The small non-coding RNA RsaE influences extracellular matrix composition in Staphylococcus epidermidis biofilm communities

PLoS Pathog. 2019 Mar 14;15(3):e1007618. doi: 10.1371/journal.ppat.1007618. eCollection 2019 Mar.

Abstract

RsaE is a conserved small regulatory RNA (sRNA) which was previously reported to represent a riboregulator of central carbon flow and other metabolic pathways in Staphylococcus aureus and Bacillus subtilis. Here we show that RsaE contributes to extracellular (e)DNA release and biofilm-matrix switching towards polysaccharide intercellular adhesin (PIA) production in a hypervariable Staphylococcus epidermidis isolate. Transcriptome analysis through differential RNA sequencing (dRNA-seq) in combination with confocal laser scanning microscopy (CLSM) and reporter gene fusions demonstrate that S. epidermidis protein- and PIA-biofilm matrix producers differ with respect to RsaE and metabolic gene expression. RsaE is spatiotemporally expressed within S. epidermidis PIA-mediated biofilms, and its overexpression triggers a PIA biofilm phenotype as well as eDNA release in an S. epidermidis protein biofilm matrix-producing strain background. dRNA-seq and Northern blot analyses revealed RsaE to exist as a major full-length 100-nt transcript and a minor processed species lacking approximately 20 nucleotides at the 5'-end. RsaE processing results in expansion of the mRNA target spectrum. Thus, full-length RsaE interacts with S. epidermidis antiholin-encoding lrgA mRNA, facilitating bacterial lysis and eDNA release. Processed RsaE, however, interacts with the 5'-UTR of icaR and sucCD mRNAs, encoding the icaADBC biofilm operon repressor IcaR and succinyl-CoA synthetase of the tricarboxylic acid (TCA) cycle, respectively. RsaE augments PIA-mediated biofilm matrix production, most likely through activation of icaADBC operon expression via repression of icaR as well as by TCA cycle inhibition and re-programming of staphylococcal central carbon metabolism towards PIA precursor synthesis. Additionally, RsaE supports biofilm formation by mediating the release of eDNA as stabilizing biofilm matrix component. As RsaE itself is heterogeneously expressed within biofilms, we consider this sRNA to function as a factor favoring phenotypic heterogeneity and supporting division of labor in S. epidermidis biofilm communities.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Bacterial Proteins / genetics
  • Bacterial Proteins / metabolism
  • Biofilms
  • Extracellular Matrix / genetics*
  • Extracellular Matrix / physiology
  • Gene Expression Profiling
  • Gene Expression Regulation, Bacterial / genetics
  • Operon / genetics
  • Phenotype
  • Polysaccharides, Bacterial / genetics
  • Polysaccharides, Bacterial / metabolism
  • RNA, Small Untranslated / genetics
  • RNA, Small Untranslated / metabolism*
  • Staphylococcal Infections / genetics
  • Staphylococcal Infections / metabolism
  • Staphylococcus / genetics
  • Staphylococcus epidermidis / genetics*
  • Staphylococcus epidermidis / metabolism

Substances

  • Bacterial Proteins
  • Polysaccharides, Bacterial
  • RNA, Small Untranslated
  • polysaccharide intercellular adhesin

Grant support

The study was supported by grants to W.Z. from the German Research Council (DFG) through grants SPP1617 (ZI 665/2), ZI 665/3-1 and Transregional Collaborative Research Centre 34 (INST 292/67; B04) as well as by the German Federal Ministry of Education and Research (BMBF), grant number 01KI1727E. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.