Legume Transcription Factor Genes: What Makes Legumes So Special?1[W]

All eukaryotic organisms have a diversity of transcription factor (TF) gene families, encoding key proteins regulating gene expression. TF families are strongly conserved across eukaryotic organisms, especially plants. The specific function of each of these TF genes is of interest due to their role

[1]  H. Kouchi,et al.  Positional cloning identifies Lotus japonicus NSP2, a putative transcription factor of the GRAS family, required for NIN and ENOD40 gene expression in nodule initiation. , 2006, DNA research : an international journal for rapid publication of reports on genes and genomes.

[2]  J. Perry,et al.  Lotus japonicus Nodulation Requires Two GRAS Domain Regulators, One of Which Is Functionally Conserved in a Non-Legume1[C][W] , 2006, Plant Physiology.

[3]  M. Luckow,et al.  The Rest of the Iceberg. Legume Diversity and Evolution in a Phylogenetic Context1 , 2003, Plant Physiology.

[4]  B. Roe,et al.  Legume genome evolution viewed through the Medicago truncatula and Lotus japonicus genomes , 2006, Proceedings of the National Academy of Sciences.

[5]  R. Shoemaker,et al.  Fractionation of synteny in a genomic region containing tandemly duplicated genes across glycine max, Medicago truncatula, and Arabidopsis thaliana. , 2008, The Journal of heredity.

[6]  Joseph R Ecker,et al.  Utilizing tiling microarrays for whole-genome analysis in plants. , 2007, The Plant journal : for cell and molecular biology.

[7]  R. Rose,et al.  The Transcription Factor MtSERF1 of the ERF Subfamily Identified by Transcriptional Profiling Is Required for Somatic Embryogenesis Induced by Auxin Plus Cytokinin in Medicago truncatula1[W][OA] , 2008, Plant Physiology.

[8]  S. Chen,et al.  Soybean WRKY-type transcription factor genes, GmWRKY13, GmWRKY21, and GmWRKY54, confer differential tolerance to abiotic stresses in transgenic Arabidopsis plants. , 2008, Plant biotechnology journal.

[9]  G. Oldroyd,et al.  Identification and Characterization of Nodulation-Signaling Pathway 2, a Gene of Medicago truncatula Involved in Nod Factor Signaling1 , 2003, Plant Physiology.

[10]  S. Tabata,et al.  Functional differentiation of Lotus japonicus TT2s, R2R3-MYB transcription factors comprising a multigene family. , 2008, Plant & cell physiology.

[11]  A. Muñoz,et al.  GRAS Proteins Form a DNA Binding Complex to Induce Gene Expression during Nodulation Signaling in Medicago truncatula[W] , 2009, The Plant Cell Online.

[12]  Robert D. Finn,et al.  InterPro: the integrative protein signature database , 2008, Nucleic Acids Res..

[13]  M. Gerstein,et al.  Structure and evolution of transcriptional regulatory networks. , 2004, Current opinion in structural biology.

[14]  R. Hellens,et al.  UNIFOLIATA regulates leaf and flower morphogenesis in pea , 1997, Current Biology.

[15]  Hank C Wu,et al.  Phosphorus Stress in Common Bean: Root Transcript and Metabolic Responses1[W][OA] , 2007, Plant Physiology.

[16]  The Arabidopsis Genome Initiative Analysis of the genome sequence of the flowering plant Arabidopsis thaliana , 2000, Nature.

[17]  M. Ohmori,et al.  The novel symbiotic phenotype of enhanced-nodulating mutant of Lotus japonicus: astray mutant is an early nodulating mutant with wider nodulation zone. , 2002, Plant & cell physiology.

[18]  R. Dixon,et al.  The LAP1 MYB transcription factor orchestrates anthocyanidin biosynthesis and glycosylation in Medicago. , 2009, The Plant journal : for cell and molecular biology.

[19]  Leah Barrera,et al.  The transcriptional regulatory code of eukaryotic cells--insights from genome-wide analysis of chromatin organization and transcription factor binding. , 2006, Current opinion in cell biology.

[20]  H. Leung,et al.  Candidate defense genes from rice, barley, and maize and their association with qualitative and quantitative resistance in rice. , 2003, Molecular plant-microbe interactions : MPMI.

[21]  B. Roe,et al.  Highly syntenic regions in the genomes of soybean, Medicago truncatula, and Arabidopsis thaliana , 2005, BMC Plant Biology.

[22]  N. Young,et al.  Translating Medicago truncatula genomics to crop legumes. , 2009, Current opinion in plant biology.

