We studied the maize leaf to understand how long-distance signals, auxin and cytokinin, control leaf growth dynamics. We constructed a mathematical model describing the transport of these hormones along the leaf growth zone and their interaction with the local gibberellin (GA) metabolism in the control of cell division. Assuming gradually declining auxin and cytokinin supply at the leaf base, the model generated spatiotemporal hormone distribution and growth patterns that matched experimental data. At the cellular level, the model predicted a basal leaf growth as a result of cell division driven by auxin and cytokinin. Superimposed on this, GA synthesis regulated growth through the control of the size of the region of active cell division. The predicted hormone and cell length distributions closely matched experimental data. To correctly predict the leaf growth profiles and final organ size of lines with reduced or elevated GA production, the model required a signal proportional to the size of the emerged part of the leaf that inhibited the basal leaf growth driven by auxin and cytokinin. Excision and shading of the emerged part of the growing leaf allowed us to demonstrate that this signal exists and depends on the perception of light intensity.
PMID: 31705666
Plant Biotechnol J , IF:8.154 , 2020 Mar , V18 (3) : P691-706 doi: 10.1111/pbi.13236
Molecular insight into cotton leaf curl geminivirus disease resistance in cultivated cotton (Gossypium hirsutum).
National Institute for Biotechnology and Genetic Engineering, Faisalabad, Pakistan.; Boyce Thompson Institute, Ithaca, NY, USA.; Plant Genetics Lab, TERRA Teaching and Research Center, Gembloux Agro-Bio Tech, University of Liege, Gembloux, Belgium.; Department of Biology, University of Alabama at Birmingham, Birmingham, AL, USA.; Genomics and Bioinformatics Research Unit, United States Department of Agriculture-Agricultural Research Service (USDA-ARS), Stoneville, MS, USA.; Crop Genetics Research Unit, United States Department of Agriculture-Agricultural Research Service (USDA-ARS), Stoneville, MS, USA.
Cultivated cotton (Gossypium hirsutum) is the most important fibre crop in the world. Cotton leaf curl disease (CLCuD) is the major limiting factor and a threat to textile industry in India and Pakistan. All the local cotton cultivars exhibit moderate to no resistance against CLCuD. In this study, we evaluated an exotic cotton accession Mac7 as a resistance source to CLCuD by challenging it with viruliferous whiteflies and performing qPCR to evaluate the presence/absence and relative titre of CLCuD-associated geminiviruses/betasatellites. The results indicated that replication of pathogenicity determinant betasatellite is significantly attenuated in Mac7 and probably responsible for resistance phenotype. Afterwards, to decipher the genetic basis of CLCuD resistance in Mac7, we performed RNA sequencing on CLCuD-infested Mac7 and validated RNA-Seq data with qPCR on 24 independent genes. We performed co-expression network and pathway analysis for regulation of geminivirus/betasatellite-interacting genes. We identified nine novel modules with 52 hubs of highly connected genes in network topology within the co-expression network. Analysis of these hubs indicated the differential regulation of auxin stimulus and cellular localization pathways in response to CLCuD. We also analysed the differential regulation of geminivirus/betasatellite-interacting genes in Mac7. We further performed the functional validation of selected candidate genes via virus-induced gene silencing (VIGS). Finally, we evaluated the genomic context of resistance responsive genes and found that these genes are not specific to A or D sub-genomes of G. hirsutum. These results have important implications in understanding CLCuD resistance mechanism and developing a durable resistance in cultivated cotton.
PMID: 31448544
Cell Rep , IF:8.109 , 2020 Mar , V30 (11) : P3904-3916.e3 doi: 10.1016/j.celrep.2020.02.087
Auxin Signaling-Mediated Apoplastic pH Modification Functions in Petal Conical Cell Shaping.
Basic Forestry and Proteomic Research Center, Fujian Provincial Key Laboratory of Plant Functional Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China; State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Key Lab of Sugarcane Biology, College of Agriculture, Guangxi University, Nanning 530004, China.; Basic Forestry and Proteomic Research Center, Fujian Provincial Key Laboratory of Plant Functional Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China.; State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Key Lab of Sugarcane Biology, College of Agriculture, Guangxi University, Nanning 530004, China; Center for Genomics and Biotechnology, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou 350002, China.; Basic Forestry and Proteomic Research Center, Fujian Provincial Key Laboratory of Plant Functional Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China; State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Key Lab of Sugarcane Biology, College of Agriculture, Guangxi University, Nanning 530004, China. Electronic address: deshu.lin@fafu.edu.cn.
The flowers of angiosperm species typically contain specialized conical cells. Although substantial progress has been achieved regarding the mechanisms underlying flower development, little is known about how petal cells achieve final conical shape. Here, we use 8-hydroxypyrene-1,3,6-trisulfonic acid trisodium salt (HPTS) as a fluorescent pH indicator for analyzing the apoplastic pH of conical cells in Arabidopsis and show that normal conical cell expansion requires auxin signaling and apoplastic pH changes. By combining imaging analysis and genetic and pharmacological experiments, we demonstrate that apoplastic acidification and alkalization correlate with an increase and decrease in tip sharpening of conical cells, respectively. Initial expansion of conical cells is accompanied by decreased apoplastic pH, which is associated with increased auxin signaling. Decreased auxin levels, transport, or signaling abolishes cell wall acidification and causes reduced tip sharpening and heights of conical cells. These findings provide an insight into apoplastic pH regulation of conical cell expansion.
PMID: 32187558
PLoS Biol , IF:7.076 , 2020 Mar , V18 (3) : Pe3000671 doi: 10.1371/journal.pbio.3000671
CsIVP functions in vasculature development and downy mildew resistance in cucumber.
State Key Laboratories of Agrobiotechnology, Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, MOE Joint Laboratory for International Cooperation in Crop Molecular Breeding, China Agricultural University, Beijing, China.; Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (South China), Ministry of Agriculture and Rural Affairs, College of Horticulture, South China Agricultural University, Guangzhou, China.; Department of Plant Nutrition, the Key Laboratory of Plant-Soil Interactions, China Agricultural University, Beijing, China.; Shanghai Center for Plant Stress Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China.; State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China.; Department of Plant Pathology, China Agricultural University, Beijing, China.; College of Horticulture, and FAFU-UCR Joint Center for Horticultural Biology and Metabolomics, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou, China.; College of Horticulture Science and Technology, Hebei Normal University of Science & Technology, Qinhuangdao, China.; Department of Plant Biology, University of California, Davis, California, United States of America.
Domesticated crops with high yield and quality are frequently susceptible to pathogen attack, whereas enhancement of disease resistance generally compromises crop yield. The underlying mechanisms of how plant development and disease resistance are coordinately programed remain elusive. Here, we showed that the basic Helix-Loop-Helix (bHLH) transcription factor Cucumis sativus Irregular Vasculature Patterning (CsIVP) was highly expressed in cucumber vascular tissues. Knockdown of CsIVP caused severe vasculature disorganization and abnormal organ morphogenesis. CsIVP directly binds to vascular-related regulators YABBY5 (CsYAB5), BREVIPEDICELLUS (CsBP), and AUXIN/INDOLEACETIC ACIDS4 (CsAUX4) and promotes their expression. Knockdown of CsYAB5 resulted in similar phenotypes as CsIVP-RNA interference (RNAi) plants, including disturbed vascular configuration and abnormal organ morphology. Meanwhile, CsIVP-RNAi plants were more resistant to downy mildew and accumulated more salicylic acid (SA). CsIVP physically interacts with NIM1-INTERACTING1 (CsNIMIN1), a negative regulator in the SA signaling pathway. Thus, CsIVP is a novel vasculature regulator functioning in CsYAB5-mediated organ morphogenesis and SA-mediated downy mildew resistance in cucumber.
PMID: 32203514
Plant Physiol , IF:6.902 , 2020 Mar , V182 (3) : P1481-1493 doi: 10.1104/pp.19.01434
AtMOB1 Genes Regulate Jasmonate Accumulation and Plant Development.
Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China.; University of Chinese Academy of Sciences, Beijing 100049, China.; Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China yfcheng@ibcas.ac.cn.; Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China.
The MOB1 proteins are highly conserved in yeasts, animals, and plants. Previously, we showed that the Arabidopsis (Arabidopsis thaliana) MOB1A gene (AtMOB1A/NCP1) plays critical roles in auxin-mediated plant development. Here, we report that AtMOB1A and AtMOB1B redundantly and negatively regulate jasmonate (JA) accumulation and function in Arabidopsis development. The two MOB1 genes exhibited similar expression patterns, and the MOB1 proteins displayed similar subcellular localizations and physically interacted in vivo. Furthermore, the atmob1a atmob1b (mob1a/1b) double mutant displayed severe developmental defects, which were much stronger than those of either single mutant. Interestingly, many JA-related genes were up-regulated in mob1a/1b, suggesting that AtMOB1A and AtMOB1B negatively regulate the JA pathways. mob1a/1b plants accumulated more JA and were hypersensitive to exogenous JA treatments. Disruption of MYC2, a key gene in JA signaling, in the mob1a/1b background partially alleviated the root defects and JA hypersensitivity observed in mob1a/1b. Moreover, the expression levels of the MYC2-repressed genes PLT1 and PLT2 were significantly decreased in the mob1a/1b double mutant. Our results showed that MOB1A/1B genetically interact with SIK1 and antagonistically modulate JA-related gene expression. Taken together, our findings indicate that AtMOB1A and AtMOB1B play important roles in regulating JA accumulation and Arabidopsis development.
PMID: 31862839
Plant Physiol , IF:6.902 , 2020 Mar , V182 (3) : P1467-1480 doi: 10.1104/pp.19.01336
ZmEHD1 Is Required for Kernel Development and Vegetative Growth through Regulating Auxin Homeostasis.
National Key Laboratory of Wheat and Maize Crop Science, Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, 450002 Zhengzhou, China.; National Engineering Laboratory for Crop Molecular Breeding, Institute of Crop Science, Chinese Academy of Agricultural Sciences, 100081 Beijing, China.; National Engineering Laboratory for Crop Molecular Breeding, Institute of Crop Science, Chinese Academy of Agricultural Sciences, 100081 Beijing, China liwenxue@caas.cn.
The roles of C-terminal Eps15 homology domain (EHD) proteins in clathrin-mediated endocytosis in plants are poorly understood. Here, we isolated a maize (Zea mays) mutant, designated ehd1, which showed defects in kernel development and vegetative growth. Positional cloning and transgenic analysis revealed that ehd1 encodes an EHD protein. Internalization of the endocytic tracer FM4-64 was substantially reduced in the ehd1 mutant and ZmEHD1 knockout mutants. We further demonstrated that ZmEHD1 and the ZmAP2 sigma subunit physically interact at the plasma membrane. Auxin distribution and ZmPIN1a-YFP localization were altered in the ehd1 mutant. Kernel indole-3-acetic acid levels were substantially lower in the ehd1 mutant than in wild-type maize. Exogenous application of 1-naphthaleneacetic acid, but not GA3 or 2-naphthaleneacetic acid, rescued the seed germination and seedling emergency phenotypic defects of ehd1 mutants. Taken together, these results indicate that ZmEHD1 regulates auxin homeostasis by mediating clathrin-mediated endocytosis through its interaction with the ZmAP2 sigma subunit, which is crucial for kernel development and vegetative growth of maize.
PMID: 31857426
Sci Total Environ , IF:6.551 , 2020 Mar , V710 : P135542 doi: 10.1016/j.scitotenv.2019.135542
High-throughput non-targeted metabolomics study of the effects of perfluorooctane sulfonate (PFOS) on the metabolic characteristics of A. thaliana leaves.
Key Laboratory for Environmental Factors Control of Agro-Product Quality Safety, Ministry of Agriculture, Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs, Tianjin 300191, China.; Shanghai AB Sciex Analytical Instrument Trading Co., Ltd, Shanghai, China.; Key Laboratory for Environmental Factors Control of Agro-Product Quality Safety, Ministry of Agriculture, Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs, Tianjin 300191, China. Electronic address: zhangyanwei14@163.com.
The ecotoxicity of perfluorooctane sulfonate (PFOS) is complex and has been reported in animals (including fish and mice), but the effects of PFOS in plants, especially the toxic mechanisms, have rarely been studied. High-throughput nontargeted metabolomics methods for comprehensive assessment were selected to study changes in metabolic characteristics in Arabidopsis thaliana leaves by exposure to different concentrations of PFOS throughout the growth period (30 days). All the metabolites were analyzed by PCA and OPLS-DA methods, by the cutoff of VIP and p-value, 53 biomarkers were found and significantly regulated, all amino acids except glutamate were inhibited and probably associated with binding to protein, auxin and cytokinin of phytohormones were significantly down-regulated. In response mechanism to oxidative stress from PFOS, the phenylpropanoid pathway were fully activated to form several polyphenols and further enhanced into several flavonoids against the reactive oxygen species (ROS) as the primary defend pathway, in addition, ascorbate, trehalose and nicotinamide also were activated and help decrease the damage from oxidative stress. These results provide insights into the mechanism underlying the phytotoxicity of PFOS.
PMID: 31785916
Plant Cell Environ , IF:6.362 , 2020 Mar , V43 (3) : P675-691 doi: 10.1111/pce.13694
Genome-wide association study reveals new genes involved in leaf trichome formation in polyploid oilseed rape (Brassica napus L.).
Provincial Key Laboratory of Crop Gene Resources, Zhejiang University, Hangzhou, China.; Institute of Crop and Nuclear Technology Utilization, Zhejiang Academy of Agricultural Sciences, Hangzhou, China.
Leaf trichomes protect against various biotic and abiotic stresses in plants. However, there is little knowledge about this trait in oilseed rape (Brassica napus). Here, we demonstrated that hairy leaves were less attractive to Plutella xylostella larvae than glabrous leaves. We established a core germplasm collection with 290 accessions for a genome-wide association study (GWAS) of the leaf trichome trait in oilseed rape. We compared the transcriptomes of the shoot apical meristem (SAM) between hairy- and glabrous-leaf genotypes to narrow down the candidate genes identified by GWAS. The single nucleotide polymorphisms and the different transcript levels of BnaA.GL1.a, BnaC.SWEET4.a, BnaC.WAT1.a and BnaC.WAT1.b corresponded to the divergence of the hairy- and glabrous-leaf phenotypes, indicating the role of sugar and/or auxin signalling in leaf trichome initiation. The hairy-leaf SAMs had lower glucose and sucrose contents but higher expression of putative auxin responsive factors than the glabrous-leaf SAMs. Spraying of exogenous auxin (8 mum) increased leaf trichome number in certain genotypes, whereas spraying of sucrose (1%) plus glucose (6%) slightly repressed leaf trichome initiation. These data contribute to the existing knowledge about the genetic control of leaf trichomes and would assist breeding towards the desired leaf surface type in oilseed rape.
PMID: 31889328
Plant Cell Environ , IF:6.362 , 2020 Mar , V43 (3) : P745-759 doi: 10.1111/pce.13658
A multidrug and toxic compound extrusion (MATE) transporter modulates auxin levels in root to regulate root development and promotes aluminium tolerance.
Department of Biological Sciences, Indian Institute of Science Education and Research (IISER) Bhopal, Bhopal, 462066, India.
MATE (multidrug and toxic compound extrusion) transporters play multiple roles in plants including detoxification, secondary metabolite transport, aluminium (Al) tolerance, and disease resistance. Here we identify and characterize the role of the Arabidopsis MATE transporter DETOXIFICATION30. AtDTX30 regulates auxin homeostasis in Arabidopsis roots to modulate root development and Al-tolerance. DTX30 is primarily expressed in roots and localizes to the plasma membrane of root epidermal cells including root hairs. dtx30 mutants exhibit reduced elongation of the primary root, root hairs, and lateral roots. The mutant seedlings accumulate more auxin in their root tips indicating role of DTX30 in maintaining auxin homeostasis in the root. Al induces DTX30 expression and promotes its localization to the distal transition zone. dtx30 seedlings accumulate more Al in their roots but are hyposensitive to Al-mediated rhizotoxicity perhaps due to saturation in root growth inhibition. Increase in expression of ethylene and auxin biosynthesis genes in presence of Al is absent in dtx30. The mutants exude less citrate under Al conditions, which might be due to misregulation of AtSTOP1 and the citrate transporter AtMATE. In conclusion, DTX30 modulates auxin levels in root to regulate root development and in the presence of Al indirectly modulates citrate exudation to promote Al tolerance.
PMID: 31677167
Genomics , IF:6.205 , 2020 Mar , V112 (2) : P2041-2051 doi: 10.1016/j.ygeno.2019.11.017
Plant virus interaction mechanism and associated pathways in mosaic disease of small cardamom (Elettaria cardamomum Maton) by RNA-Seq approach.
