Transcriptional profiling of genes responsive to abscisic acid and gibberellin in rice: phenotyping and comparative analysis between rice and Arabidopsis.

We collected and completely sequenced 32,127 full-length complementary DNA clones from Oryza sativa L. ssp. japonica cv. "Nipponbare." Mapping of these clones to genomic DNA revealed approximately 20,500 transcriptional units (TUs) in the rice genome. For each TU, we selected 60-mers using an algorithm that took into account some DNA conditions such as base composition and sequence complexity. Using in situ synthesis technology, we constructed oligonucleotide arrays with these TUs on glass slides. We targeted RNAs prepared from normally grown rice callus and from callus treated with abscisic acid (ABA) or gibberellin (GA). We identified 200 ABA-responsive and 301 GA-responsive genes, many of which had never before been annotated as ABA or GA responsive in other expression analysis. Comparison of these genes revealed antagonistic regulation of almost all by both hormones; these had previously been annotated as being responsible for protein storage and defense against pathogens. Comparison of the cis-elements of genes responsive to one or antagonistic to both hormones revealed that the antagonistic genes had cis-elements related to ABA and GA responses. The genes responsive to only one hormone were rich in cis-elements that supported ABA and GA responses. In a search for the phenotypes of mutants in which a retrotransposon was inserted in these hormone-responsive genes, we identified phenotypes related to seed formation or plant height, including sterility, vivipary, and dwarfism. In comparison of cis-elements for hormone response genes between rice and Arabidopsis thaliana, we identified cis-elements for dehydration-stress response as Arabidopsis specific and for protein storage as rice specific.

[1]  G. Heck,et al.  Barley embryo globulin 1 gene, Beg1: Characterization of cDNA, chromosome mapping and regulation of expression , 1993, Molecular and General Genetics MGG.

[2]  K. Shinozaki,et al.  Monitoring Expression Profiles of Rice Genes under Cold, Drought, and High-Salinity Stresses and Abscisic Acid Application Using cDNA Microarray and RNA Gel-Blot Analyses1[w] , 2003, Plant Physiology.

[3]  M. Delseny,et al.  Characterization of a gene encoding an abscisic acid‐inducible type‐2 lipid transfer protein from rice , 1998, FEBS letters.

[4]  Yujun Zhang,et al.  Sequence and analysis of rice chromosome 4 , 2002, Nature.

[5]  H. Vanacker,et al.  A role for salicylic acid and NPR1 in regulating cell growth in Arabidopsis. , 2001, The Plant journal : for cell and molecular biology.

[6]  H. Obata,et al.  EFFECTS OF ZINC DEFICIENCY ON THE NITROGEN METABOLISM OF MERISTEMATIC TISSUES OF RICE PLANTS WITH REFERENCE TO PROTEIN SYNTHESIS , 1986 .

[7]  A. Oliphant,et al.  A draft sequence of the rice genome (Oryza sativa L. ssp. japonica). , 2002, Science.

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

[9]  K. Skriver,et al.  Novel Plant Ca-binding Protein Expressed in Response to Abscisic Acid and Osmotic Stress (*) , 1996, The Journal of Biological Chemistry.

[10]  R. Stoughton,et al.  Experimental annotation of the human genome using microarray technology , 2001, Nature.

[11]  M. Ueguchi-Tanaka,et al.  Molecular analysis of the NAC gene family in rice , 2000, Molecular and General Genetics MGG.

[12]  Kenichi Higo,et al.  PLACE: a database of plant cis-acting regulatory DNA elements , 1998, Nucleic Acids Res..

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

[14]  M. Iwata,et al.  Cloning and characterization of a probenazole-inducible gene for an intracellular pathogenesis-related protein in rice. , 1996, Plant & cell physiology.

[15]  Claudio Scazzocchio,et al.  Operator derepressed mutations in the proline utilisation gene cluster of Aspergillus nidulans , 2004, Molecular and General Genetics MGG.

[16]  F. Speleman,et al.  Accurate normalization of real-time quantitative RT-PCR data by geometric averaging of multiple internal control genes , 2002, Genome Biology.

[17]  S. Dudoit,et al.  Normalization for cDNA microarray data: a robust composite method addressing single and multiple slide systematic variation. , 2002, Nucleic acids research.

[18]  Jerry Li,et al.  Within the fold: assessing differential expression measures and reproducibility in microarray assays , 2002, Genome Biology.

[19]  S. Lin,et al.  A high-density rice genetic linkage map with 2275 markers using a single F2 population. , 1998, Genetics.

