A conserved RpoS-dependent small RNA controls the synthesis of major porin OmpD
Open Access
- 16 December 2011
- journal article
- research article
- Published by Oxford University Press (OUP) in Nucleic Acids Research
- Vol. 40 (8), 3623-3640
- https://doi.org/10.1093/nar/gkr1156
Abstract
A remarkable feature of many small non-coding RNAs (sRNAs) of Escherichia coli and Salmonella is their accumulation in the stationary phase of bacterial growth. Several stress response regulators and sigma factors have been reported to direct the transcription of stationary phase-specific sRNAs, but a widely conserved sRNA gene that is controlled by the major stationary phase and stress sigma factor, σ S (RpoS), has remained elusive. We have studied in Salmonella the conserved SdsR sRNA, previously known as RyeB, one of the most abundant stationary phase-specific sRNAs in E. coli. Alignments of the sdsR promoter region and genetic analysis strongly suggest that this sRNA gene is selectively transcribed by σ S . We show that SdsR down-regulates the synthesis of the major Salmonella porin OmpD by Hfq-dependent base pairing; SdsR thus represents the fourth sRNA to regulate this major outer membrane porin. Similar to the InvR, MicC and RybB sRNAs, SdsR recognizes the ompD mRNA in the coding sequence, suggesting that this mRNA may be primarily targeted downstream of the start codon. The SdsR-binding site in ompD was localized by 3′-RACE, an experimental approach that promises to be of use in predicting other sRNA–target interactions in bacteria.Keywords
This publication has 116 references indexed in Scilit:
- Small RNAs endow a transcriptional activator with essential repressor functions for single-tier control of a global stress regulonProceedings of the National Academy of Sciences of the United States of America, 2011
- The Base-Pairing RNA Spot 42 Participates in a Multioutput Feedforward Loop to Help Enact Catabolite Repression in Escherichia coliMolecular Cell, 2011
- Evidence for an autonomous 5′ target recognition domain in an Hfq-associated small RNAProceedings of the National Academy of Sciences of the United States of America, 2010
- Integrating anaerobic/aerobic sensing and the general stress response through the ArcZ small RNAThe EMBO Journal, 2010
- Positive regulation by small RNAs and the role of HfqProceedings of the National Academy of Sciences of the United States of America, 2010
- Translational Regulation of Gene Expression by an Anaerobically Induced Small Non-coding RNA in Escherichia coli*Published by Elsevier BV ,2010
- The role of Hfq in bacterial pathogensCurrent Opinion in Microbiology, 2010
- Sigma E controls biogenesis of the antisense RNA MicANucleic Acids Research, 2007
- Translational control and target recognition by Escherichia coli small RNAs in vivoNucleic Acids Research, 2007
- Target prediction for small, noncoding RNAs in bacteriaNucleic Acids Research, 2006