Xanthomonas oryzae pv. oryzae strain:HB1009
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA302093 | ENA |
REPOSITORIES: ENA
Dataset's files
primary
| Action | DRS | |||
|---|---|---|---|---|
| SRR2915666_1.fastq.gz | Fastqsanger.gz | |||
| SRR2915666_2.fastq.gz | Fastqsanger.gz |
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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 | ArrayExpress
Project description:Xanthomonas oryzae pv. oryzae, which causes rice bacterial leaf blight, and Xanthomonas oryzae pv. oryzicola, which causes rice bacterial leaf streak, are important plant-pathogenic bacteria. A member of the adaptor protein family, ankyrin protein, has been investigated largely in humans but rarely in plant-pathogenic bacteria. In this study, a novel ankyrin-like protein, AnkB, was identified in X. oryzae pv. oryzae and X. oryzae pv. oryzicola. The expression of ankB was significantly upregulated when these bacteria were treated with phenazine-1-carboxylic acid (PCA). ankB is located 58 bp downstream of the gene catB (which encodes a catalase) in both bacteria, and the gene expression of catB and catalase activity were reduced following ankB deletion in X. oryzae pv. oryzae and X. oryzae pv. oryzicola. Furthermore, we demonstrated that AnkB directly interacts with CatB by glutathione S-transferase (GST) pulldown assays. Deletion of ankB increased the sensitivity of X. oryzae pv. oryzae and X. oryzae pv. oryzicola to H2O2 and PCA, decreased bacterial biofilm formation, swimming ability, and exopolysaccharide (EPS) production, and also reduced virulence on rice. Together our results indicate that the ankyrin-like protein AnkB has important and conserved roles in antioxidant systems and pathogenicity in X. oryzae pv. oryzae and X. oryzae pv. oryzicola.IMPORTANCE This study demonstrates that the ankyrin protein AnkB directly interacts with catalase CatB in Xanthomonas oryzae pv. oryzae and Xanthomonas oryzae pv. oryzicola. Ankyrin protein AnkB can affect the gene expression of catB, catalase activity, and sensitivity to H2O2 In Xanthomonas spp., the locations of genes ankB and catB and the amino acid sequence of AnkB are highly conserved. It is suggested that in prokaryotes, AnkB plays a conserved role in the defense against oxidative stress.
2018-01-01 | S-EPMC5795068 | BioStudies
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. Overall design: 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 | GSE27809 | GEO
Project description:The rice pathogen recognition receptor, XA21, confers resistance to Xanthomonas oryzae pv. oryzae strains producing the type one system-secreted molecule, AvrXA21. X. oryzae pv. oryzae requires a regulatory two-component system (TCS) called RaxRH to regulate expression of eight rax (required for AvrXA21 activity) genes and to sense population cell density. To identify other key components in this critical regulatory circuit, we assayed proteins expressed in a raxR gene knockout strain. This survey led to the identification of the phoP gene encoding a response regulator that is up-regulated in the raxR knockout strain. Next we generated a phoP knockout strain and found it to be impaired in X. oryzae pv. oryzae virulence and no longer able to activate the response regulator HrpG (hypersensitive reaction and pathogenicity G) in response to low levels of Ca2+. The impaired virulence of the phoP knockout strain can be partially complemented by constitutive expression of hrpG, indicating that PhoP controls a key aspect of X. oryzae pv. oryzae virulence through regulation of hrpG. A gene encoding the cognate putative histidine protein kinase, phoQ, was also isolated. Growth curve analysis revealed that AvrXA21 activity is impaired in a phoQ knockout strain as reflected by enhanced growth of this strain in rice lines carrying XA21. These results suggest that the X. oryzae pv. oryzae PhoPQ TCS functions in virulence and in the production of AvrXA21 in partnership with RaxRH.
