Methionine biosynthesis in Staphylococcus aureus is tightly controlled by a hierarchical network involving an initiator tRNA-specific T-box riboswitch

PLoS Pathog. 2013 Sep;9(9):e1003606. doi: 10.1371/journal.ppat.1003606. Epub 2013 Sep 12.

Abstract

In line with the key role of methionine in protein biosynthesis initiation and many cellular processes most microorganisms have evolved mechanisms to synthesize methionine de novo. Here we demonstrate that, in the bacterial pathogen Staphylococcus aureus, a rare combination of stringent response-controlled CodY activity, T-box riboswitch and mRNA decay mechanisms regulate the synthesis and stability of methionine biosynthesis metICFE-mdh mRNA. In contrast to other Bacillales which employ S-box riboswitches to control methionine biosynthesis, the S. aureus metICFE-mdh mRNA is preceded by a 5'-untranslated met leader RNA harboring a T-box riboswitch. Interestingly, this T-box riboswitch is revealed to specifically interact with uncharged initiator formylmethionyl-tRNA (tRNAi(fMet)) while binding of elongator tRNA(Met) proved to be weak, suggesting a putative additional function of the system in translation initiation control. met leader RNA/metICFE-mdh operon expression is under the control of the repressor CodY which binds upstream of the met leader RNA promoter. As part of the metabolic emergency circuit of the stringent response, methionine depletion activates RelA-dependent (p)ppGpp alarmone synthesis, releasing CodY from its binding site and thereby activating the met leader promoter. Our data further suggest that subsequent steps in metICFE-mdh transcription are tightly controlled by the 5' met leader-associated T-box riboswitch which mediates premature transcription termination when methionine is present. If methionine supply is limited, and hence tRNAi(fMet) becomes uncharged, full-length met leader/metICFE-mdh mRNA is transcribed which is rapidly degraded by nucleases involving RNase J2. Together, the data demonstrate that staphylococci have evolved special mechanisms to prevent the accumulation of excess methionine. We hypothesize that this strict control might reflect the limited metabolic capacities of staphylococci to reuse methionine as, other than Bacillus, staphylococci lack both the methionine salvage and polyamine synthesis pathways. Thus, methionine metabolism might represent a metabolic Achilles' heel making the pathway an interesting target for future anti-staphylococcal drug development.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • 5' Untranslated Regions
  • Bacterial Proteins / genetics
  • Bacterial Proteins / metabolism
  • DNA, Bacterial / metabolism
  • Down-Regulation
  • Isoenzymes / metabolism
  • Methionine / biosynthesis*
  • Models, Biological*
  • Mutation
  • Peptide Chain Initiation, Translational
  • Promoter Regions, Genetic
  • RNA Stability
  • RNA, Bacterial / metabolism*
  • RNA, Spliced Leader / metabolism
  • RNA, Transfer, Met / metabolism*
  • Repressor Proteins / genetics
  • Repressor Proteins / metabolism
  • Ribonucleases / metabolism
  • Riboswitch*
  • Staphylococcus aureus / enzymology
  • Staphylococcus aureus / metabolism*
  • T-Box Domain Proteins / genetics
  • T-Box Domain Proteins / metabolism*
  • Up-Regulation

Substances

  • 5' Untranslated Regions
  • Bacterial Proteins
  • CodY protein, Staphylococcus aureus
  • DNA, Bacterial
  • Isoenzymes
  • RNA, Bacterial
  • RNA, Spliced Leader
  • RNA, Transfer, Met
  • Repressor Proteins
  • Riboswitch
  • T-Box Domain Proteins
  • fMet-tRNA(fMet)
  • Methionine
  • Ribonucleases

Grant support

This study was supported by grants from the Deutsche Forschungsgemeinschaft through SFB-TR34, SPP1617 and Wo578/7-1 as well as by the Department for Employment and Learning (Northern Ireland). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.