[23]  F. Sánchez,et al.  Essential role of MYB transcription factor: PvPHR1 and microRNA: PvmiR399 in phosphorus-deficiency signalling in common bean roots. , 2008, Plant, cell & environment.

[24]  M. Crespi,et al.  Differential Expression of the TFIIIA Regulatory Pathway in Response to Salt Stress between Medicago truncatula Genotypes1[W] , 2007, Plant Physiology.

[25]  F. Frugier,et al.  EFD Is an ERF Transcription Factor Involved in the Control of Nodule Number and Differentiation in Medicago truncatula[W] , 2008, The Plant Cell Online.

[26]  J. Ray,et al.  A sequence based synteny map between soybean and Arabidopsis thaliana , 2007, BMC Genomics.

[27]  Sarah A. Teichmann,et al.  DBD––taxonomically broad transcription factor predictions: new content and functionality , 2007, Nucleic Acids Res..

[28]  M. Gribskov,et al.  The Genome of Black Cottonwood, Populus trichocarpa (Torr. & Gray) , 2006, Science.

[29]  S. Tabata,et al.  A plant receptor-like kinase required for both bacterial and fungal symbiosis , 2002, Nature.

[30]  Leif Schauser,et al.  A plant regulator controlling development of symbiotic root nodules , 1999, Nature.

[31]  Cathy H. Wu,et al.  The Universal Protein Resource (UniProt) , 2005, Nucleic Acids Res..

[32]  Jun Yang,et al.  Floral Patterning in Lotus japonicus1[w] , 2005, Plant Physiology.

[33]  J. Dubcovsky,et al.  A cluster of 11 CBF transcription factors is located at the frost tolerance locus Fr-Am2 in Triticum monococcum , 2006, Molecular Genetics and Genomics.

[34]  Takashi Ito,et al.  Structure and Function of the PB1 Domain, a Protein Interaction Module Conserved in Animals, Fungi, Amoebas, and Plants , 2007, Science's STKE.

[35]  Sara L. Zimmer,et al.  The Chlamydomonas Genome Reveals the Evolution of Key Animal and Plant Functions , 2007, Science.

[36]  Scott A. Taylor,et al.  PROLIFERATING INFLORESCENCE MERISTEM, a MADS-Box Gene That Regulates Floral Meristem Identity in Pea1 , 2002, Plant Physiology.

[37]  R. Shoemaker,et al.  Comparative physical mapping reveals features of microsynteny between Glycine max, Medicago truncatula, and Arabidopsis thaliana. , 2004, Genome.

[38]  Aili Li,et al.  Phylogeny, gene structures, and expression patterns of the ERF gene family in soybean (Glycine max L.) , 2008, Journal of experimental botany.

[39]  Mark Stitt,et al.  Real-time RT-PCR profiling of over 1400 Arabidopsis transcription factors: unprecedented sensitivity reveals novel root- and shoot-specific genes. , 2004, The Plant journal : for cell and molecular biology.

[40]  M. Crespi,et al.  The Medicago truncatula CRE1 Cytokinin Receptor Regulates Lateral Root Development and Early Symbiotic Interaction with Sinorhizobium meliloti[W] , 2006, The Plant Cell Online.

[41]  Arsen O. Batagov,et al.  The Sym35 Gene Required for Root Nodule Development in Pea Is an Ortholog of Nin from Lotus japonicus 1 , 2003, Plant Physiology.

[42]  Tao Chen,et al.  A Novel ARID DNA-Binding Protein Interacts with SymRK and Is Expressed during Early Nodule Development in Lotus japonicus1[C][W][OA] , 2008, Plant Physiology.

[43]  J. Beltrán,et al.  Analysis of PEAM4, the pea AP1 functional homologue, supports a model for AP1-like genes controlling both floral meristem and floral organ identity in different plant species. , 2001, The Plant journal : for cell and molecular biology.

[44]  T. Bisseling,et al.  NSP1 of the GRAS Protein Family Is Essential for Rhizobial Nod Factor-Induced Transcription , 2005, Science.

[45]  Eleazar Eskin,et al.  Using Network Component Analysis to Dissect Regulatory Networks Mediated by Transcription Factors in Yeast , 2009, PLoS Comput. Biol..

[46]  Mihaela M. Martis,et al.  The Sorghum bicolor genome and the diversification of grasses , 2009, Nature.

[47]  Bogumil J. Karas,et al.  A Cytokinin Perception Mutant Colonized by Rhizobium in the Absence of Nodule Organogenesis , 2007, Science.

[48]  X. Ye,et al.  GmDREB2, a soybean DRE-binding transcription factor, conferred drought and high-salt tolerance in transgenic plants. , 2007, Biochemical and biophysical research communications.

