MicroRNAs in the Rhizobia Legume Symbiosis
PLANT PHYSIOLOGYPublished 29 September 2009Open access
Stacey A. Simon, Blake C. Meyers, D. Janine Sherrier
Citations67
SJR quartileQ1
SJR score2.16
SNIP1.66
Generate an AI Snapshot to get a quick, structured summary of this paper.
Study Snapshot
ObjectiveStudy objective
MethodsResearch methodology
PopulationPopulation studied
Sample sizeSample sizes
OutcomesStudy outcomes here
ResultsStudy results comes here
LimitationsResearch study limitations comes here
A concise AI-generated summary of the paper will appear here once you click Generate AI Snapshot.
TL;DR
Legumes are agronomically valuable crops for food and fodder production worldwide because they are rich in protein, oil, fiber, and micronutrients.
Abstract
LEGUME SYMBIOSES
Keywords
Agricultural and Biological Sciences
NatureThe plant immune system
13,103 Citations2006Jonathan D. G. Jones, Jeffery L. Dangl
A detailed understanding of plant immune function will underpin crop improvement for food, fibre and biofuels production and provide extraordinary insights into molecular recognition, cell biology and evolution across biological kingdoms.
Nucleic Acids ResearchmiRBase: microRNA sequences, targets and gene nomenclature
4,785 Citations2005Sam Griffiths‐Jones
The miRBase database aims to provide integrated interfaces to comprehensive microRNA sequence data, annotation and predicted gene targets, and acts as an independent arbiter of microRNA gene nomenclature.
Nucleic Acids ResearchmiRBase: tools for microRNA genomics
4,403 Citations2007Sam Griffiths‐Jones, Harpreet K. Saini +2 more
The overlap of miRNA sequences with annotated transcripts, both protein- and non-coding, are described and graphical views of the locations of a wide range of genomic features in model organisms allow for the first time the prediction of the likely boundaries of many miRNA primary transcripts.
Annual Review of Plant BiologyMicroRNAs AND THEIR REGULATORY ROLES IN PLANTS
2,738 Citations2006Matthew W. Jones-Rhoades, David P. Bartel +1 more
The importance of miRNA-directed gene regulation during plant development is now particularly clear and typically at the cores of gene regulatory networks, targeting genes that are themselves regulators, such as those encoding transcription factors and F-box proteins.
Molecular CellComputational Identification of Plant MicroRNAs and Their Targets, Including a Stress-Induced miRNA
2,300 Citations2004Matthew W. Jones-Rhoades, David P. Bartel
Comparative genomic approaches were developed to systematically identify both miRNAs and their targets that are conserved in Arabidopsis thaliana and rice, and the expression of miR395, the sulfurylase-targeting miRNA, increases upon sulfate starvation, showing that miRNAAs can be induced by environmental stress.
CellmicroRNA-Directed Phasing during Trans-Acting siRNA Biogenesis in Plants
2,294 Citations2005Edwards Allen, Zhixin Xie +2 more
Data support a model in which miRNA-guided formation of a 5' or 3' terminus within pre-ta-siRNA transcripts, followed by RDR6-dependent formation of dsRNA and Dicer-like processing, yields phased ta-siRNAs that negatively regulate other genes.
Nucleic Acids ResearchThe microRNA Registry
2,248 Citations2003Sam Griffiths‐Jones
The miRNA Registry provides a service for the assignment of miRNA gene names prior to publication and a comprehensive and searchable database of published miRNA sequences is accessible via a web interface.
NatureThe F-box protein TIR1 is an auxin receptor
2,070 Citations2005Nihal Dharmasiri, Sunethra Dharmasiri +1 more
TIR1 is an auxin receptor that mediates Aux/IAA degradation and auxin-regulated transcription and the loss of TIR1 and three related F-box proteins eliminates saturable auxin binding in plant extracts.
ScienceA Plant miRNA Contributes to Antibacterial Resistance by Repressing Auxin Signaling
1,971 Citations2006Lionel Navarro, Patrice Dunoyer +6 more
It is shown that a flagellin-derived peptide induces a plant microRNA (miRNA) that negatively regulates messenger RNAs for the F-box auxin receptors TIR1, AFB2, and AFB3, implicating auxin in disease susceptibility and miRNA-mediated suppression of auxin signaling in resistance.
