Integrative "omics"-approach discovers dynamic and regulatory features of bacterial stress responses

PLoS Genet. 2013 Jun;9(6):e1003576. doi: 10.1371/journal.pgen.1003576. Epub 2013 Jun 20.

Abstract

Bacteria constantly face stress conditions and therefore mount specific responses to ensure adaptation and survival. Stress responses were believed to be predominantly regulated at the transcriptional level. In the phototrophic bacterium Rhodobacter sphaeroides the response to singlet oxygen is initiated by alternative sigma factors. Further adaptive mechanisms include post-transcriptional and post-translational events, which have to be considered to gain a deeper understanding of how sophisticated regulation networks operate. To address this issue, we integrated three layers of regulation: (1) total mRNA levels at different time-points revealed dynamics of the transcriptome, (2) mRNAs in polysome fractions reported on translational regulation (translatome), and (3) SILAC-based mass spectrometry was used to quantify protein abundances (proteome). The singlet oxygen stress response exhibited highly dynamic features regarding short-term effects and late adaptation, which could in part be assigned to the sigma factors RpoE and RpoH2 generating distinct expression kinetics of corresponding regulons. The occurrence of polar expression patterns of genes within stress-inducible operons pointed to an alternative of dynamic fine-tuning upon stress. In addition to transcriptional activation, we observed significant induction of genes at the post-transcriptional level (translatome), which identified new putative regulators and assigned genes of quorum sensing to the singlet oxygen stress response. Intriguingly, the SILAC approach explored the stress-dependent decline of photosynthetic proteins, but also identified 19 new open reading frames, which were partly validated by RNA-seq. We propose that comparative approaches as presented here will help to create multi-layered expression maps on the system level ("expressome"). Finally, intense mass spectrometry combined with RNA-seq might be the future tool of choice to re-annotate genomes in various organisms and will help to understand how they adapt to alternating conditions.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Gene Expression Regulation, Bacterial / drug effects
  • Heat-Shock Proteins / genetics*
  • Heat-Shock Proteins / metabolism
  • Oligonucleotide Array Sequence Analysis
  • Photosynthesis / genetics*
  • Proteome
  • Quorum Sensing
  • RNA, Messenger / genetics
  • Rhodobacter sphaeroides / genetics*
  • Rhodobacter sphaeroides / metabolism
  • Rhodobacter sphaeroides / physiology
  • Sigma Factor / genetics*
  • Sigma Factor / metabolism
  • Singlet Oxygen / metabolism
  • Singlet Oxygen / pharmacology*
  • Stress, Physiological / drug effects*
  • Transcription, Genetic

Substances

  • Heat-Shock Proteins
  • Proteome
  • RNA, Messenger
  • Sigma Factor
  • heat-shock sigma factor 32
  • Singlet Oxygen

Grant support

Funding was provided by DFG (www.dfg.de) grant Kl563/20-2 to GK. Work in the group of MK was supported by the Max-Planck-Society (www.mpg.de) and the Excellence Initiative LOEWE (www.hmwk.hessen.de). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.