Dataset Information

Genome subtraction for the identification of potential antimicrobial targets in Xanthomonas oryzae pv. oryzae PXO99A pathogenic to rice.

ABSTRACT: In pathogenic bacteria, identification of essential proteins which are non-homologous to the host plants represents potential antimicrobial targets. We applied subtractive genomics approach for the identification of novel antimicrobial targets in Xanthomonas oryzae pv. oryzae PXO99A, the causative agent of bacterial blight in rice. Comparative analysis was performed through BLAST available with the NCBI. The analysis revealed that 27 essential protein sequences out of 4,988 sequences of X. oryzae pv. oryzae PXO99A are non-homologous to Oryza sativa. Subsequent analysis of 27 essential proteins revealed their involvement in different metabolic activities such as transport activity, DNA binding, structural constituent of ribosome, cell division, translation, and plasma membrane. These 27 proteins were analyzed for virulence and novelty and out of 27, three essential non-homologous proteins were found to be the novel antimicrobial targets.

SUBMITTER: Keshri V

PROVIDER: S-EPMC3909572 | biostudies-literature | 2014 Feb

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

Genome subtraction for the identification of potential antimicrobial targets in Xanthomonas oryzae pv. oryzae PXO99A pathogenic to rice.

Keshri V V Singh Dhananjaya P DP Prabha R R Rai A A Sharma A K AK

3 Biotech 20130404 1

In pathogenic bacteria, identification of essential proteins which are non-homologous to the host plants represents potential antimicrobial targets. We applied subtractive genomics approach for the identification of novel antimicrobial targets in Xanthomonas oryzae pv. oryzae PXO99A, the causative agent of bacterial blight in rice. Comparative analysis was performed through BLAST available with the NCBI. The analysis revealed that 27 essential protein sequences out of 4,988 sequences of X. oryza ...[more]

PMID: 28324466

Similar Datasets

Project description:BackgroundXanthomonas oryzae pv oryzae is a devastating pathogen of rice and has been extensively studied as a model pathogen of monocotyledons. Expressional studies in both the contenders have been undertaken in past to understand the molecular mechanism underlying the compatible and incompatible interactions in the pathosystem. Continuous update on database and gene annotations necessitates constant updating on the roles of the new entities as well as reinterpretation of regulations of the previous ones. Moreover the past endeavors have addressed the middle or late defense responses of the rice plant whereas in the present study an attempt has been made to investigate the early defense responses taking place immediately after inoculation.ResultsMicroarray was used to study the transcriptional modulations in eighteen days old rice seedling leaves of both susceptible and resistant genotypes one hour after inoculation. In resistant plants as compared to susceptible ones 274 genes were found to be differentially expressed. Annotations could be assigned to 112 up- and 73 down-regulated transcripts and gene interaction maps were generated for 86 transcripts. Expressional data and interaction maps were used to develop a hypothetical scheme of the molecular events taking place during early defense response. Network analysis with the differential transcripts showed up-regulation of major clusters of cell signaling proteins and transcription factors while growth and basal metabolic components were largely found to be down-regulated.ConclusionsThis study provides an understanding of the early defense signaling in rice cells. Components of the calcium and lipid signaling as well as MAPK cascade were modulated, by signals from surface receptors and cytosolic R-proteins, to arouse jasmonic acid and ethylene signaling and suppress auxin signaling through various transcription factors. Abscisic acid modulation was also evident through the expression regulation of transcription factors involved with its functions. Moreover adjustments in expression levels of components of primary as well as secondary metabolism, protein trafficking and turnout were apparent, highlighting the complexity of defense response.

Project description:BackgroundPlant-pathogen interactions at early stages of infection are important to the fate of interaction. Xanthomonas oryzae pv. oryzae (Xoo) causes bacterial blight, which is a devastating disease in rice. Although in vivo and in vitro systems have been developed to study rice-Xoo interactions, both systems have limitations. The resistance mechanisms in rice can be better studied by the in vivo approach, whereas the in vitro systems are suitable for pathogenicity studies on Xoo. The current in vitro system uses minimal medium to activate the pathogenic signal (expression of pathogenicity-related genes) of Xoo, but lacks rice-derived factors needed for Xoo activation. This fact emphasizes the need of developing a new in vitro system that allow for an easy control of both pathogenic activation and for the experiment itself.ResultsWe employed an in vitro system that can activate pathogenicity-related genes in Xoo using rice leaf extract (RLX) and combined the in vitro assay with RNA-Seq to analyze the time-resolved genome-wide gene expression of Xoo. RNA-Seq was performed with samples from seven different time points within 1 h post-RLX treatment and the expression of up- or downregulated genes in RNA-Seq was validated by qRT-PCR. Global analysis of gene expression and regulation revealed the most dramatic changes in functional categories of genes related to inorganic ion transport and metabolism, and cell motility. Expression of many pathogenicity-related genes was induced within 15 min upon contact with RLX. hrpG and hrpX expression reached the maximum level within 10 and 15 min, respectively. Chemotaxis and flagella biosynthesis-related genes and cyclic-di-GMP controlling genes were downregulated for 10 min and were then upregulated. Genes related to inorganic ion uptake were upregulated within 5 min. We introduced a non-linear regression fit to generate continuous time-resolved gene expression levels and tested the essentiality of the transcriptionally upregulated genes by a pathogenicity assay of lesion length using single-gene knock-out Xoo strains.ConclusionsThe in vitro system combined with RNA-Seq generated a genome-wide time-resolved pathogenic gene expression profile within 1 h of initial rice-Xoo interactions, demonstrating the expression order and interaction dependency of pathogenic genes. This combined system can be used as a novel tool to study the initial interactions between rice and Xoo during bacterial blight progression.

Dataset Information

Genome subtraction for the identification of potential antimicrobial targets in Xanthomonas oryzae pv. oryzae PXO99A pathogenic to rice.

Publications

Genome subtraction for the identification of potential antimicrobial targets in Xanthomonas oryzae pv. oryzae PXO99A pathogenic to rice.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets