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Whole WRKY gene family transcription analysis in rice during biotic and abiotic stress.

ABSTRACT: The WRKY gene family has a very ancient origin but has faced extensive duplication only in the plant kingdom so much that Arabidopsis (Arabidopsis thaliana) has 74 copies of WRKY genes encoding transcription factors while 109 can be found in Rice (Oryza sativa L.). Several studies in the last decade has pointed their involvement in an heterogeneous number of biological processes, from development to hormone signalling, dormancy and senescence, but a wide number of WRKY genes are transcriptionally regulated during biotic or abiotic stresses. To investigate involvement of WRKY genes upon host and non-host infection (different strain of Magnaporthe grisea) and osmotic stress in Rice, we performed a gene family transcription analysis using custom microarray. Results indicate that a relevant part of WRKY genes are involved during at least one of these stresses, that there is little difference in transcriptional regulation between host and non-host infection or between different tissues upon the same osmotic stress. Moreover, are evident groups of genes that, often with opposite behaviour, are co-regulated in all or most of the studied conditions. We thus formulated the hypothesis that WRKY genes might be part of co-regulatory networks with other WRKY genes. Keywords: stress response

ORGANISM(S): Oryza sativa Japonica Group

PROVIDER: GSE5819 | GEO | 2007/04/10

SECONDARY ACCESSION(S): PRJNA97207

REPOSITORIES: GEO

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Whole WRKY gene family transcription analysis in rice during biotic and abiotic stress.

Project description:The WRKY gene family has a very ancient origin but has faced extensive duplication only in the plant kingdom so much that Arabidopsis (Arabidopsis thaliana) has 74 copies of WRKY genes encoding transcription factors while 109 can be found in Rice (Oryza sativa L.). Several studies in the last decade has pointed their involvement in an heterogeneous number of biological processes, from development to hormone signalling, dormancy and senescence, but a wide number of WRKY genes are transcriptionally regulated during biotic or abiotic stresses. To investigate involvement of WRKY genes upon host and non-host infection (different strain of Magnaporthe grisea) and osmotic stress in Rice, we performed a gene family transcription analysis using custom microarray. Results indicate that a relevant part of WRKY genes are involved during at least one of these stresses, that there is little difference in transcriptional regulation between host and non-host infection or between different tissues upon the same osmotic stress. Moreover, are evident groups of genes that, often with opposite behaviour, are co-regulated in all or most of the studied conditions. We thus formulated the hypothesis that WRKY genes might be part of co-regulatory networks with other WRKY genes. Keywords: stress response We analyzed 40 arrays and tested 6 conditions: BR29 (Non-host Pathogen), BR32 (Non-host Pathogen), FR13 (Host pathogen), Osmotic leaves 5 hours, Osmotic roots 1 hour and Osmotic roots 5 hours. 2 biological replicated were analyzed and between 2 to 4 technical replicates applied for each biological sample.

2007-04-09 | E-GEOD-5819 | biostudies-arrayexpress

WRKY type transcription factor OsWRKY28 overexpression effect on rice leaves 48 h after Magnaporthe Oryzae infection

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A group of WRKY transcription factors form a protein complex with PHD-containing proteins to repress the transcription of stress responsive genes [ChIP-Seq]

Project description:In higher plants, WRKY is a large transcription factor family involved in multiple biological processes by mediating either transcriptional activation or repression. Although the conserved WRKY domain is known to mediate the binding of WRKY transcription factors to DNA, little is known about how the other domains are involved in the regulation of transcription. We find that the group IId WRKY transcription factors interact with PHD-containing OBE proteins and form redundant WRKY-OBE complexes in Arabidopsis thaliana. We find that a conserved coiled-coil motif in the group IId WRKY transcription factors functions as an OBE-interacting domain (OID), which is involved in transcriptional repression and target gene selection. The WRKY-OBE complexes mediate transcriptional repression at a large number of stress responsive genes and are required for maintaining normal plant growth and development. While the growth of high order of wrky mutants is retarded at the early seedling stage, the low order of wrky mutants show reduced plant height and increased drought tolerance, which is consistent with the increased expression of stress responsive genes, including DREB1A, DREB1B, and DREB1C. Moreover, we found that the expression levels of most of group IId WRKY genes are markedly reduced in drought stress conditions relative to non-stress conditions. These results together suggest that the WRKY-OBE repress the transcription of stress responsive genes primarily under non-stress conditions, thereby coordinating plant growth and drought stress tolerance under variable environmental conditions.

