Regulatory RNAs in Bacteria

Cell - Tập 136 Số 4 - Trang 615-628 - 2009
L. Waters1, Gisela Storz1
1Cell Biology and Metabolism Program, Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, MD 20892, USA

Tóm tắt

Từ khóa


Tài liệu tham khảo

Aiba, 2007, Mechanism of RNA silencing by Hfq-binding small RNAs, Curr. Opin. Microbiol., 10, 134, 10.1016/j.mib.2007.03.010

Altuvia, 2007, Identification of bacterial small non-coding RNAs: Experimental approaches, Curr. Opin. Microbiol., 10, 257, 10.1016/j.mib.2007.05.003

Altuvia, 1997, A small, stable RNA induced by oxidative stress: Role as a pleiotropic regulator and antimutator, Cell, 90, 45, 10.1016/S0092-8674(00)80312-8

Andersson, 2008, Virus population dynamics and acquired virus resistance in natural microbial communities, Science, 320, 1047, 10.1126/science.1157358

Babitzke, 2007, CsrB sRNA family: Sequestration of RNA-binding regulatory proteins, Curr. Opin. Microbiol., 10, 156, 10.1016/j.mib.2007.03.007

Barrangou, 2007, CRISPR provides acquired resistance against viruses in prokaryotes, Science, 315, 1709, 10.1126/science.1138140

Bejerano-Sagie, 2007, The role of small RNAs in quorum sensing, Curr. Opin. Microbiol., 10, 189, 10.1016/j.mib.2007.03.009

Blount, 2006, Riboswitches as antibacterial drug targets, Nat. Biotechnol., 24, 1558, 10.1038/nbt1268

Boisset, 2007, Staphylococcus aureus RNAIII coordinately represses the synthesis of virulence factors and the transcription regulator Rot by an antisense mechanism, Genes Dev., 21, 1353, 10.1101/gad.423507

Bouvier, 2008, Small RNA binding to 5′ mRNA coding region inhibits translation initiation, Mol. Cell, 32, 827, 10.1016/j.molcel.2008.10.027

Brantl, 2007, Regulatory mechanisms employed by cis-encoded antisense RNAs, Curr. Opin. Microbiol., 10, 102, 10.1016/j.mib.2007.03.012

Brennan, 2007, Hfq structure, function and ligand binding, Curr. Opin. Microbiol., 10, 125, 10.1016/j.mib.2007.03.015

Brouns, 2008, Small CRISPR RNAs guide antiviral defense in prokaryotes, Science, 321, 960, 10.1126/science.1159689

Collins, 2007, Mechanism of mRNA destabilization by the glmS ribozyme, Genes Dev., 21, 3356, 10.1101/gad.1605307

De Lay, 2008, The Crp-activated small noncoding regulatory RNA CyaR (RyeE) links nutritional status to group behavior, J. Bacteriol., 191, 461, 10.1128/JB.01157-08

Dühring, 2006, An internal antisense RNA regulates expression of the photosynthesis gene isiA, Proc. Natl. Acad. Sci. USA, 103, 7054, 10.1073/pnas.0600927103

Fozo, 2008, Small toxic proteins and the antisense RNAs that repress them, Microbiol. Mol. Biol. Rev., 72, 579, 10.1128/MMBR.00025-08

Fozo, 2008, Repression of small toxic protein synthesis by the Sib and OhsC small RNAs, Mol. Microbiol., 70, 1076, 10.1111/j.1365-2958.2008.06394.x

Gerdes, 2007, RNA antitoxins, Curr. Opin. Microbiol., 10, 117, 10.1016/j.mib.2007.03.003

Gildehaus, 2007, Studies on the function of the riboregulator 6S RNA from E. coli: RNA polymerase binding, inhibition of in vitro transcription and synthesis of RNA-directed de novo transcripts, Nucleic Acids Res., 35, 1885, 10.1093/nar/gkm085

Görke, 2008, Noncoding RNA control of the making and breaking of sugars, Genes Dev., 22, 2914, 10.1101/gad.1717808

Gottesman, 2005, Micros for microbes: Non-coding regulatory RNAs in bacteria, Trends Genet., 21, 399, 10.1016/j.tig.2005.05.008

