Riboregulation in Escherichia coli : DsrA RNA acts by RNA:RNA interactions at multiple loci

Abstract

DsrA is an 87-nt untranslated RNA that regulates both the global transcriptional silencer and nucleoid protein H-NS and the stationary phase and stress response sigma factor RpoS ( s ). We demonstrate that DsrA acts via specific RNA:RNA base pairing interactions at the hns locus to antagonize H-NS translation. We also give evidence that supports a role for RNA:RNA interactions at the rpoS locus to enhance RpoS translation. Negative regulation of hns by DsrA is achieved by the RNA:RNA interaction blocking translation of hns RNA. In contrast, results suggest that positive regulation of rpoS by DsrA occurs by formation of an RNA structure that activates a cis-acting translational operator. Sequences within DsrA complementary to three additional genes, argR, ilvIH, and rbsD, suggest that DsrA is a riboregulator of gene expression that acts coordinately via RNA:RNA interactions at multiple loci.

Anti-silencing: overcoming H-NS-mediated repression of transcription in Gram-negative enteric bacteria

“…1h). It does this by direct RNA-RNA interaction with the hns mRNA (Lease et al, 1998). This explains an earlier observation that DsrA acts as an anti-silencer in the case of H-NS-repressed genes in E. coli (Sledjeski & Gottesman, 1995).…”

A small RNA regulates multiple ABC transporter mRNAs by targeting C/A-rich elements inside and upstream of ribosome-binding sites

“…sRNAs can also affect the expression of larger sets of genes by targeting the mRNAs of global transcriptional regulators; e.g., RpoS or FhlA (Lease et al 1998;Majdalani et al 1998;Argaman and Altuvia 2000). In contrast, our understanding of how sRNAs could directly control multiple mRNAs by an antisense mechanism has been limited by the low number of validated sRNA-target interactions and hence difficulty to reliably predict new targets.…”

“…However, it was early recognized that some E. coli sRNAs could regulate multiple mRNAs. For example, DsrA was shown to directly act on the hns and rpoS mRNAs (Lease et al 1998;Majdalani et al 1998), and constitutive overexpression of OxyS altered the expression of >40 genes (Altuvia et al 1997). Recent biocomputational and experimental approaches predicted more sRNAs to target multiple mRNAs.…”

“…This additional layer of gene expression control could mediate the coregulation of mRNAs that belong to different transcriptional regulons. However, evidence for direct interactions of sRNAs with multiple mRNAs has been rare in enterobacteria (Lease et al 1998) and has come primarily from investigations of RNAIII of the Gram-positive pathogen Staphylococcus aureus (Boisset et al 2007).…”

Thioredoxin post-transcriptional regulation by H19 provides a new function to mRNA-like non-coding RNA

“…However, H19 is not an antisense mRNA and its participation in IGF-II imprinting has been ruled out (Jones et al, 1998). In Prokaryotes and in the case of antisense RNA, the common feature is that these riboregulators are involved in the recognition of nucleic acid targets via complementary base pairing and this association is not always responsible for a negative regulation, but can also activate the translation by removing an inhibitory secondary structure (Lease et al, 1998). This mechanism does not seem to be implicated in the H19 riboregulation, as we did not detect primary structure complementarity between the H19 transcript and Trx mRNA by dotplot (data not shown).…”