Noncoding RNA

Abstract

Regulatory RNAs, present in many bacterial genomes and particularly in pathogenic bacteria such as Staphylococcus aureus, control the expression of genes encoding virulence factors or metabolic proteins. They are extremely diverse and include noncoding RNAs (sRNA), antisense RNAs, and some 5' or 3' untranslated regions of messenger RNAs that act as sensors for metabolites, tRNAs, or environmental conditions (e.g., temperature, pH). In this review we focus on specific examples of sRNAs of S. aureus that illustrate how numerous sRNAs and associated proteins are embedded in complex networks of regulation. In addition, we discuss the CRISPR-Cas systems defined as an RNA-interference-like mechanism, which also exist in staphylococcal strains.

FIGURE 1

Several mechanisms of RNA regulation in S. aureus. (a) Schematic drawing of the flavin mononucleotide riboswitch. The 5′ UTR adopts a particular structure recognized by the flavin mononucleotide, which in turn leads to the stabilization of a stem-loop structure sequestrating the SD sequence to inhibit translation. 30S is for the small ribosomal subunit. (b) An example of a T-box motif as found in the 5′ UTR of many mRNAs encoding aminoacyl-tRNA synthetases. Nonaminoacylated tRNA binds to the leader region at two sites and stabilizes an antiterminator structure, allowing transcription of the downstream gene. The drawing is adapted from reference 4. (c) The 3′ UTR of the biofilm repressor IcaR possesses a cytosine-rich motif, which binds to the SD sequence and hinders ribosomes from its binding site on the mRNA (see text for details). (d) Overlapping 5′ UTRs of tagG and tagH mRNAs are processed by the endoribonuclease III (Rnase III). Shorter 5′ ends might facilitate ribosome recruitment. (e) The antitoxin RNA SprF1 interacts at the 3′ end of the toxin encoded by sprG1 and triggers its degradation. (f) A cluster of five sRNAs was sequenced in the S. aureus Newman strain that encodes a putative toxin-antitoxin system (see text for details). (g,h) sRNAs act by an antisense mechanism. Binding of the 5′ UTR of RNAIII to the 5′ UTR of hla mRNA liberates its SD and activated translation (g), whereas the 3′ domain of RNAIII acts as a repressor domain, which contains C-rich motifs for base-pairing with the SD sequence of mRNA as coa mRNA depicted in the figure (h). Green bar, SD sequence; black circle, RNase III (for references and more details, see text).

FIGURE 2

Examples of the complex network between sRNAs and transcriptional factors in S. aureus in response to stress. Arrows show activation and bars show repression. Blue, transcriptional regulators; green, two-component systems; red, regulatory sRNAs. Red lines corresponded to posttranscriptional regulation, and black lines, to transcriptional regulation. Dotted lines are for the target mRNAs that were not experimentally validated. Only sRNA-dependent mRNA targets encoding transcriptional factors are depicted in the figure.

FIGURE 3

(a) Genomic organization of the loci for the type III-A CRISPR system of S. aureus strain 08BA02176. Type III is the typical S. aureus CRISPR organization. The scheme was obtained using CRISPRone (72), and the genome sequence was deposited in GenBank (accession number 08BA02176; RefSeq accession number GCF_000296595.1). (b) Genomic organization of the loci for the type II-C CRISPR system of S. aureus strain M06/0171. The CRISPR-Cas genes were found on an SCCmec inserted into the 3′ end of the chromosomally located orfX gene. The scheme was obtained using CRISPRone (72), and the SCCmec sequence was deposited in GenBank (GenBank accession number HE980450.1). (c) Cartoon (RNA and DNA) and surface (Cas9) representations of the SaCas9-sgRNA-target DNA complex (pdb file 5AXW) (80). The SaCas9 sgRNA consists of the crRNA guide region (crGUIDE represented in pale yellow) forming a heteroduplex with the target DNA strand (tDNA in magenta) and the repeat/antirepeat helix (blue, the repeat crRNA-derived strand, green, the antirepeat trascrRNA-derived strand). The protospacer adjacent region-containing DNA duplex is red. Cas9 domains are colored as follows: cyan, WED domain; pale orange, REC domain; gray, NUC domain. Molecular graphics images were prepared using PyMol.