Xanthomonas oryzae pv. oryzae PXO99A
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PROVIDER: PRJNA131967 | ENA |
REPOSITORIES: ENA
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Project description:Xanthomonas oryzae pv. oryzae strain PXO99A, so called Xoo, is disable to infect in rice cultivar carrying Xa21 gene. A set of experiments indicated that Ax21 is quorum sensing factor in PXO99 strain. To observe fine-tuned details how Ax21 controls expression of PXO99 in response to change of cell population density, transcriptional profiling analysis was perform by using published two channel oligo Xo microarray platform (Seo et al.,2008 BMC microbiology). Keywords: Comparative transcription profiling between low cell density and high cell density with same genetic background
2012-01-01 | GSE24989 | GEO
Project description:OsEDS1 is a key regulator of SA-mediated immunity in plants. The OsEDS1 knockout mutant (Oseds1) was characterized and shown to have increased susceptibility to Xanthomonas oryzae pv. oryzae (Xoo) and Xanthomonas oryzae pv. oryzicola (Xoc), suggesting the positive role of OsEDS1 in regulating rice disease resistance. To identify differentially regulated downstream of Oseds1, we performed transcriptome deep sequencing (RNA-seq) of wild type (ZH11) and Oseds1 inoculated with Xanthomonas oryzae pv. Oryzae (PXO99A).
2023-11-25 | GSE248248 | GEO
Project description:Xanthomonas oryzae pv. oryzae strain PXO99A, so called Xoo, is disable to infect in rice cultivar carrying Xa21 gene. A set of experiments indicated that Ax21 is quorum sensing factor in PXO99 strain. To observe fine-tuned details how Ax21 controls expression of PXO99 in response to change of cell population density, transcriptional profiling analysis was perform by using published two channel oligo Xo microarray platform (Seo et al.,2008 BMC microbiology). Keywords: Comparative transcription profiling between low cell density and high cell density with same genetic background Three biological and dye-swap replicates, total six samples for each dataset. Two datasets contained; (i) PXO99 at 106 CFU/ml vs 108 CFU/ml, and (ii) PXO99∆ax21at 106 CFU/ml vs PXO99∆ax21 108 CFU/ml. 106 CFU/ml and 108 CFU/ml are cell density used in this study as representation of low and high cell density. All bacteria cultures were grown in PS (Peptone sucrose) broth media.
2012-01-01 | E-GEOD-24989 | biostudies-arrayexpress
Project description: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
2010-09-09 | E-GEOD-14498 | biostudies-arrayexpress
Project description: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
2009-01-31 | GSE14498 | GEO
Project description:This SuperSeries is composed of the following subset Series: GSE9640: Transcriptome Profiling of Xanthomonas oryzae pv. oryzae and Xanthomonas oryzae pv. oryzicola on two different medias GSE9643: Transcriptome Profiling of Xanthomonas oryzae pv. oryzae knockout mutants at different hybridization conditions and PMTs Keywords: SuperSeries Refer to individual Series
2010-05-26 | E-GEOD-9658 | biostudies-arrayexpress
Project description:Transcription profiling of the DSF regulon in Xanthomonas oryzae pv. oryzae (Xoo) using wild type and the rpfF mutant. Cell-cell signaling mediated by the quorum sensing molecule known as Diffusible Signaling factor (DSF) is required for virulence of Xanthomonas group of plant pathogens. DSF in different Xanthomonas and the closely related plant pathogen Xylella fastidiosa regulates diverse traits in a strain specific manner. The transcriptional profiling performed in this study is to elucidate the traits regulated by DSF from the Indian isolate of Xanthomonas oryzae pv. oryzae, which exhibits traits very different from other Xanthomonas group of plant pathogen. In this study, transcription analysis was done between a wild type Xanthomonas oryzae pv. oryzae strain and an isogenic strain that has a mutation in the DSF biosynthetic gene rpfF.
2011-04-02 | GSE27809 | GEO
Project description:Transcription profiling of RaxR-regulon members of Xanthomonas oryzae pv. oryzae PXO99A
| PRJNA111557 | ENA
Project description:In bacteria, two-component regulatory system (TCSs) is generally characterized by a simple phosphotransfer scheme, composed of a sensor domain (a histidine kinase) and a response domain (a response regulator), which is responsible for detection of external stimuli. PhoP-PhoQ TCS of Xanthomonas oryzae pv. oryzae (Xoo), a causal agent of bacterial leaf blight disease in rice, was previously shown to be negatively regulated by RaxR-RaxH, another TCS that senses population cell density as well as modulates the activity of AvrXA21, a bacterial effector, recognized by a bacterial blight resistance gene, Xa21. In this work, whole-genome microarray was performed to analyze transcription profiling and identify member of PhoP regulon under Mg2+ and Ca2+ limited condition. This analysis revealed that PhoP governs broad cellular pathways including stress defense response, cation transportation, general metabolism, broad regulatory system, bacterial motility, and bacterial virulence. Array results provide a set of candidate genes, further biochemical pathway analysis, and signaling pathway crosstalks that need to be characterized to understand PhoP-dependent mechanisms and also suggest a putative regulatory loop between two phoP-phoQ and raxR-raxH TCSs. Implication of this analysis suggested that Xoo adopt PhoP-PhoQ system to perceive extracellular signals from certain environment such as low concentration of metal ions, and to regulate intracellular signals of other regulatory systems. Keywords: Comparative transcription profiling under limited Mg2+ Ca2+ condition Three biological and dye-swap replicates, total six samples for each dataset. Three datasets contained; (i) phoP knockout mutant vs. wildtype PXO99A in low concentration (10 µM) of MgCl2 and CaCl2, (ii) phoP knockout mutant in low (10 µM) vs. high (10mM) concentration of MgCl2 and CaCl2, and (iii) PXO99A in low (10 µM) vs. high (10mM) concentration of MgCl2 and CaCl2.
2008-07-16 | E-GEOD-12099 | biostudies-arrayexpress
Project description:Transcription profiling of the DSF regulon in Xanthomonas oryzae pv. oryzae (Xoo) using wild type and the rpfF mutant. Cell-cell signaling mediated by the quorum sensing molecule known as Diffusible Signaling factor (DSF) is required for virulence of Xanthomonas group of plant pathogens. DSF in different Xanthomonas and the closely related plant pathogen Xylella fastidiosa regulates diverse traits in a strain specific manner. The transcriptional profiling performed in this study is to elucidate the traits regulated by DSF from the Indian isolate of Xanthomonas oryzae pv. oryzae, which exhibits traits very different from other Xanthomonas group of plant pathogen. In this study, transcription analysis was done between a wild type Xanthomonas oryzae pv. oryzae strain and an isogenic strain that has a mutation in the DSF biosynthetic gene rpfF. Agilent one-color experiment, Organism: Xanthomonas oryzae, Agilent-025096 Genotypic Technology Pvt. Ltd. designed Custom Xanthomonas oryzae 8x15k, Labeling kit: Agilent Quick-Amp labeling Kit (p/n5190-0442).
2011-04-02 | E-GEOD-27809 | biostudies-arrayexpress