Emerging functions for the Staphylococcus aureus RNome

Abstract

Staphylococcus aureus is a leading pathogen for animals and humans, not only being one of the most frequently isolated bacteria in hospital-associated infections but also causing diseases in the community. To coordinate the expression of its numerous virulence genes for growth and survival, S. aureus uses various signalling pathways that include two-component regulatory systems, transcription factors, and also around 250 regulatory RNAs. Biological roles have only been determined for a handful of these sRNAs, including cis, trans, and cis-trans acting RNAs, some internally encoding small, functional peptides and others possessing dual or multiple functions. Here we put forward an inventory of these fascinating sRNAs; the proteins involved in their activities; and those involved in stress response, metabolisms, and virulence.

Figure 1. A variety of mechanisms of actions for the S. aureus sRNAs.

(A) Cis-encoded sRNAs bind via perfect complementarities with mRNA targets at the translation initiation sequence, preventing ribosome binding and therefore translation. (B) Trans-acting sRNAs. The trans-encoded sRNAs bind and block the ribosome binding site by interrupted pairings, using one or two hairpin(s) to repress translation initiation. (C) Cis-encoded antisense sRNAs acting in trans. In the SprA1/A1_AS TA module, SprA1_AS prevents SprA1 translation to prevent toxic peptide expression. On the two interacting sRNAs, the cis and trans pairing-regions are indicated in blue and red, respectively.

Figure 2. RsaE controls central metabolic pathways.

RsaE regulates, directly or indirectly, the expression of several genes involved in amino acid synthesis, peptides transport, carbohydrate metabolism, and the TCA cycle. RsaE directly regulates the TCA cycle by inhibiting sucD mRNA translation coding for one of the subunits of the succinyl-Coa synthase. It alters the purine biosynthetic pathway via the down-regulation of some enzymes involved in the folate-dependent, one-carbon metabolism. RsaE uses multiple binding sites for the regulation of the opp3BCDFA mRNA expressing an oligopeptide transporter involved in nutrient transport. RsaE pairs directly with sites overlapping the ribosome binding site of the upstream (opp3B) and distal (opp3A) genes from the operon to inhibit their translations. RsaE modulates the intracellular pool of amino acid by down-regulating the expression of an oligopeptide transporter and by up-regulating genes that produce amino acid synthesis enzymes. In some S. aureus strains, RsaE expression is controlled by the agr quorum-sensing system in response to autoinducing peptide (AIP), and it depends on the σ^B regulon. The plain and dashed lines indicate the direct and indirect gene regulations, respectively (red bars: inhibitions, black arrows: stimulations).

Figure 3. Schematic overview of the multiple interactions between sRNAs and transcriptional regulators involved in spa (protein A) and hla (α-hemolysin) expression in S. aureus strain 8325-4.

The arrows indicate the stimulations and the bars, the repressions. The direct effects of two sRNAs on gene expression are indicated in red. RNAIII represses rot and spa translation by direct pairing interactions , . Rot requires SarT to stimulate SarS in the presence of SarA , . In contrast to SarA, Rot and SarS are direct activators of spa expression , . In the exponential phase of growth, spa transcription is stimulated by Rot and by SarS. In the post-exponential phase, spa transcription and translation are repressed by SarA and RNAIII, respectively, and the direct inactivation of Rot by RNAIII leads to the repression of the Rot and the SarS-dependent transcription activations of spa. hla is up-regulated by SarA and down-regulated by SarS . Rot and SarT repress hla transcription by a sae-dependent way . In the post-exponential phase of growth, RNAIII enhances hla translation by direct pairings at the hla mRNA 5′UTR and stimulates hla transcription by down-regulating the expression of SarT and Rot. AgrA, the master transcriptional regulator of quorum sensing, stimulates RNAIII expression but also represses ArtR expression. ArtR indirectly activates hla transcription by repressing sarT translation . SarA stimulates the AgrA-dependent expression of RNAIII . SarT directly represses SarU which activates agr (RNAIII) transcription .

Figure 4. sRNAs from the S. aureus RNome implicated in bacterial virulence.

Multitasking RNAIII is the effector of quorum sensing to perceive bacterial population density and regulates multiple targets involved in peptidoglycan metabolism, adhesion, exotoxins production, and virulence. RNAIII internally encodes hemolysin δ (blue). RNAIII contains at least three repressor domains (red) containing accessible UCCC motifs that interact, by antisense pairings, with the ribosome binding sites of numerous target mRNAs for translational repression (Tr.R), some triggering endoribonuclease III (RNase III) cleavages to induce target mRNA degradations and irreversible gene expression decay. Translation of at least two exotoxins is activated by RNAIII, one encoded (hlδ), and another (hlα) by translation activation (Tr.A). SprD is expressed from the genome of a converting phage and interacts, by antisense pairings, with the 5′ part of the sbi mRNA encoding an immune evasion molecule. SprD possesses an important role in S. aureus virulence, but the mechanism of its control is yet to be elucidated, with Sbi being only one player among others. The 891-nucleotide long SSR42 affects extracellular virulence expression, hemolysis, neutrophil virulence, and pathogenesis and contains a putative internal ORF. The mechanisms of target regulation remain to be elucidated. The SCCmec-encoded psm-mec RNA suppresses agrA translation and attenuates MRSA virulence, acting as a dual-function RNA regulator.