title: 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.
abstract: BACKGROUND
  Serratia 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.
  
  
  RESULTS
  In 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.
  
  
  CONCLUSIONS
  Using 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.
authors.forename: Nabil M
authors.initials: NM
authors.lastname: Wilf
authors.forename: Adam J
authors.initials: AJ
authors.lastname: Reid
authors.forename: Joshua P
authors.initials: JP
authors.lastname: Ramsay
authors.forename: Neil R
authors.initials: NR
authors.lastname: Williamson
authors.forename: Nicholas J
authors.initials: NJ
authors.lastname: Croucher
authors.forename: Laurent
authors.initials: L
authors.lastname: Gatto
authors.forename: Svenja S
authors.initials: SS
authors.lastname: Hester
authors.forename: David
authors.initials: D
authors.lastname: Goulding
authors.forename: Lars
authors.initials: L
authors.lastname: Barquist
authors.forename: Kathryn S
authors.initials: KS
authors.lastname: Lilley
authors.forename: Robert A
authors.initials: RA
authors.lastname: Kingsley
authors.forename: Gordon
authors.initials: G
authors.lastname: Dougan
authors.affiliation: Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QW, UK. gpcs2@cam.ac.uk.
authors.forename: George Pc
authors.initials: GP
authors.lastname: Salmond
mesh_terms: D000900:Anti-Bacterial Agents / Q000096:biosynthesis*; D001426:Bacterial Proteins / Q000235:genetics* / Q000378:metabolism*; D001435:Bacteriophages / Q000235:genetics / Q000378:metabolism; D016000:Cluster Analysis; D004579:Electron Transport / Q000235:genetics; D005407:Flagella / Q000235:genetics / Q000378:metabolism; D015964:Gene Expression Regulation, Bacterial; D016680:Genome, Bacterial; D035001:Host Factor 1 Protein / Q000235:genetics* / Q000378:metabolism*; D009154:Mutation; D009876:Operon; D011353:Prodigiosin / Q000378:metabolism; D020543:Proteome; D016601:RNA-Binding Proteins / Q000235:genetics / Q000378:metabolism; D012045:Regulatory Sequences, Nucleic Acid; D017423:Sequence Analysis, RNA; D012705:Serratia / Q000235:genetics* / Q000378:metabolism* / Q000472:pathogenicity / Q000821:virology; D059467:Transcriptome; D014774:Virulence / Q000235:genetics; D037521:Virulence Factors / Q000235:genetics / Q000378:metabolism
chemical_list: D000900:Anti-Bacterial Agents; D001426:Bacterial Proteins; D035001:Host Factor 1 Protein; D020543:Proteome; D016601:RNA-Binding Proteins; D037521:Virulence Factors; D011353:Prodigiosin