ICAR-Indian Agricultural Statistics Research Institute, New Delhi 110012, India.; ICAR- Indian Institute of Spices Research, Kozhikode, Kerala 673012, India.; ICAR-Indian Agricultural Statistics Research Institute, New Delhi 110012, India. Electronic address: Dinesh.Kumar@icar.gov.in.
Small cardamom (Elettaria cardamomum), grown in limited coastal tropical countries is one of the costliest and widely exported agri-produce having global turnover of >10 billion USD. Mosaic/marble disease is one of the major impediments that requires understanding of disease at molecular level. Neither whole genome sequence nor any genomic resources are available, thus RNA seq approach can be a rapid and economical alternative. De novo transcriptome assembly was done with Illumina Hiseq data. A total of 5317 DEGs, 2267 TFs, 114 pathways and 175,952 genic region putative markers were obtained. Gene regulatory network analysis deciphered molecular events involved in marble disease. This is the first transcriptomic report revealing disease mechanism mediated by perturbation in auxin homeostasis and ethylene signalling leading to senescence. The web-genomic resource (SCMVTDb) catalogues putative molecular markers, candidate genes and transcript information. SCMVTDb can be used in germplasm improvement against mosaic disease in endeavour of small cardamom productivity. Availability of genomic resource, SCMVTDb: http://webtom.cabgrid.res.in/scmvtdb/.
PMID: 31770586
Plant J , IF:6.141 , 2020 Mar , V101 (6) : P1411-1429 doi: 10.1111/tpj.14605
Mediator subunit OsMED14_1 plays an important role in rice development.
National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India.; Department of Plant Molecular Biology, University of Delhi South Campus, Benito Juarez Marg, New Delhi, 110021, India.
Mediator, a multisubunit co-activator complex, regulates transcription in eukaryotes and is involved in diverse processes in Arabidopsis through its different subunits. Here, we have explored developmental aspects of one of the rice Mediator subunit gene OsMED14_1. We analyzed its expression pattern through RNA in situ hybridization and pOsMED14_1:GUS transgenics that showed its expression in roots, leaves, anthers and seeds prominently at younger stages, indicating possible involvement of this subunit in multiple aspects of rice development. To understand the developmental roles of OsMED14_1 in rice, we generated and studied RNAi-based knockdown rice plants that showed multiple effects including less height, narrower leaves and culms with reduced vasculature, lesser lateral root branching, defective microspore development, reduced panicle branching and seed set, and smaller seeds. Histological analyses showed that slender organs were caused by reduction in both cell number and cell size in OsMED14_1 knockdown plants. Flow cytometric analyses and expression analyses of cell cycle-related genes revealed that defective cell-cycle progression led to these defects. Expression analyses of auxin-related genes and indole-3-acetic acid (IAA) immunolocalization study indicated altered auxin level in these knockdown plants. Reduction of lateral root branching in knockdown plants was corrected by exogenous IAA supplement. OsMED14_1 physically interacts with transcription factors YABBY5, TAPETUM DEGENERATION RETARDATION (TDR) and MADS29, possibly regulating auxin homeostasis and ultimately leading to lateral organ/leaf, microspore and seed development.
PMID: 31702850
Plant J , IF:6.141 , 2020 Mar , V101 (5) : P1118-1134 doi: 10.1111/tpj.14579
The formation of perinucleolar bodies is important for normal leaf development and requires the zinc-finger DNA-binding motif in Arabidopsis ASYMMETRIC LEAVES2.
Division of Biological Science, Graduate School of Science, Nagoya University, Nagoya, Aichi, 464-8602, Japan.; Graduate School of Bioscience and Biotechnology, Chubu University, Kasugai, Aichi, 487-8501, Japan.; Department of Applied Biological Science, Faculty of Science and Technology, Tokyo University of Science, Noda, Chiba, 278-8510, Japan.; Department of Biological Sciences, Graduate School of Science, Osaka University, 1-1 Machikaneyama-cho, Toyonaka, Osaka, 560-0043, Japan.; Central Research Institute, Ishihara Sangyo Kaisha, Ltd., 2-3-1 Nishi-Shibukawa, Kusatsu, Shiga, 525-0025, Japan.; Graduate School of Medical Sciences, Kanazawa University, Kakuma-machi, Kanazawa, Ishikawa, 920-1192, Japan.; JST, PRESTO, Furo-cho, Chikusa-ku, Nagoya, Aichi, 464-8601, Japan.; Institute of Transformative Bio-Molecules (ITbM), Nagoya University, Furo-cho, Chiku00sa-ku, Nagoya, Aichi, 464-8601, Japan.; Department of Biological Sciences, Graduate School of Science, University of Tokyo, 7-3-1 Hongo, Bukyo-ku, Tokyo, 113-0033, Japan.; Division of Biological Sciences, Faculty of Science, Hokkaido University, Sapporo, 060-0810, Japan.; Department of Biology, Faculty of Agriculture and Life Science, Hirosaki University, 3 Bunkyo-cho, Hirosaki, 036-8561, Japan.
In Arabidopsis, the ASYMMETRIC LEAVES2 (AS2) protein plays a key role in the formation of flat symmetric leaves via direct repression of the abaxial gene ETT/ARF3. AS2 encodes a plant-specific nuclear protein that contains the AS2/LOB domain, which includes a zinc-finger (ZF) motif that is conserved in the AS2/LOB family. We have shown that AS2 binds to the coding DNA of ETT/ARF3, which requires the ZF motif. AS2 is co-localized with AS1 in perinucleolar bodies (AS2 bodies). To identify the amino acid signals in AS2 required for formation of AS2 bodies and function(s) in leaf formation, we constructed recombinant DNAs that encoded mutant AS2 proteins fused to yellow fluorescent protein. We examined the subcellular localization of these proteins in cells of cotyledons and leaf primordia of transgenic plants and cultured cells. The amino acid signals essential for formation of AS2 bodies were located within and adjacent to the ZF motif. Mutant AS2 that failed to form AS2 bodies also failed to rescue the as2-1 mutation. Our results suggest the importance of the formation of AS2 bodies and the nature of interactions of AS2 with its target DNA and nucleolar factors including NUCLEOLIN1. The partial overlap of AS2 bodies with perinucleolar chromocenters with condensed ribosomal RNA genes implies a correlation between AS2 bodies and the chromatin state. Patterns of AS2 bodies in cells during interphase and mitosis in leaf primordia were distinct from those in cultured cells, suggesting that the formation and distribution of AS2 bodies are developmentally modulated in plants.
PMID: 31639235
J Exp Bot , IF:5.908 , 2020 Mar doi: 10.1093/jxb/eraa130
Seasonal N remobilization and the role of auxin transport in poplar trees.
Department of Plant Science and Landscape Architecture, University of Maryland, College Park, MD.; OARDC Metabolite Analysis Center, Department of Horticulture and Crop Science, The Ohio State University, Wooster, OH.; Department of Environmental Science and Technology, University of Maryland, College Park, MD.; College of Forestry, Agriculture and Natural Resources, University of Arkansas at Monticello, Monticello, AR.; Department of Radiology, Washington University in St Louis, MO.
Seasonal nitrogen (N) cycling in Populus, involves Bark Storage Proteins (BSP) that accumulate in bark phloem parenchyma in the fall and decline when shoot growth resumes in the spring. Little is known about the contribution of BSP to growth or the signals regulating N remobilization from BSP. Knockdown of BSP accumulation via RNAi and N-sink manipulations were used to understand how BSP storage influences shoot growth. Reduced accumulation of BSP delayed bud break and reduced shoot growth following dormancy. Further, 13N tracer studies also showed that BSP accumulation is an important factor in N partitioning from senescing leaves to bark. Thus, BSP accumulation has a role in both N remobilization during N partitioning from senescing leaves to bark and from bark to expanding shoots once growth commences following dormancy. The bark transcriptome during BSP catabolism and N remobilization was enriched in genes associated with auxin transport and signaling, and manipulation of the source of auxin or auxin transport revealed a role for auxin in regulating BSP catabolism and N remobilization. Therefore, N remobilization appears to be regulated by auxin produced in expanding buds and shoots that is transported to bark where it regulates protease gene expression and BSP catabolism.
PMID: 32161967
J Exp Bot , IF:5.908 , 2020 Mar , V71 (6) : P1928-1942 doi: 10.1093/jxb/eraa003
DNA methylation is involved in the regulation of pepper fruit ripening and interacts with phytohormones.
Department of Vegetable Science, College of Horticulture, China Agricultural University, Beijing, P.R. China.; Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, Department of Vegetable Science, College of Horticulture, China Agricultural University, Beijing, P.R. China.
There is growing evidence to suggest that epigenetic tags, especially DNA methylation, are critical regulators of fruit ripening. To examine whether this is the case in sweet pepper (Capsicum annuum) we conducted experiments at the transcriptional, epigenetic, and physiological levels. McrBC PCR, bisulfite sequencing, and real-time PCR demonstrated that DNA hypomethylation occurred in the upstream region of the transcription start site of some genes related to pepper ripening at the turning stage, which may be attributed to up-regulation of CaDML2-like and down-regulation of CaMET1-like1, CaMET1-like2, CaCMT2-like, and CaCMT4-like. Silencing of CaMET1-like1 by virus-induced gene silencing led to DNA hypomethylation, increased content of soluble solids, and accumulation of carotenoids in the fruit, which was accompanied by changes in expression of genes involved in capsanthin/capsorubin biosynthesis, cell wall degradation, and phytohormone metabolism and signaling. Endogenous ABA increased during fruit ripening, whereas endogenous IAA showed an opposite trend. No ethylene signal was detected during ripening. DNA hypomethylation repressed the expression of auxin and gibberellin biosynthesis genes as well as cytokinin degradation genes, but induced the expression of ABA biosynthesis genes. In mature-green pericarp, exogenous ABA induced expression of CaDML2-like but repressed that of CaCMT4-like. IAA treatment promoted the transcription of CaMET1-like1 and CaCMT3-like. Ethephon significantly up-regulated the expression of CaDML2-like. Treatment with GA3 and 6-BA showed indistinct effects on DNA methylation at the transcriptional level. On the basis of the results, a model is proposed that suggests a high likelihood of a role for DNA methylation in the regulation of ripening in the non-climacteric pepper fruit.
PMID: 31907544
J Exp Bot , IF:5.908 , 2020 Mar , V71 (6) : P1899-1914 doi: 10.1093/jxb/erz552
Morphological and stage-specific transcriptome analyses reveal distinct regulatory programs underlying yam (Dioscorea alata L.) bulbil growth.
Key Laboratory for Plant Genetic Improvement, Institute of Subtropical Crops, Zhejiang Academy of Agricultural Sciences, Wenzhou, China.; School of Pharmacy, Wenzhou Medical University, Wenzhou, China.; Quzhou Academy of Agricultural Sciences, Quzhou, China.; Key Laboratory of Modern Preparation of Traditional Chinese Medicine, Jiangxi University of Traditional Chinese Medicine, Nanchang, China.
In yam (Dioscorea spp) species, bulbils at leaf axils are the most striking species-specific axillary structure and exhibit important ecological niches. Genetic regulation underlying bulbil growth remains largely unclear so far. Here, we characterize yam (Dioscorea alata L.) bulbil development using histological analysis, and perform full transcriptional profiling on key developmental stages together with phytohormone analyses. Using the stage-specific scoring algorithm, we have identified 3451 stage-specifically expressed genes that exhibit a tight link between major transcriptional changes and stages. Co-expressed gene clusters revealed an obvious over-representation of genes associated with cell division and expansion at the initiation stage of bulbils (T1). Transcriptional changes of hormone-related genes highly coincided with hormone levels, indicating that bulbil initiation and growth are coordinately controlled by multiple phytohormones. In particular, localized auxin is transiently required to trigger bulbil initiation, and be further depleted or exported from bulbils to promote growth by up-regulation of genes involved in auxinconjugation and efflux. The sharp increase in supply of sucrose and an enhanced trehalose-6-phophate pathway at T1 were observed, suggesting that sucrose probably functions as a key signal and promotes bulbil initiation. Analysis of the expression of transcription factors (TFs) predicated 149 TFs as stage-specifically expressed; several T1-specific TFs (from Aux/IAA, E2F, MYB, and bHLH families) have been shown to play key roles in triggering bulbil formation. Together, our work provides a crucial angle for in-depth understanding of the molecular programs underlying yam's unique bulbil development processes. Stage-specific gene sets can be queried to obtain key candidates regulating bulbil growth, serving as valuable resources for further functional research.
PMID: 31832647
Development , IF:5.611 , 2020 Mar , V147 (6) doi: 10.1242/dev.181669
Auxin fluxes through plasmodesmata modify root-tip auxin distribution.
Division of Plant and Crop Sciences, School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough LE12 5RD, UK.; Division of Plant and Crop Sciences, School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough LE12 5RD, UK leah.band@nottingham.ac.uk.; Centre for Mathematical Medicine and Biology, School of Mathematical Sciences, University of Nottingham, Nottingham NG7 2RD, UK.
Auxin is a key signal regulating plant growth and development. It is well established that auxin dynamics depend on the spatial distribution of efflux and influx carriers on the cell membranes. In this study, we employ a systems approach to characterise an alternative symplastic pathway for auxin mobilisation via plasmodesmata, which function as intercellular pores linking the cytoplasm of adjacent cells. To investigate the role of plasmodesmata in auxin patterning, we developed a multicellular model of the Arabidopsis root tip. We tested the model predictions using the DII-VENUS auxin response reporter, comparing the predicted and observed DII-VENUS distributions using genetic and chemical perturbations designed to affect both carrier-mediated and plasmodesmatal auxin fluxes. The model revealed that carrier-mediated transport alone cannot explain the experimentally determined auxin distribution in the root tip. In contrast, a composite model that incorporates both carrier-mediated and plasmodesmatal auxin fluxes re-capitulates the root-tip auxin distribution. We found that auxin fluxes through plasmodesmata enable auxin reflux and increase total root-tip auxin. We conclude that auxin fluxes through plasmodesmata modify the auxin distribution created by efflux and influx carriers.
PMID: 32229613
Development , IF:5.611 , 2020 Mar , V147 (6) doi: 10.1242/dev.185710
A coherent feed-forward loop drives vascular regeneration in damaged aerial organs of plants growing in a normal developmental context.
School of Biology, Indian Institute of Science Education and Research, Thiruvananthapuram 695551, India.; Plant Developmental Biology, Wageningen University Research, Wageningen 6708 PB, The Netherlands.; National Centre for Biological Sciences, Tata Institute of Fundamental Research, 15, Bengaluru, 560065, India.; Department of Biological Sciences, University of Alberta, Edmonton, Alberta T6G 2E9, Canada.; Department of Biological Sciences, University of South Carolina, Columbia, SC 29208, USA.; The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University, Rehovot 76100, Israel.; Institute of Biotechnology HiLIFE, University of Helsinki, 00014 Helsinki, Finland.; Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, Viikki Plant Science Centre, University of Helsinki, 00014 Helsinki, Finland.; School of Biology, Indian Institute of Science Education and Research, Thiruvananthapuram 695551, India kalika@iisertvm.ac.in.
Aerial organs of plants, being highly prone to local injuries, require tissue restoration to ensure their survival. However, knowledge of the underlying mechanism is sparse. In this study, we mimicked natural injuries in growing leaves and stems to study the reunion between mechanically disconnected tissues. We show that PLETHORA (PLT) and AINTEGUMENTA (ANT) genes, which encode stem cell-promoting factors, are activated and contribute to vascular regeneration in response to these injuries. PLT proteins bind to and activate the CUC2 promoter. PLT proteins and CUC2 regulate the transcription of the local auxin biosynthesis gene YUC4 in a coherent feed-forward loop, and this process is necessary to drive vascular regeneration. In the absence of this PLT-mediated regeneration response, leaf ground tissue cells can neither acquire the early vascular identity marker ATHB8, nor properly polarise auxin transporters to specify new venation paths. The PLT-CUC2 module is required for vascular regeneration, but is dispensable for midvein formation in leaves. We reveal the mechanisms of vascular regeneration in plants and distinguish between the wound-repair ability of the tissue and its formation during normal development.
PMID: 32108025
Development , IF:5.611 , 2020 Mar , V147 (6) doi: 10.1242/dev.183277
Spatiotemporal control of cell growth by CUC3 shapes leaf margins.
Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Universite Paris-Saclay, 78000, Versailles, France leo.serra@slcu.cam.ac.uk catherine.rechenmann@cnrs-dir.fr.
