Genome sequence of the rice-pathogenic bacterium Acidovorax avenae subsp. avenae RS-1.
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ABSTRACT:
SUBMITTER: Xie GL
PROVIDER: S-EPMC3165674 | biostudies-literature | 2011 Sep
REPOSITORIES: biostudies-literature
Publications
Genome sequence of the rice-pathogenic bacterium Acidovorax avenae subsp. avenae RS-1.
Xie Guan-Lin GL Zhang Guo-Qing GQ Liu He H Lou Miao-Miao MM Tian Wen-Xiao WX Li Bin B Zhou Xue-Ping XP Zhu Bo B Jin Gu-Lei GL
Journal of bacteriology 20110708 18
Acidovorax avenae subsp. avenae is a phytobacterium which is the causative agent of several plant diseases with economic significance. Here, we present the draft genome sequence of strain RS-1, which was isolated from rice shoots in a rice field in China. This strain can cause bacterial stripe of rice. ...[more]
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Project description:This study investigated the transcriptomic response of rice pathogen Acidovorax avenae subsp. avenae (Aaa) strain RS-1 to ß-lactam antibiotics in particular Ampicillin (Amp) and the result highlights the importance of Amp-induced differentially expressed genes in the virulence of Aaa strain RS-1.
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Project description:Determining how a bacterial pathogen responds to its host and other bacterial species by altering gene expression is key to understand its pathogenesis and environmental adaption. Here, we used RNA-Seq to comprehensively and quantitatively assess the transcriptional response of the rice bacterial pathogen Acidovorax avenae subsp. avenae strain RS-1 cultivated in vitro, in vivo and in co-culture with rice rhizobacterium Burkholderia seminalis R456. Results revealed a surprisingly large number of regulatory differences between these conditions indicating adaptation of A. avenae subsp. avenae to specific ecological conditions. In particular, a number of potential virulence factors such as type 3 secretion system proteins were specifically expressed under in vivo conditions, whereas genes whose protein products are involved in inter-bacterial interaction such as auxin efflux carrier, small mechanosensitive ion channel protein, and ureidoglycolate hydrolase were among those specifically up-regulated under co-culture conditions. In addition, global genomic analysis of strain RS-1 identified 406 putative non-coding (nc) RNA genes. Interestingly, 8 ncRNA genes that were uniquely expressed under in vivo may be linked to pathogenicity while 4 ncRNA genes that were uniquely expressed under coculture conditions may be involved in adaption to co-cultivation with B. seminalis. Expression data obtained by RNA-Seq were also confirmed for selected genes by quantitative real-time PCR and two-dimensional gel electrophoresis as well as knockout analysis.
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Project description:Response of bacterial pathogen to environmental bacteria and its host is critical for understanding of microbial adaption and pathogenesis. Here, we used RNA-Seq to comprehensively and quantitatively assess the transcriptional response of Acidovorax avenae subsp. avenae strain RS-1 cultivated in vitro, in vivo and in co-culture with rice rhizobacterium Burkholderia seminalis R456. Results revealed a slight response to other bacteria, but a strong response to host. In particular, a large number of virulence associated genes encoding Type I to VI secretion systems, 118 putative non-coding RNAs, and 7 genomic islands (GIs) were differentially expressed in vivo based on comparative genomic and transcriptomic analyses. Furthermore, the loss of virulence for knockout mutants of 11 differentially expressed T6SS genes emphasized the importance of these genes in bacterial pathogenicity. In addition, the reliability of expression data obtained by RNA-Seq was supported by quantitative real-time PCR of the 25 selected T6SS genes. Overall, this study highlighted the role of differentially expressed genes in elucidating bacterial pathogenesis based on combined analysis of RNA-Seq data and knockout of T6SS genes.
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Project description:Determining how a bacterial pathogen responds to its host and other bacterial species by altering gene expression is key to understand its pathogenesis and environmental adaption. Here, we used RNA-Seq to comprehensively and quantitatively assess the transcriptional response of the rice bacterial pathogen Acidovorax avenae subsp. avenae strain RS-1 cultivated in vitro, in vivo and in co-culture with rice rhizobacterium Burkholderia seminalis R456. Results revealed a surprisingly large number of regulatory differences between these conditions indicating adaptation of A. avenae subsp. avenae to specific ecological conditions. In particular, a number of potential virulence factors such as type 3 secretion system proteins were specifically expressed under in vivo conditions, whereas genes whose protein products are involved in inter-bacterial interaction such as auxin efflux carrier, small mechanosensitive ion channel protein, and ureidoglycolate hydrolase were among those specifically up-regulated under co-culture conditions. In addition, global genomic analysis of strain RS-1 identified 406 putative non-coding (nc) RNA genes. Interestingly, 8 ncRNA genes that were uniquely expressed under in vivo may be linked to pathogenicity while 4 ncRNA genes that were uniquely expressed under coculture conditions may be involved in adaption to co-cultivation with B. seminalis. Expression data obtained by RNA-Seq were also confirmed for selected genes by quantitative real-time PCR and two-dimensional gel electrophoresis as well as knockout analysis. Aaa strain RS-1 and B. seminalis strain R456 was isolated from diseased rice plants (Li et al., 2011; Xie et al., 2011) and rice rhizosphere (Zhang et al., 2007; Li et al., 2011), respectively, in our previous studies, and were stored in 20-30% sterile glycerol at -80°C. The samples of Aaa strain RS-1 for in vitro and in vivo analysis were prepared as described before (Ibrahim et al., 2012). The co-culture analysis of Aaa strain RS-1 with B. seminalis strain R456 were conducted according to Ruiz et al. (2009) and Di Cagno et al. (2009). Briefly, Aaa strain RS-1 and B. seminalis strain R456 was inoculated and incubated in chambers of a double culture vessel apparatus separated by a 0.4-μm membrane filter (Millipore Isopore™). In order to avoid the possible contamination during in vivo and co-culture operation, all bacterial samples were further confirmed based on the sequence analysis of 16S-rRNA (Li et al., 2011). Then samples were processed for RNA harvesting, mRNA purification and cDNA synthesis.
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