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Rice Gene Network Inferred from Expression Profiling of Plants Overexpressing OsWRKY13

ABSTRACT: Accumulating information indicates that plant disease resistance signaling pathway frequently interact with other pathways regulating developmental processes or abiotic stress responses. However, the molecular mechanisms of these types of crosstalk remain poorly understood in most cases. Here we report that OsWRKY13, an activator of rice resistance to both bacterial and fungal pathogens, functions as a convergent point of the crosstalk between pathogen-induced salicylate-dependent defense pathway and at least five other physiological pathways. Genome-wide analysis of the expression profiling of OsWRKY13-overexpressing lines showed that OsWRKY13 directly or indirectly regulates the expression of more than 500 genes, which are potentially involved in different physiological processes according to the classification of Gene Ontology database. Comparing the expression patterns of genes functioning in known pathways or cellular processes upon pathogen infection and the phenotypes between OsWRKY13-overexpressing and susceptible wild-type plants, we find that OsWRKY13 is also regulator of other physiological processes during pathogen infection. OsWRKY13-involved disease resistance pathway synergistically interacts with glutathione/glutaredoxin system and flavonoid biosynthesis pathway via OsWRKY13 to monitor redox homeostasis and may enhance the biosynthesis of antimicrobial flavonoid phytoalexins. Meanwhile, OsWRKY13-invloved disease resistance pathway antagonistically interacts with SNAC1-mediated abiotic-stress defense pathway, JA signaling pathway, and terpenoid metabolism pathway via OsWRKY13 to suppress salt and cold defense responses as well as may retard rice growth and development. Keywords: abiotic stress, bacterial blight, microarray, Oryza sativa, signal transduction, WRKY transcription factor

ORGANISM(S): Oryza sativa

PROVIDER: GSE8380 | GEO | 2008/07/02

SECONDARY ACCESSION(S): PRJNA101419

REPOSITORIES: GEO

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Project description:Accumulating information indicates that plant disease resistance signaling pathway frequently interact with other pathways regulating developmental processes or abiotic stress responses. However, the molecular mechanisms of these types of crosstalk remain poorly understood in most cases. Here we report that OsWRKY13, an activator of rice resistance to both bacterial and fungal pathogens, functions as a convergent point of the crosstalk between pathogen-induced salicylate-dependent defense pathway and at least five other physiological pathways. Genome-wide analysis of the expression profiling of OsWRKY13-overexpressing lines showed that OsWRKY13 directly or indirectly regulates the expression of more than 500 genes, which are potentially involved in different physiological processes according to the classification of Gene Ontology database. Comparing the expression patterns of genes functioning in known pathways or cellular processes upon pathogen infection and the phenotypes between OsWRKY13-overexpressing and susceptible wild-type plants, we find that OsWRKY13 is also regulator of other physiological processes during pathogen infection. OsWRKY13-involved disease resistance pathway synergistically interacts with glutathione/glutaredoxin system and flavonoid biosynthesis pathway via OsWRKY13 to monitor redox homeostasis and may enhance the biosynthesis of antimicrobial flavonoid phytoalexins. Meanwhile, OsWRKY13-invloved disease resistance pathway antagonistically interacts with SNAC1-mediated abiotic-stress defense pathway, JA signaling pathway, and terpenoid metabolism pathway via OsWRKY13 to suppress salt and cold defense responses as well as may retard rice growth and development. Experiment Overall Design: To determine the genes directly or indirectly regulated by OsWRKY13 genome-widely, we performed the microarray analysis using the Affymetrix Genechip Rice Genome Array containing total 57381 probe sets. Two independent OsWRKY13-overexpressing rice lines, D11UM 1-1 and D11UM 7-2 (Qiu et al., 2007), and wild-type Mudanjiang 8, which was susceptible to Xoo and M. grisea, were used for the analyses.The experiment was repeated three times.

Project description:Harpin proteins from Gram-negative plant pathogenic bacteria can activate distinct signaling pathways and cause multiple effects in plants. In this document, we observed the transcriptome profile in transgenic NJH12 and wide type R109 using a customized 57 k rice cDNA microarray and found 225 differentially expressed transcripts related to the responses to biotic and abiotic stresses, including programmed cell death (PCD), defense responses associated with the recognition of pathogen-derived elicitors secondary metabolite biosynthesis, and defense signalling pathways mediated by abscisic acid (ABA), reactive oxygen species (ROS), nitric oxide (NO), polyamines (PAs) and Ca2+, suggesting that the disease resistance and drought tolerance mediated by Harpin protein in hrf1-expressing NJH12 rice has a crosstalk through several signaling pathways. The homozygous T3 NJH12 line is a transgenic rice line generated by transforming rice cultivar R109 with hrf1-containing pBMH9 using Agrobacterium-mediated transformation (Shao et al., 2008). Three T3 progeny of the transgenic NJH12 used in this study were grown in a sterile incubator at 28 ℃ in the greenhouse with a 16 h light/8 h dark cycle. Rice leaves were collected at the four-leaf stage and stored in liquid nitrogen prior to RNA extraction. Wild-type rice R109 was used as the negative control. The experiments for each transgenic line and wild type were repeated three times by three independently grown sets of plants for preparing RNA samples used for independent hybridization to the microarrays. Total RNA was extracted with TRIZOL reagent (Invitrogen, Gaithersburg, MD). The RNA quality was assessed by formaldehyde agarose gel electrophoresis and concentration was quantitated by spectrophotometric analysis. Total RNA was kept at −80 ℃ and sent to the Affymetrix core facility, where quality-control analysis was carried out before cDNA synthesis from the mRNA, labeling (through synthesis of cRNA with incorporation of biotinylated ribonucleotide analogs), and hybridization to the GeneChip Rice Genome Array (Affymetrix). This chip contains 57, 381 probe sets to query 51, 279 transcripts, which was designed based on the 59, 712 gene predictions of TIGR’s osa1 version 2.0 release. The chip was washed and then stained with streptavidin-phycoerythrin on an Affymetrix Fluidics Station 400, followed by scanning on a GeneChip Scanner 3000 (Affymetrix). The results were quantified and normalized using MicroArray Suite 5.0 (GCOS1.4) software (Affymetrix). The gene annotation and pathway identiﬁcation were performed according to the method described by Shi et al. (2006) and Miao et al. (2010b).

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Rice Gene Network Inferred from Expression Profiling of Plants Overexpressing OsWRKY13

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