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A group of WRKY transcription factors form a protein complex with PHD-containing proteins to repress the transcription of stress responsive genes [RNA-Seq]

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Expression profiling of a lesion mimic genotype, splNF4050-8, that confers blast resistance in rice

Project description:Lesion mimic mutants in rice are widely known as spotted leaf (spl) mutants, of which several genotypes exhibit enhanced resistance to different races of Magnaporthe grisea. Besides naturally occurring spotted leaf mutants, tissue culture-induced reverse genetic repositories also act as sources of lesion mimic mutants in rice. We systematically evaluated a large collection of Tos17 mutant panel lines, developed and maintained at the National Institute of Agrobiological Sciences, Tsukuba, Japan, for their reaction to three different races of M. grisea and identified a lesion mimic mutant, NF4050-8, that showed lesions similar to naturally occurring spl5 mutant and enhanced resistance to all three blast races tested. Microarray analysis of ~44,000 rice genes in NF4050-8 with Nipponbare as control during the progressive lesion appearance stage revealed significant up-regulation of numerous defense/pathogenesis-related genes as well as several WRKY domain-containing genes and down-regulation of haem peroxidase gene. Subsequent real-time PCR analysis of WRKY45 and PR1b genes in NF4050-8 and spl5 suggested possible constitutive activation of a defense signaling pathway downstream of Salicylic Acid (SA) but independent of NH1 in these mutant lines of rice.

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Arabidopsis thaliana anti-all-WRKY pull-downs from whole seedlings

Project description:The experiments were performed to monitor dynamics in WRKY transcription factor abundancies upon treatment with flg22, a peptide derived from the bacterial flagella. Mock-treated or WT seedlings treated for 2 h with flg22 were used to prepare crude nuclear lysates. Then pull downs were performed with an anti-all-WRKY antiserum to enrich for WRKY transcription factor proteins prior to MS.

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WRKY type transcription factor OsWRKY28 overexpression effect on rice leaves 48 h after Magnaporthe Oryzae infection

Project description:Analysis of transgenic rice overexpressing OsWRKY28, a WRKY type transcription factor. Results provide insight into the role of OsWRKY28 in the defense signaling against rice blast fungus. Expression profiling in wild-type and OsWRKY28 overexpressing rice leaves infected with or without Magnaporthe Oryzae was analyzed using one-color method with three biological replicates.

2012-09-30 | E-GEOD-39635 | biostudies-arrayexpress

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Project description:We used this microarray to monitor rice miRNA expression profile under osmotic stress. Most of rice miRNAs have no significant change. miR-169f showed osmotic-responsive up-regulation. However, the others members of miR-169 family displays no responses to the osmotic stress. Keywords: microRNA,rice,osmotic stress,miR-169

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Expression profiling of a lesion mimic genotype, splNF4050-8, that confers blast resistance in rice

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WRKY transcription factors in early MAMP-triggered immunity (RNA-Seq)

Project description:We determined on a genome-wide scale the flg22-induced in vivo DNA-binding dynamics of three of the most prominent WRKY factors, WRKY18, WRKY40 and WRKY33. The three WRKY factors each bound to more than 1000 gene loci predominantly at W-box elements, the known WRKY binding motif. Transcriptional analysis also revealed that WRKY18 and WRKY40 function redundantly as negative regulators of flg22-induced genes.

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