RARTF: database and tools for complete sets of Arabidopsis transcription factors.

More than 5% of all genes in the Arabidopsis thaliana genome have been assumed to code for transcription factors. However, it has been difficult to accurately identify them. To construct proper sets of transcription factors, we used PSI-BLAST and InterProScan, and also checked several families manually. Especially to determine major Arabidopsis transcription factors (MYB, AP2/EREBP, bHLH, NAC, MADS, bZIP, WRKY), we compared the PSI-BLAST search results with those in recent reports. Finally, we identified 1968 proteins as transcription factors (7.4% of all Arabidopsis genes). We established a database named RARTF (RIKEN Arabidopsis Transcription Factor database, http://rarge.gsc.riken.jp/rartf/) based on the identified transcription factors. In RARTF, we provide information on the functional motif of transcription factors, full-length cDNAs, alternative pre-mRNA splicing events and Ac/Ds transposon-tagged mutants. We also provide expression profiles of 400 transcription factor genes in six experiments. We will report expression profiles of all transcription factor genes in various plant tissues under various stress and hormone conditions in the near future.

[1]  M. Ohme-Takagi,et al.  Arabidopsis Ethylene-Responsive Element Binding Factors Act as Transcriptional Activators or Repressors of GCC Box–Mediated Gene Expression , 2000, Plant Cell.

[2]  Jia Liu,et al.  The TIGR rice genome annotation resource: annotating the rice genome and creating resources for plant biologists , 2003, Nucleic Acids Res..

[3]  K. Akiyama,et al.  Monitoring the expression pattern of around 7,000 Arabidopsis genes under ABA treatments using a full-length cDNA microarray , 2002, Functional & Integrative Genomics.

[4]  D. Engelke,et al.  A CBF5 mutation that disrupts nucleolar localization of early tRNA biosynthesis in yeast also suppresses tRNA gene-mediated transcriptional silencing. , 2000, Proceedings of the National Academy of Sciences of the United States of America.

[5]  A. Steinmetz,et al.  A LIM-domain protein from sunflower is localized to the cytoplasm and/or nucleus in a wide variety of tissues and is associated with the phragmoplast in dividing cells , 2004, Plant Molecular Biology.

[6]  M. Holdsworth,et al.  Identification and analysis of proteins that interact with the Avena fatua homologue of the maize transcription factor VIVIPAROUS 1. , 2000, The Plant journal : for cell and molecular biology.

[7]  K. Akiyama,et al.  Monitoring the expression profiles of 7000 Arabidopsis genes under drought, cold and high-salinity stresses using a full-length cDNA microarray. , 2002, The Plant journal : for cell and molecular biology.

[8]  Kazuo Shinozaki,et al.  A collection of 11 800 single-copy Ds transposon insertion lines in Arabidopsis. , 2004, The Plant journal : for cell and molecular biology.

[9]  R. Frye,et al.  Phylogenetic classification of prokaryotic and eukaryotic Sir2-like proteins. , 2000, Biochemical and biophysical research communications.

[10]  K. Shinozaki,et al.  Molecular responses to dehydration and low temperature: differences and cross-talk between two stress signaling pathways. , 2000, Current opinion in plant biology.

[11]  Rolf Apweiler,et al.  InterProScan - an integration platform for the signature-recognition methods in InterPro , 2001, Bioinform..

[12]  E. Lam,et al.  TGA3 is a distinct member of the TGA family of bZIP transcription factors in Arabidopsis thaliana , 1994, Plant Molecular Biology.

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

[14]  R. Stracke,et al.  The R2R3-MYB gene family in Arabidopsis thaliana. , 2001, Current opinion in plant biology.

[15]  G. Haughn,et al.  LEAFY, a Homeotic Gene That Regulates Inflorescence Development in Arabidopsis. , 1991, The Plant cell.

[16]  Y. Nakamura,et al.  Structural analysis of a Lotus japonicus genome. I. Sequence features and mapping of fifty-six TAC clones which cover the 5.4 mb regions of the genome. , 2001, DNA research : an international journal for rapid publication of reports on genes and genomes.

[17]  M. Gerstein,et al.  A Genome-Wide Analysis of Blue-Light Regulation of Arabidopsis Transcription Factor Gene Expression during Seedling Development , 2003 .

[18]  Alex Bateman,et al.  The InterPro Database, 2003 brings increased coverage and new features , 2003, Nucleic Acids Res..

[19]  Shoshi Kikuchi,et al.  Comprehensive analysis of NAC family genes in Oryza sativa and Arabidopsis thaliana. , 2003, DNA research : an international journal for rapid publication of reports on genes and genomes.

