Browse
Submit Data
Databases
API
Help

Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

16 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Gene expression changes induced in Rice (Oryza sativa) leaves by lipopolysaccharide (LPS) extracted from Xanthomonas oryzae pv. oryzae (Xoo) strain BXO43

ABSTRACT: Lipopolysaccharide is a Microbe Associated Molecular Pattern (MAMP) that is known to induce defense responses in plants. We have shown that treatment of rice leaves with Xoo LPS induces callose deposition, reactive oxygen production and enhances resistance against subsequent infection by the pathogen. We have performed transcriptional profiling of rice leaves that are treated with Xoo LPS to identify differentially expressed genes. Xoo LPS was injected into mid-veins of rice leaves and RNA was isolated 15 hours later.

ORGANISM(S): Oryza sativa

SUBMITTER: Ramesh Sonti

PROVIDER: E-GEOD-61832 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Gene expression changes induced in Rice (Oryza sativa) leaves following treatment with any one of the following: wild type Xoo, lipopolysaccharide (LPS) and exopolysaccaride (EPS) deficient Xoo mutant; LPS proficient but EPS deficient Xoo mutant

Project description:Lipopolysaccharide is a Microbe Associated Molecular Pattern (MAMP) that is known to induce defense responses in plants. In rice we have shown that Xoo LPS induce callose deposition, reactive oxygen production and induced resistance response. The exopolysaccaride (EPS) secreted by Xoo might be involved in supressing these defense responses. We have performed transcriptional profiling of rice leaf gene expression changes after treatment with Xoo strains BXO1003 (LPS-, EPS-), BXO1002 (LPS+ EPS-) and BXO43 (wild type) along with milliQ treated leaves to identify the genes that are differentially expressed. RNA was isolated from mid veins of rice leaves 15 hours after injecting them with Xoo strains BXO1003 (LPS-, EPS-), BXO1002 (EPS-), BXO43 (wild type) or milli-Q water. The rice gene expression in each of the treatment was normalized based on the gene expression in the milli-Q treatment.

2015-06-30 | E-GEOD-61833 | biostudies-arrayexpress

Time-resolved combined analysis of transcriptome and proteome of the pathogenicity-activated plant pathogen Xanthomonas oryzae pv. oryzae

Project description:Xanthomonas oryzae pv. oryzae (Xoo) is a rice pathogen causing bacterial blight, which outbreaks in most rice cultivating countries and reduces yield up to 50% due to no effective pesticide. Urgent responses of Xoo upon the initial contacts with rice at infection site are essential for pathogenesis. We studied the time-resolved gene expression of both transcriptome and proteome in the pathogenicity-activated Xoo cells with an in vitro assay system. Genes related to cell mobility, inorganic ion transport and effectors are early response genes to help Xoo cells invade into damaged rice leaf tissues, obtain rare cofactors, and evade rice immune responses. Although the time-resolved gene expression pattern of Xoo is conserved in both mRNA and protein, there are varied time gaps in genes between the expression peaks of mRNA and protein, which implies there is an additional translational selection step of specific mRNAs for rapid translation. The expression pattern of genes from a polycistronic mRNA in the same gene cluster is strictly conserved. The time-resolved gene expression study of Xoo in both transcriptome and proteome provides a valuable information about the pathogenic responses of Xoo at the initial stage of Xoo-rice interaction.

2021-09-09 | PXD020135 | Pride

Comparative Proteome Profiling of Susceptible anComparative Proteome Profiling of Susceptible and Resistant Rice Cultivars Identified an Arginase Involved in Rice Defense Against Xanthomonas oryzae pv. oryzae d Resistant Rice Cultivars Identified an Arginase Involved in Rice Defense Against Xanthomonas oryzae pv. oryzae