2008-01-01 | S-EPMC2258857 | BioStudies
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 | ArrayExpress
Project description:BACKGROUND: Xanthomonas oryzae pv. oryzae, the causal agent of bacterial blight disease, is a serious pathogen of rice. Here we describe a fluorescent marker system to study virulence and pathogenicity of X. oryzae pv. oryzae. RESULTS: A fluorescent X. oryzae pv. oryzae Philippine race 6 strain expressing green fluorescent protein (GFP) (PXO99GFP) was generated using the gfp gene under the control of the neomycin promoter in the vector, pPneo-gfp. The PXO99GFPstrain displayed identical virulence and avirulence properties as the wild type control strain, PXO99. Using fluorescent microscopy, bacterial multiplication and colonization were directly observed in rice xylem vessels. Accurate and rapid determination of bacterial growth was assessed using fluoremetry and an Enzyme-Linked ImmunoSorbant Assay (ELISA). CONCLUSION: Our results indicate that the fluorescent marker system is useful for assessing bacterial infection and monitoring bacterial multiplication in planta.
1000-01-01 | S-EPMC2569045 | BioStudies
Project description:Xanthomonadins are yellow, membrane-bound pigments produced by members of the genus Xanthomonas. We identified an ethyl methanesulfonate-induced Xanthomonas oryzae pv. oryzae mutant (BXO65) that is deficient for xanthomonadin production and virulence on rice, as well as auxotrophic for aromatic amino acids (Pig(-) Vir(-) Aro(-)). Reversion analysis indicated that these multiple phenotypes are due to a single mutation. A genomic library of the wild-type strain was used to isolate a 7.0-kb clone that complements BXO65. By transposon mutagenesis, marker exchange, sequence analysis, and subcloning, the complementing activity was localized to a 849-bp open reading frame (ORF). This ORF is homologous to the aroE gene, which encodes shikimate dehydrogenase in various bacterial species. Shikimate dehydrogenase activity was present in the wild-type strain and the mutant with the complementing clone, whereas no activity was found in BXO65. This clone also complemented an Escherichia coli aroE mutant for prototrophy, indicating that aroE is functionally conserved in X. oryzae pv. oryzae and E. coli. The nucleotide sequence of the 2.9-kb region containing aroE revealed that a putative DNA helicase gene is located adjacent to aroE. Our results indicate that aroE is required for normal levels of virulence and xanthomonadin production in X. oryzae pv. oryzae.
2001-01-01 | S-EPMC92557 | BioStudies
Project description:Xanthomonas oryzae pv. oryzae is the causative agent of bacterial leaf blight of rice. The application of bacteriophages may provide an effective tool against this bacterium. Here, we report the complete genome sequences of 10 newly isolated OP2-like X. oryzae pv. oryzae bacteriophages.
2019-01-01 | S-EPMC6606903 | BioStudies
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
Project description:We have cloned a hrp gene cluster from Xanthomonas oryzae pv. oryzae. Bacteria with mutations in the hrp region have reduced growth in rice leaves and lose the ability to elicit a hypersensitive response (HR) on the appropriate resistant cultivars of rice and the nonhost plant tomato. A 12,165-bp portion of nucleotide sequence from the presumed left end and extending through the hrpB operon was determined. The region was most similar to hrp genes from Xanthomonas campestris pv. vesicatoria and Ralstonia solanacearum. Two new hrp-associated loci, named hpa1 and hpa2, were located beyond the hrpA operon. The hpa1 gene encoded a 13-kDa glycine-rich protein with a composition similar to those of harpins and PopA. The product of hpa2 was similar to lysozyme-like proteins. Perfect PIP boxes were present in the hrpB and hpa1 operons, while a variant PIP box was located upstream of hpa2. A strain with a deletion encompassing hpa1 and hpa2 had reduced pathogenicity and elicited a weak HR on nonhost and resistant host plants. Experiments using single mutations in hpa1 and hpa2 indicated that the loss of hpa1 was the principal cause of the reduced pathogenicity of the deletion strain. A 1,519-bp insertion element was located immediately downstream of hpa2. Hybridization with hpa2 indicated that the gene was present in all of the strains of Xanthomonas examined. Hybridization experiments with hpa1 and IS1114 indicated that these sequences were detectable in all strains of X. oryzae pv. oryzae and some other Xanthomonas species.
2000-01-01 | S-EPMC101866 | BioStudies