Regulatory RNAs in Bacteria

By L. Waters, G. Storz. Cell, 2009

1,562 citations recorded by the source corpus.

RNA regulators in bacteria are a heterogenous group of molecules that act by various mechanisms to modulate a wide range of physiological responses. One class comprises riboswitches, which are parts of the mRNAs they regulate. These leader sequences fold into structures amenable to conformational changes upon the binding of small molecules. Riboswitches thus sense and respond to the availability of various nutrients in the cell. Other small transcripts bind to proteins, among them global regulators, and antagonize their functions. The largest and most extensively studied set of small RNA regulators act through base pairing with RNAs, usually modulating the translation and stability of mRNAs. The majority of these small RNAs regulate responses to changes in environmental conditions. Finally, a recently discovered group of RNA regulators, known as the CRISPR RNAs, contain short regions of homology to bacteriophage and plasmid sequences. CRISPR RNAs interfere with bacteriophage infection and plasmid conjugation by targeting the homologous foreign DNA through an unknown mechanism. Here we discuss what is known about these RNA regulators, as well as the many intriguing questions that remain to be addressed.

Subfields: Ecology, Genetics, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/eb2c215ed68a974171eeb9660fcf3b4ac31ae424

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Citations in the corpus

Geobacter: the microbe electric's physiology, ecology, and practical applications. (2011, background): “Riboswitches, noncoding RNA elements found in the untranslated region of mRNA, are known to sense and bind cellular metabolites to control gene expression (Lioliou et al., 2010; Waters and Storz, 2009).”
Global mapping of transcription start sites and promoter motifs in the symbiotic α-proteobacterium Sinorhizobium meliloti 1021 (2013, neutral): “Promoter sequences direct the transcription of both coding and noncoding RNAs by acting as target sites for specific RNA polymerase binding and activity [1-3].”
Optimization of enzymatic reaction conditions for generating representative pools of cDNA from small RNA (2010, background): “For instance, the CRISPR/CAS system uses small RNA guides in protein effector complexes to suppress foreign DNA (van der Oost et al. 2009; Waters and Storz 2009), and the structural homologs from prokaryotes have guided our current understanding of eukaryotic Argonaute function (Song et al.”
Implications of streamlining theory for microbial ecology (2014, background): “Other regulatory noncoding RNAs can be trans-acting and interact with proteins and riboswitches (Waters and Storz, 2009).”
Bacterial Quorum-Sensing Network Architectures (2009, neutral): “Until recently, sRNA-mediated gene regulation was underappreciated in bacteria (30, 135).”
A comparison of the endotoxin biosynthesis and protein oxidation pathways in the biogenesis of the outer membrane of Escherichia coli and Neisseria meningitidis (2012, neutral): “Small non-coding RNAs (sRNAs), such as MgrR, are fast becoming recognized as key components of regulatory circuits that act as a fast acting “switches” to respond to stress signals (reviewed in Waters and Storz, 2009).”
Genome-wide identification of novel small RNAs in Pseudomonas aeruginosa (2013, background): “Bacterial sRNAs, which typically range from 70 to 500 nt in length, have been mainly found to function in post-transcriptional control of gene expression and control a variety of processes including metabolic reactions, stress responses and pathogenesis in response to environmental signals (reviewed”
TonB-dependent transporters: regulation, structure, and function (2010, background): “In the last decade, sRNAs have been recognized as major regulators of gene expression (37, 85).”
Regulation by Small RNAs in Bacteria: Expanding Frontiers (2011, neutral): “The most extensively studied sRNAs, often called trans-encoded sRNAs, are those that regulate mRNAs by short, imperfect base-pairing interactions (reviewed in Waters and Storz, 2009).”
A genome-wide survey of sRNAs in the symbiotic nitrogen-fixing alpha-proteobacterium Sinorhizobium meliloti (2010, background): “Thus, in most cases antisense sRNAs modulate expression of the overlapping sense gene on transcriptional or posttranscriptional level, although trans targets may also be affected [42,56].”
Non-coding RNAs as regulators of embryogenesis (2011, background): “Our expanding knowledge of ncRNA function in metazoans and the numerous studies of ncRNAs in prokaryote”
Extracting intracellular diffusive states and transition rates from single-molecule tracking data (2013, methodology): “To test the method on a biological system, we studied the RNA helper protein Hfq 11,12 (UniProtKB: P0A6X3), which mediates posttranscriptional gene regulation by facilitat ing interactions between mRNA and noncoding small RNA (sRNA).”
CRISPR/Cas system and its role in phage-bacteria interactions. (2010, background): “It became obvious, however, that noncoding sequences were also of critical importance for cell function and regulation (69, 80, 90).”
CRISPR-Cas systems in bacteria and archaea: versatile small RNAs for adaptive defense and regulation. (2011, background): “Likewise, there is growing evidence of the diverse regulatory roles that small noncoding RNAs play in bacteria (34, 116).”