Project description:Xanthomonas oryzae pv. oryzae (Xoo), the causative agent of bacterial blight disease, is one of the major threats to rice productivity. Yet, the molecular mechanism of rice-Xoo interaction is elusive. Here, we report comparative proteome profiles of Xoo susceptible (Dongjin) and resistant (Hwayeong) cultivars of rice in response to two-time points (3 and 6 days) of Xoo infection. Low-abundance proteins were enriched using a protamine sulfate (PS) precipitation method and isolated proteins were quantified by a label-free quantitative analysis, leading to the identification of 3846 protein groups. Of these, 1128 proteins were significantly changed between mock and Xoo infected plants of Dongjin and Hwayeong cultivars. Based on the abundance pattern and functions of the identified proteins, a total of 23 candidate proteins were shortlisted that potentially participate in plant defense against Xoo in the resistant cultivar. Of these candidate proteins, a mitochondrial arginase-1 showed Hwayeong specific abundance and was significantly accumulated following Xoo inoculation. Overexpression of arginase-1 in susceptible rice cultivar (Dongjin) resulted in enhanced tolerance against Xoo as compared to the wild-type (WT). In addition, expression analysis of defense-related genes encoding PR1, glucanase I, and chitinase II by qRT-PCR showed their enhanced expression in the overexpression lines as compared to WT. Mitochondrial localization of the selected arginase was further confirmed by fluorescent microscopy using GFP-tagged arginase. Taken together, our results uncover the proteome changes in the rice cultivars and highlight the functions of arginase in plant defense against Xoo.

2022-01-06 | PXD027569 | Pride

Dynamic and coordinated expression changes of rice small RNAs in response to Xanthomonas oryzae pv. oryzae

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

Gene expression changes induced in Rice (Oryza sativa) leaves by lipopolysaccharide (LPS) extracted from Xanthomonas oryzae pv. oryzae (Xoo) strain BXO43

Project description:Lipopolysaccharide is a Microbe Associated Molecular Pattern (MAMP) that is known to induce defense responses in plants. We have shown that treatment of rice leaves with Xoo LPS induces callose deposition, reactive oxygen production and enhances resistance against subsequent infection by the pathogen. We have performed transcriptional profiling of rice leaves that are treated with Xoo LPS to identify differentially expressed genes.

2015-06-30 | GSE61832 | GEO

Whole genome expression profiling of rice leaves treated with Xanthomonas oryzae pv. oryzae secreted cell wall degrading lipase/esteraseA (LipA) at early time points, 30 min. and 120 min.

Project description:Treatment of rice tissues with purified preparations of a Xanthomonas oryzae pv. oryzae (Xoo) secreted plant cell wall degrading enzyme, Lipase/Esterase (LipA), elicits cell wall damage induced innate immune responses. LipA activity is required for induction of defense responses. In order to characterize the early events during elaboration of cell wall degrading enzyme, Lipase/Esterase (LipA) induced innate immune response in rice, we have performed global gene expression profiling of rice leaves treated with purified LipA at early time points, 30 minutes and 120min, after treatment. Whole genome transcriptional profiling was performed using Affymetrix Rice GeneChips Leaves of two weeks old green house grown susceptible rice cultivar (Taichung Native-1; TN-1) were infiltrated with either 30-40μl of purified Xoo Lipase/Esterase (LipA)(500μg/ml) or with buffer (10mM potassium phosphate buffer pH 6.0) alone (as described in Jha et al. 2007; MPMI vol 20, pp 31-40). The plants were shifted to a growth chamber (28oC; 80% relative humidity; 12/12h light/dark cycle) 48 hours before the treatment. 20-30 leaf pieces covering the infiltrated zone from each of the treatments were harvested 30 min. and 120 min. after infiltration. Total RNA isolated from the pooled samples was subjected for expression analysis using Affymetrix GeneChip System. The experiment was repeated with three different biological replicates using RNA isolated from three batches of rice leaves treated with the freshly purified Xoo Lipase/Esterase (LipA)and the buffer Gene Expression profiling of rice leaves undergoing an innate immune respone induced by LipA (Lipase/Esterase A) enzyme

2015-06-30 | E-GEOD-53940 | biostudies-arrayexpress

Transcriptome analysis of rice ABA deficient mutant Osaba1-1 and wild-type before and 72h after Xanthomonas oryzae pv. oryzae (Xoo) infection

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

Expression data from infected (Xanthomonas oryzae pv. Oryzae (P10)) leaf in japonica rice (cv. Y73)