Grundy, 2006, From ribosome to riboswitch: Control of gene expression in bacteria by RNA structural rearrangements, Crit. Rev. Biochem. Mol. Biol., 41, 329, 10.1080/10409230600914294

Guillier, 2008, The 5′ end of two redundant sRNAs is involved in the regulation of multiple targets, including their own regulator, Nucleic Acids Res., 36, 6781, 10.1093/nar/gkn742

Hammer, 2007, Regulatory small RNAs circumvent the conventional quorum sensing pathway in pandemic Vibrio cholerae, Proc. Natl. Acad. Sci. USA, 104, 11145, 10.1073/pnas.0703860104

Hebert, 2008, Beyond silencing–engineering applications of RNA interference and antisense technology for altering cellular phenotype, Curr. Opin. Biotechnol., 19, 500, 10.1016/j.copbio.2008.08.006

Heroven, 2008, A Csr-type regulatory system, including small non-coding RNAs, regulates the global virulence regulator RovA of Yersinia pseudotuberculosis through RovM, Mol. Microbiol., 68, 1179, 10.1111/j.1365-2958.2008.06218.x

Holbrook, 2008, Structural principles from large RNAs, Annu. Rev. Biophys., 37, 445, 10.1146/annurev.biophys.36.040306.132755

Horvath, 2008, Diversity, activity, and evolution of CRISPR loci in Streptococcus thermophilus, J. Bacteriol., 190, 1401, 10.1128/JB.01415-07

Isaacs, 2006, RNA synthetic biology, Nat. Biotechnol., 24, 545, 10.1038/nbt1208

Johansen, 2006, Conserved small non-coding RNAs that belong to the sE regulon: Role in down-regulation of outer membrane proteins, J. Mol. Biol., 364, 1, 10.1016/j.jmb.2006.09.004

Johansen, 2008, Down-regulation of outer membrane proteins by non-coding RNAs: Unraveling the cAMP-CRP- and σE-dependent CyaR-ompX regulatory case, J. Mol. Biol., 383, 1, 10.1016/j.jmb.2008.06.058

Johansson, 2002, An RNA thermosensor controls expression of virulence genes in Listeria monocytogenes, Cell, 110, 551, 10.1016/S0092-8674(02)00905-4

Kalamorz, 2007, Feedback control of glucosamine-6-phosphate synthase GlmS expression depends on the small RNA GlmZ and involves the novel protein YhbJ in Escherichia coli, Mol. Microbiol., 65, 1518, 10.1111/j.1365-2958.2007.05888.x

Kawamoto, 2005, Implication of membrane localization of target mRNA in the action of a small RNA: Mechanism of post-transcriptional regulation of glucose transporter in Escherichia coli, Genes Dev., 19, 328, 10.1101/gad.1270605

Kawamoto, 2006, Base-pairing requirement for RNA silencing by a bacterial small RNA and acceleration of duplex formation by Hfq, Mol. Microbiol., 61, 1013, 10.1111/j.1365-2958.2006.05288.x

Kawano, 2007, An antisense RNA controls synthesis of an SOS-induced toxin evolved from an antitoxin, Mol. Microbiol., 64, 738, 10.1111/j.1365-2958.2007.05688.x

Kazantsev, 2006, Bacterial RNase P: A new view of an ancient enzyme, Nat. Rev. Microbiol., 4, 729, 10.1038/nrmicro1491

Khemici, 2008, The RNase E of Escherichia coli is a membrane-binding protein, Mol. Microbiol., 70, 799, 10.1111/j.1365-2958.2008.06454.x

Landt, 2008, Small non-coding RNAs in Caulobacter crescentus, Mol. Microbiol., 68, 600, 10.1111/j.1365-2958.2008.06172.x

Lapouge, 2008, Gac/Rsm signal transduction pathway of gamma-proteobacteria: From RNA recognition to regulation of social behaviour, Mol. Microbiol., 67, 241, 10.1111/j.1365-2958.2007.06042.x

Legewie, 2008, Small RNAs establish delays and temporal thresholds in gene expression, Biophys. J., 95, 3232, 10.1529/biophysj.108.133819

