Dual-Function RNAs

Abstract

Bacteria are known to use RNA, either as mRNAs encoding proteins or as noncoding small RNAs (sRNAs), to regulate numerous biological processes. However, a few sRNAs have two functions: they act as base-pairing RNAs and encode a small protein with additional regulatory functions. Thus, these so called "dual-function" sRNAs can serve as both a riboregulator and an mRNA. In some cases, these two functions can act independently within the same pathway, while in other cases, the base-pairing function and protein function act in different pathways. Here, we discuss the five known dual-function sRNAs-SgrS from enteric species, RNAIII and Psm-mec from Staphylococcus aureus, Pel RNA from Streptococcus pyogenes, and SR1 from Bacillus subtilis-and review their mechanisms of action and roles in regulating diverse biological processes. We also discuss the prospect of finding additional dual-function sRNAs and future challenges in studying the overlap and competition between the functions.

FIGURE 1

Sugar-phosphate stress due to intracellular accumulation of phosphosugars triggers expression of the transcription factor SgrR. SgrR, in turn, induces transcription of the 227-nt sRNA SgrS, which also encodes a small, 43-aa protein, SgrT (blue). The other features of this sRNA include the base-pairing region (red) and the Hfq-binding region [poly(U) tail]. To relieve the sugar-phosphate stress, SgrS represses translation of mRNAs coding for sugar transporters (PtsG and ManXYZ) and other mRNAs involved in various metabolic pathways (Asd, AdiY, FolE, and PurR) to help restore metabolic homeostasis during stress conditions. SgrS also activates translation of a phosphatase (YigL) that dephosphorylates the phosphosugars for export out of the cell. SgrT, meanwhile, is expressed from SgrS later and inhibits the activity of the glucose transporter PtsG; thereby, both the sRNA and the encoded small protein act together in the same pathway to combat sugar-phosphate stress.

FIGURE 2

RNAIII is part of the global regulatory locus known as the accessory gene regulator (agr) locus, which encodes the components of an autoregulatory quorum-sensing system. The agr locus consists of two divergent transcripts, RNAII and RNAIII, which initiate from promoters P2 and P3, respectively. Increases in cell density lead to phosphorylation and activation of the DNA-binding response regulator AgrA. Phosphorylated AgrA in turn activates transcription from the P2 and P3 promoters, P3 activation leading to expression of RNAIII, the major effector molecule of the agr response. The secondary structure of the 514-nt RNAIII consists of 14 stem-loop structures with multiple base-pairing regions (red). RNAIII encodes a 26-aa δ-hemolysin protein (blue, hld) but also acts as a posttranscriptional regulator of several mRNAs, most of which impact virulence. The RNA activates expression of Map, α-hemolysin, and MgrA proteins by either promoting a more open secondary structure surrounding the RBS by base-pairing in the case of map and hla mRNAs or by stabilizing the RNA in the case of mgrA. RNAIII is also involved in translation inhibition and RNA degradation of various mRNAs involved in the early stages of infection.

FIGURE 3

Psm-mec is located on staphylococcal cassette chromosome (SCCmec), next to the mecI/mecR1/mecA genes, which confer methicillin resistance and its regulation. The 143- to 157-nt sRNA also encodes PSM-mec, a 22-aa cytolytic toxin with the ORF making up most of the transcript (blue). The protein plays a role in S. aureus infection and immune evasion, while the sRNA represses the translation of agrA mRNA by inhibiting translation and affecting the stability of the mRNA.

FIGURE 4

The SR1 gene is encoded between pdhD and speA. Its transcription is repressed by CcpA and CcpN under glycolytic conditions. The 205-nt sRNA expressed under gluconeogenic conditions and in the presence of l-arginine also encodes a small, 39-aa protein, SR1P (blue). The ORF and the base-pairing region overlap on this sRNA. In the presence of arginine, SR1 represses translation of the ahrC mRNA, the transcriptional activator of two arginine catabolic operons, rocABC and rocDEF. The small protein SR1P plays a role in gluconeogenic conditions by binding to GapA and stabilizing the gapA operon mRNA from degradation by an unknown mechanism. It also binds RNase J1 and enhances its activity. Thus, the activities of the small protein and base-pairing RNA affect different pathways.

FIGURE 5

Pel/SagA sRNA is expressed from the pleiotropic effect locus of S. pyogenes, comprising the sagABCEDEFGHI operon. This 459-nt sRNA also encodes a 53-aa protein called streptolysin S (purple). Pel sRNA activates transcription of various mRNAs coding for different virulence factors, like Sic, Nga, and M protein, by an unknown mechanism. The sRNA also modulates maturation of cysteine protease SpeB.