[20]  T. Gojobori,et al.  The genome sequence and structure of rice chromosome 1 , 2002, Nature.

[21]  Yudong D. He,et al.  Expression profiling using microarrays fabricated by an ink-jet oligonucleotide synthesizer , 2001, Nature Biotechnology.

[22]  K. Akama,et al.  Rice (Oryza sativa) contains a novel isoform of glutamate decarboxylase that lacks an authentic calmodulin-binding domain at the C-terminus. , 2001, Biochimica et biophysica acta.

[23]  J. Kawai,et al.  Genomics approach to abscisic acid- and gibberellin-responsive genes in rice. , 2003, DNA research : an international journal for rapid publication of reports on genes and genomes.

[24]  E. Meyerowitz,et al.  MADS domain proteins in plant development. , 1997, Biological chemistry.

[25]  J. Giraudat,et al.  ABSCISIC ACID SIGNAL TRANSDUCTION. , 1998, Annual review of plant physiology and plant molecular biology.

[26]  Beixin Mo,et al.  β-Mannosidase (EC 3.2.1.25) activity during and following germination of tomato (Lycopersicon esculentum Mill.) seeds. Purification, cloning and characterization , 2002, Planta.

[27]  M. E. Foley,et al.  Cloning and characterization of differentially expressed genes in imbibed dormant and afterripened Avena fatua embryos , 1995, Plant Molecular Biology.

[28]  C. Jang,et al.  Molecular characterization of a cDNA encoding putative calcium binding protein, HvCaBP1, induced during kernel development in barley (Hordeum vulgare L.) , 2003, Plant Cell Reports.

[29]  Dawood B Dudekula,et al.  In situ-synthesized novel microarray optimized for mouse stem cell and early developmental expression profiling. , 2003, Genome research.

[30]  Masahiro Ishikawa,et al.  Rice Expression Database: the gateway to rice functional genomics , 2002 .

[31]  Y. Yamaguchi,et al.  Four rice genes encoding cysteine synthase: isolation and differential responses to sulfur, nitrogen and light. , 1999, Gene.

[32]  Takuji Sasaki,et al.  INE: a rice genome database with an integrated map view , 2000, Nucleic Acids Res..

[33]  M. Crespi,et al.  Ankyrin protein kinases: a novel type of plant kinase gene whose expression is induced by osmotic stress in alfalfa , 2003, Plant Molecular Biology.

[34]  J. Kawai,et al.  Collection, Mapping, and Annotation of Over 28,000 cDNA Clones from japonica Rice , 2003, Science.

[35]  S. Jacobsen,et al.  Gibberellins regulate the abundance of RNAs with sequence similarity to proteinase inhibitors, dioxygenases and dehydrogenases , 2004, Planta.

[36]  M. Guerinot,et al.  GmZIP1 Encodes a Symbiosis-specific Zinc Transporter in Soybean* , 2002, The Journal of Biological Chemistry.

[37]  Shoshi Kikuchi,et al.  The Rice PIPELINE: a unification tool for plant functional genomics , 2004, Nucleic Acids Res..

[38]  P. Kapranov,et al.  A protein phosphatase 2C gene, LjNPP2C1, from Lotus japonicus induced during root nodule development. , 1999, Proceedings of the National Academy of Sciences of the United States of America.

[39]  A. Miyao,et al.  Target Site Specificity of the Tos17 Retrotransposon Shows a Preference for Insertion within Genes and against Insertion in Retrotransposon-Rich Regions of the Genome Article, publication date, and citation information can be found at www.plantcell.org/cgi/doi/10.1105/tpc.012559. , 2003, The Plant Cell Online.

[40]  A. Lovegrove,et al.  Gibberellin and abscisic acid signalling in aleurone. , 2000, Trends in plant science.

[41]  F. Skoog,et al.  A revised medium for rapid growth and bio assays with tobacco tissue cultures , 1962 .

[42]  P. Hugenholtz.  Exploring prokaryotic diversity in the genomic era , 2002, Genome Biology.

[43]  Michele Morgante,et al.  Genome-wide gene expression profiling in Arabidopsis thaliana reveals new targets of abscisic acid and largely impaired gene regulation in the abi1-1 mutant , 2002, Journal of Cell Science.

[44]  F. Cohen,et al.  Molecular Phylogeny and Evolution of the Plant-Specific Seven-Transmembrane MLO Family , 2002, Journal of Molecular Evolution.