Negative allosteric regulation of Enterococcus faecalis small alarmone synthetase RelQ by single-stranded RNA

Proc Natl Acad Sci U S A. 2017 Apr 4;114(14):3726-3731. doi: 10.1073/pnas.1617868114. Epub 2017 Mar 20.


The alarmone nucleotides guanosine pentaphosphate (pppGpp) and tetraphosphate (ppGpp), collectively referred to as (p)ppGpp, are key regulators of bacterial growth, stress adaptation, pathogenicity, and antibiotic tolerance. We show that the tetrameric small alarmone synthetase (SAS) RelQ from the Gram-positive pathogen Enterococcus faecalis is a sequence-specific RNA-binding protein. RelQ's enzymatic and RNA binding activities are subject to intricate allosteric regulation. (p)ppGpp synthesis is potently inhibited by the binding of single-stranded RNA. Conversely, RelQ's enzymatic activity destabilizes the RelQ:RNA complex. pppGpp, an allosteric activator of the enzyme, counteracts the effect of RNA. Tetramerization of RelQ is essential for this regulatory mechanism, because both RNA binding and enzymatic activity are abolished by deletion of the SAS-specific C-terminal helix 5α. The interplay of pppGpp binding, (p)ppGpp synthesis, and RNA binding unites two archetypal regulatory paradigms within a single protein. The mechanism is likely a prevalent but previously unappreciated regulatory switch used by the widely distributed bacterial SAS enzymes.

Keywords: (p)ppGpp; RNA–protein interaction; allosteric regulation; nucleotide signaling; stringent response.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Allosteric Regulation
  • Bacterial Proteins / chemistry
  • Bacterial Proteins / metabolism
  • Base Sequence
  • Binding Sites
  • Enterococcus faecalis / chemistry
  • Enterococcus faecalis / enzymology*
  • Gene Expression Regulation, Bacterial
  • Guanosine Pentaphosphate / metabolism*
  • Ligases / chemistry*
  • Ligases / metabolism*
  • Models, Molecular
  • Protein Binding
  • Protein Multimerization
  • RNA, Bacterial / metabolism
  • RNA, Messenger / metabolism*
  • Substrate Specificity


  • Bacterial Proteins
  • RNA, Bacterial
  • RNA, Messenger
  • Guanosine Pentaphosphate
  • Ligases