Regulatory RNAs in the Less Studied Streptococcal Species: From Nomenclature to Identification

Abstract

Streptococcal species are Gram-positive bacteria involved in severe and invasive diseases in humans and animals. Although, this group includes different pathogenic species involved in life-threatening infections for humans, it also includes beneficial species, such as Streptococcus thermophilus, which is used in yogurt production. In bacteria virulence factors are controlled by various regulatory networks including regulatory RNAs. For clearness and to develop logical thinking, we start this review with a revision of regulatory RNAs nomenclature. Previous reviews are mostly dealing with Streptococcus pyogenes and Streptococcus pneumoniae regulatory RNAs. We especially focused our analysis on regulatory RNAs in Streptococcus agalactiae, Streptococcus mutans, Streptococcus thermophilus and other less studied Streptococcus species. Although, S. agalactiae RNome remains largely unknown, sRNAs (small RNAs) are supposed to mediate regulation during environmental adaptation and host infection. In the case of S. mutans, sRNAs are suggested to be involved in competence regulation, carbohydrate metabolism, and Toxin-Antitoxin systems. A new category of miRNA-size small RNAs (msRNAs) was also identified for the first time in this species. The analysis of S. thermophilus sRNome shows that many sRNAs are associated to the bacterial immune system known as CRISPR-Cas system. Only few of the other different Streptococcus species have been the subject of studies pointed toward the characterization of regulatory RNAs. Finally, understanding bacterial sRNome can constitute one step forward to the elaboration of new strategies in therapy such as substitution of antibiotics in the management of S. agalactiae neonatal infections, prevention of S. mutans dental caries or use of S. thermophilus CRISPR-Cas system in genome editing applications.

Keywords: Regulatory RNA nomenclature; Streptococcus agalactiae; Streptococcus mutans; Streptococcus thermophilus; non-coding RNA; small RNAs.

FIGURE 1

(A) cis-acting sRNAs (caRNAs) and their mechanism of action. (a) 5′ UTR-mediated transcriptional regulation. (Left) In the absence of ligand, transcription is initiated through a permissive stem-loop region, an aptamer region in the 5′ UTR (blue) of an open reading frame (ORF, red). In the presence of ligand, the aptamer region assumes a conformational change and is stabilized by the direct recognition of ligand. The complex (5′ UTR/Ligand) leads to the formation of a U-rich hairpin that acts as a transcriptional terminator. (Right) In the absence of ligand, the transcription is initially attenuated. The recognition of the ligand by the U-rich hairpin leads to the disruption of the stem-loop and thus to the transcription anti-termination or activation. (b) 5′ UTR-mediated translational regulation. (Left) In the absence of ligand, the aptamer region forms an anti-terminator hairpin. The ribosome binding site (RBS, green) is available, and mRNA translation is initiated. Upon ligand binding, the access to the RBS is hindered, preventing translation. (Right) In the absence of ligand, translation is inhibited due to a sequestered RBS. The recognition of the ligand by the stem-loop releases the RBS and translation can be initiated. In other cases, the ligand can be replaced by a temperature-dependent mechanism, where the mRNA adopts a secondary structure that hinders the access to the RBS (Listeria monocytogenes). (B) Mechanisms of mRNA regulation by antisense RNAs (asRNA). (Left upper) The binding of asRNA (blue) to the TIR (translation initiation region) leads to translation repression. The RNA duplex (asRNA-sense RNA) can be degraded by RNase III, a double strand specific endoribonuclease conserved in all the three kingdoms (Cho and Kim, 2015); or by RNase E which belong to the Gram-negative bacteria degradosome (Stazic et al., 2011). (Left lower) The asRNA can bind to the 5′ end of the target mRNA and causes changes in the target RNA structure leading to transcription termination. (Right) The complex asRNA-Hfq can also stabilize target mRNA for translation activation. (C) trans-encoded sRNAs (treRNAs)-based regulatory mechanisms of mRNA expression. treRNAs act through an imperfect basepairing to mRNA targets. The treRNA/mRNA duplex is stabilized by Hfq and can either repress (a–b), (c) activate or (d) stabilize mRNA translation. (e) It was also demonstrated that treRNAs can bind to proteins to inhibit and/or modify their activity. (f) tracrRNAs are a treRNA involved in the maturation of crRNAs through the interaction with the complex CRISPR-Cas9, pre-crRNA and RNase III. The processed crRNAs target the invading DNA.