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

• Published in: Proceedings of the National Academy of Sciences - PNAS Vol. 114; no. 14; pp. 3726 - 3731
• Main Authors: Beljantseva, Jelena, Kudrin, Pavel, Andresen, Liis, Shingler, Victoria, Atkinson, Gemma C., Tenson, Tanel, Hauryliuk, Vasili
• Format: Journal Article
• Language: English
• Published: United States National Academy of Sciences 04.04.2017
• Subjects: (p)ppGpp; Allosteric Regulation; Bacterial Proteins - chemistry; Bacterial Proteins - metabolism; Base Sequence; Binding Sites; Biological Sciences; Enterococcus faecalis; Enterococcus faecalis - chemistry; Enterococcus faecalis - enzymology; Enzymatic activity; Enzymes; Gene Expression Regulation, Bacterial; Gram-positive bacteria; Guanosine Pentaphosphate - metabolism; Ligases - chemistry; Ligases - metabolism; Models, Molecular; nucleotide signaling; Pathogens; Protein Binding; Protein Multimerization; Proteins; Ribonucleic acid; RNA; RNA, Bacterial - metabolism; RNA, Messenger - metabolism; RNA-protein interaction; stringent response; Substrate Specificity; RNA–protein interaction; nucleotide signaling; (p)ppGpp; allosteric regulation; stringent response
• ISSN: 0027-8424; 1091-6490; 1091-6490
• DOI: 10.1073/pnas.1617868114

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.