The Plant CellNovel and Stress-Regulated MicroRNAs and Other Small RNAs from Arabidopsis[W]
1,942 Citations2004Ramanjulu Sunkar, Jian‐Kang Zhu
It is suggested that a large number of miRNAs and other small regulatory RNAs are encoded by the Arabidopsis genome and that some of them may play important roles in plant responses to environmental stresses as well as in development and genome maintenance.
RNAA uniform system for microRNA annotation
1,902 Citations2003Victor Ambros, Bonnie Bartel +11 more
Guidelines are presented for the identification and annotation of new miRNAs from diverse organisms, particularly so that mi RNAs can be reliably distinguished from other RNAs such as small interfering RNAs.
The Plant CellCriteria for Annotation of Plant MicroRNAs
1,220 Citations2008Blake C. Meyers, Michael J. Axtell +19 more
The specific criteria required for the annotation of plant miRNAs are updated, including experimental and computational data, as well as refinements to standard nomenclature.
The Plant CellMicroRNA Directs mRNA Cleavage of the Transcription Factor <i>NAC1</i> to Downregulate Auxin Signals for Arabidopsis Lateral Root Development
997 Citations2005Hui‐Shan Guo, Qi Xie +2 more
It is shown that miR164 guides the cleavage of endogenous and transgenic NAC1 mRNA, producing 3′-specific fragments, which indicates that auxin induction ofmiR164 provides a homeostatic mechanism to clear Nac1 mRNA to downregulate auxin signals.
DevelopmentModulation of floral development by a gibberellin-regulated microRNA
839 Citations2004Patrick Achard, Alan J. Herr +2 more
It is proposed that miR159 is a phytohormonally regulated homeostatic modulator of GAMYB activity, and hence of GAmyB-dependent developmental processes.
Nature GeneticsFunctions of microRNAs and related small RNAs in plants
818 Citations2006Allison C. Mallory, Hervé Vaucheret
This review focuses on the regulatory roles of plant miRNAs during development, in the adaptive response to stresses and in the miRNA pathway itself, which participates in post-transcriptional control of gene expression.
Development<i>Arabidopsis microRNA167</i>controls patterns of<i>ARF6</i>and<i>ARF8</i>expression, and regulates both female and male reproduction
757 Citations2006Miin‐Feng Wu, Qing Tian +1 more
The essential patterning function of miR167 contrasts with cases from animals in which miRNAs reinforce or maintain transcriptionally established gene expression patterns, and for fertility of both ovules and anthers.
Proceedings of the National Academy of SciencesCell-specific nitrogen responses mediate developmental plasticity
617 Citations2008Miriam L. Gifford, Alexis Dean +3 more
Cellular profiling of five Arabidopsis root cell types in response to an influx of a critical resource, nitrogen, is used to uncover a vast and predominantly cell-specific response to nitrogen, revealing a previously cryptic component of cell- specific responses to nitrogen.
FEBS LettersmicroRNA biogenesis and function in plants
564 Citations2005Xuemei Chen
The high degree of sequence complementarity between plant miRNAs and their target mRNAs has facilitated the bioinformatic prediction of miRNA targets, many of which have been subsequently validated.
Proceedings of the National Academy of SciencesThe <i>Arabidopsis</i> double-stranded RNA-binding protein HYL1 plays a role in microRNA-mediated gene regulation
525 Citations2004Meng-Hsuan Han, Saiprasad Goud +2 more
Observations provide evidence that the HYL1 protein is part of a nuclear macromolecular complex that is involved in miRNA-mediated gene regulation, and suggest that mi RNA-mediated changes in mRNA stability play a vital role in plant hormone signaling.
Genes & Development<i>MtHAP2-1</i> is a key transcriptional regulator of symbiotic nodule development regulated by microRNA169 <i>in Medicago truncatula</i>
506 Citations2006Jean‐Philippe Combier, Florian Frugier +9 more
It is suggested that the miR169-mediated restriction of MtHAP2-1 expression to the nodule meristematic zone is essential for the differentiation of nodule cells.
