Molecular call and response: The physiology of bacterial small RNAs

Richards, Gregory R.; Vanderpool, Carin K.

doi:10.1016/j.bbagrm.2011.07.013

Cited by 70 publications

(72 citation statements)

References 80 publications

(113 reference statements)

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“…We conclude that the function of PcrZ is to balance the response of photosynthesis genes to redox signals. Such fine-tuning of regulatory networks by the action of sRNAs is widely used by bacteria, e.g., for regulation of iron homeostasis or carbon metabolism (38). Because PrrA directly activates photosynthesis genes and at the same time PcrZ, which negatively affects photosynthesis gene expression, this action constitutes an incoherent feed-forward loop as frequently found in bacteria (39).…”

Section: Discussionmentioning

confidence: 99%

Regulation of bacterial photosynthesis genes by the small noncoding RNA PcrZ

Mank

Berghoff

Hermanns

et al. 2012

Proc. Natl. Acad. Sci. U.S.A.

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The small RNA PcrZ (photosynthesis control RNA Z) of the facultative phototrophic bacterium Rhodobacter sphaeroides is induced upon a drop of oxygen tension with similar kinetics to those of genes for components of photosynthetic complexes. High expression of PcrZ depends on PrrA, the response regulator of the PrrB/ PrrA two-component system with a central role in redox regulation in R. sphaeroides. In addition the FnrL protein, an activator of some photosynthesis genes at low oxygen tension, is involved in redox-dependent expression of this small (s)RNA. Overexpression of full-length PcrZ in R. sphaeroides affects expression of a small subset of genes, most of them with a function in photosynthesis. Some mRNAs from the photosynthetic gene cluster were predicted to be putative PcrZ targets and results from an in vivo reporter system support these predictions. Our data reveal a negative effect of PcrZ on expression of its target mRNAs. Thus, PcrZ counteracts the redox-dependent induction of photosynthesis genes, which is mediated by protein regulators. Because PrrA directly activates photosynthesis genes and at the same time PcrZ, which negatively affects photosynthesis gene expression, this is one of the rare cases of an incoherent feed-forward loop including an sRNA. Our data identified PcrZ as a trans acting sRNA with a direct regulatory function in formation of photosynthetic complexes and provide a model for the control of photosynthesis gene expression by a regulatory network consisting of proteins and a small noncoding RNA.α-proteobacteria | protochlorophyllide reductase

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Section: Discussionmentioning

confidence: 99%

Regulation of bacterial photosynthesis genes by the small noncoding RNA PcrZ

Mank

Berghoff

Hermanns

et al. 2012

Proc. Natl. Acad. Sci. U.S.A.

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“…The activity of SgrS allows cells to cope with stress and continue growing, whereas mutants lacking sgrS are severely growth inhibited under stress conditions (6,10). SgrS possesses two separate functions that can contribute independently to recovery from stress (5,12). The first function is base pairing with several mRNA targets (13)(14)(15), including ptsG and manXYZ, which encode sugar transporters of the phosphoenolpyruvate phosphotransferase system.…”

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confidence: 99%

“…SgrS is a well-studied sRNA found in enteric bacteria and is expressed in response to a metabolic stress known as "glucosephosphate" (GP) stress (5,6). GP stress is a condition associated with imbalanced glycolytic flux resulting in the accumulation of sugar phosphates.…”

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confidence: 99%

Small RNA binding-site multiplicity involved in translational regulation of a polycistronic mRNA

Rice

Balasubramanian

Vanderpool

2012

Proc. Natl. Acad. Sci. U.S.A.

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In animal systems, mRNAs subject to posttranscriptional regulation by small RNAs (sRNAs) often possess multiple binding sites with imperfect complementarity to a given sRNA. In contrast, small RNA-mRNA interactions in bacteria and plants typically involve a single binding site. In a previous study, we demonstrated that the Escherichia coli sRNA SgrS base pairs with a site in the coding region of the first gene of a polycistronic message, manXYZ. This interaction was shown to be responsible for translational repression of manX and to contribute to destabilization of the manXYZ mRNA. In the current study, we report that translational repression of the manY and manZ genes by SgrS requires a second binding site located in the manX-manY intergenic region. Pairing at this site can repress translation of manY and manZ even when mRNA degradation is blocked. Base pairing between SgrS and the manX site does not affect translation of manY or manZ. Pairing at both sites is required for optimal SgrS-mediated degradation of the fulllength manXYZ mRNA and for a particular stress phenotype. These results suggest that bacterial sRNAs may use target-site multiplicity to enhance the efficiency and stringency of regulation. Moreover, use of multiple binding sites may be particularly important for coordinating regulation of multiple genes encoded in operons.glucose-phosphate stress | Hfq | phosphoenolpyruvate phosphotransferase system | RNase E N ow accepted as fundamentally important players in regulation of gene expression, regulatory RNAs are present in organisms across all domains of life. In many eukaryotic organisms, siRNAs and microRNAs (miRNAs) control gene expression at the posttranscriptional level in diverse pathways (1-3). In bacteria, small RNAs (sRNAs) similarly control gene expression posttranscriptionally, and the principles (if not the details) of sRNA regulatory mechanisms have much in common with miRNA and siRNA regulation. Like miRNAs, many bacterial sRNAs function by base pairing with mRNA targets to affect their translation and stability. Both miRNAs and bacterial sRNAs usually regulate multiple mRNAs through interactions involving short regions (7-10 bases) of imperfect complementarity. In most instances, base pairing between sRNAs or miRNAs and their mRNA targets negatively affects target expression by modulating translation and mRNA stability (2, 4). Bacterial sRNAs usually repress target mRNA translation by base pairing with and sequestering sequences of the ribosome-binding site (RBS) in the 5′ UTR of the mRNA, making it unavailable for ribosome binding. Subsequent mRNA degradation is initiated by the endoribonuclease RNase E and its associated proteins, collectively referred to as the "degradosome" (4).SgrS is a well-studied sRNA found in enteric bacteria and is expressed in response to a metabolic stress known as "glucosephosphate" (GP) stress (5, 6). GP stress is a condition associated with imbalanced glycolytic flux resulting in the accumulation of sugar phosphates. The stress occurs when certain phosp...

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“…sRNAs regulate expression through a wide array of mechanisms, such as protein sequestration, conformational changes in mRNA (riboswitches), and base pairing with mRNA targets, the latter of which generally leads to enhancement of translation (in the case of positive regulation) or translational repression and/or mRNA degradation (in the case of negative regulation) (for reviews, see references 17, 50, and 65). Although many mechanisms of regulation by sRNAs are well understood, much remains to be learned about the biological functions of many of these regulatory responses and their effects on the physiology of the cell (46).…”

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confidence: 99%