How a shape arises from the coordinated behavior of cells is one of the most fascinating questions in developmental biology. In plants, fine spatial and temporal controls of cell proliferation and cell expansion sustain differential growth that defines organ shape and size. At the leaf margin of Arabidopsis thaliana, interplay between auxin transport and transcription factors named CUP SHAPED COTYLEDON (CUCs), which are involved in the establishment of boundary domain identity, were reported to trigger differential growth, leading to serration. Cellular behaviors behind these differential growths remain scarcely described. Here, we used 3D and time lapse imaging on young leaves at different stages of development to determine the sequence of cellular events resulting in leaf serrations. In addition, we showed that the transcription factor CUC3 is a negative regulator of cell growth and that its expression dynamics in a small number of cells at the leaf margin is tightly associated with the control of differential growth.
PMID: 32094116
J Ginseng Res , IF:5.487 , 2020 Mar , V44 (2) : P321-331 doi: 10.1016/j.jgr.2019.01.004
Overexpression of ginseng patatin-related phospholipase pPLAIIIbeta alters the polarity of cell growth and decreases lignin content in Arabidopsis.
Department of Plant Biotechnology, College of Agriculture and Life Science, Chonnam National University, Gwangju, Republic of Korea.
Background: The patatin-related phospholipase AIII family (pPLAIIIs) genes alter cell elongation and cell wall composition in Arabidopsis and rice plant, suggesting diverse commercial purposes of the economically important medicinal ginseng plant. Herein, we show the functional characterization of a ginseng pPLAIII gene for the first time and discuss its potential applications. Methods: pPLAIIIs were identified from ginseng expressed sequence tag clones and further confirmed by search against ginseng database and polymerase chain reaction. A clone showing the highest homology with pPLAIIIbeta was shown to be overexpressed in Arabidopsis using Agrobacterium. Quantitative polymerase chain reaction was performed to analyze ginseng pPLAIIIbeta expression. Phenotypes were observed using a low-vacuum scanning electron microscope. Lignin was stained using phloroglucinol and quantified using acetyl bromide. Results: The PgpPLAIIIbeta transcripts were observed in all organs of 2-year-old ginseng. Overexpression of ginseng pPLAIIIbeta (PgpPLAIIIbeta-OE) in Arabidopsis resulted in small and stunted plants. It shortened the trichomes and decreased trichome number, indicating defects in cell polarity. Furthermore, OE lines exhibited enlarged seeds with less number per silique. The YUCCA9 gene was downregulated in the OE lines, which is reported to be associated with lignification. Accordingly, lignin was stained less in the OE lines, and the expression of two transcription factors related to lignin biosynthesis was also decreased significantly. Conclusion: Overexpression of pPLAIIIbeta retarded cell elongation in all the tested organs except seeds, which were longer and thicker than those of the controls. Shorter root length is related to auxin-responsive genes, and its stunted phenotype showed decreased lignin content.
PMID: 32148415
Antioxidants (Basel) , IF:5.014 , 2020 Mar , V9 (3) doi: 10.3390/antiox9030235
Some Physiological and Biochemical Mechanisms during Seed-to-Seedling Transition in Tomato as Influenced by Garlic Allelochemicals.
College of Horticulture, Northwest A&F University, Yangling 712100, China.; College of Natural Resources and Environment, Northwest A&F University, Yangling 712100, China.; Key Laboratory of Urban Agriculture (South), School of Agriculture and Biology, Ministry of Agriculture & Bor S. Luh Food Safety Research Center, SJTU, Shanghai 200240, China.; Department of Agriculture, Abdul Wali Khan University, Mardan 23200, Pakistan.; Department of Soil and Environmental Sciences, The University of Agriculture, Peshawar 25120, Pakistan.; State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Institute of Soil and Water Conservation, Northwest A&F University, Yangling 712100, China.
The effects of aqueous garlic extracts (AGEs), diallyl disulfide (DADS), and allicin (AAS) were investigated during seed-to-seedling transition of tomato. Independent bioassays were performed including seed priming with AGE (0, 100, and 200 microgmL(-)(1)), germination under the allelochemical influence of AGE, DADS, and AAS, and germination under volatile application of AGE. Noticeable differences in germination indices and seedling growth (particularly root growth and fresh weights) were observed in a dose-dependent manner. When germinated under 50 mM NaCl, seeds primed with AGE exhibited induced defense via antioxidant enzyme activities (superoxide dismutase (SOD), peroxidase (POD), and catalase (CAT)), lipid peroxidation (malondialdehyde content (MDA)), and H2O2 scavenging. Enzyme-linked immunosorbent analysis (ELISA) of the endogenous phytohormones auxin (IAA), abscisic acid (ABA), cytokinin (ZR), and gibberellic acid (GA3) in the roots and shoots of the obtained seedlings and the relative expression levels of auxin-responsive protein (IAA2), like-auxin (LAX5), mitogen-activated protein kinase (MAPK7 and MPK2), respiratory burst oxidase homolog (RBOH1), CHI3 and SODCC1 suggested allelopathic functions in stimulating growth responses. Our findings suggest that garlic allelochemicals act as plant biostimulants to enhance auxin biosynthesis and transportation, resulting in root growth promotion. Additionally, the relative expressions of defense-related genes, antioxidant enzymes activities and phytohormonal regulations indicate activation of the defense responses in tomato seedlings resulting in better growth and development. These results, thus, provide a basis to understand the biological functions of garlic allelochemicals from the induced resistance perspective in plants.
PMID: 32178294
J Integr Plant Biol , IF:4.885 , 2020 Mar doi: 10.1111/jipb.12927
Phytohormone dynamics in developing endosperm influence rice grain shape and quality.
School of Life Science and Technology, Shanghai Tech University, Shanghai, 201210, China.; Hunan Provincial Key Laboratory of Phytohormones and Growth Development, Hunan Agricultural University, Changsha, 410128, China.; Key Laboratory of Plant Molecular Physiology, Institute of Botany, the Chinese Academy of Sciences, Beijing, 100093, China.; Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.; Joint Center for Single Cell Biology/School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China.; National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, the Chinese Academy of Sciences, Shanghai, 200032, China.
Hormones are important signaling molecules regulating developmental processes and responses to environmental stimuli in higher plants. Rice endosperm, the portion of the seed surrounding the embryo, is the main determinant of rice grain shape and yield; however, the dynamics and exact functions of phytohormones in developing endosperm remain elusive. Through a systemic study including transcriptome analysis, hormone measurement, and transgene-based endosperm-specific expression of phytohormone biosynthetic enzymes, we demonstrated that dynamic phytohormone levels play crucial roles in the developing rice endosperm, particularly in regard to grain shape and quality. We detected diverse, differential, and dramatically changing expression patterns of genes related to hormone biosynthesis and signaling during endosperm development, especially at early developmental stages. Liquid chromatography measurements confirmed the dynamic accumulation of hormones in developing endosperm. Further transgenic analysis performed on plants expressing hormone biosynthesis genes driven by an endosperm-specific promoter revealed differential effects of the hormones, especially auxin and brassinosteroids, in regulating grain shape and quality. Our studies help elucidate the distinct roles of hormones in developing endosperm and provide novel and useful tools for influencing crop seed shape and yield.
PMID: 32198820
Ecotoxicol Environ Saf , IF:4.872 , 2020 Mar , V191 : P110213 doi: 10.1016/j.ecoenv.2020.110213
Indole-3-acetic acid promotes cadmium (Cd) accumulation in a Cd hyperaccumulator and a non-hyperaccumulator by different physiological responses.
Faculty of Environmental Science and Engineering, Kunming University of Science and Technology, Kunming, 650500, China; Yunnan Key Lab of Soil Carbon Sequestration and Pollution Control, Kunming, 650500, China. Electronic address: ranjk1226@163.com.; Faculty of Environmental Science and Engineering, Kunming University of Science and Technology, Kunming, 650500, China. Electronic address: 1563934296@qq.com.; Faculty of Environmental Science and Engineering, Kunming University of Science and Technology, Kunming, 650500, China; Yunnan Key Lab of Soil Carbon Sequestration and Pollution Control, Kunming, 650500, China. Electronic address: whb1974@kust.edu.cn.; Faculty of Environmental Science and Engineering, Kunming University of Science and Technology, Kunming, 650500, China; Yunnan Key Lab of Soil Carbon Sequestration and Pollution Control, Kunming, 650500, China. Electronic address: whj79@126.com.; Faculty of Environmental Science and Engineering, Kunming University of Science and Technology, Kunming, 650500, China; Yunnan Key Lab of Soil Carbon Sequestration and Pollution Control, Kunming, 650500, China. Electronic address: lqc0657@126.com.
To study the effects of indole-3-acetic acid (IAA) on cadmium (Cd) accumulation and the physiological responses of the Cd hyperaccumulator Solanum nigrum and non-hyperaccumulator Solanum melongena, a pot experiment was conducted in soil containing 2 mg kg(-1) Cd in which different concentrations of IAA (0, 10, 20, or 40 mg L(-1)) were sprayed on plant leaves. The results showed that Cd accumulation in shoots of S. nigrum was significantly increased by 30% after the addition of 10 mg L(-1) IAA under 2 mg kg(-1) Cd stress compared to that in the control, but shoot Cd accumulation showed no significant change in S. melongena after this IAA treatment. Additionally, the growth and the proline content in the two species were significantly increased by 20 mg L(-1) IAA. The activities of peroxidase and catalase in leaves of S. nigrum and the activity of superoxide dismutase (SOD) in S. melongena were significantly increased and their malondialdehyde content was significantly decreased compared to those in the control. The root activity of S. nigrum was significantly improved after 10 and 20 mg L(-1) IAA treatments, but no significant difference was observed in S. melongena. The correlation analysis results showed that the Cd concentration in leaves of S. nigrum was significantly and positively correlated with the carotenoid and proline contents, and there was also a significant positive correlation between the Cd concentration and SOD activity in leaves of S. melongena. Therefore, S. nigrum is an ideal plant for the phytoextraction of Cd-contaminated soil assisted by IAA. IAA promotes Cd accumulation in plant shoots by enhancing the accumulation of carotenoids and proline in S. nigrum and maintaining a high leaf SOD activity in S. melongena.
PMID: 31978764
Int J Mol Sci , IF:4.556 , 2020 Mar , V21 (6) doi: 10.3390/ijms21062188
Genome-Wide Identification and Analysis on YUCCA Gene Family in Isatis indigotica Fort. and IiYUCCA6-1 Functional Exploration.
National Engineering Laboratory for Resources Development of Endangered Crude Drugs in Northwest China, The Key Laboratory of Medicinal Resources and Natural Pharmaceutical Chemistry, The Ministry of Education, College of Life Sciences, Shaanxi Normal University, Xi'an 710119, China.
Auxin is one of the most critical hormones in plants. YUCCA (Tryptophan aminotransferase of Arabidopsis (TAA)/YUCCA) enzymes catalyze the key rate-limiting step of the tryptophan-dependent auxin biosynthesis pathway, from IPA (Indole-3-pyruvateacid) to IAA (Indole-3-acetic acid). Here, 13 YUCCA family genes were identified from Isatis indigotica, which were divided into four categories, distributing randomly on chromosomes (2n = 14). The typical and conservative motifs, including the flavin adenine dinucleotide (FAD)-binding motif and flavin-containing monooxygenases (FMO)-identifying sequence, existed in the gene structures. IiYUCCA genes were expressed differently in different organs (roots, stems, leaves, buds, flowers, and siliques) and developmental periods (7, 21, 60, and 150 days after germination). Taking IiYUCCA6-1 as an example, the YUCCA genes functions were discussed. The results showed that IiYUCCA6-1 was sensitive to PEG (polyethylene glycol), cold, wounding, and NaCl treatments. The over-expressed tobacco plants exhibited high auxin performances, and some early auxin response genes (NbIAA8, NbIAA16, NbGH3.1, and NbGH3.6) were upregulated with increased IAA content. In the dark, the contents of total chlorophyll and hydrogen peroxide in the transgenic lines were significantly lower than in the control group, with NbSAG12 downregulated and some delayed leaf senescence characteristics, which delayed the senescence process to a certain extent. The findings provide comprehensive insight into the phylogenetic relationships, chromosomal distributions, and expression patterns and functions of the YUCCA gene family in I. indigotica.
PMID: 32235744
Int J Mol Sci , IF:4.556 , 2020 Mar , V21 (7) doi: 10.3390/ijms21072307
Epigenetic Regulation of Auxin-Induced Somatic Embryogenesis in Plants.
University of Silesia in Katowice, Faculty of Natural Sciences, Institute of Biology, Biotechnology and Environmental Protection, Jagiellonska 28, 40-032 Katowice, Poland.
Somatic embryogenesis (SE) that is induced in plant explants in response to auxin treatment is closely associated with an extensive genetic reprogramming of the cell transcriptome. The significant modulation of the gene transcription profiles during SE induction results from the epigenetic factors that fine-tune the gene expression towards embryogenic development. Among these factors, microRNA molecules (miRNAs) contribute to the post-transcriptional regulation of gene expression. In the past few years, several miRNAs that regulate the SE-involved transcription factors (TFs) have been identified, and most of them were involved in the auxin-related processes, including auxin metabolism and signaling. In addition to miRNAs, chemical modifications of DNA and chromatin, in particular the methylation of DNA and histones and histone acetylation, have been shown to shape the SE transcriptomes. In response to auxin, these epigenetic modifications regulate the chromatin structure, and hence essentially contribute to the control of gene expression during SE induction. In this paper, we describe the current state of knowledge with regard to the SE epigenome. The complex interactions within and between the epigenetic factors, the key SE TFs that have been revealed, and the relationships between the SE epigenome and auxin-related processes such as auxin perception, metabolism, and signaling are highlighted.
PMID: 32225116
Int J Mol Sci , IF:4.556 , 2020 Mar , V21 (6) doi: 10.3390/ijms21062099
Hormesis in Plants: The Role of Oxidative Stress, Auxins and Photosynthesis in Corn Treated with Cd or Pb.
Plant Ecophysiology Team, Faculty of Natural Sciences, Institute of Biology, Biotechnology and Environmental Protection, University of Silesia in Katowice, 40-032 Katowice, Poland.; Institute for Ecology of Industrial Areas, 40-844 Katowice, Poland.; Department of Plant Physiology, Institute of Biology, Warsaw University of Life Sciences WULS-SGGW, 02-776 Warsaw, Poland.
Hormesis, which describes the stimulatory effect of low doses of toxic substances on growth, is a well-known phenomenon in the plant and animal kingdoms. However, the mechanisms that are involved in this phenomenon are still poorly understood. We performed preliminary studies on corn coleoptile sections, which showed a positive correlation between the stimulation of growth by Cd or Pb and an increase in the auxin and H2O2 content in the coleoptile sections. Subsequently, we grew corn seedlings in hydroponic culture and tested a wide range of Cd or Pb concentrations in order to determine hormetic growth stimulation. In these seedlings the gas exchange and the chlorophyll a fluorescence, as well as the content of chlorophyll, flavonol, auxin and hydrogen peroxide, were measured. We found that during the hormetic stimulation of growth, the response of the photosynthetic apparatus to Cd and Pb differed significantly. While the application of Cd mostly caused a decrease in various photosynthetic parameters, the application of Pb stimulated some of them. Nevertheless, we discovered that the common features of the hormetic stimulation of shoot growth by heavy metals are an increase in the auxin and flavonol content and the maintenance of hydrogen peroxide at the same level as the control plants.
PMID: 32204316
Int J Mol Sci , IF:4.556 , 2020 Mar , V21 (6) doi: 10.3390/ijms21062067
Comparative Transcriptome Analysis Provides Insights into the Seed Germination in Cotton in Response to Chilling Stress.
State Key Laboratory of Cotton Biology, Institute of Cotton Research of CAAS, Anyang, Henan 455000, China.; MOA Key Laboratory of Crop Eco-physiology and Farming system in the Middle Reaches of Yangtze River, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430000, China.
Gossypium hirsutum L., is a widely cultivated cotton species around the world, but its production is seriously threatened by its susceptibility to chilling stress. Low temperature affects its germination, and the underlying molecular mechanisms are rarely known, particularly from a transcriptional perspective. In this study, transcriptomic profiles were analyzed and compared between two cotton varieties, the cold-tolerant variety KN27-3 and susceptible variety XLZ38. A total of 7535 differentially expressed genes (DEGs) were identified. Among them, the transcripts involved in energy metabolism were significantly enriched during germination based on analysis of Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways, such as glycolysis/gluconeogenesis, tricarboxylic acid cycle (TCA cycle), and glyoxylate cycle (GAC). Results from further GO enrichment analysis show the earlier appearance of DNA integration, meristem growth, cotyledon morphogenesis, and other biological processes in KN27-3 compared with XLZ38 under chilling conditions. The synthesis of asparagine, GDP-mannose, and trehalose and the catabolic process of raffinose were activated. DEGs encoding antioxidants (spermidine) and antioxidase (CAT1, GPX4, DHAR2, and APX1) were much more up-regulated in embryos of KN27-3. The content of auxin (IAA), cis-zeatin riboside (cZR), and trans-zeatin riboside (tZR) in KN27-3 are higher than that in XLZ38 at five stages (from 12 h to 54 h). GA3 was expressed at a higher level in KN27-3 from 18 h to 54 h post imbibition compared to that in XLZ38. And abscisic acid (ABA) content of KN27-3 is lower than that in XLZ38 at five stages. Results from hormone content measurements and the related gene expression analysis indicated that IAA, CTK, and GA3 may promote germination of the cold-tolerant variety, while ABA inhibits it. These results expand the understanding of cottonseed germination and physiological regulations under chilling conditions by multiple pathways.
