Another layer of complexity inStaphylococcus aureusmethionine biosynthesis control: unusual RNase III-driven T-box riboswitch cleavage determinesmetoperon mRNA stability and decay

Abstract

In Staphylococcus aureus, de novo methionine biosynthesis is regulated by a unique hierarchical pathway involving stringent-response controlled CodY repression in combination with a T-box riboswitch and RNA decay. The T-box riboswitch residing in the 5′ untranslated region (met leader RNA) of the S. aureus metICFE-mdh operon controls downstream gene transcription upon interaction with uncharged methionyl-tRNA. met leader and metICFE-mdh (m)RNAs undergo RNase-mediated degradation in a process whose molecular details are poorly understood. Here we determined the secondary structure of the met leader RNA and found the element to harbor, beyond other conserved T-box riboswitch structural features, a terminator helix which is target for RNase III endoribonucleolytic cleavage. As the terminator is a thermodynamically highly stable structure, it also forms posttranscriptionally in met leader/ metICFE-mdh read-through transcripts. Cleavage by RNase III releases the met leader from metICFE-mdh mRNA and initiates RNase J-mediated degradation of the mRNA from the 5′-end. Of note, metICFE-mdh mRNA stability varies over the length of the transcript with a longer lifespan towards the 3′-end. The obtained data suggest that coordinated RNA decay represents another checkpoint in a complex regulatory network that adjusts costly methionine biosynthesis to current metabolic requirements.

The 3′UTR‐derived sRNA RsaG coordinates redox homeostasis and metabolism adaptation in response to glucose‐6‐phosphate uptake in Staphylococcus aureus

“…Hence, RNases J1/J2 are not only essential for stress responses by controlling mRNA degradation but they also contribute to generate sRNA from mRNAs. Very recently, a rather similar degradation mechanism was described in the maturation of the T-box riboswitch in the 5′UTR of the metlCFE-mdh operon (Wencker et al, 2021). Indeed, in the absence of methionine and after cleavage of the met leader by RNase III, the RNases J1/J2 mediate degradation of the mRNA from the 5′-end generating more stable transcripts toward the 3′-end.…”

A Riboswitch-Driven Era of New Antibacterials

“…For instance, some riboswitches that are widely distributed among different bacterial species (i.e., TPP, FMN riboswitches) could be used as broad-spectrum antibacterial targets, while others that are found specifically in individual genus or species could constitute selective drugs (e.g., targeting preQ-1 or purine-riboswitches) [ 26 ]. Recently, it was reported that T-boxes in Staphylococcus aureus contain species-specific structural features that play a central role in riboswitch structural conformation and function, allowing the adaptation to specific metabolic environments, making them promising, lineage-specific drug targets [ 27 , 28 , 29 , 30 ]. Furthermore, some riboswitches regulate the expression of several genes that are fundamental for bacterial survival.…”

Streptococcus suis TrpX is part of a tryptophan uptake system, and its expression is regulated by a T-box regulatory element

“…The trpX T-box comprises 461 nt and is relatively large in size compared to other T-boxes 21 . However, a T-box with a similar size (440 nt) which is involved in methionine biosynthesis has been found in Staphylococcus aureus 63 .…”

“…Similar results were found in S. aureus where the deletion of the antiterminator and terminator stretch led to an activated transcription independent of methionine concentration. Therefore, the T-box riboswitch mechanism depends on an effective termination site 63 .…”