Small regulatory RNAs from low-GC Gram-positive bacteria

Abstract

Small regulatory RNAs (sRNAs) that act by base-pairing were first discovered in so-called accessory DNA elements--plasmids, phages, and transposons--where they control replication, maintenance, and transposition. Since 2001, a huge body of work has been performed to predict and identify sRNAs in a multitude of bacterial genomes. The majority of chromosome-encoded sRNAs have been investigated in E. coli and other Gram-negative bacteria. However, during the past five years an increasing number of sRNAs were found in Gram-positive bacteria. Here, we outline our current knowledge on chromosome-encoded sRNAs from low-GC Gram-positive species that act by base-pairing, i.e., an antisense mechanism. We will focus on sRNAs with known targets and defined regulatory mechanisms with special emphasis on Bacillus subtilis.

Keywords: Bacillus subtilis; Streptococcus pneumoniae; base-pairing sRNA; low GC Gram-positive bacteria; small regulatory RNA.

Figure 1. Mechanisms employed by sRNAs encoded from low-GC Gram-positive bacteria. All currently known mechanisms for sRNAs encoded from chromosomes are summarized. For additional mechanisms employed by plasmid-encoded sRNAs, see reference . Antisense RNAs are drawn in red, sense RNAs in blue. Black triangles denote promoters. Light blue, ribosome binding sites (RBS). Yellow symbols indicate ribosomes. Green arrows denote RNase III cleavage; black arrows indicate unknown RNase action. The violet symbol represents RNase R. For details, see text. B, C, E, F, and H are based on reference .

Figure 2. SR1 and SR4, a trans- and a cis-encoded sRNA from B. subtilis. As in Figure 1, the antisense RNAs are indicated in red, the sense RNAs in blue, RBS in light blue, ribosomes are in yellow, RNase III in green, and RNase R in violet. (A) SR1, a trans-encoded sRNA, is the first identified dual-function sRNA from B. subtilis. +, activation; -, repression. CcpA and CcpN repress sr1 transcription under glycolytic conditions. TF is a novel transcription factor that activates sr1 transcription at cold-shock. (B) SR4, a cis-encoded sRNA, is the antitoxin of the type I TA system bsrG/SR4. It is the first antitoxin for which two independent functions have been found. For details, see text.