PMID: 32197292
Int J Mol Sci , IF:4.556 , 2020 Mar , V21 (5) doi: 10.3390/ijms21051807
Root Development and Stress Tolerance in rice: The Key to Improving Stress Tolerance without Yield Penalties.
School of Biological Sciences and Technology, Chonnam National University, Gwangju 61186, Korea.; The National Academy of Sciences, Seoul 06579, Korea.
Roots anchor plants and take up water and nutrients from the soil; therefore, root development strongly affects plant growth and productivity. Moreover, increasing evidence indicates that root development is deeply involved in plant tolerance to abiotic stresses such as drought and salinity. These findings suggest that modulating root growth and development provides a potentially useful approach to improve plant abiotic stress tolerance. Such targeted approaches may avoid the yield penalties that result from growth-defense trade-offs produced by global induction of defenses against abiotic stresses. This review summarizes the developmental mechanisms underlying root development and discusses recent studies about modulation of root growth and stress tolerance in rice.
PMID: 32155710
Theor Appl Genet , IF:4.439 , 2020 Mar , V133 (3) : P951-966 doi: 10.1007/s00122-019-03519-6
Structural genome analysis in cultivated potato taxa.
Department of Plant Science, McGill University, Sainte-Anne-de-Bellevue, Montreal, QC, H9X 3V9, Canada.; Fredericton Research and Development Centre, Agriculture and Agri-Food Canada, Fredericton, Canada.; International Potato Center, Lima, Peru.; Department of Plant Science, McGill University, Sainte-Anne-de-Bellevue, Montreal, QC, H9X 3V9, Canada. martina.stromvik@mcgill.ca.
KEY MESSAGE: Twelve potato accessions were selected to represent two principal views on potato taxonomy. The genomes were sequenced and analyzed for structural variation (copy number variation) against three published potato genomes. The common potato (Solanum tuberosum L.) is an important staple crop with a highly heterozygous and complex tetraploid genome. The other taxa of cultivated potato contain varying ploidy levels (2X-5X), and structural variations are common in the genomes of these species, likely contributing to the diversification or agronomic traits during domestication. Increased understanding of the genomes and genomic variation will aid in the exploration of novel agronomic traits. Thus, sequencing data from twelve potato landraces, representing the four ploidy levels, were used to identify structural genomic variation compared to the two currently available reference genomes, a double monoploid potato genome and a diploid inbred clone of S. chacoense. The results of a copy number variation analysis showed that in the majority of the genomes, while the number of deletions is greater than the number of duplications, the number of duplicated genes is greater than the number of deleted ones. Specific regions in the twelve potato genomes have a high density of CNV events. Further, the auxin-induced SAUR genes (involved in abiotic stress), disease resistance genes and the 2-oxoglutarate/Fe(II)-dependent oxygenase superfamily proteins, among others, had increased copy numbers in these sequenced genomes relative to the references.
PMID: 31893289
Cells , IF:4.366 , 2020 Mar , V9 (3) doi: 10.3390/cells9030641
Molecular Rewiring of the Jasmonate Signaling Pathway to Control Auxin-Responsive Gene Expression.
State Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees, Ministry of Education, College of Forestry, Central South University of Forestry and Technology, Changsha 410004, China.; Key Laboratory of Saline-Alkali Vegetation Ecology Restoration (SAVER), Ministry of Education, College of Life Science, Northeast Forestry University, Harbin 150040, China.
The plant hormone jasmonic acid (JA) has an important role in many aspects of plant defense response and developmental process. JA triggers interaction between the F-box protein COI1 and the transcriptional repressors of the JAZ family that leads the later to proteasomal degradation. The Jas-motif of JAZs is critical for mediating the COI1 and JAZs interaction in the presence of JA. Here, by using the protoplast transient gene expression system we reported that the Jas-motif of JAZ1 was necessary and sufficient to target a foreign reporter protein for COI1-facilitated degradation. We fused the Jas-motif to the SHY2 transcriptional repressor of auxin signaling pathway to create a chimeric protein JaSHY. Interestingly, JaSHY retained the transcriptional repressor function while become degradable by the JA coreceptor COI1 in a JA-dependent fashion. Moreover, the JA-induced and COI1-facilitated degradation of JaSHY led to activation of a synthetic auxin-responsive promoter activity. These results showed that the modular components of JA signal transduction pathway can be artificially redirected to regulate auxin signaling pathway and control auxin-responsive gene expression. Our work provides a general strategy for using synthetic biology approaches to explore and design cell signaling networks to generate new cellular functions in plant systems.
PMID: 32155843
Cells , IF:4.366 , 2020 Mar , V9 (3) doi: 10.3390/cells9030606
The Winner Takes It All: Auxin-The Main Player during Plant Embryogenesis.
Department of Cytophysiology, Faculty of Biology and Environmental Protection, University of Lodz, 90-236 Lodz, Poland.
In plants, the first asymmetrical division of a zygote leads to the formation of two cells with different developmental fates. The establishment of various patterns relies on spatial and temporal gene expression, however the precise mechanism responsible for embryonic patterning still needs elucidation. Auxin seems to be the main player which regulates embryo development and controls expression of various genes in a dose-dependent manner. Thus, local auxin maxima and minima which are provided by polar auxin transport underlie cell fate specification. Diverse auxin concentrations in various regions of an embryo would easily explain distinct cell identities, however the question about the mechanism of cellular patterning in cells exposed to similar auxin concentrations still remains open. Thus, specification of cell fate might result not only from the cell position within an embryo but also from events occurring before and during mitosis. This review presents the impact of auxin on the orientation of the cell division plane and discusses the mechanism of auxin-dependent cytoskeleton alignment. Furthermore, close attention is paid to auxin-induced calcium fluxes, which regulate the activity of MAPKs during postembryonic development and which possibly might also underlie cellular patterning during embryogenesis.
PMID: 32138372
Microorganisms , IF:4.152 , 2020 Mar , V8 (4) doi: 10.3390/microorganisms8040471
Pseudomonas PS01 Isolated from Maize Rhizosphere Alters Root System Architecture and Promotes Plant Growth.
Faculty of Biology and Biotechnology, University of Science-Ho Chi Minh City, Ho Chi Minh City 700000, Vietnam.; Vietnam National University, Ho Chi Minh City 700000, Vietnam.
The objectives of this study were to evaluate the plant growth promoting effects on Arabidopsis by Pseudomonas sp. strains associated with rhizosphere of crop plants grown in Mekong Delta, Vietnam. Out of all the screened isolates, Pseudomonas PS01 isolated from maize rhizosphere showed the most prominent plant growth promoting effects on Arabidopsis and maize (Zea mays). We also found that PS01 altered root system architecture (RSA). The full genome of PS01 was resolved using high-throughput sequencing. Phylogenetic analysis identified PS01 as a member of the Pseudomonas putida subclade, which is closely related to Pseudomonas taiwanensis.. PS01 genome size is 5.3 Mb, assembled in 71 scaffolds comprising of 4820 putative coding sequence. PS01 encodes genes for the indole-3-acetic acid (IAA), acetoin and 2,3-butanediol biosynthesis pathways. PS01 promoted the growth of Arabidopsis and altered the root system architecture by inhibiting primary root elongation and promoting lateral root and root hair formation. By employing gene expression analysis, genetic screening and pharmacological approaches, we suggested that the plant-growth promoting effects of PS01 and the alteration of RSA might be independent of bacterial auxin and could be caused by a combination of different diffusible compounds and volatile organic compounds (VOCs). Taken together, our results suggest that PS01 is a potential candidate to be used as bio-fertilizer agent for enhancing plant growth.
PMID: 32224990
Microorganisms , IF:4.152 , 2020 Mar , V8 (3) doi: 10.3390/microorganisms8030382
Complete Genome Sequence of Pseudomonas psychrotolerans CS51, a Plant Growth-Promoting Bacterium, Under Heavy Metal Stress Conditions.
School of Applied Biosciences, Kyungpook National University, Daegu 41566, Korea.; Natural and Medical Sciences Research Center, University of Nizwa, Nizwa 616, Oman.; Department of Botany, Garden Campus, Abdul Wali Khan University Mardan, Mardan 23200, Pakistan.
In the current study, we aimed to elucidate the plant growth-promoting characteristics of Pseudomonas psychrotolerans CS51 under heavy metal stress conditions (Zn, Cu, and Cd) and determine the genetic makeup of the CS51 genome using the single-molecule real-time (SMRT) sequencing technology of Pacific Biosciences. The results revealed that inoculation with CS51 induced endogenous indole-3-acetic acid (IAA) and gibberellins (GAs), which significantly enhanced cucumber growth (root shoot length) and increased the heavy metal tolerance of cucumber plants. Moreover, genomic analysis revealed that the CS51 genome consisted of a circular chromosome of 5,364,174 base pairs with an average G+C content of 64.71%. There were around 4774 predicted protein-coding sequences (CDSs) in 4859 genes, 15 rRNA genes, and 67 tRNA genes. Around 3950 protein-coding genes with function prediction and 733 genes without function prediction were identified. Furthermore, functional analyses predicted that the CS51 genome could encode genes required for auxin biosynthesis, nitrate and nitrite ammonification, the phosphate-specific transport system, and the sulfate transport system, which are beneficial for plant growth promotion. The heavy metal resistance of CS51 was confirmed by the presence of genes responsible for cobalt-zinc-cadmium resistance, nickel transport, and copper homeostasis in the CS51 genome. The extrapolation of the curve showed that the core genome contained a minimum of 2122 genes (95% confidence interval = 2034.24 to 2080.215). Our findings indicated that the genome sequence of CS51 may be used as an eco-friendly bioresource to promote plant growth in heavy metal-contaminated areas.
PMID: 32182882
Plant Cell Physiol , IF:4.062 , 2020 Mar , V61 (3) : P644-658 doi: 10.1093/pcp/pcz231
SAUR49 Can Positively Regulate Leaf Senescence by Suppressing SSPP in Arabidopsis.
Tianjin Key Laboratory of Protein Sciences, Department of Plant Biology and Ecology, College of Life Sciences, Nankai University, Tianjin 300071, China.
The involvement of SMALL AUXIN-UP RNA (SAUR) proteins in leaf senescence has been more and more acknowledged, but the detailed mechanisms remain unclear. In the present study, we performed yeast two-hybrid assays and identified SAUR49 as an interactor of SENESCENCE SUPPRESSED PROTEIN PHOSPHATASE (SSPP), which is a PP2C protein phosphatase that negatively regulates Arabidopsis leaf senescence by suppressing the leucine-rich repeat receptor-like protein kinase SENESCENCE-ASSOCIATED RECEPTOR-LIKE KINASE (SARK), as reported previously by our group. The interaction between SAUR49 and SSPP was further confirmed in planta. Functional characterization revealed that SAUR49 is a positive regulator of leaf senescence. The accumulation level of SAUR49 protein increased during natural leaf senescence in Arabidopsis. The transcript level of SAUR49 was upregulated during SARK-induced premature leaf senescence but downregulated during SSPP-mediated delayed leaf senescence. Overexpression of SAUR49 significantly accelerated both natural and dark-induced leaf senescence in Arabidopsis. More importantly, SAUR49 overexpression completely reversed SSPP-induced delayed leaf senescence. In addition, overexpression of SAUR49 reversed the decreased plasma membrane H+-ATPase activity mediated by SSPP. Taken together, the results showed that SAUR49 functions in accelerating the leaf senescence process via the activation of SARK-mediated leaf senescence signaling by suppressing SSPP. We further identified four other SSPP-interacting SAURs, SAUR30, SAUR39, SAUR41 and SAUR72, that may act redundantly with SAUR49 in regulating leaf senescence. All these observations indicated that certain members of the SAUR family may serve as an important hub that integrates various hormonal and environmental signals with senescence signals in Arabidopsis.
PMID: 31851355
Plant Cell Physiol , IF:4.062 , 2020 Mar , V61 (3) : P606-615 doi: 10.1093/pcp/pcz229
Metabolic Regulation and Development of Energy Cane Setts upon Auxin Stimulus.
Brazilian Biorenewables National Laboratory (LNBR), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas 13083-970, Brazil.; Genomics and bioEnergy Laboratory, Department of Genetics, Evolution, Microbiology and Immunology, Institute of Biology, University of Campinas (Unicamp), Campinas 13083-864, Brazil.; Center for Ecophysiology and Biophysics, Agronomic Institute of Campinas (IAC), Campinas 13001-970, Brazil.
Energy cane is a bioenergy crop with an outstanding ability to bud sprouting and increasing yield in ratoon cycles even in marginal lands. Bud fate control is key to biomass production and crop profits due to vegetative propagation and tiller dependency, as well as phenotype plasticity to withstand harsh environmental conditions. During the establishment stage (plant cane cycle), energy cane has a tendency for low root:shoot ratio, which might hamper the ability to cope with stress. Auxin is known to modulate bud sprouting and stimulate rooting in sugarcane. Hence, we treated a slow and a fast bud sprouting energy cane cultivars with auxin or controls (with and without water soaking) for 6 h prior to planting and evaluate plant growth parameters and metabolic profiling using two techniques (gas chromatography with time-of-flight mass spectrometer and nuclear magnetic resonance) to characterize the effect and identify metabolite markers associated with bud inhibition and outgrowth. Auxin inhibited bud burst and promote rooting in setts changing the root:shoot ratio of plantlets. Metabolome allowed the identification of lactate, succinate and aspartate family amino acids as involved in bud fate control through the potential modulation of oxygen and energy status. Investigating environmental and biochemical factors that regulate bud fate can be incremental to other monocot species. Our study provides new insights into bud quiescence and outgrowth in cane hybrids, with the potential to leverage our understanding of yield-related traits, crop establishment and adaptation to global climate change.
PMID: 31830271
Plant Cell Physiol , IF:4.062 , 2020 Mar , V61 (3) : P596-605 doi: 10.1093/pcp/pcz223
GH3 Auxin-Amido Synthetases Alter the Ratio of Indole-3-Acetic Acid and Phenylacetic Acid in Arabidopsis.
Department of Bioregulation and Biointeraction, Graduate School of Agriculture, Tokyo University of Agriculture and Technology, Fuchu, 183-8509 Japan.; Laboratory of Biochemistry, Wageningen University & Research, Wageningen 6708 WE, the Netherlands.; Institute of Agriculture, Tokyo University of Agriculture and Technology, Fuchu, 183-8509 Japan.; JSPS International Research Fellow, The Japan Society for the Promotion of Science (JSPS), Chiyoda-ku, Japan.; Department of Biochemistry, Okayama University of Science, Okayama, 700-0005 Japan.; Institute of Global Innovation Research, Tokyo University of Agriculture and Technology, Fuchu, 183-8509 Japan.; RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa, 230-0045 Japan.
Auxin is the first discovered plant hormone and is essential for many aspects of plant growth and development. Indole-3-acetic acid (IAA) is the main auxin and plays pivotal roles in intercellular communication through polar auxin transport. Phenylacetic acid (PAA) is another natural auxin that does not show polar movement. Although a wide range of species have been shown to produce PAA, its biosynthesis, inactivation and physiological significance in plants are largely unknown. In this study, we demonstrate that overexpression of the CYP79A2 gene, which is involved in benzylglucosinolate synthesis, remarkably increased the levels of PAA and enhanced lateral root formation in Arabidopsis. This coincided with a significant reduction in the levels of IAA. The results from auxin metabolite quantification suggest that the PAA-dependent induction of GRETCHEN HAGEN 3 (GH3) genes, which encode auxin-amido synthetases, promote the inactivation of IAA. Similarly, an increase in IAA synthesis, via the indole-3-acetaldoxime pathway, significantly reduced the levels of PAA. The same adjustment of IAA and PAA levels was also observed by applying each auxin to wild-type plants. These results show that GH3 auxin-amido synthetases can alter the ratio of IAA and PAA in plant growth and development.
PMID: 31808940
Plant Cell Physiol , IF:4.062 , 2020 Mar , V61 (3) : P519-535 doi: 10.1093/pcp/pcz217
Nickel Toxicity Targets Cell Wall-Related Processes and PIN2-Mediated Auxin Transport to Inhibit Root Elongation and Gravitropic Responses in Arabidopsis.