Lenz, 2004, The small RNA chaperone Hfq and multiple small RNAs control quorum sensing in Vibrio harveyi and Vibrio cholerae, Cell, 118, 69, 10.1016/j.cell.2004.06.009

Levine, 2007, Quantitative characteristics of gene regulation by small RNA, PLoS Biol., 5, e229, 10.1371/journal.pbio.0050229

Livny, 2007, Identification of small RNAs in diverse bacterial species, Curr. Opin. Microbiol., 10, 96, 10.1016/j.mib.2007.03.005

Livny, 2008, High-throughput, kingdom-wide prediction and annotation of bacterial non-coding RNAs, PLoS ONE, 3, e3197, 10.1371/journal.pone.0003197

Lucchetti-Miganeh, 2008, The post-transcriptional regulator CsrA plays a central role in the adaptation of bacterial pathogens to different stages of infection in animal hosts, Microbiology, 154, 16, 10.1099/mic.0.2007/012286-0

Makarova, 2006, A putative RNA-interference-based immune system in prokaryotes: Computational analysis of the predicted enzymatic machinery, functional analogies with eukaryotic RNAi, and hypothetical mechanisms of action, Biol. Direct., 16, 7, 10.1186/1745-6150-1-7

Maki, 2008, RNA, but not protein partners, is directly responsible for translational silencing by a bacterial Hfq-binding small RNA, Proc. Natl. Acad. Sci. USA, 105, 10332, 10.1073/pnas.0803106105

Mandal, 2004, Gene regulation by riboswitches, Nat. Rev. Mol. Cell Biol., 5, 451, 10.1038/nrm1403

Mandin, 2007, Identification of new noncoding RNAs in Listeria monocytogenes and prediction of mRNA targets, Nucleic Acids Res., 35, 962, 10.1093/nar/gkl1096

Marraffini, 2008, CRISPR interference limits horizontal gene transfer in staphylococci by targeting DNA, Science, 322, 1843, 10.1126/science.1165771

Massé, 2002, A small RNA regulates the expression of genes involved in iron metabolism in Escherichia coli, Proc. Natl. Acad. Sci. USA, 99, 4620, 10.1073/pnas.032066599

Massé, 2005, Effect of RyhB small RNA on global iron use in Escherichia coli, J. Bacteriol., 187, 6962, 10.1128/JB.187.20.6962-6971.2005

Massé, 2007, Small RNAs controlling iron metabolism, Curr. Opin. Microbiol., 10, 140, 10.1016/j.mib.2007.03.013

Mehta, 2008, A quantitative comparison of sRNA-based and protein-based gene regulation, Mol. Syst. Biol., 4, 221, 10.1038/msb.2008.58

Mitarai, 2007, Efficient degradation and expression prioritization with small RNAs, Phys. Biol., 4, 164, 10.1088/1478-3975/4/3/003

Mizuno, 1984, A unique mechanism regulating gene expression: translational inhibition by a complementary RNA transcript (micRNA), Proc. Natl. Acad. Sci. USA, 81, 1966, 10.1073/pnas.81.7.1966

Mohanty, 2004, The Sm-like protein Hfq regulates polyadenylation dependent mRNA decay in Escherichia coli, Mol. Microbiol., 54, 905, 10.1111/j.1365-2958.2004.04337.x

Montange, 2008, Riboswitches: Emerging themes in RNA structure and function, Annu. Rev. Biophys., 37, 117, 10.1146/annurev.biophys.37.032807.130000

Moore, 2007, The tmRNA system for translational surveillance and ribosome rescue, Annu. Rev. Biochem., 76, 101, 10.1146/annurev.biochem.75.103004.142733

Morita, 1999, Translational induction of heat shock transcription factor s32: Evidence for a built-in RNA thermosensor, Genes Dev., 13, 655, 10.1101/gad.13.6.655

Morita, 2005, RNase E-based ribonucleoprotein complexes: Mechanical basis of mRNA destabilization mediated by bacterial noncoding RNAs, Genes Dev., 19, 2176, 10.1101/gad.1330405

Morita, 2006, Translational repression is sufficient for gene silencing by bacterial small noncoding RNAs in the absence of mRNA destruction, Proc. Natl. Acad. Sci. USA, 103, 4858, 10.1073/pnas.0509638103