[49]  S. Carroll Chance and necessity: the evolution of morphological complexity and diversity , 2001, Nature.

[50]  The UniProt Consortium,et al.  The Universal Protein Resource (UniProt) 2009 , 2008, Nucleic Acids Res..

[51]  A. Barski,et al.  Genomic location analysis by ChIP‐Seq , 2009, Journal of cellular biochemistry.

[52]  G. Stacey,et al.  Identification of 118 Arabidopsis transcription factor and 30 ubiquitin-ligase genes responding to chitin, a plant-defense elicitor. , 2007, Molecular plant-microbe interactions : MPMI.

[53]  Michael K. Udvardi,et al.  Dissection of Symbiosis and Organ Development by Integrated Transcriptome Analysis of Lotus japonicus Mutant and Wild-Type Plants , 2009, PloS one.

[54]  J. F. Marsh,et al.  Medicago truncatula NIN Is Essential for Rhizobial-Independent Nodule Organogenesis Induced by Autoactive Calcium/Calmodulin-Dependent Protein Kinase1 , 2007, Plant Physiology.

[55]  R. Shoemaker,et al.  Estimates of conserved microsynteny among the genomes of Glycine max, Medicago truncatula and Arabidopsis thaliana , 2003, Theoretical and Applied Genetics.

[56]  J. Beltrán,et al.  Isolation of mtpim Proves Tnt1 a Useful Reverse Genetics Tool in Medicago truncatula and Uncovers New Aspects of AP1-Like Functions in Legumes1 , 2006, Plant Physiology.

[57]  D. Soltis,et al.  Rosid radiation and the rapid rise of angiosperm-dominated forests , 2009, Proceedings of the National Academy of Sciences.

[58]  B. Roe,et al.  Estimating genome conservation between crop and model legume species. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[59]  Kathryn VandenBosch,et al.  An ERF Transcription Factor in Medicago truncatula That Is Essential for Nod Factor Signal Transduction[W] , 2007, The Plant Cell Online.

[60]  G. Weiller,et al.  A gene expression atlas of the model legume Medicago truncatula. , 2008, The Plant journal : for cell and molecular biology.

[61]  Rex T. Nelson,et al.  Gene duplication and paleopolyploidy in soybean and the implications for whole genome sequencing , 2007, BMC Genomics.

[62]  J. Gouzy,et al.  Expression Profiling in Medicago truncatula Identifies More Than 750 Genes Differentially Expressed during Nodulation, Including Many Potential Regulators of the Symbiotic Program1[w] , 2004, Plant Physiology.

[63]  J. Hofer,et al.  Legume Transcription Factors: Global Regulators of Plant Development and Response to the Environment1[W] , 2007, Plant Physiology.

[64]  K. Marcker,et al.  VsENBP1 regulates the expression of the early nodulin PsENOD12B , 1999, Plant Molecular Biology.

[65]  Youzhi Ma,et al.  Cold-induced modulation and functional analyses of the DRE-binding transcription factor gene, GmDREB3, in soybean (Glycine max L.) , 2008, Journal of experimental botany.

[66]  W. McCombie,et al.  Syntenic Relationships between Medicago truncatulaand Arabidopsis Reveal Extensive Divergence of Genome Organization1,212 , 2003, Plant Physiology.

[67]  M. Crespi,et al.  Cytokinin: secret agent of symbiosis. , 2008, Trends in plant science.

[68]  Clive Brown,et al.  Toward the $1000 human genome , 2005 .

[69]  C. Poulsen,et al.  A protein binding AT-rich sequence in the soybean leghemoglobin c3 promoter is a general cis element that requires proximal DNA elements to stimulate transcription. , 1994, The Plant cell.

[70]  G. Tóth,et al.  Significant microsynteny with new evolutionary highlights is detected between Arabidopsis and legume model plants despite the lack of macrosynteny , 2005, Molecular Genetics and Genomics.

[71]  B. Mueller‐Roeber,et al.  A quantitative RT-PCR platform for high-throughput expression profiling of 2500 rice transcription factors , 2007, Plant Methods.

[72]  James R. Knight,et al.  Genome sequencing in microfabricated high-density picolitre reactors , 2005, Nature.

[73]  J. Poulain,et al.  The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla , 2007, Nature.

[74]  A. Timmers,et al.  The HCL gene of Medicago truncatula controls Rhizobium-induced root hair curling. , 2001, Development.

[75]  M. Crespi,et al.  Identification of transcription factors involved in root apex responses to salt stress in Medicago truncatula , 2008, Molecular Genetics and Genomics.