PLANT PHYSIOLOGYIdentification of Nutrient-Responsive Arabidopsis and Rapeseed MicroRNAs by Comprehensive Real-Time Polymerase Chain Reaction Profiling and Small RNA Sequencing
499 Citations2009Bikram Datt Pant, Magdalena Musialak‐Lange +6 more
The Plant CellA Mutation in the Arabidopsis <i>HYL1</i> Gene Encoding a dsRNA Binding Protein Affects Responses to Abscisic Acid, Auxin, and Cytokinin
489 Citations2000Cheng Lu, Nina V. Fedoroff
Evidence is presented that the HYL1 gene is ABA-regulated and encodes a nuclear dsRNA binding protein that contains two double-stranded RNA (dsRNA) binding motifs, a nuclear localization motif, and a C-terminal repeat structure suggestive of a protein–protein interaction domain that is hypothesized to be a regulatory protein functioning at the transcriptional or post-transcriptional level.
The Plant JournalSulphur starvation induces the expression of microRNA‐395 and one of its target genes but in different cell types
403 Citations2008Cintia Goulart Kawashima, Naoko Yoshimoto +5 more
Results illustrate that negative temporal correlation between the expression level of a miRNA and its target gene in a complex tissue cannot be a requirement for target gene validation and suggest that translocation of miR395 from leaves to roots through the phloem is not necessary for plants growing on -S soil/medium.
Current Opinion in Plant BiologyThe developmental role of microRNA in plants
395 Citations2004Catherine Kidner, Robert A. Martienssen
Over the past year, the list of known miRNAs, confirmed targets and developmental effects has expanded, as has the realization that they are conserved during evolution and that small RNAs can play a direct role in cell-cell signaling.
BMC Plant BiologyIn silico identification of conserved microRNAs in large number of diverse plant species
381 Citations2008Ramanjulu Sunkar, Guru Jagadeeswaran
By combining the expression analysis with the computational approach, it is found that 6 miRNAs and 2 small RNAs that have been identified only in Arabidopsis thus far, are also conserved in Brassica spp.
Genome ResearchMicroRNAs and other small RNAs enriched in the <i>Arabidopsis</i> RNA-dependent RNA polymerase<i>-</i>2 mutant
343 Citations2006Cheng Lu, Karthik Kulkarni +9 more
Deep sequencing of mutants provides a genetic approach for the dissection and characterization of diverse small RNA populations and the identification of low abundance miRNAs.
BMC GenomicsNovel and nodulation-regulated microRNAs in soybean roots
323 Citations2008Senthil Subramanian, Yan Fu +4 more
Construction and analysis of a small RNA library led to the identification of 20 conserved and 35 novel miRNA families in soybean and enable investigation of the role of miRNAs in rhizobial symbiosis.
The Plant JournalMicroRNA166 controls root and nodule development in <i>Medicago truncatula</i>
309 Citations2008Adnane Boualem, Philippe Laporte +7 more
Plant polycistronic miRNA precursors, although rare, can be processed, and MIR166-mediated post-transcriptional regulation is a new regulatory pathway involved in the regulation of legume root architecture.
DevelopmentHASTY, the<i>Arabidopsis</i>ortholog of exportin 5/MSN5, regulates phase change and morphogenesis
291 Citations2003Krista Bollman, Milo J. Aukerman +4 more
The hst loss-of-function phenotype suggests that this protein regulates the nucleocytoplasmic transport of molecules involved in several different morphogenetic pathways, as well as molecules generally required for root and shoot growth.
The Plant JournalDisruption and overexpression of <i>auxin response factor 8</i> gene of <i>Arabidopsis</i> affect hypocotyl elongation and root growth habit, indicating its possible involvement in auxin homeostasis in light condition
267 Citations2004Chang-En Tian, Hideki Muto +5 more
Sensitivity to auxin was unaltered in arf8-1 hypocotyls with respect to growth inhibition caused by exogenously applied auxin and growth promotion induced by higher temperatures, and ARF8 may control the free IAA level in a negative feedback fashion by regulating GH3 gene expression.
Plant Molecular BiologyConserved and novel miRNAs in the legume Phaseolus vulgaris in response to stress
264 Citations2009Catalina Arenas‐Huertero, Beatriz Pérez +7 more
It is proposed that the novel miRNAs present in common bean and other legumes, are involved in regulation of legume-specific processes including adaptation to diverse external cues.