Department of Physiology & Cell Biology, Leibniz Institute of Plant Genetics and Crop Plant Research, Corrensstr. 3, Gatersleben 06466, Germany.; Department of Plant Physiology, Plant Science and Biodiversity Center, Slovak Academy of Sciences, Di inverted question mark(1/2)bravski inverted question mark(1/2) Cesta 9, Bratislava 84523, Slovakia.; Department of Nuclear Physics and Biophysics, Faculty of Mathematics, Physics and Informatics of Comenius University, Mlynski inverted question mark(1/2) Dolina F1, Bratislava 84248, Slovakia.
Contamination of soils with heavy metals, such as nickel (Ni), is a major environmental concern due to increasing pollution from industrial activities, burning of fossil fuels, incorrect disposal of sewage sludge, excessive manure application and the use of fertilizers and pesticides in agriculture. Excess Ni induces leaf chlorosis and inhibits plant growth, but the mechanisms underlying growth inhibition remain largely unknown. A detailed analysis of root development in Arabidopsis thaliana in the presence of Ni revealed that this heavy metal induces gravitropic defects and locally inhibits root growth by suppressing cell elongation without significantly disrupting the integrity of the stem cell niche. The analysis of auxin-responsive reporters revealed that excess Ni inhibits shootward auxin distribution. Furthermore, we found that PIN2 is very sensitive to Ni, as the presence of this heavy metal rapidly reduced PIN2 levels in roots. A transcriptome analysis also showed that Ni affects the expression of many genes associated with plant cell walls and that Ni-induced transcriptional changes are largely independent of iron (Fe). In addition, we raised evidence that excess Ni increases the accumulation of reactive oxygen species and disturbs the integrity and orientation of microtubules. Together, our results highlight which processes are primarily targeted by Ni to alter root growth and development.
PMID: 31750920
Sci Rep , IF:3.998 , 2020 Mar , V10 (1) : P4917 doi: 10.1038/s41598-020-61913-3
Enhancement of soybean nodulation by seed treatment with non-thermal plasmas.
Instituto de Investigaciones en Biociencias Agricolas y Ambientales (INBA), Facultad de Agronomia, Universidad de Buenos Aires (UBA), Consejo Nacional de Investigaciones Cientificas y Tecnicas (CONICET), San Martin, 4453, Buenos Aires, Argentina.; Universidad Tecnologica Nacional, CONICET, Facultad Regional Venado Tuerto, Departamento de Ingenieria Electromecanica, Grupo de Descargas Electricas, Laprida 651, Venado Tuerto, Santa Fe, Argentina.; Laboratorio de Regulacion Genica y Celulas Madre, Instituto de Medicina Traslacional, Trasplante y Bioingenieria (IMeTTyB), Universidad Favaloro-CONICET, Buenos Aires, Argentina.; Instituto de Investigaciones en Biociencias Agricolas y Ambientales (INBA), Facultad de Agronomia, Universidad de Buenos Aires (UBA), Consejo Nacional de Investigaciones Cientificas y Tecnicas (CONICET), San Martin, 4453, Buenos Aires, Argentina. kbale@agro.uba.ar.
Soybean (Glycine max (L.) Merrill) is one of the most important crops worldwide providing dietary protein and vegetable oil. Most of the nitrogen required by the crop is supplied through biological N2 fixation. Non-thermal plasma is a fast, economical, and environmental-friendly technology that can improve seed quality, plant growth, and crop yield. Soybean seeds were exposed to a dielectric barrier discharge plasma operating at atmospheric pressure air with superimposed flows of O2 or N2 as carrying gases. An arrangement of a thin phenolic sheet covered by polyester films was employed as an insulating barrier. We focused on the ability of plasma to improve soybean nodulation and biological nitrogen fixation. The total number of nodules and their weight were significantly higher in plants grown from treated seeds than in control. Plasma treatments incremented 1.6 fold the nitrogenase activity in nodules, while leghaemoglobin content was increased two times, indicating that nodules were fixing nitrogen more actively than control. Accordingly, the nitrogen content in nodules and the aerial part of plants increased by 64% and 23%, respectively. Our results were supported by biometrical parameters. The results suggested that different mechanisms are involved in soybean nodulation improvement. Therefore, the root contents of isoflavonoids, glutathione, auxin and cytokinin, and expansin (GmEXP1) gene expression were determined. We consider this emerging technology is a suitable pre-sowing seed treatment.
PMID: 32188896
Sci Rep , IF:3.998 , 2020 Mar , V10 (1) : P3860 doi: 10.1038/s41598-020-60865-y
Auxin perception in Agave is dependent on the species' Auxin Response Factors.
Unidad de Biotecnologia, Centro de Investigacion Cientifica de Yucatan, Calle 43 # 130 x 32 y 34, Col. Chuburna de Hidalgo, 97205, Merida, Yucatan, Mexico.; Unidad de Biotecnologia, Centro de Investigacion Cientifica de Yucatan, Calle 43 # 130 x 32 y 34, Col. Chuburna de Hidalgo, 97205, Merida, Yucatan, Mexico. clelia@cicy.mx.
Auxins are one of the most important and studied phytohormones in nature. Auxin signaling and perception take place in the cytosol, where the auxin is sensed. Then, in the nucleus, the auxin response factors (ARF) promote the expression of early-response genes. It is well known that not all plants respond to the same amount and type of auxins and that the response can be very different even among plants of the same species, as we present here. Here we investigate the behavior of ARF in response to various auxins in Agave angustifolia Haw., A. fourcroydes Lem. and A. tequilana Weber var. Azul. By screening the available database of A. tequilana genes, we have identified 32 ARF genes with high sequence identity in the conserved domains, grouped into three main clades. A phylogenetic tree was inferred from alignments of the 32 Agave ARF protein sequences and the evolutionary relationship with other species was analyzed. AteqARF 4, 15, 21, and 29 were selected as a representative diverse sample coming from each of the different subclades that comprise the two main clades of the inferred phylogenetic reconstruction. These ARFs showed differential species-specific expression patterns in the presence of indole-3-acetic acid (IAA) and 2,4-dichlorophenoxyacetic acid (2,4-D). Interestingly, A. angustifolia showed different phenotypes in the presence and absence of auxins. In the absence of auxin, A. angustifolia produces roots, while shoots are developed in the presence of IAA. However, in the presence of 2,4-D, the plant meristem converts into callus. According to our results, it is likely that AteqARF15 participates in this outcome.
PMID: 32123284
Plant Cell Rep , IF:3.825 , 2020 Mar , V39 (3) : P381-391 doi: 10.1007/s00299-019-02497-9
An essential role for Arabidopsis Trs33 in cell growth and organization in plant apical meristems.
State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of the State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100 091, China.; Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA.; Department of Biology, McGill University, 1205 Dr Penfield Avenue, Montreal, QC, H3A 1B1, Canada.; Department of Biology, McGill University, 1205 Dr Penfield Avenue, Montreal, QC, H3A 1B1, Canada. hugo.zheng@mcgill.ca.; State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of the State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100 091, China. lumz@caf.ac.cn.; State Key Laboratory of Subtropical Silviculture, School of Forestry and Biotechnology, Zhejiang A&F University, Hanzhou, Zhejiang, 311300, China. lumz@caf.ac.cn.
KEY MESSAGE: Trafficking protein particle (TRAPP) complexes subunit gene AtTrs33 plays an important role in keeping apical meristematic activity and dominance in Arabidopsis. TRAPP complexes, composed of multimeric subunits, are guanine-nucleotide exchange factors for certain Rab GTPases and are believed to be involved in the regulation of membrane trafficking, but the cases in Arabidopsis are largely unknown. Trs33, recently proposed to be a component of TRAPP IV, is non-essential in yeast cells. A single copy of Trs33 gene, AtTrs33, was identified in Arabidopsis. GUS activity assay indicated that AtTrs33 was ubiquitously expressed. Based on a T-DNA insertion line, we found that loss-of-function of AtTrs33 is lethal for apical growth. Knock-down or knock-in of AtTrs33 affects apical meristematic growth and fertility, which indicates that AtTrs33 plays an important role in keeping apical meristematic activity and dominance in Arabidopsis. Analysis of auxin responses and PIN1/2 localization indicate that impaired apical meristematic activity and dominance were caused by altered auxin responses through non-polarized PIN1 localization. The present study reported that AtTrs33 plays an essential role in Arabidopsis cell growth and organization, which is different with its homologue in yeast. These findings provide new insights into the functional divergence of TRAPP subunits.
PMID: 31828377
Genes (Basel) , IF:3.759 , 2020 Mar , V11 (3) doi: 10.3390/genes11030337
Quantitative Trait Loci (QTLs) Associated with Microspore Culture in Raphanus sativus L. (Radish).
Department of Crop Science, College of Agricultural and Life Sciences, Chungnam National University, Daejeon 34134, Korea.; National Institute of Horticultural & Herbal Science, Rural Development Administration (RDA), Wanju 55365, Korea.; Department of Horticultural Science, College of Agricultural and Life Sciences, Chungnam National University, Daejeon 34134, Korea.; Department of Smart Agriculture Systems, College of Agricultural and Life Sciences, Chungnam National University, Daejeon 34134, Korea.
The radish is a highly self-incompatible plant, and consequently it is difficult to produce homozygous lines. Bud pollination in cross-fertilization plants should be done by opening immature pollen and attaching pollen to mature flowers. It accordingly takes a lot of time and effort to develop lines with fixed alleles. In the current study, a haploid breeding method has been applied to obtain homozygous plants in a short period of time by doubling chromosomes through the induction of a plant body in the haploid cells, in order to shorten the time to breed inbred lines. We constructed genetic maps with an F1 population derived by crossing parents that show a superior and inferior ability to regenerate microspores, respectively. Genetic maps were constructed from the maternal and parental maps, separately, using the two-way pseudo-testcross model. The phenotype of the regeneration rate was examined by microspore cultures and a quantitative trait loci (QTL) analysis was performed based on the regeneration rate. From the results of the culture of microspores in the F1 population, more than half of the group did not regenerate, and only a few showed a high regeneration rate. A total of five significant QTLs were detected in the F1 population, and five candidate genes were found based on the results. These candidate genes are divided into two classes, and appear to be related to either PRC2 subunits or auxin synthesis.
PMID: 32245207
Genes (Basel) , IF:3.759 , 2020 Mar , V11 (3) doi: 10.3390/genes11030272
Down Regulation and Loss of Auxin Response Factor 4 Function Using CRISPR/Cas9 Alters Plant Growth, Stomatal Function and Improves Tomato Tolerance to Salinity and Osmotic Stress.
Laboratoire de Biotechnologie et Physiologie Vegetales, Centre de Biotechnologie Vegetale et Microbienne Biodiversite et Environnement, Faculte des Sciences, Universite Mohammed V de Rabat, Rabat 1014, Morocco.; GBF, Universite de Toulouse, INRA, 31326 Castanet-Tolosan, France.; Departamento de Biologia Vegetal, Universidade Federal de Vicosa, 36570-900 Vicosa, Brazil.
Auxin controls multiple aspects of plant growth and development. However, its role in stress responses remains poorly understood. Auxin acts on the transcriptional regulation of target genes, mainly through Auxin Response Factors (ARF). This study focuses on the involvement of SlARF4 in tomato tolerance to salinity and osmotic stress. Using a reverse genetic approach, we found that the antisense down-regulation of SlARF4 promotes root development and density, increases soluble sugars content and maintains chlorophyll content at high levels under stress conditions. Furthermore, ARF4-as displayed higher tolerance to salt and osmotic stress through reduced stomatal conductance coupled with increased leaf relative water content and Abscisic acid (ABA) content under normal and stressful conditions. This increase in ABA content was correlated with the activation of ABA biosynthesis genes and the repression of ABA catabolism genes. Cu/ZnSOD and mdhar genes were up-regulated in ARF4-as plants which can result in a better tolerance to salt and osmotic stress. A CRISPR/Cas9 induced SlARF4 mutant showed similar growth and stomatal responses as ARF4-as plants, which suggest that arf4-cr can tolerate salt and osmotic stresses. Our data support the involvement of ARF4 as a key factor in tomato tolerance to salt and osmotic stresses and confirm the use of CRISPR technology as an efficient tool for functional reverse genetics studies.
PMID: 32138192
Plant Physiol Biochem , IF:3.72 , 2020 Mar , V148 : P368-378 doi: 10.1016/j.plaphy.2020.01.031
Tomato root development and N assimilation depend on C and ABA content under different N sources.
Grupo de Bioquimica y Biotecnologia, Area de Fisiologia Vegetal, Departamento de Ciencias Agrarias y Del Medio Natural, ESTCE, Universitat Jaume I, 12071, Castellon, Spain. Electronic address: gonzalan@uji.es.; Grupo de Bioquimica y Biotecnologia, Area de Fisiologia Vegetal, Departamento de Ciencias Agrarias y Del Medio Natural, ESTCE, Universitat Jaume I, 12071, Castellon, Spain. Electronic address: scalschi@uji.es.; Grupo de Bioquimica y Biotecnologia, Area de Fisiologia Vegetal, Departamento de Ciencias Agrarias y Del Medio Natural, ESTCE, Universitat Jaume I, 12071, Castellon, Spain. Electronic address: garciap@camn.uji.es.; Grupo de Bioquimica y Biotecnologia, Area de Fisiologia Vegetal, Departamento de Ciencias Agrarias y Del Medio Natural, ESTCE, Universitat Jaume I, 12071, Castellon, Spain. Electronic address: camanes@uji.es.
Root plasticity is controlled by hormonal homeostasis and nutrient availability. In this work, we have determined the influence of different N regimens on growth parameters and on the expression of genes involved in auxin transport and N-assimilation in tomato seedlings. NH4(+) nutrition led to an inhibitory effect on root fresh weight (FW), lateral root (LR) number and root density, while an increase in the primary root (PR) length was observed. The expression of N assimilation genes GS2 and ASN1, is affected by NH4(+) nutrition. Moreover, in order to relieve the toxic effect of NH4(+) on root development, glucose or 2-oxoglutarate was supplied as a C source during NH4(+) treatment. The addition of 2-oxoglutarate improved root parameters compared to the NH4(+) regimen. N-assimilation gene analysis showed that NH4(+)-fed tomato plants try to alleviate the toxic effect by concurrently upregulating ASN1 and anaplerotic PEPC2 expression, whereas when 2-oxoglutarate is supplied, ASN1 induction was not observed. The addition of both C skeletons induced the expression of the ROS-scavenging genes GSH and SOD. In addition, since ABA plays a role in root development, the ABA-synthesis-defective mutant flacca was studied under NO3(-) and NH4(+) regimens. It displayed a decrease in LR number under NO3(-) conditions, whereas, the NH4(+)-fed seedlings showed a decrease solely in PR length that was reverted when ABA was exogenously supplied. Moreover, flacca seedlings displayed a reprogramming of the N/C assimilation genes. Altogether, these results reflect the importance of N and C sources and ABA homeostasis in root development of tomato seedlings.
PMID: 32028134
Plant Physiol Biochem , IF:3.72 , 2020 Mar , V148 : P302-311 doi: 10.1016/j.plaphy.2020.01.021
Differential gene expression profiling of one- and two-dimensional apogamous gametophytes of the fern Dryopteris affinis ssp. affinis.
Department of Plant and Microbial Biology & Zurich-Basel Plant Science Center, University of Zurich, Zollikerstrasse 107, CH-8008, Zurich, Switzerland.; Area of Plant Physiology, Department of Organisms and Systems Biology, University of Oviedo, c) Catedratico R Uria s/n, 33071, Oviedo, Spain.; Department of Ecology, Environment and Plant Sciences, Stockholm University, SE-106 91, Stockholm, Sweden.; Area of Plant Physiology, Department of Organisms and Systems Biology, University of Oviedo, c) Catedratico R Uria s/n, 33071, Oviedo, Spain. Electronic address: fernandezelena@uniovi.es.
Apomixis was originally defined as the replacement of sexual reproduction by an asexual process that does not involve fertilization but, in angiosperms, it is often used in the more restricted sense of asexual reproduction through seeds. In ferns, apomixis combines the production of unreduced spores (diplospory) and the formation of sporophytes from somatic cells of the prothallium (apogamy). The genes that control the onset of apogamy in ferns are largely unknown. In this study, we describe the gametophyte transcriptome of the apogamous fern Dryopteris affinis ssp. affinis using an RNA-Seq approach to compare the gene expression profiles of one- and two-dimensional gametophytes, the latter containing apogamic centers. After collapsing highly similar de novo transcripts, we obtained 166,191 unigenes, of which 30% could be annotated using public databases. Multiple quality metrics indicate a good quality of the de novo transcriptome with a low level of fragmentation. Our data show a total of 10,679 genes (6% of all genes) to be differentially expressed between gametophytes of filamentous (one-dimensional) and prothallial (two-dimensional) architecture. 6,110 genes were up-regulated in two-dimensional relative to one-dimensional gametophytes, some of which are implicated in the regulation of meristem growth, auxin signaling, reproduction, and sucrose metabolism. 4,570 genes were down-regulated in two-dimensional versus one-dimensional gametophytes, which are enriched in stimulus and defense genes, as well as genes involved in epigenetic gene regulation and ubiquitin degradation. Our results provide insights into free-living gametophyte development, focusing on the filamentous-to-prothallus growth transition, and provide a useful resource for further investigations of asexual reproduction.
