Small Regulatory RNAs in Bacteria

Nicholas Delihas, State University of New York, Stony Brook, New York, USA

Published online: March 2009

DOI: 10.1002/9780470015902.a0000970.pub2

Intergenic regions of bacteria contain small regulatory ribonucleic acid (srRNA) genes whose transcripts control expression of distal genes. These transcripts, referred to here as srRNAs, primarily act at the level of translation where they bind messenger RNAs (mRNAs). srRNAs can inhibit or activate a target mRNA. Base pairing with mRNAs is imperfect and includes looped out and/or bulged nucleotide positions and noncanonical base pairs as well. The RNA chaparone protein Hfq is involved in many RNA/RNA interactions and ribonucleases, RNase E and RNase III, have been implicated in the destabilization of several target mRNAs. Gene transcription can also be controlled by an srRNA via binding to the RNA polymerase–sigma factor complex and blocking a functional site on the enzyme complex. Many srRNA genes are transcriptionally activated by environmental stress factors and have complex promoter and upstream regulatory sites involved in this activation. The control of outer membrane protein synthesis in response to stress is one major function of bacterial srRNAs.

Key Concepts

Properties of small regulatory RNA genes; control of gene expression at the level of translation and transcription by RNA; RNA/RNA interactions; imperfect RNA base pairing and noncanonical base pairs; bacterial cell response to environmental stress conditions; mechanisms of mRNA translational inactivation and degradation; macromolecular responses and phenotypic changes in a cell.

Keywords: small regulatory RNA; gene regulation; RNA/RNA interactions; translation; transcription

Figure 1. Generalized representation of an srRNA transcript interacting with a target mRNA. Hfq is the RNA-binding protein that facilitates the RNA/RNA interaction. RBS is the ribosome-binding site on the mRNA. Translation is blocked and in many cases the mRNA is degraded.
Figure 2. Representation of the activation of translation of an mRNA by srRNA. The RBS is normally sequestered in the base pairing of the 5¢ UTR stem loop. When the srRNA is transcribed, it can bind to the 5¢ end of the mRNA and produce a conformational change resulting in the exposure of the RBS.
Figure 3. Interaction of the E. coli micF RNA with the target ompF mRNA. The RNA/RNA duplex structure was determined experimentally. RBS refers to the ribosome-binding site on the mRNA and AUG is the translation start codon. Regulatory and target RNAs from related species of bacteria form similar duplex structures. Modified from Delihas et al. (1997).
Figure 4. Diagrammatic representation of the regulation of ompA RNA by micA RNA. Modified from Udekwu et al. (2005). Left: micA RNA competes for binding to the RBS of ompA mRNA. Hfq facilitates RNA/RNA binding. Right: Model of translation from ompA mRNA (top) and inhibition and initiation of ompA mRNA degradation (bottom). ‘E’ represents RNase E cleavage sites. Reproduced by permission of Cold Spring Harbor Press.
Figure 5. (a) Diagramatic representation of rpoS mRNA showing the RBS sequestered by base pairing that is shown in sections I, II and III. Normal RNase III cleavage sites are also shown. (b) The binding of DsrA RNA to the upstream sequence of rpoS mRNA exposes the RBS (positions –8 to –12) and creates new RNase III cleavage sites. Modified from Resch et al. (2008). Reproduced by permission of the RNA Society.
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Related Sub-Topics:

Nucleic Acid Structure | Transcription | Transcriptional Regulation | RNA Structure and Function | Noncoding RNA | Posttranscriptional Modification | Biomolecular Interactions | Information Flow | Nucleic Acids: Structure, Function, Metabolism
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Article Title: Small Regulatory RNAs in Bacteria
 
How to Cite close
Delihas, Nicholas(Mar 2009) Small Regulatory RNAs in Bacteria. In: eLS. John Wiley & Sons Ltd, Chichester. http://www.els.net [doi: 10.1002/9780470015902.a0000970.pub2]