Implication of CcpN in the regulation of a novel untranslated RNA (SR1) in Bacillus subtilis

Abstract

SummaryAntisense-RNAs have been investigated in detail over the past 20 years as the principal regulators in accessory DNA elements such as plasmids, phages and transposons. However, only a few examples of chromosomally encoded bacterial antisense RNAs were known. Meanwhile, ª ª ª ª 70 small non-coding RNAs from the Escherichia coli genome have been found, the functions of the majority of which remain to be elucidated. Only one systematic search has been performed for Gram-positive bacteria, so far. Here, we report the identification of a novel small (205 nt) nontranslated RNA -SR1 -encoded in the Bacillus subtilis genome. SR1 was predicted by a computational approach and verified by Northern blotting. Knockout or overexpression of SR1 did not affect growth. SR1 was derepressed under conditions of gluconeogenesis, but repressed under glycolytic conditions. Two regulatory levels could be identified, one involving CcpA, the second, more important, involving the recently identified regulator CcpN.

Regulatory RNAs in Bacillus subtilis: a Gram-Positive Perspective on Bacterial RNA-Mediated Regulation of Gene Expression

“…The presence of potential binding sites for other protein factors can also give clues to the regulatory process controlled by a particular RNA. For instance, for B. subtilis, this was reported for the Fur-dependent FsrA sRNA, which regulates the iron-sparing response (43), and the gluconeogenesis sRNA SR1, which is regulated by CcpA and CcpN (44).…”

“…Instead, there are seven regions of complementarity between the coding part of ahrC and the 3= end of SR1. SR1 has been reported to be exclusively expressed under gluconeogenic conditions, because of its repression by CcpN and CcpA (44). SR1 was later found to encode a 39-amino-acid peptide that increases mRNA stability of the gapA operon by binding to the GapA protein via an unknown mechanism.…”

Carbon Catabolite Control of the Metabolic Network inBacillus subtilis

“…127) B. subtilis possesses NADH-and NADPH-dependent glyceraldehyde-3-P dehydrogenases, which are specific for glycolysis and gluconeogenesis and are encoded by gapA and gapB respectively. 131) This protein also represses sr1, 132) which encodes a small non-coding regulatory RNA that inhibits the translation of ahrC encoding a transcriptional regulator that activates the rocABC and rocDEF operons for arginine catabolism and represses the gene cluster for arginine biosynthesis. 108,[133][134][135] CcpN is active when cells are growing on a glycolytic substrate, even if the medium also contains a gluconeogenic substrate.…”

CodY Activates Transcription of a Small RNA inBacillus subtilis

“…Recently, we have demonstrated that SR1, which was found by using a computational approach and subsequent Northern blotting (24), acts by base pairing with its primary target, ahrC mRNA encoding the transcriptional activator of the rocABC and rocDEF arginine catabolic operons (17). Seven complementary regions between SR1 and ahrC were identified, and the most 5Ј region, region G, is located 97 nucleotides (nt) downstream from the ahrC ribosome binding site.…”

“…In Bacillus subtilis, 24 sRNAs are known (1,24,35,39,40), and targets for 5 of them have been identified; RatA controls the toxin TxpA (39), SR1 controls the transcription activator AhrC (17) (see below), FsrA regulates sdhCAB, citB, yvfW, and leuCD (11), and BsrA and BsrB are two 6S RNAs (1). In Staphylococcus aureus, in addition to RNAIII (3), 12 novel sRNAs from pathogenicity islands have been detected (33).…”