PMID: 32000107
Plant Physiol Biochem , IF:3.72 , 2020 Mar , V148 : P273-281 doi: 10.1016/j.plaphy.2020.01.028
Expression analysis of the BpARF genes in Betula platyphylla under drought stress.
State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, 26 Hexing Road, Harbin, 150040, China; Forestry Science Institute of Heilongjiang Province, 134 Haping Road, Harbin, 150081, China.; State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, 26 Hexing Road, Harbin, 150040, China.; State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, 26 Hexing Road, Harbin, 150040, China. Electronic address: wangyucheng@ms.xjb.ac.cn.; State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, 26 Hexing Road, Harbin, 150040, China. Electronic address: yangcp@nefu.edu.cn.
Auxin response factors (ARFs) play an important role in modulating plant growth and development processes by regulating the expression of auxin-responsive genes. However, the modes of action of ARFs in birch (Betula platyphylla) remain largely unknown. In this study, fifteen ARF genes were identified in the birch (B. platyphylla) genome. Bioinformatics analysis revealed that the 15 BpARF genes were unevenly distributed on 7 chromosomes. The 15 BpARF proteins clustered into 6 groups, and all of them contained ARF and B3 motifs. The cis-acting elements present within the promoters of the BpARF genes were mostly related to stress resistance. Expression analysis revealed that most of the BpARF genes were significantly upregulated or downregulated in response to drought treatment in at least one organ. In particular, the expression of BpARF1 was significantly induced by drought stress. The function of BpARF1 was further studied via a transient transformation system. Under drought stress conditions, compared with vector control plants, BpARF1 RNA interference (RNAi)-inhibited plants presented reduced reactive oxygen species (ROS) accumulation, enhanced peroxide (POD) and superoxide dismutase (SOD) activities, increased ascorbic acid (AsA) and proline contents, and reduced electrolyte leakage and water loss rates. Conversely, BpARF1 overexpression plants displayed the opposite physiological changes. These results suggest that the silencing of BpARF1 can improve the drought tolerance of B. platyphylla.
PMID: 31986481
BMC Genomics , IF:3.594 , 2020 Mar , V21 (1) : P212 doi: 10.1186/s12864-020-6633-x
Genome-wide discovery and functional prediction of salt-responsive lncRNAs in duckweed.
Institute of Tropical Bioscience and Biotechnology, MOA Key Laboratory of Tropical Crops Biology and Genetic Resources, Hainan Bioenergy Center, Chinese Academy of Tropical Agricultural Sciences, Xueyuan Road 4, Haikou, 571101, China.; Hainan Academy of Tropical Agricultural Resource, Chinese Academy of Tropical Agricultural Sciences, Xueyuan Road 4, Haikou, 571101, China.; Institute of Tropical Bioscience and Biotechnology, MOA Key Laboratory of Tropical Crops Biology and Genetic Resources, Hainan Bioenergy Center, Chinese Academy of Tropical Agricultural Sciences, Xueyuan Road 4, Haikou, 571101, China. dingzehong@itbb.org.cn.; Hainan Academy of Tropical Agricultural Resource, Chinese Academy of Tropical Agricultural Sciences, Xueyuan Road 4, Haikou, 571101, China. dingzehong@itbb.org.cn.; Institute of Tropical Bioscience and Biotechnology, MOA Key Laboratory of Tropical Crops Biology and Genetic Resources, Hainan Bioenergy Center, Chinese Academy of Tropical Agricultural Sciences, Xueyuan Road 4, Haikou, 571101, China. zhangjiaming@itbb.org.cn.; Hainan Academy of Tropical Agricultural Resource, Chinese Academy of Tropical Agricultural Sciences, Xueyuan Road 4, Haikou, 571101, China. zhangjiaming@itbb.org.cn.
BACKGROUND: Salt significantly depresses the growth and development of the greater duckweed, Spirodela polyrhiza, a model species of floating aquatic plants. Physiological responses of this plant to salt stress have been characterized, however, the roles of long noncoding RNAs (lncRNAs) remain unknown. RESULTS: In this work, totally 2815 novel lncRNAs were discovered in S. polyrhiza by strand-specific RNA sequencing, of which 185 (6.6%) were expressed differentially under salinity condition. Co-expression analysis indicated that the trans-acting lncRNAs regulated their co-expressed genes functioning in amino acid metabolism, cell- and cell wall-related metabolism, hormone metabolism, photosynthesis, RNA transcription, secondary metabolism, and transport. In total, 42 lncRNA-mRNA pairs that might participate in cis-acting regulation were found, and these adjacent genes were involved in cell wall, cell cycle, carbon metabolism, ROS regulation, hormone metabolism, and transcription factor. In addition, the lncRNAs probably functioning as miRNA targets were also investigated. Specifically, TCONS_00033722, TCONS_00044328, and TCONS_00059333 were targeted by a few well-studied salt-responsive miRNAs, supporting the involvement of miRNA and lncRNA interactions in the regulation of salt stress responses. Finally, a representative network of lncRNA-miRNA-mRNA was proposed and discussed to participate in duckweed salt stress via auxin signaling. CONCLUSIONS: This study is the first report on salt-responsive lncRNAs in duckweed, and the findings will provide a solid foundation for in-depth functional characterization of duckweed lncRNAs in response to salt stress.
PMID: 32138656
Plant Sci , IF:3.591 , 2020 Mar , V292 : P110385 doi: 10.1016/j.plantsci.2019.110385
Exogenous application of abscisic acid to shoots promotes primary root cell division and elongation.
Laboratory of Photosynthesis and Environment, CAS Centre for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China.; National Key Laboratory of Plant Molecular Genetics, CAS Centre for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China.; Laboratory of Photosynthesis and Environment, CAS Centre for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China. Electronic address: wmcai@sibs.ac.cn.
Root-derived abscisic acid (ABA) is known to regulate shoot physiology, such as stomata closure. Conversely, the basipetal regulatory effect of shoot-derived ABA is poorly understood. Herein, we report that simulation of shoot-ABA accumulation by exogenous application of ABA to shoots basipetally stimulates primary root (PR) growth. ABA applied to shoots accelerates root cell division, as evidenced by the increase in meristem size and cell number and the intensity of CYCB1;1::GFP (a mitosis marker). Root ABA content was not changed following shoot ABA application, although the ABA reporter line RAB18::GFP showed an increase in ABA in the cotyledons. Shoot-ABA application increases basipetal auxin transport by 114 %. Shoot-ABA-promoted PR growth can be abolished by attenuating basipetal auxin flux using 2,3,5-triiodobenzoic acid (TIBA, an auxin transport inhibitor), demonstrating that ABA promotes PR growth by increasing basipetal auxin transport. Root cell elongation, evaluated by the total length of the first 7 cells in the elongation zone (EZ), was increased by 56 % following shoot-ABA application. The cell walls of the root EZ were alkalinized by ABA, as exhibited by 8-hydroxypyrene-1,3,6-trisulfonic acid trisodium salt staining. Higher pH promotes both PR growth and cell elongation. Thus, shoot-ABA promotes cell elongation by alkalinizing the cell wall. In light of our results, we provide a representative detailed model of the basipetal regulatory effect of ABA on PR growth.
PMID: 32005390
Plant Sci , IF:3.591 , 2020 Mar , V292 : P110381 doi: 10.1016/j.plantsci.2019.110381
Auxin and ethylene regulation of fruit set.
Laboratory Genomics and Biotechnology of Fruits, INRA, Toulouse INP, University of Toulouse, Castanet-Tolosan, France.; Laboratory Genomics and Biotechnology of Fruits, INRA, Toulouse INP, University of Toulouse, Castanet-Tolosan, France. Electronic address: mohamed.zouine@ensat.fr.; Laboratory Genomics and Biotechnology of Fruits, INRA, Toulouse INP, University of Toulouse, Castanet-Tolosan, France. Electronic address: christian.chervin@ensat.fr.
With the forecasted fast increase in world population and global climate change, providing sufficient amounts of quality food becomes a major challenge for human society. Seed and fruit crop yield is determined by developmental processes including flower initiation, pollen fertility and fruit set. Fruit set is defined as the transition from flower to young fruit, a key step in the development of sexually reproducing higher plants. Plant hormones have important roles during flower pollination and fertilization, leading to fruit set. Moreover, it is well established that fruit set can be triggered by phytohormones like auxin and gibberellins (GAs), in the absence of fertilization, both hormones being commonly used to produce parthenocarpic fruits and to increase fruit yield. Additionally, a number of studies highlighted the role of ethylene in plant reproductive organ development. The present review integrates current knowledge on the roles of auxin and ethylene in different steps of the fruit set process with a specific emphasis on the interactions between the two hormones. A deeper understanding of the interplay between auxin and ethylene may provide new leads towards designing strategies for a better control of fruit initiation and ultimately yield.
PMID: 32005386
BMC Plant Biol , IF:3.497 , 2020 Mar , V20 (1) : P115 doi: 10.1186/s12870-020-2315-8
Genome-wide survey of the bHLH super gene family in Brassica napus.
College of Agronomy and Biotechnology, Southwest University, Chongqing, 400715, China.; Academy of Agricultural Sciences, Southwest University, Chongqing, 400715, China.; College of Agronomy and Biotechnology, Southwest University, Chongqing, 400715, China. haidu81@126.com.; Academy of Agricultural Sciences, Southwest University, Chongqing, 400715, China. haidu81@126.com.
BACKGROUND: The basic helix-loop-helix (bHLH) gene family is one of the largest transcription factor families in plants and is functionally characterized in diverse species. However, less is known about its functions in the economically important allopolyploid oil crop, Brassica napus. RESULTS: We identified 602 potential bHLHs in the B. napus genome (BnabHLHs) and categorized them into 35 subfamilies, including seven newly separated subfamilies, based on phylogeny, protein structure, and exon-intron organization analysis. The intron insertion patterns of this gene family were analyzed and a total of eight types were identified in the bHLH regions of BnabHLHs. Chromosome distribution and synteny analyses revealed that hybridization between Brassica rapa and Brassica oleracea was the main expansion mechanism for BnabHLHs. Expression analyses showed that BnabHLHs were widely in different plant tissues and formed seven main patterns, suggesting they may participate in various aspects of B. napus development. Furthermore, when roots were treated with five different hormones (IAA, auxin; GA3, gibberellin; 6-BA, cytokinin; ABA, abscisic acid and ACC, ethylene), the expression profiles of BnabHLHs changed significantly, with many showing increased expression. The induction of five candidate BnabHLHs was confirmed following the five hormone treatments via qRT-PCR. Up to 246 BnabHLHs from nine subfamilies were predicted to have potential roles relating to root development through the joint analysis of their expression profiles and homolog function. CONCLUSION: The 602 BnabHLHs identified from B. napus were classified into 35 subfamilies, and those members from the same subfamily generally had similar sequence motifs. Overall, we found that BnabHLHs may be widely involved in root development in B. napus. Moreover, this study provides important insights into the potential functions of the BnabHLHs super gene family and thus will be useful in future gene function research.
PMID: 32171243
BMC Plant Biol , IF:3.497 , 2020 Mar , V20 (1) : P114 doi: 10.1186/s12870-020-02330-6
Physiological and transcriptomic analyses reveal the mechanisms underlying the salt tolerance of Zoysia japonica Steud.
Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, 210014, China.; Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, 210014, China. ghlnmg@sina.com.
BACKGROUND: Areas with saline soils are sparsely populated and have fragile ecosystems, which severely restricts the sustainable development of local economies. Zoysia grasses are recognized as excellent warm-season turfgrasses worldwide, with high salt tolerance and superior growth in saline-alkali soils. However, the mechanism underlying the salt tolerance of Zoysia species remains unknown. RESULTS: The phenotypic and physiological responses of two contrasting materials, Zoysia japonica Steud. Z004 (salt sensitive) and Z011 (salt tolerant) in response to salt stress were studied. The results show that Z011 was more salt tolerant than was Z004, with the former presenting greater K(+)/Na(+) ratios in both its leaves and roots. To study the molecular mechanisms underlying salt tolerance further, we compared the transcriptomes of the two materials at different time points (0 h, 1 h, 24 h, and 72 h) and from different tissues (leaves and roots) under salt treatment. The 24-h time point and the roots might make significant contributions to the salt tolerance. Moreover, GO and KEGG analyses of different comparisons revealed that the key DEGs participating in the salt-stress response belonged to the hormone pathway, various TF families and the DUF family. CONCLUSIONS: Zoysia salt treatment transcriptome shows the 24-h and roots may make significant contributions to the salt tolerance. The auxin signal transduction family, ABA signal transduction family, WRKY TF family and bHLH TF family may be the most important families in Zoysia salt-stress regulation.
PMID: 32169028
BMC Plant Biol , IF:3.497 , 2020 Mar , V20 (1) : P98 doi: 10.1186/s12870-020-2311-z
Transcriptome and metabolite analyses provide insights into zigzag-shaped stem formation in tea plants (Camellia sinensis).
College of Horticulture, Fujian Agriculture and Forestry University/Key Laboratory of Tea Science in Universities of Fujian Province, Fuzhou, 350002, China.; College of Tea and Food Science, Wuyi University, Wuyishan, 354300, China.; College of Horticulture, Fujian Agriculture and Forestry University/Key Laboratory of Tea Science in Universities of Fujian Province, Fuzhou, 350002, China. yccyyx@163.com.
BACKGROUND: Shoot orientation is important for plant architecture formation, and zigzag-shaped shoots are a special trait found in many plants. Zigzag-shaped shoots have been selected and thoroughly studied in Arabidopsis; however, the regulatory mechanism underlying zigzag-shaped shoot development in other plants, especially woody plants, is largely unknown. RESULTS: In this study, tea plants with zigzag-shaped shoots, namely, Qiqu (QQ) and Lianyuanqiqu (LYQQ), were investigated and compared with the erect-shoot tea plant Meizhan (MZ) in an attempt to reveal the regulation of zigzag-shaped shoot formation. Tissue section observation showed that the cell arrangement and shape of zigzag-shaped stems were aberrant compared with those of normal shoots. Moreover, a total of 2175 differentially expressed genes (DEGs) were identified from the zigzag-shaped shoots of the tea plants QQ and LYQQ compared to the shoots of MZ using transcriptome sequencing, and the DEGs involved in the "Plant-pathogen interaction", "Phenylpropanoid biosynthesis", "Flavonoid biosynthesis" and "Linoleic acid metabolism" pathways were significantly enriched. Additionally, the DEGs associated with cell expansion, vesicular trafficking, phytohormones, and transcription factors were identified and analysed. Metabolomic analysis showed that 13 metabolites overlapped and were significantly changed in the shoots of QQ and LYQQ compared to MZ. CONCLUSIONS: Our results suggest that zigzag-shaped shoot formation might be associated with the gravitropism response and polar auxin transport in tea plants. This study provides a valuable foundation for further understanding the regulation of plant architecture formation and for the cultivation and application of horticultural plants in the future.
PMID: 32131737
Planta , IF:3.39 , 2020 Mar , V251 (4) : P90 doi: 10.1007/s00425-020-03381-7
Functional dissection of the DORNROSCHEN-LIKE enhancer 2 during embryonic and phyllotactic patterning.
Developmental Biology, Biocenter, University of Cologne, Zulpicher Str 47b, 50674, Cologne, Germany.; Max Planck Institute for Plant Breeding Research, Carl-von-Linne-Weg 10, 50829, Cologne, Germany.; Institute for Molecular Physiology, Heinrich-Heine-Universitat, Universitatsstrasse 1, 40225, Dusseldorf, Germany.; Developmental Biology, Biocenter, University of Cologne, Zulpicher Str 47b, 50674, Cologne, Germany. werr@uni-koeln.de.