[76]  J. Bennetzen,et al.  The Physcomitrella Genome Reveals Evolutionary Insights into the Conquest of Land by Plants , 2008, Science.

[77]  Huanming Yang,et al.  A Draft Sequence of the Rice Genome (Oryza sativa L. ssp. indica) , 2002, Science.

[78]  Hank C Wu,et al.  A community resource for high-throughput quantitative RT-PCR analysis of transcription factor gene expression in Medicago truncatula , 2008, Plant Methods.

[79]  F. J. Bruijn,et al.  Interaction of a nodule specific, trans‐acting factor with distinct DNA elements in the soybean leghaemoglobin Ibc3 5′ upstream region , 1988, The EMBO journal.

[80]  M. Pineda,et al.  Nuclear factors interact with conserved A/T-rich elements upstream of a nodule-enhanced glutamine synthetase gene from French bean. , 1990, The Plant cell.

[81]  M. Cho,et al.  Pathogen-induced binding of the soybean zinc finger homeodomain proteins GmZF-HD1 and GmZF-HD2 to two repeats of ATTA homeodomain binding site in the calmodulin isoform 4 (GmCaM4) promoter , 2007, Nucleic acids research.

[82]  Stefan R. Henz,et al.  A gene expression map of Arabidopsis thaliana development , 2005, Nature Genetics.

[83]  S. Tabata,et al.  A Positive Regulatory Role for LjERF1 in the Nodulation Process Is Revealed by Systematic Analysis of Nodule-Associated Transcription Factors of Lotus japonicus1[W] , 2008, Plant Physiology.

[84]  S. Chen,et al.  The soybean Dof-type transcription factor genes, GmDof4 and GmDof11, enhance lipid content in the seeds of transgenic Arabidopsis plants. , 2007, The Plant journal : for cell and molecular biology.

[85]  L. Schauser,et al.  Evolution of NIN-Like Proteins in Arabidopsis, Rice, and Lotus japonicus , 2005, Journal of Molecular Evolution.

[86]  T. Joshi,et al.  Large-Scale Analysis of Putative Soybean Regulatory Gene Expression Identifies a Myb Gene Involved in Soybean Nodule Development1[W][OA] , 2009, Plant Physiology.

[87]  E. Journet,et al.  Four Genes of Medicago truncatula Controlling Components of a Nod Factor Transduction Pathway , 2000, Plant Cell.

[88]  R. Shoemaker,et al.  Bridging Model and Crop Legumes through Comparative Genomics , 2005, Plant Physiology.

[89]  D. Grant,et al.  Genome organization in dicots: genome duplication in Arabidopsis and synteny between soybean and Arabidopsis. , 2000, Proceedings of the National Academy of Sciences of the United States of America.

[90]  F. J. Bruijn,et al.  Primary structure and promoter analysis of leghemoglobin genes of the stem-nodulated tropical legume Sesbania rostrata: Conserved coding sequences, cis-elements and trans-acting factors , 1988, Molecular and General Genetics MGG.

[91]  W. Scheible,et al.  Repressor- and Activator-Type Ethylene Response Factors Functioning in Jasmonate Signaling and Disease Resistance Identified via a Genome-Wide Screen of Arabidopsis Transcription Factor Gene Expression[w] , 2005, Plant Physiology.

[92]  E. Stockinger,et al.  Fine mapping of a HvCBF gene cluster at the frost resistance locus Fr-H2 in barley , 2007, Theoretical and Applied Genetics.

[93]  R. R. Samaha,et al.  Arabidopsis transcription factors: genome-wide comparative analysis among eukaryotes. , 2000, Science.

[94]  J. F. Marsh,et al.  Nodulation Signaling in Legumes Requires NSP2, a Member of the GRAS Family of Transcriptional Regulators , 2005, Science.

[95]  R. Shoemaker,et al.  Placing paleopolyploidy in relation to taxon divergence: a phylogenetic analysis in legumes using 39 gene families. , 2005, Systematic biology.

[96]  J. Downie,et al.  Coordinating nodule morphogenesis with rhizobial infection in legumes. , 2008, Annual review of plant biology.

[97]  M. Gerstein,et al.  Genomic analysis of regulatory network dynamics reveals large topological changes , 2004, Nature.

[98]  B. Zhu,et al.  Identification and characterization of a novel heat shock transcription factor gene, GmHsfA1, in soybeans (Glycine max) , 2006, Journal of Plant Research.

[99]  Jessica A Schlueter,et al.  Mining EST databases to resolve evolutionary events in major crop species. , 2004, Genome.