BMC GenomicsHigh-throughput sequencing of Medicago truncatula short RNAs identifies eight new miRNA families
264 Citations2008György Szittya, Simon Moxon +5 more
Deep sequencing of short RNAs from M. truncatula leaves identified eight new miRNAs indicating that specific miRN as well as 26 novel miRNA candidates that were potentially generated from 32 loci.
The Plant CellGenome-Wide<i>Medicago truncatula</i>Small RNA Analysis Revealed Novel MicroRNAs and Isoforms Differentially Regulated in Roots and Nodules
250 Citations2009Christine Lelandais‐Brière, Loreto Naya +6 more
Deep sequencing of small RNAs from root apexes and nodules of M. truncatula was used to identify 100 novel candidate miRNAs encoded by 265 hairpin precursors, and new atypical precursor classes producing only specific 21- and 24-nucleotide smallRNAs were found.
MethodsConstruction of small RNA cDNA libraries for deep sequencing
240 Citations2007Cheng Lu, Blake C. Meyers +1 more
The methods used in the laboratory to construct small RNA cDNA libraries for high-throughput sequencing using technologies such as MPSS, 454 or SBS are described.
The Plant JournalMicroRNAs in loblolly pine ( <i>Pinus taeda</i> L.) and their association with fusiform rust gall development
228 Citations2007Shanfa Lu, Ying‐Hsuan Sun +2 more
A new genetic basis for host-pathogen interactions in the development of fusiform rust gall is revealed and 82 plant disease-related transcripts that may also response to miRNA regulation in pine are predicted.
PLANT PHYSIOLOGYMechanism of Infection Thread Elongation in Root Hairs of<i>Medicago truncatula</i>and Dynamic Interplay with Associated Rhizobial Colonization
210 Citations2008Joëlle Fournier, Ton Timmers +4 more
In vivo studies have shown that gaps within the bacterial file are a common feature during the early stages of IT development, and that segments of the file are able to slide collectively down the thread.
Plant Cell & EnvironmentEssential role of MYB transcription factor: PvPHR1 and microRNA: PvmiR399 in phosphorus‐deficiency signalling in common bean roots
203 Citations2008Oswaldo Valdés‐López, Catalina Arenas‐Huertero +6 more
The analysis of DICER-like1 (PvDCL1) silenced bean composite plants suppressed for accumulation of PvmiR399 and other miRNAs suggested that miR399 is a negative regulator of the ubiquitin E2 conjugase: PvPHO2 expression.
Biochemical and Biophysical Research CommunicationsInsights into the mechanism of plant development: Interactions of miRNAs pathway with phytohormone response
148 Citations2009Qing Liu, Yujie Chen
Progress on the current known relationship of miRNAs with phytohormone signaling is highlighted, and the potential roles of some specific mi RNAs in hormone signaling were also discussed.
Biochemical and Biophysical Research CommunicationsIdentification and expression analysis of miRNAs from nitrogen-fixing soybean nodules
148 Citations2008Yanwei Wang, Pingchuan Li +4 more
It is suggested that miRNAs play critical and diverse roles in SNF, nutrient acquisition, and plant development, as well as genes that are involved in multiple biological processes.
FEBS LettersEndogenous small RNAs and antibacterial immunity in plants
119 Citations2008Hailing Jin
Certain endogenous small RNAs in plants are induced or repressed in response to pathogen attack and subsequently regulate the expression of genes involved in disease resistance and defense responses by mediating transcriptional or post‐transcriptional gene silencing.
Plant Signaling & BehaviorPositioning the nodule, the hormone dictum
105 Citations2009Yiliang Ding, Giles Oldroyd
How the tissue specific nature of hormonal action dictates where, when and how a nodule is formed is reviewed and discussed.
Nucleic Acids ResearchOligoHeatMap (OHM): an online tool to estimate and display hybridizations of oligonucleotides onto DNA sequences
70 Citations2008Olivier Croce, François Chevenet +1 more
OHM (OligoHeatMap) is an online tool able to provide estimates of Tm for a set of oligomers and aSet of aligned sequences, not only as text files of complete results but also in a graphical way: Tm values are translated into colors and displayed as a heat map image, either stand alone or to be used by softwares such as TreeDyn to be included in a phylogenetic tree.