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

[21]  S. Tabata,et al.  Structural analysis of a Lotus japonicus genome. V. Sequence features and mapping of sixty-four TAC clones which cover the 6.4 mb regions of the genome. , 2003, DNA research : an international journal for rapid publication of reports on genes and genomes.

[22]  K. Akiyama,et al.  Functional Annotation of a Full-Length Arabidopsis cDNA Collection , 2002, Science.

[23]  P. Tighe,et al.  The Arabidopsis MALE STERILITY1 (MS1) gene is a transcriptional regulator of male gametogenesis, with homology to the PHD-finger family of transcription factors. , 2001, The Plant journal : for cell and molecular biology.

[24]  Joseph M. Dale,et al.  Empirical Analysis of Transcriptional Activity in the Arabidopsis Genome , 2003, Science.

[25]  Terry Gaasterland,et al.  Alternative splicing of mouse transcription factors affects their DNA-binding domain architecture and is tissue specific , 2004, Genome Biology.

[26]  D. Shasha,et al.  A Gene Expression Map of the Arabidopsis Root , 2003, Science.

[27]  F. Parcy,et al.  bZIP transcription factors in Arabidopsis. , 2002, Trends in plant science.

[28]  K. Shinozaki,et al.  Arabidopsis basic leucine zipper transcription factors involved in an abscisic acid-dependent signal transduction pathway under drought and high-salinity conditions. , 2000, Proceedings of the National Academy of Sciences of the United States of America.

[29]  K. Akiyama,et al.  Monitoring expression profiles of Arabidopsis gene expression during rehydration process after dehydration using ca 7000 full-length cDNA microarray. , 2003, The Plant journal : for cell and molecular biology.

[30]  T. Sakurai,et al.  Identification of Arabidopsis Genes Regulated by High Light–Stress Using cDNA Microarray¶ , 2003, Photochemistry and photobiology.

[31]  Hans-Werner Mewes,et al.  MIPS Arabidopsis thaliana Database (MAtDB): an integrated biological knowledge resource for plant genomics , 2004, Nucleic Acids Res..

[32]  N. Gutterson,et al.  Regulation of disease resistance pathways by AP2/ERF transcription factors. , 2004, Current opinion in plant biology.

[33]  G. Martin,et al.  Tomato Transcription Factors Pti4, Pti5, and Pti6 Activate Defense Responses When Expressed in Arabidopsis Article, publication date, and citation information can be found at www.plantcell.org/cgi/doi/10.1105/tpc.000794. , 2002, The Plant Cell Online.

[34]  D. Horner,et al.  Molecular and Phylogenetic Analyses of the Complete MADS-Box Transcription Factor Family in Arabidopsis Article, publication date, and citation information can be found at www.plantcell.org/cgi/doi/10.1105/tpc.011544. , 2003, The Plant Cell Online.

[35]  Imre E Somssich,et al.  WRKY transcription factors: from DNA binding towards biological function. , 2004, Current opinion in plant biology.

[36]  Bernd Weisshaar,et al.  Update on the Basic Helix-Loop-Helix Transcription Factor Gene Family in Arabidopsis thaliana , 2003, The Plant Cell Online.

[37]  Jungwon Yoon,et al.  The Arabidopsis Information Resource (TAIR): a model organism database providing a centralized, curated gateway to Arabidopsis biology, research materials and community , 2003, Nucleic Acids Res..

[38]  Masakazu Satou,et al.  Genome-wide analysis of alternative pre-mRNA splicing in Arabidopsis thaliana based on full-length cDNA sequences. , 2004, Nucleic acids research.

[39]  Benjamin A. Shoemaker,et al.  CDD: a database of conserved domain alignments with links to domain three-dimensional structure , 2002, Nucleic Acids Res..

[40]  K. Shinozaki,et al.  DNA-binding specificity of the ERF/AP2 domain of Arabidopsis DREBs, transcription factors involved in dehydration- and cold-inducible gene expression. , 2002, Biochemical and biophysical research communications.

[41]  D. Landsman,et al.  AT-hook motifs identified in a wide variety of DNA-binding proteins. , 1998, Nucleic acids research.

[42]  Tetsuya Sakurai,et al.  RARGE: a large-scale database of RIKEN Arabidopsis resources ranging from transcriptome to phenome , 2004, Nucleic Acids Res..

[43]  G. Tuskan,et al.  Poplar genomics is getting popular: the impact of the poplar genome project on tree research. , 2004, Plant biology.

[44]  B. Haas,et al.  Full-length messenger RNA sequences greatly improve genome annotation , 2002, Genome Biology.

[45]  D. Wagner,et al.  SPLAYED, a Novel SWI/SNF ATPase Homolog, Controls Reproductive Development in Arabidopsis , 2002, Current Biology.