Unknown,Transcriptomics,Genomics,Proteomics

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Transcription profiling of RaxR-regulon members of Xanthomonas oryzae pv. oryzae PXO99A

ABSTRACT: Xanthomonas oryzae pv. oryzae strain PXO99A, so called Xoo, is disable to infect in rice cultivar carrying Xa21 gene. Disrupted mutant of raxR gene, response regulator of two-component regulatory system (TCS), in Xoo was previously shown to partially retrieve back the bacterial capability to establish in Xa21 rice. RaxR was shown to mediate the expression of other rax gene operon members and also its expression is changed dependent on cell population density. In this study, we investigated the regulatory mechanisms mediated by RaxR using whole-genome transcriptional profiling analysis in comparison of (i) PXO99R (PXO99 strain lacking RaxR) vs. PXO99, (ii) PXO99Rox (PXO99 strain overexpressing RaxR) vs. PXO99, and (iii) PXO99Rox vs. PXO99R. As a result of array analysis, we revealed that RaxR is not only required for AvrXa21 activitiy, it also plays roles in regulatory functions, for example, pathogenicity, motility, and stress tolerance. Then, we generated knock out mutants of RaxR regulon members to validate regulatory functions of RaxR and to extend other biological impacts of RaxR beyond the Xoo AvrXa21 activity. The combined interpretation from array analysis and mutant functional validation presents the complexity of regulatory pathways between AvrXa21 activity and other biological activities in Xoo. Keywords: Comparative transcription profiling between modified genetic mutant and wild type Three biological and dye-swap replicates, total six samples for each dataset. Three datasets contained; (i) raxR knockout mutant vs. wildtype PXO99A in PSB, nutrient rich media (ii) RaxR constitutively express mutant vs. wildtype PXO99A in PSB, nutrient rich media, and (iii) raxR knockout mutant vs. RaxR constitutively express mutant in PSB, nutrient rich media

ORGANISM(S): Xanthomonas oryzae pv. oryzae PXO99A

SUBMITTER: Pamela Ronald

PROVIDER: E-GEOD-14498 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Project description:X. oryzae pv. oryzae (Xoo) is the causal agent of bacterial blight of rice. X. oryzae pv. oryzicola (Xoc) is the causal agent of bacterial streak of rice. Fourteen day old rice leaves were inoculated with one of five strains of Xanthomonas oryzae. Seven strains of Xoo were used; three wild type strains (PXO99A, T7174, and PXO86) and strains PXO99AME7, which has a nonfunctional type III secretion system and is non-pathogenic, , PXO99AME1, a pthXo6 and avrXa27 double mutant, PXO99ME2, a pthXo1 mutant, and PXO99ME5, a reduced virulence strain with uncharacterized mutation in a TAL effector. One strain of Xoc (BLS303) was tested. Controls include an inoculation with water (MOCK) and no inoculation. T7174 is our label for the Japanese isolate MAFF311018. Third leaves are inoculated with a needless syringe at adjacent sites along the upper leaf blade. Six leaves from separate plants are pooled. RNA samples were collected 24 h after treatment. ****[PLEXdb(http://www.plexdb.org) has submitted this series at GEO on behalf of the original contributor, Ginny Antony. The equivalent experiment is OS66 at PLEXdb.] cultivar: Nipponbare - strain: PXO99A(3-replications); cultivar: Nipponbare - strain: PXO99AME7(3-replications); cultivar: Nipponbare - strain: PXO99AME5(3-replications); cultivar: Nipponbare - strain: MOCK(3-replications); cultivar: Nipponbare - strain: NO TREATMENT(2-replications); cultivar: Nipponbare - strain: T7174(3-replications); cultivar: Nipponbare - strain: PXO86(3-replications); cultivar: Nipponbare - strain: BLS303(3-replications); cultivar: Nipponbare - strain: PXO99AME1(3-replications); cultivar: Nipponbare - strain: PXO99AME2(3-replications); cultivar: Nipponbare - strain: PXO99A-2(3-replications); cultivar: IR24 - strain: PXO99A(3-replications); cultivar: IR24 - strain: PXO99AME7(3-replications); cultivar: IR24 - strain: PXO99AME5(3-replications); cultivar: IR24 - strain: MOCK(3-replications); cultivar: IR24 - strain: NO TREATMENT(3-replications); cultivar: IR24 - strain: T7174(3-replications); cultivar: IR24 - strain: PXO86(3-replications); cultivar: IR24 - strain: BLS303(3-replications); cultivar: IR24 - strain: PXO99AME1(3-replications); cultivar: IR24 - strain: PXO99AME2(3-replications); cultivar: IR24 - strain: PXO99A-2(3-replications)

Project description:Bacterial blight, caused by Xanthomonas oryzae pv. oryzae (Xoo), is the most destructive bacterial disease of rice. The cloned rice gene Xa21 confers resistance to a broad spectrum of Xoo races. To identify other genes involved in Xa21-mediated immunity, a whole-genome oligonucleotide microarray of rice was used to profile the expression of rice genes between incompatible interactions and mock treatments at 0, 4, 8, 24, 72 and 120 hours post inoculation (hpi) or between incompatible and compatible interactions at 4 hpi, respectively. A total of 441 differentially expressed genes, designated as XDGs (Xa21 mediated Differentially expressed Genes), were identified. Based on their functional annotations, the XDGs were assigned to 14 categories some of which encode resistance/defense related proteins and signaling regulators. Interestingly, most signaling-related genes were down-regulated at 4 and 8 hpi, suggesting that negative regulation of cellular signaling may play a role in the Xa21-mediated defense response. Moreover, a number of pathogenesis-related genes were induced at 72 and 120 hpi. Comparison of expression profiles mediated by other resistance genes revealed an interesting common responses in the plant immune system. Comparison analyses also suggest possible overlaps with hormone signaling pathways and with defense systems including basal defense and hypersensitive responses. We investigated the transcriptional characteristics of Xa21-mediated defense responses in rice using whole-genome oligonucleotide microarray, by comparing the expression profiles between incompatible interactions and mock treatments at five time-points and between incompatible and compatible interactions at 4 hours post inoculation. Microarray hybridization at each time point was carried out in three replications including two biological replications and one technological replication. To detect the genes that are significantly regulated and to eliminate those that have inconsistent expression data among replicated experiments, a cutoff of 1.5 fold change and 1.96 for intensity-dependent Z-scores were required in at least two experimental samples.

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Transcription profiling of RaxR-regulon members of Xanthomonas oryzae pv. oryzae PXO99A

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