Project description:Previously, we successfully introduce the bacterial blight resistance trait from Oryza meyeriana into O. sativa using asymmetric somatic hybridization with O. meyeriana as the donor species. After years of breeding, a progeny named Y73 was generated with recurrent parent O. sativa L. ssp. japonica cv. Dalixiang, and it shows high resistance to broad-spectrum of bacterial blight pathogens Xanthomonas oryzae pv. Oryzae (Xoo). However, the resistance mechanism of Y73 is remain undiscovered. To provide insights into the high resistance phenotype of these plants, we examined the transcriptome response in leaves of Y73 to the bacterial blight infection in this study. Xoo inoculated and mock inoculated rice plants were grown in growth room and the global analysis of gene expression events in rice leaves at 24 hours post inoculation (hpi) were analyzed using Affymetrix Rice GeneChip microarrays. We used microarrays to detail the global programme of gene expression underlying Xoo infection in rice Y73. To find out pathways and genes involved in its high and board-spectrum resistance, microanalysis were carried out on Y73 after Xoo infection at 24 hours post inoculation (hpi). Three independant replicates were perfomed for each treatments.

2012-02-27 | E-GEOD-36093 | biostudies-arrayexpress

Time-resolved genome-wide pathogenic gene expression analysis of the plant pathogen Xanthomonas oryzae pv. oryzae (Xoo) via RNA-Seq

Project description:Host-pathogen interactions, in particular during the early stages of infection, are important for the fate of both the invading pathogen and host. In pathogens, these interactions activate diverse pathogenic signals to cause disease in the host and evade the inevitably activated immune responses of the infected host. In this study, we used in vitro assay system and RNA-seq to analyze the time-resolved genome-wide gene expressions of Xanthomonas oryzae pv. oryzae (Xoo) evoked by the interactions with rice leaf extracts. RNA-seq analysis was carried out with samples of 7 different time points within 1 h. The RNA-seq data were verified by qRT-PCR. The in vitro system successfully initiated the pathogenic signals in Xoo cell culture. Many pathogenicity-related genes were expressed within 15 min. The hrpG gene was transcribed at maximum level within 10 min, and hrpX gene expression reached maximum level in 15 min. Chemotaxis and flagellar biosynthesis-related genes and cyclic-di-GMP synthesizing genes having GGDEF motif, were down-regulated until 10 min and after then up-regulated. Genes related to iron uptake and two component systems of phoB-phoR, phoP-phoQ, and pmrA-pmrB were up-regulated before 5 min. Data of multiple time points enabled non-linear regression fit of the time-resolved expression data, with which we newly developed the continuous time-resolved heat map to help the comparison of gene expression profiles. Essentiality of the transcriptionally up-regulated genes was also analyzed by the pathogenicity assay using the Xoo knockout strains, which showed not necessarily all the up-regulated genes were required for pathogenicity. the time-dependent, 0, 5, 10, 15, 30, 45, and 60 min, transcriptome analysis of genome-wide Xanthomonas oryzae pv. oryzae genes from the pathogenic interactions with RLX via RNA-Seq

2015-09-22 | E-GEOD-61607 | biostudies-arrayexpress

Transcriptional profiling of Cellulase induced hypersensitive reaction like response in rice

Project description:Cellulase, a Type II secretion system secreted protein of Xanthomonas oryzae pv. oryzae (Xoo; the casual of bacterial leaf blight of rice) is a potent inducer of rice defense responses such as hypersensitive response like reactions (HR), callose depositions, cell death associated with nuclear fragmentations and impart functional resistance against further Xoo inoculation In order to understand the molecular events associated with cellulase induced HR in rice, whole genome transcriptional profiling was performed using Affymetrix Rice GeneChips Keywords: Expression profiling of a hypersensitive reaction like response Leaves of 20 days old green house grown susceptible rice cultivar (Taichung Native-1; TN-1) were infiltrated with either 30-40μl of purified Xoo cellulase (5μg/ml) or with buffer (10mM potassium phosphate buffer pH 6.0) alone (as described in Jha et al. 2007; MPMI vol 20, pp 31-40). The plants were shifted to a growth chamber (28oC; 80% relative humidity; 12/12h light/dark cycle) 48 hours before the treatment. 20-30 leaf pieces covering the infiltrated zone from each of the treatments were harvested 12 h after infiltration. Total RNA isolated from the pooled samples was subjected for expression analysis using Affymetrix GeneChip System. The experiment was repeated with three different biological replicates using RNA isolated from three batches of rice leaves treated with the freshly purified Xoo cellulase and the buffer

2009-12-24 | E-GEOD-8216 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data