RNA-seq reveals the RNA binding proteins, Hfq and RsmA, play various roles in virulence, antibiotic production and genomic flux in Serratia sp. ATCC 39006

BMC Genomics

Research Article

Svenja S Hester¹  Laurent Gatto¹  Kathryn S Lilley¹  Nabil M Wilf²  George PC Salmond²  Neil R Williamson²  Joshua P Ramsay³  David Goulding⁴  Gordon Dougan⁴  Adam J Reid⁴  Robert A Kingsley⁴  Nicholas J Croucher⁴  Lars Barquist⁴ 

[1] Cambridge Centre for Proteomics, University of Cambridge, Cambridge, UK;Department of Biochemistry, University of Cambridge, Tennis Court Road, CB2 1QW, Cambridge, UK;Department of Biochemistry, University of Cambridge, Tennis Court Road, CB2 1QW, Cambridge, UK;School of Biomedical Sciences, CHIRI Biosciences Research Precinct, Curtin University, Perth, WA, Australia;The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus Hinxton, Cambridge, UK;

关键词: Quorum Sense;    Mobile Genetic Element;    Prodigiosin;    Early Stationary Phase;    Pectate Lyase;   

DOI  :  10.1186/1471-2164-14-822

 received in 2013-08-27, accepted in 2013-11-14,  发布年份 2013

来源: Springer

【 摘 要 】

BackgroundSerratia sp. ATCC 39006 (S39006) is a Gram-negative enterobacterium that is virulent in plant and animal models. It produces a red-pigmented trypyrrole secondary metabolite, prodigiosin (Pig), and a carbapenem antibiotic (Car), as well as the exoenzymes, pectate lyase and cellulase. Secondary metabolite production in this strain is controlled by a complex regulatory network involving quorum sensing (QS). Hfq and RsmA (two RNA binding proteins and major post-transcriptional regulators of gene expression) play opposing roles in the regulation of several key phenotypes within S39006. Prodigiosin and carbapenem production was abolished, and virulence attenuated, in an S39006 ∆hfq mutant, while the converse was observed in an S39006 rsmA transposon insertion mutant.ResultsIn order to define the complete regulon of Hfq and RsmA, deep sequencing of cDNA libraries (RNA-seq) was used to analyse the whole transcriptome of S39006 ∆hfq and rsmA::Tn mutants. Moreover, we investigated global changes in the proteome using an LC-MS/MS approach. Analysis of differential gene expression showed that Hfq and RsmA directly or indirectly regulate (at the level of RNA) 4% and 19% of the genome, respectively, with some correlation between RNA and protein expression. Pathways affected include those involved in antibiotic regulation, virulence, flagella synthesis, and surfactant production. Although Hfq and RsmA are reported to activate flagellum production in E. coli and an adherent-invasive E. coli hfq mutant was shown to have no flagella by electron microscopy, we found that flagellar production was increased in the S39006 rsmA and hfq mutants. Additionally, deletion of rsmA resulted in greater genomic flux with increased activity of two mobile genetic elements. This was confirmed by qPCR and analysis of rsmA culture supernatant revealed the presence of prophage DNA and phage particles. Finally, expression of a hypothetical protein containing DUF364 increased prodigiosin production and was controlled by a putative 5′ cis-acting regulatory RNA element.ConclusionUsing a combination of transcriptomics and proteomics this study provides a systems-level understanding of Hfq and RsmA regulation and identifies similarities and differences in the regulons of two major regulators. Additionally our study indicates that RsmA regulates both core and variable genome regions and contributes to genome stability.

【 授权许可】

Unknown   
© Wilf et al.; licensee BioMed Central Ltd. 2013. This article is published under license to BioMed Central Ltd. This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.