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Burkholderia seminalis

ABSTRACT: Burkholderia seminalis Transcriptome or Gene expression

PROVIDER: PRJNA235910 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR1130477_1.fastq.gz	Fastqsanger.gz
	SRR1130477_2.fastq.gz	Fastqsanger.gz
	SRR1130248_1.fastq.gz	Fastqsanger.gz
	SRR1130248_2.fastq.gz	Fastqsanger.gz
	SRR1130349_1.fastq.gz	Fastqsanger.gz

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Transcriptome analysis of rice pathogen Acidovorax avenae subsp. avenae cultivated in vitro, in vivo and in co-culture with the rice rhizobacterium Burkholderia seminalis

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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