MAIN CONCLUSION: The Arabidopsis DORNROSCHEN-LIKE enhancer 2 comprises a high-occupancy target region in the IM periphery that integrates signals for the spiral phyllotactic pattern and cruciferous arrangement of sepals. Transcription of the DORNROSCHEN-LIKE (DRNL) gene marks lateral organ founder cells (LOFCs) in the peripheral zone of the inflorescence meristem (IM) and enhancer 2 (En2) in the DRNL promoter upstream region essentially contributes to this phyllotactic transcription pattern. Further analysis focused on the phylogenetically highly conserved 100-bp En2(core) element, which was sufficient to promote the phyllotactic pattern, but was recalcitrant to further shortening. Here, we show that En2(core) functions independent of orientation and create a series of mutations to study consequences on the transcription pattern. Their analysis shows that, first, in addition to in the inflorescence apex, En2(core) acts in the embryo; second, cis-regulatory target sequences are distributed throughout the 100-bp element, although substantial differences exist in their function between embryo and IM. Third, putative core auxin response elements (AuxREs) spatially activate or restrict DRNL expression, and fourth, according to chromatin configuration data, En2(core) enhancer activity in LOFCs correlates with an open chromatin structure at the DRNL transcription start. In combination, mutational and chromatin analyses imply that En2(core) comprises a high-occupancy target (HOT) region for transcription factors, which implements phyllotactic information for the spiral LOFC pattern in the IM periphery and coordinates the cruciferous array of floral sepals. Our data disfavor a contribution of activating auxin response factors (ARFs) but do not exclude auxin as a morphogenetic signal.
PMID: 32236749
Planta , IF:3.39 , 2020 Mar , V251 (4) : P84 doi: 10.1007/s00425-020-03376-4
The physiological mechanism underlying root elongation in response to nitrogen deficiency in crop plants.
College of Resources and Environmental Sciences, National Academy of Agriculture Green Development, Key Laboratory of Plant-Soil Interactions, Ministry of Education, China Agricultural University, Beijing, 100193, China.; College of Resources and Environmental Sciences, National Academy of Agriculture Green Development, Key Laboratory of Plant-Soil Interactions, Ministry of Education, China Agricultural University, Beijing, 100193, China. miguohua@cau.edu.cn.
MAIN CONCLUSION: In response to low nitrogen stress, multiple hormones together with nitric oxide signaling pathways work synergistically and antagonistically in crop root elongation. Changing root morphology allows plants to adapt to soil nutrient availability. Nitrogen is the most important essential nutrient for plant growth. An important adaptive strategy for crops responding to nitrogen deficiency is root elongation, thereby accessing increased soil space and nitrogen resources. Multiple signaling pathways are involved in this regulatory network, working together to fine-tune root elongation in response to soil nitrogen availability. Based on existing research, we propose a model to explain how different signaling pathways interact to regulate root elongation in response to low nitrogen stress. In response to a low shoot nitrogen status signal, auxin transport from the shoot to the root increases. High auxin levels in the root tip stimulate the production of nitric oxide, which promotes the synthesis of strigolactones to accelerate cell division. In this process, cytokinin, ethylene, and abscisic acid play an antagonistic role, while brassinosteroids and auxin play a synergistic role in regulating root elongation. Further study is required to identify the QTLs, genes, and favorable alleles which control the root elongation response to low nitrogen stress in crops.
PMID: 32189077
Planta , IF:3.39 , 2020 Mar , V251 (3) : P73 doi: 10.1007/s00425-020-03367-5
Endogenous auxin determines the pattern of adventitious shoot formation on internodal segments of ipecac.
Graduate School of Life Sciences, Toyo University, 1-1-1 Izumino, Itakura-machi, Ora-gun, Gunma, 374-0193, Japan.; Department of Applied Biosciences, Toyo University, 1-1-1 Izumino, Itakura-machi, Ora-gun, Gunma, 374-0193, Japan.; Department of Biochemistry, Okayama University of Science, 1-1 Ridai-cho, Kita-ku, Okayama, Okayama, 700-0005, Japan.; Institute of Global Innovation Research, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu-shi, Tokyo, 183-8509, Japan.; RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan.; Graduate School of Life Sciences, Toyo University, 1-1-1 Izumino, Itakura-machi, Ora-gun, Gunma, 374-0193, Japan. umehara@toyo.jp.; Department of Applied Biosciences, Toyo University, 1-1-1 Izumino, Itakura-machi, Ora-gun, Gunma, 374-0193, Japan. umehara@toyo.jp.
MAIN CONCLUSION: Endogenous auxin determines the pattern of adventitious shoot formation. Auxin produced in the dominant shoot is transported to the internodal segment and suppresses growth of other shoots. Adventitious shoot formation is required for the propagation of economically important crops and for the regeneration of transgenic plants. In most plant species, phytohormones are added to culture medium to induce adventitious shoots. In ipecac (Carapichea ipecacuanha (Brot.) L. Andersson), however, adventitious shoots can be formed without phytohormone treatment. Thus, ipecac culture allows us to investigate the effects of endogenous phytohormones during adventitious shoot formation. In phytohormone-free culture, adventitious shoots were formed on the apical region of the internodal segments, and a high concentration of IAA was detected in the basal region. To explore the relationship between endogenous auxin and adventitious shoot formation, we evaluated the effects of auxin transport inhibitors, auxin antagonists, and auxin biosynthesis inhibitors on adventitious shoot formation in ipecac. Auxin antagonists and biosynthesis inhibitors strongly suppressed adventitious shoot formation, which was restored by exogenously applied auxin. Auxin biosynthesis and transport inhibitors significantly decreased the IAA level in the basal region and shifted the positions of adventitious shoot formation from the apical region to the middle region of the segments. These data indicate that auxin determines the positions of the shoots formed on internodal segments of ipecac. Only one of the shoots formed grew vigorously; this phenomenon is similar to apical dominance. When the largest shoot was cut off, other shoots started to grow. Naphthalene-1-acetic acid treatment of the cut surface suppressed shoot growth, indicating that auxin produced in the dominant shoot is transported to the internodal segment and suppresses growth of other shoots.
PMID: 32140780
Plant Mol Biol , IF:3.302 , 2020 Mar , V102 (4-5) : P537-551 doi: 10.1007/s11103-020-00963-7
SlCAND1, encoding cullin-associated Nedd8-dissociated protein 1, regulates plant height, flowering time, seed germination, and root architecture in tomato.
Bioengineering College, Chongqing University, Chongqing, 400044, China.; Key Laboratory of Biorheological Science and Technology, Ministry of Education, Chongqing University, Chongqing, 400044, China.; Bioengineering College, Chongqing University, Chongqing, 400044, China. yangyinwu@cqu.edu.cn.; Key Laboratory of Biorheological Science and Technology, Ministry of Education, Chongqing University, Chongqing, 400044, China. yangyinwu@cqu.edu.cn.
KEY MESSAGE: Silencing of SlCAND1 expression resulted in dwarfish, loss of apical dominance, early flowering, suppression of seed germination, and abnormal root architecture in tomato Cullin-RING E3 ligases (CRLs)-dependent ubiquitin proteasome system mediates degradation of numerous proteins that controls a wide range of developmental and physiological processes in eukaryotes. Cullin-associated Nedd8-dissociated protein 1 (CAND1) acts as an exchange factor allowing substrate recognition part exchange and plays a vital role in reactivating CRLs. The present study reports on the identification of SlCAND1, the only one CAND gene in tomato. SlCAND1 expression is ubiquitous and positively regulated by multiple plant hormones. Silencing of SlCAND1 expression using RNAi strategy resulted in a pleiotropic and gibberellin/auxin-associated phenotypes, including dwarf plant with reduced internode length, loss of apical dominance, early flowering, low seed germination percentage, delayed seed germination speed, short primary root, and increased lateral root proliferation and elongation. Moreover, application of exogenous GA3 or IAA could partly rescue some SlCAND1-silenced phenotypes, and the expression levels of gibberellin/auxin-related genes were altered in SlCAND1-RNAi lines. These facts revealed that SlCAND1 is required for gibberellin/auxin-associated regulatory network in tomato. Although SlCAND1 is crucial for multiple developmental processes during vegetative growth stage, SlCAND1-RNAi lines didn't exhibit visible effect on fruit development and ripening. Meanwhile, we discussed that multiple physiological functions of SlCAND1 in tomato are different to previous report of its ortholog in Arabidopsis. Our study adds a new perspective on the functional roles of CAND1 in plants, and strongly supports the hypothesis that CAND1 and its regulated ubiquitin proteasome system are pivotal for plant vegetative growth but possibly have different roles in diverse plant species.
PMID: 31916084
Biochem Biophys Res Commun , IF:2.985 , 2020 Mar , V524 (1) : P83-88 doi: 10.1016/j.bbrc.2020.01.041
Arogenate dehydratases can modulate the levels of phenylacetic acid in Arabidopsis.
Department of Bioregulation and Biointeraction, Graduate School of Agriculture, Tokyo University of Agriculture and Technology, Fuchu, Tokyo, 183-8509, Japan.; Faculty of Agriculture, Yamagata University, Tsuruoka, Yamagata, 997-8555, Japan; RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa, 230-0045, Japan.; RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa, 230-0045, Japan.; Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, 100 Guilin Road, Shanghai, 200234, China.; Department of Biochemistry, Okayama University of Science, Okayama, 700-0005, Japan.; RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa, 230-0045, Japan; Institute of Global Innovation Research, Tokyo University of Agriculture and Technology, Fuchu, Tokyo, 183-8509, Japan. Electronic address: kasahara@go.tuat.ac.jp.
Phenylacetic acid (PAA) is one type of natural auxin and widely exists in plants. Previous biochemical studies demonstrate that PAA in plants is synthesized from phenylalanine (Phe) via phenylpyruvate (PPA), but the PAA biosynthetic genes and its regulation remain unknown. In this article, we show that the AROGENATE DEHYDRATASE (ADT) family, which catalyzes the conversion of arogenate to Phe, can modulate the levels of PAA in Arabidopsis. We found that overexpression of ADT4 or ADT5 remarkably increased the amounts of PAA. Due to an increase in PAA levels, ADT4ox and ADT5ox plants can partially restore the auxin-deficient phenotypes caused by treatments with an inhibitor of the biosynthesis of indole-3-acetic acid (IAA), a main auxin in plants. In contrast, the levels of PAA were significantly reduced in adt multiple knockout mutants. Moreover, the levels of PPA are substantially increased in ADT4 or ADT5 overexpression plants but reduced in adt multiple knockout mutants, suggesting that PPA is a key intermediate of PAA biosynthesis. These results provide an evidence that members of the ADT family of Arabidopsis can modulate PAA level via the PPA-dependent pathway.
PMID: 31980164
Plants (Basel) , IF:2.762 , 2020 Mar , V9 (3) doi: 10.3390/plants9030398
In Vitro Rooting of Capparis spinosa L. as Affected by Genotype and by the Proliferation Method Adopted During the Multiplication Phase.
Department of Agricultural, Food and Forest Sciences (SAAF), University of Palermo, 90128 Palermo, Italy.; Department of Architecture (DARCH), University of Palermo, 90128 Palermo, Italy.
The in vitro rooting of three caper (Capparis spinosa L.) selected biotypes, grown in a commercial orchard on the Sicilian island of Salina (38 degrees 33'49" N), was performed using-as base material for rooting experiments-shoot explants proceeding from two different in vitro culture systems: solid medium and liquid culture in a PlantForm bioreactor (TIS). The regenerated shoots of each accession were submitted to different auxin treatments (NAA, IBA, IAA - 1 or 2 mg L(-1); NAA+IBA 0.75 and 0.25 mg L(-1), respectively), supplemented with sucrose or fructose (mg L(-1)). The highest rooting rate in terms of root percentage (67%) was reached with the explants of the selected accession 'Sal 39' proceeding from liquid culture in PlantForm and induced in the MS medium with sucrose, as a carbon source, supplemented with NAA 0.75 mg L(-1) + IBA 0.25 mg L(-1), after six days in a climatic growth chamber at 25 +/- 1 degrees C in the dark and then placed under a cool white fluorescent lamp, with a PPFD of 35 mumol m(-1) s(-1) and a photoperiod of 16 h. On the other hand, poor rooting rate was generally achieved under all the tested experimental conditions with the other biotypes, 'Sal 37' and 'Sal 35', demonstrating the strong role exerted by the previously adopted proliferation method and by the genotype for successful caper in vitro rooting.
PMID: 32210124
Plants (Basel) , IF:2.762 , 2020 Mar , V9 (3) doi: 10.3390/plants9030379
Capacity of Pseudomonas Strains to Degrade Hydrocarbons, Produce Auxins and Maintain Plant Growth under Normal Conditions and in the Presence of Petroleum Contaminants.
Ufa Institute of Biology, Ufa Federal Research Centre, Russian Academy of Sciences, Ufa 450054, Russia.
The phytoremediation of soil contaminated with petroleum oil products relies on co-operation between plants and rhizosphere bacteria, including the plant growth-promoting effect of the bacteria. We studied the capacity of strains of Pseudomonas, selected as oil degraders, to produce plant hormones and promote plant growth. Strains with intermediate auxin production were the most effective in stimulating the seedling growth of seven plant species under normal conditions. Bacterial seed treatment resulted in about a 1.6-fold increase in the weight of barley seedlings, with the increment being much lower in other plant species. The strains P. plecoglossicida 2.4-D and P. hunanensis IB C7, characterized by highly efficient oil degradation (about 70%) and stable intermediate in vitro auxin production in the presence of oil, were selected for further study with barley. These strains increased the seed germination percentage approximately two-fold under 5% oil concentration in the soil, while a positive effect on further seedling growth was significant when the oil concentration was raised to 8%. This resulted in a 1.3-1.7-fold increase in the seedling mass after 7 days of growth, depending on the bacterial strain. Thus, strains of oil-degrading bacteria selected for their intermediate and stable production of auxin were found to be effective ameliorators of plant growth inhibition resulting from petroleum stress.
PMID: 32204485
Plants (Basel) , IF:2.762 , 2020 Mar , V9 (3) doi: 10.3390/plants9030349
Characterization of the Auxin Efflux Transporter PIN Proteins in Pear.
College of Horticulture, Qingdao Key Lab of Genetic Improvement and Breeding of Horticultural Plants, Qingdao Agricultural University, Qingdao 266109, China.; Institute of Soil and Fertilizer & Resource and Environment, Jiangxi Academy of Agriculture Sciences, Nanchang 330200, China.; College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China.
PIN-FORMED (PIN) encodes a key auxin polar transport family that plays a crucial role in the outward transport of auxin and several growth and development processes, including dwarfing trees. We identified a dwarfing pear rootstock 'OHF51' (Pyrus communis), which limits the growth vigor of the 'Xueqing' (Pyrus bretschneideri x Pyrus pyrifolia) scion, and isolated 14 putative PbPINs from the pear Pyrus bretschneideri. The phylogenic relationships, structure, promoter regions, and expression patterns were analyzed. PbPINs were classified into two main groups based on the protein domain structure and categorized into three major groups using the neighbor-joining algorithm. Promoter analysis demonstrated that PbPINs might be closely related to plant growth and development. Through quantitative real-time PCR (qRT-PCR) analysis, we found that the expression patterns of 14 PbPINs varied upon exposure to different organs in dwarfing and vigorous stocks, 'OHF51' and 'QN101' (Pyrus betulifolia), indicating that they might play varying roles in different tissues and participated in the regulation of growth vigor. These results provide fundamental insights into the characteristics and evolution of the PINs family, as well as the possible relationship between dwarfing ability and auxin polar transport.
PMID: 32164258
Plants (Basel) , IF:2.762 , 2020 Mar , V9 (3) doi: 10.3390/plants9030321
Some Urea Derivatives Positively Affect Adventitious Root Formation: Old Concepts and the State of the Art.
Dipartimento di Scienze Chimiche, della Vita e della Sostenibilita Ambientale, Universita di Parma, Parco Area delle Scienze 11/A, 43124 Parma, Italy.
The success of vegetative propagation programmes strongly depends on adventitious rooting, a postembryonic developmental process whereby new roots can be induced from differentiated cells in positions where normally they do not arise. This auxin-dependent organogenesis has been studied at molecular, cellular, and developmental levels, and our knowledge of the process has improved in recent years. However, bioactive compounds that enhance adventitious root formation and possibly reduce undesirable auxinic side effects are still needed to ameliorate this process. From this point of view, our structure-activity relationship studies concerning urea derivatives revealed that some of them, more specifically, the N,N'-bis-(2,3-methylenedioxyphenyl)urea (2,3-MDPU), the N,N'-bis-(3,4-methylenedioxyphenyl)urea (3,4-MDPU), the 1,3-di(benzo[d]oxazol-5-yl)urea (5-BDPU), and the 1,3-di(benzo[d]oxazol-6-yl)urea (6-BDPU), constitute a category of adventitious rooting adjuvants. The results of our studies are presented here, in order either to highlight the positive effects of the supplementation of these urea derivatives, or to better understand the nature of their interaction with auxin.
