Structural basis for inhibition of a response regulator of σS stability by a ClpXP antiadaptor

Genes Dev. 2019 Jun 1;33(11-12):718-732. doi: 10.1101/gad.320168.118. Epub 2019 Apr 11.

Abstract

The stationary phase promoter specificity subunit σS (RpoS) is delivered to the ClpXP machinery for degradation dependent on the adaptor RssB. This adaptor-specific degradation of σS provides a major point for regulation and transcriptional reprogramming during the general stress response. RssB is an atypical response regulator and the only known ClpXP adaptor that is inhibited by multiple but dissimilar antiadaptors (IraD, IraP, and IraM). These are induced by distinct stress signals and bind to RssB in poorly understood manners to achieve stress-specific inhibition of σS turnover. Here we present the first crystal structure of RssB bound to an antiadaptor, the DNA damage-inducible IraD. The structure reveals that RssB adopts a compact closed architecture with extensive interactions between its N-terminal and C-terminal domains. The structural data, together with mechanistic studies, suggest that RssB plasticity, conferred by an interdomain glutamate-rich flexible linker, is critical for regulation of σS degradation. Structural modulation of interdomain linkers may thus constitute a general strategy for tuning response regulators.

Keywords: ClpXP; adaptor; antiadaptor; bacteria; biochemistry; crystallography; stress response.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Bacterial Proteins / chemistry
  • Bacterial Proteins / metabolism*
  • Crystallography, X-Ray
  • DNA-Binding Proteins / antagonists & inhibitors
  • DNA-Binding Proteins / chemistry*
  • DNA-Binding Proteins / metabolism
  • Escherichia coli Proteins / antagonists & inhibitors
  • Escherichia coli Proteins / chemistry*
  • Escherichia coli Proteins / metabolism
  • Models, Molecular
  • Protein Conformation
  • Protein Conformation, alpha-Helical
  • Protein Domains
  • Protein Stability
  • Sigma Factor / chemistry*
  • Sigma Factor / metabolism*
  • Transcription Factors / antagonists & inhibitors
  • Transcription Factors / chemistry*
  • Transcription Factors / metabolism

Substances

  • Bacterial Proteins
  • DNA-Binding Proteins
  • Escherichia coli Proteins
  • IraD protein, E coli
  • Sigma Factor
  • Transcription Factors
  • rssB protein, E coli
  • sigma factor KatF protein, Bacteria