Rice roots: Non-colonized (sterile) control vs. infected with Xanthomonas oryzae pv. oryzae strain PXO99 (Xan)
Ontology highlight
ABSTRACT:
ORGANISM(S): Oryza sativa Oryza sativa Japonica Group
PROVIDER: GSE136706 | GEO | 2019/09/01
REPOSITORIES: GEO
Similar Datasets
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: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: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
2009-01-31 | GSE14498 | GEO
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:ABA deficient mutant Osaba1-1 exhibits great resistance to Xanthomonas oryzae pv. oryzae (Xoo) infection. To investigate gene expression profile changes at whole genome level between Osaba1-1 and wild-type (Nipponbare) rice during Xoo infection, we employed microarray expression profiling as a discovery platform. Osaba1-1 and wild-type rice plants about 6.5 leaf stage were used in this experiment. For Xoo inoculation, tips (about 3cm) of the fifth and sixth fully expanded leaves were cut off, and then immersed into Xoo (PXO99 strain) inoculum (suspended in sterile distilled water containing 10mM MgCl2, OD≈0.5) immediately for about fifteen seconds. Inoculated rice leaves were collected (approximately 2 cm leaf fragment from the inoculation site) at 0h and 72h post inoculation. Three independent replicate samples were collected at each time point for microarray.
2015-05-15 | E-GEOD-63337 | biostudies-arrayexpress
Project description:We performed RNA-Seq of leaves of Oryza sativa L. ssp. japonica cv. Nipponbare 48 hours after inoculation with Xanthomonas oryzae pv. oryzicola strain BLS354, the causal agent of bacterial leaf streak. Results provide insight into the molecular basis of bacterial leaf streak, particularly the role of transcription activator-like effectors in the disease. Examination of mRNA levels in Oryza sativa L. ssp. japonica cv. Nipponbare leaves at 48 hours after inoculation with Xanthomonas oryzae pv. oryzicola strain BLS354 with three biological replicates compared to three replicates of mock inoculated O. sativa as the control.
2016-07-07 | E-GEOD-75131 | biostudies-arrayexpress
Project description:ABA deficient mutant Osaba1-1 exhibits great resistance to Xanthomonas oryzae pv. oryzae (Xoo) infection. To investigate gene expression profile changes at whole genome level between Osaba1-1 and wild-type (Nipponbare) rice during Xoo infection, we employed microarray expression profiling as a discovery platform.
2015-05-15 | GSE63337 | GEO
Project description:Endogenous small RNAs are newly identified players in plant immune responses, yet their roles in rice (Oryza sativa) responding to pathogens are still less understood, especially for pathogens that can cause severe yield losses. Here, we examined the small RNA expression profiles of rice leaves at 2, 6, 12, and 24 hours post infection of Xanthomonas oryzae pv. oryzae (Xoo) virulent strain PXO99, the causal agent of rice bacterial blight disease. Dynamic expression changes of some miRNAs and trans-acting siRNAs (ta-siRNAs) were identified, together with a few novel miRNA targets, including a disease resistance gene targeted by osa-miR159a.1. Coordinated expression changes were observed among some miRNA and ta-siRNAs in response to Xoo infection, with small RNAs exhibiting the same expression pattern tended to regulate genes in the same or functional correlated signaling pathways, including auxin and GA signaling pathways, nutrition and defense related pathways, etc. Highly abundant small RNAs with pathogen-responsive expression changes were identified from the exonic region of a protein-coding gene, which may present a new class of functional small RNAs. These findings reveal the dynamic and complex roles of small RNAs in rice-pathogen interactions, and identified new targets for regulating plant immune responses. Examination of the small RNA expression profiles of rice leaves at 2, 6, 12, and 24 hours post infection of Xanthomonas oryzae pv. oryzae (Xoo) virulent strain PXO99
2015-08-31 | E-GEOD-58385 | 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