PMID: 32143271
Plants (Basel) , IF:2.762 , 2020 Mar , V9 (3) doi: 10.3390/plants9030318
In Vitro Regeneration Potential of White Lupin (Lupinus albus) from Cotyledonary Nodes.
Center for Plant Water-Use and Nutrition Regulation, College of Life Sciences, Joint International Research Laboratory of Water and Nutrient in Cops, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China.; Sanming Academy of Agriculture Sciences, Sanming, Fujian 350002, China.; Institute of Nuclear Agricultural Sciences, Key Laboratory of Nuclear Agricultural Sciences of Ministry of Agriculture and Zhejiang Province, Zhejiang University, Hangzhou 310058, China;kashif@zju.edu.cn (K.A.).
The tissue culture regeneration system of Lupinus albus has always been considered as recalcitrant material due to its genotype-dependent response and low regeneration efficiency that hamper the use of genetic engineering. Establishment of repeatable plant regeneration protocol is a prerequisite tool for successful application of genetic engineering. This aim of this study was to develop standardized, efficient protocol for successful shoot induction from cotyledonary node of white lupin. In this study, 5 day old aseptically cultured seedlings were used to prepare three explants (half cotyledonary node, HCN; whole cotyledonary node, WCN; and traditional cotyledonary node, TCN), cultured on four concentrations of M519 medium (M519, (1/2) M519, (1/3) M519, and (1/4) M519), containing four carbohydrate sources (sucrose, fructose, maltose, and glucose), and stimulated with various combinations of KT (kinetin), and NAA (naphthalene acetic acid) for direct shoot regeneration. High frequency of 80% shoot regeneration was obtained on (1/2) M519 medium (KT 4.0 mg L(-1) + NAA 0.1 mg L(-1)) by using HCN as an explant. Interestingly, combinations of (KT 4.0 mg L(-1) + NAA 0.1 mg L(-1) + BAP 1.67 mg L(-1)), and (KT 2.0 mg L(-1) + NAA 0.1 mg L(-1)) showed similar shoot regeneration frequency of 60%. Augmentation of 0.25 g L(-1) activated charcoal (AC) not only reduced browning effect but also improved shoot elongation. Among the all carbohydrate sources, sucrose showed the highest regeneration frequency with HCN. Additionally, 80% rooting frequency was recorded on (1/2) M519 containing IAA 1.0 mg L(-1) + KT 0.1 mg L(-1) (indole acetic acid) after 28 days of culturing. The present study describes establishment of an efficient and successful protocol for direct plant regeneration of white lupin from different cotyledonary nodes.
PMID: 32138269
Plants (Basel) , IF:2.762 , 2020 Mar , V9 (3) doi: 10.3390/plants9030308
Shedding the Last Layer: Mechanisms of Root Cap Cell Release.
Department of Botany and Plant Pathology and Center for Plant Biology, Purdue University, West Lafayette, IN 47907, USA.
The root cap, a small tissue at the tip of the root, protects the root from environmental stress and functions in gravity perception. To perform its functions, the position and size of the root cap remains stable throughout root growth. This occurs due to constant root cap cell turnover, in which the last layer of the root cap is released, and new root cap cells are produced. Cells in the last root cap layer are known as border cells or border-like cells, and have important functions in root protection against bacterial and fungal pathogens. Despite the importance of root cap cell release to root health and plant growth, the mechanisms regulating this phenomenon are not well understood. Recent work identified several factors including transcription factors, auxin, and small peptides with roles in the production and release of root cap cells. Here, we review the involvement of the known players in root cap cell release, compare the release of border-like cells and border cells, and discuss the importance of root cap cell release to root health and survival.
PMID: 32121604
J Glob Antimicrob Resist , IF:2.706 , 2020 Mar , V20 : P28-30 doi: 10.1016/j.jgar.2019.11.017
Draft genome sequence reveals co-occurrence of multiple antimicrobial resistance and plant probiotic traits in rice root endophytic strain Burkholderia sp. LS-044 affiliated to Burkholderia cepacia complex.
Department of Soil and Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, 145, XingDa Rd., Taichung, 40227, Taiwan.; Department of Agricultural, Food and Nutritional Science, University of Alberta, 1427 College Plaza, Edmonton, Alberta, Canada.; Tetanti AgriBiotech Inc., No. 1 Gongyequ 10th Road, Xitun District, Taichung City 40755, Taiwan.; Department of Soil and Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, 145, XingDa Rd., Taichung, 40227, Taiwan; Innovation and Development Center of Sustainable Agriculture, National Chung Hsing University, Taichung 402, Taiwan. Electronic address: ccyoung@mail.nchu.edu.tw.
OBJECTIVES: Members of the Burkholderia cepacia complex (Bcc) have been isolated from various environmental and clinical samples and reportedly pose a threat to human health. Here we examine the draft genome sequence of Burkholderia sp. LS-044, an antibiotic-resistant endophytic strain affiliated to the Bcc (ST895) inhabiting rice (Oryza sativa ssp. japonica cv. Tainung 71) root. METHODS: Antimicrobial susceptibility of LS-044 was evaluated comparatively with other Burkholderia sp. (CC-Al74 and CC-3XP9) using commercial ATB PSE 5 test strips. The genome of LS-044 was sequenced using an Illumina MiSeq platform. Plant probiotic and antimicrobial resistance genes were screened by Rapid Annotation using Subsystem Technology (RAST), CARD 2017, NCBI and/or UniProt. RESULTS: Plant-associated members of Bcc (LS-044 and CC-Al74) exhibited greater resistance to the majority of antibiotics tested. The draft genome sequence of LS-044 contained 8.78 Mbp in 62 contigs having a G + C content of 66.5%, 8868 coding sequences and 75 RNAs. The genome harboured genes coding for LysR-type beta-lactamase transcription regulator, classes A, C and D beta-lactamases, several metal-dependent beta-lactamases, antibiotic efflux proteins, and proteins conferring resistance to colistin, streptothricin, colicin and fluoroquinolones. Similarly, it also possessed genes for copper homeostasis, copper-cobalt-zinc-cadmium-chromium resistance and reduction of mercury. Genes involved in flagellar motility, hydrolysis of murein and chitin, production of siderophore and auxin, and metabolism of aromatic compounds were also found. CONCLUSION: Genome sequence data revealed an interlinked occurrence of plant probiotic traits and antimicrobial resistance in the rice root endophyte LS-044.
PMID: 31809939
Rapid Commun Mass Spectrom , IF:2.2 , 2020 Mar , V34 (6) : Pe8616 doi: 10.1002/rcm.8616
Development of a relative quantification method for infrared matrix-assisted laser desorption electrospray ionization mass spectrometry imaging of Arabidopsis seedlings.
Department of Chemistry, FTMS Laboratory for Human Health Research, North Carolina State University, Raleigh, NC, 27695, USA.; Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, 27695, USA.; Program in Genetics, North Carolina State University, Raleigh, NC, 27695, USA.; Molecular Education, Technology, and Research Innovation Center (METRIC), North Carolina State University, Raleigh, NC, 27695, USA.
RATIONALE: Mass spectrometry imaging of young seedlings is an invaluable tool in understanding how mutations affect metabolite accumulation in plant development. However, due to numerous biological considerations, established methods for the relative quantification of analytes using infrared matrix-assisted laser desorption electrospray ionization (IR-MALDESI) mass spectrometry imaging are not viable options. In this study, we report a method for the quantification of auxin-related compounds using stable-isotope-labelled (SIL) indole-3-acetic acid (IAA) doped into agarose substrate. METHODS: Wild-type Arabidopsis thaliana seedlings, sur2 and wei8 tar2 loss-of-function mutants, and YUC1 gain-of-function line were grown for 3 days in the dark in standard growth medium. SIL-IAA was doped into a 1% low-melting-point agarose gel and seedlings were gently laid on top for IR-MALDESI imaging with Orbitrap mass spectrometry analysis. Relative quantification was performed post-acquisition by normalization of auxin-related compounds to SIL-IAA in the agarose. Amounts of auxin-related compounds were compared between genotypes to distinguish the effects of the mutations on the accumulation of indolic metabolites of interest. RESULTS: IAA added to agarose was found to remain stable, with repeatability and abundance features of IAA comparable with those of other compounds used in other methods for relative quantification in IR-MALDESI analyses. Indole-3-acetaldoxime was increased in sur2 mutants compared with wild-type and other mutants. Other auxin-related metabolites were either below the limits of quantification or successfully quantified but showing little difference among mutants. CONCLUSIONS: Agarose was shown to be an appropriate sampling surface for IR-MALDESI mass spectrometry imaging of Arabidopsis seedlings. SIL-IAA doping of agarose was demonstrated as a viable technique for relative quantification of metabolites in live seedlings or tissues with similar biological considerations.
PMID: 31658400
J Microbiol Biotechnol , IF:1.992 , 2020 Mar , V30 (3) : P417-426 doi: 10.4014/jmb.1906.06055
Genomics and LC-MS Reveal Diverse Active Secondary Metabolites in Bacillus amyloliquefaciens WS-8.
College of life science, Hebei University, Baoding 071002, P.R.China.; Institute of Biology, Hebei Academy of Science, Shijiazhuang 050081, P.R.China.; Main Crops Disease of Microbial Control Engineering Technology Research Center in Hebei Province, Shijiazhuang 050081, P.R.China.; Hebei Normal University, Shijiazhuang 050024, P.R.China.
Bacillus amyloliquefaciens is an important plant disease-preventing and growth-promoting microorganism. B. amyloliquefaciens WS-8 can stimulate plant growth and has strong antifungal properties. In this study, we sequenced the complete genome of B. amyloliquefaciens WS-8 by Pacific Biosciences RSII (PacBio) Single Molecule Real-Time (SMRT) sequencing. The genome consists of one chromosome (3,929,787 bp) and no additional plasmids. The main bacteriostatic substances were determined by genome, transcriptome, and mass spectrometry data. We thereby laid a theoretical foundation for the utilization of the strain. By genomic analysis, we identified 19 putative biosynthetic gene clusters for secondary metabolites, most of which are potentially involved in the biosynthesis of numerous bioactive metabolites, including difficidin, fengycin, and surfactin. Furthermore, a potential class II lanthipeptide biosynthetic gene cluster and genes that are involved in auxin biosynthesis were found. Through the analysis of transcriptome data, we found that the key bacteriostatic genes, as predicted in the genome, exhibited different levels of mRNA expression. Through metabolite isolation, purification, and exposure experiments, we found that a variety of metabolites of WS-8 exert an inhibitory effect on the necrotrophic fungus Botrytis cinerea, which causes gray mold; by mass spectrometry, we found that the main substances are mainly iturins and fengycins. Therefore, this strain has the potential to be utilized as an antifungal agent in agriculture.
PMID: 31601062
Rev Sci Instrum , IF:1.48 , 2020 Mar , V91 (3) : P034504 doi: 10.1063/1.5120573
ARABIDOMICS-A new experimental platform for molecular analyses of plants in drop towers, on parabolic flights, and sounding rockets.
Gravitational Biology, Institute of Aerospace Medicine, German Aerospace Center (DLR), 51147 Cologne, Germany.; Department of Molecular Ecology, Max-Planck-Institute for Chemical Ecology, 07745 Jena, Germany.; Core Facility Genomics of the Medical Faculty, Westfalische Wilhelms-University, Munster, Germany.; Institute for Molecular Biosciences, Goethe University Frankfurt am Main, 60438 Frankfurt am Main, Germany.
Plants represent an essential part of future life support systems that will enable human space travel to distant planets and their colonization. Therefore, insights into changes and adaptations of plants in microgravity are of great importance. Despite considerable efforts, we still know very little about how plants respond to microgravity environments on the molecular level, partly due to a lack of sufficient hardware and flight opportunities. The plant Arabidopsis thaliana, the subject of this study, represents a well-studied model organism in gravitational biology, particularly for the analysis of transcriptional and metabolic changes. To overcome the limitations of previous plant hardware that often led to secondary effects and to allow for the extraction not only of RNA but also of phytohormones and proteins, we developed a new experimental platform, called ARABIDOMICS, for exposure and fixation under altered gravity conditions. Arabidopsis seedlings were exposed to hypergravity during launch and microgravity during the free-fall period of the MAPHEUS 5 sounding rocket. Seedlings were chemically fixed inflight at defined time points, and RNA and phytohormones were subsequently analyzed in the laboratory. RNA and phytohormones extracted from the fixed biological samples were of excellent quality. Changes in the phytohormone content of jasmonate, auxin, and several cytokinins were observed in response to hypergravity and microgravity.
PMID: 32259966
Plant Biotechnol (Tokyo) , IF:0.901 , 2020 Mar , V37 (1) : P25-30 doi: 10.5511/plantbiotechnology.19.1209a
A simple method to establish an efficient medium suitable for potato regeneration.
Department of Biological Science and Technology, Tokyo University of Science, Katsushika, Tokyo 125-8585, Japan.
Potato (Solanum tuberosum) is one of the important crop plants, and many potato cultivars consist of a tetraploid genome with high heterozygosity. The techniques of transformation and genome editing require plant regeneration. However, no efficient regeneration method has been established except for some specific cultivars, such as 'Sayaka'. In general, it is necessary to determine the adequate concentrations of auxin and cytokinin for plant regeneration. We established an efficient method using a 24-well microplate that easily enabled determination of the concentrations of these plant growth regulators suitable for shoot regeneration. Using this method, the optimal concentrations of these factors were analyzed for two representative potato cultivars, 'Sayaka' and 'Konafubuki'. This analysis revealed there was a large difference in the optimal concentrations between them. Based on this result, a specialized medium for the efficient regeneration of 'Konafubuki' cultivars was proposed. This assay method was also applied for determination of hygromycin sensitivity of these potato cultivars, and it was observed that 'Konafubuki' was rather sensitive to hygromycin. These findings suggested that the selection of a 'Konafubuki' transformant could be achieved using a medium containing a lower amount of hygromycin than that used for 'Sayaka'.
PMID: 32362745
J Genet Genomics , 2020 Mar , V47 (3) : P157-165 doi: 10.1016/j.jgg.2020.02.009
Two homologous INDOLE-3-ACETAMIDE (IAM) HYDROLASE genes are required for the auxin effects of IAM in Arabidopsis.
Section of Cell and Developmental Biology, University of California San Diego, La Jolla, CA, 92093-0116, USA.; Department of Bioregulation and Biointeraction, Graduate School of Agriculture, Tokyo University of Agriculture and Technology, Fuchu, 183-8509, Japan.; RIKEN Center for Sustainable Resource Science, Kanagawa, 230-0045, Japan.; Section of Cell and Developmental Biology, University of California San Diego, La Jolla, CA, 92093-0116, USA; School of Life Sciences, Jilin Normal University, Siping, 136000, China.; Section of Cell and Developmental Biology, University of California San Diego, La Jolla, CA, 92093-0116, USA; Key Laboratory of Plant Ecology, Northeast Forestry University, Harbin, 150040, China.; Section of Cell and Developmental Biology, University of California San Diego, La Jolla, CA, 92093-0116, USA; State Key Laboratory of Silkworm Genome Biology, Institute of Sericulture and Systems Biology, Southwest University, Chongqing, 400716, China.; RIKEN Center for Sustainable Resource Science, Kanagawa, 230-0045, Japan; Institute of Global Innovation Research, Tokyo University of Agriculture and Technology, Tokyo, 183-8509, Japan.; Section of Cell and Developmental Biology, University of California San Diego, La Jolla, CA, 92093-0116, USA. Electronic address: yundezhao@ucsd.edu.
Indole-3-acetamide (IAM) is the first confirmed auxin biosynthetic intermediate in some plant pathogenic bacteria. Exogenously applied IAM or production of IAM by overexpressing the bacterial iaaM gene in Arabidopsis causes auxin overproduction phenotypes. However, it is still inconclusive whether plants use IAM as a key precursor for auxin biosynthesis. Herein, we reported the isolation IAMHYDROLASE1 (IAMH1) gene in Arabidopsis from a forward genetic screen for IAM-insensitive mutants that display normal auxin sensitivities. IAMH1 has a close homolog named IAMH2 that is located right next to IAMH1 on chromosome IV in Arabidopsis. We generated iamh1 iamh2 double mutants using our CRISPR/Cas9 gene editing technology. We showed that disruption of the IAMH genes rendered Arabidopsis plants resistant to IAM treatments and also suppressed the iaaM overexpression phenotypes, suggesting that IAMH1 and IAMH2 are the main enzymes responsible for converting IAM into indole-3-acetic acid (IAA) in Arabidopsis. The iamh double mutants did not display obvious developmental defects, indicating that IAM does not play a major role in auxin biosynthesis under normal growth conditions. Our findings provide a solid foundation for clarifying the roles of IAM in auxin biosynthesis and plant development.
PMID: 32327358