title: Transcriptome analysis of Acidovorax avenae subsp. avenae cultivated in vivo and co-culture with Burkholderia seminalis.
abstract: 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.
authors.affiliation: 1] State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, 310058, Hangzhou, China [2].
authors.forename: Bin
authors.initials: B
authors.lastname: Li
authors.affiliation: 1] State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, 310058, Hangzhou, China [2].
authors.forename: Muhammad
authors.initials: M
authors.lastname: Ibrahim
authors.affiliation: State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, 310058, Hangzhou, China.
authors.forename: Mengyu
authors.initials: M
authors.lastname: Ge
authors.affiliation: State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, 310058, Hangzhou, China.
authors.forename: Zhouqi
authors.initials: Z
authors.lastname: Cui
authors.affiliation: State Key Laboratory Breeding Base for Zhejiang Sustainable Plant Pest and Disease Control, Key Laboratory of Detection for Pesticide Residues, Ministry of Agriculture, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China.
authors.forename: Guochang
authors.initials: G
authors.lastname: Sun
authors.affiliation: Institute of Digital Agriculture, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China.
authors.forename: Fei
authors.initials: F
authors.lastname: Xu
authors.affiliation: Faculty of Agriculture and Horticulture, Humboldt-Universität zu Berlin, 14195 Berlin, Germany.
authors.forename: Michael
authors.initials: M
authors.lastname: Kube
mesh_terms: D001426:Bacterial Proteins / Q000235:genetics / Q000378:metabolism; D058947:Bacterial Secretion Systems / Q000235:genetics; D019117:Burkholderia / Q000502:physiology*; D042621:Comamonadaceae / Q000235:genetics / Q000378:metabolism*; D020869:Gene Expression Profiling; D015964:Gene Expression Regulation, Bacterial; D005798:Genes, Bacterial; D054884:Host-Pathogen Interactions; D056265:Microbial Interactions; D012275:Oryza / Q000382:microbiology; D010935:Plant Diseases / Q000382:microbiology; D027343:Rhizome / Q000382:microbiology; D059467:Transcriptome
chemical_list: D001426:Bacterial Proteins; D058947:Bacterial Secretion Systems