Murphy, 2007, RyhB, an iron-responsive small RNA molecule, regulates Shigella dysenteriae virulence, Infect. Immun., 75, 3470, 10.1128/IAI.00112-07

Novick, 2008, Quorum sensing in staphylococci, Annu. Rev. Genet., 42, 541, 10.1146/annurev.genet.42.110807.091640

Nudler, 2004, The riboswitch control of bacterial metabolism, Trends Biochem. Sci., 29, 11, 10.1016/j.tibs.2003.11.004

Opdyke, 2004, GadY, a small RNA reglator of the acid response in Escherichia coli, J. Bacteriol., 186, 6698, 10.1128/JB.186.20.6698-6705.2004

Padalon-Brauch, 2008, Small RNAs encoded within genetic islands of Salmonella typhimurium show host-induced expression and role in virulence, Nucleic Acids Res., 36, 1913, 10.1093/nar/gkn050

Pfeiffer, 2007, A small non-coding RNA of the invasion gene island (SPI-1) represses outer membrane protein synthesis from the Salmonella core genome, Mol. Microbiol., 66, 1174, 10.1111/j.1365-2958.2007.05991.x

Pichon, 2005, Small RNA genes expressed from Staphylococcus aureus genomic and pathogenicity islands with specific expression among pathogenic strains, Proc. Natl. Acad. Sci. USA, 102, 14249, 10.1073/pnas.0503838102

Pichon, 2008, Small RNA gene identification and mRNA target predictions in Bacteria, Bioinformatics, 24, 2807, 10.1093/bioinformatics/btn560

Pontes, 2008, siRNA and miRNA processing: New functions for Cajal bodies, Curr. Opin. Genet. Dev., 18, 197, 10.1016/j.gde.2008.01.008

Prévost, 2007, The small RNA RyhB activates the translation of shiA mRNA encoding a permease of shikimate, a compound involved in siderophore synthesis, Mol. Microbiol., 64, 1260, 10.1111/j.1365-2958.2007.05733.x

Reichenbach, 2008, The small RNA GlmY acts upstream of the sRNA GlmZ in the activation of glmS expression and is subject to regulation by polyadenylation in Escherichia coli, Nucleic Acids Res., 36, 2570, 10.1093/nar/gkn091

Romby, 2006, The role of RNAs in the regulation of virulence-gene expression, Curr. Opin. Microbiol., 9, 229, 10.1016/j.mib.2006.02.005

Sharma, 2007, A small RNA regulates multiple ABC transporter mRNAs by targeting C/A-rich elements inside and upstream of ribosome-binding sites, Genes Dev., 21, 2804, 10.1101/gad.447207

Shimoni, 2007, Regulation of gene expression by small non-coding RNAs: A quantitative view, Mol. Syst. Biol., 3, 138, 10.1038/msb4100181

Simons, 1983, Translational control of IS10 transposition, Cell, 34, 683, 10.1016/0092-8674(83)90401-4

Sittka, 2008, Deep sequencing analysis of small noncoding RNA and mRNA targets of the global post-transcriptional regulator, Hfq, PLoS Genet., 4, e1000163, 10.1371/journal.pgen.1000163

Song, 2008, A new Vibrio cholerae sRNA modulates colonization and affects release of outer membrane vesicles, Mol. Microbiol., 70, 100, 10.1111/j.1365-2958.2008.06392.x

Soper, 2008, The rpoS mRNA leader recruits Hfq to facilitate annealing with DsrA sRNA, RNA, 14, 1907, 10.1261/rna.1110608

Sorek, 2008, CRISPR–A widespread system that provides acquired resistance against phages in bacteria and archaea, Nat. Rev. Microbiol., 6, 181, 10.1038/nrmicro1793

Stork, 2007, Transcription termination within the iron transport-biosynthesis operon of Vibrio anguillarum requires an antisense RNA, J. Bacteriol., 189, 3479, 10.1128/JB.00619-06

Stougaard, 1981, RNAs involved in copy-number control and incompatibility of plasmid R1, Proc. Natl. Acad. Sci. USA, 78, 6008, 10.1073/pnas.78.10.6008

Sudarsan, 2008, Riboswitches in eubacteria sense the second messenger cyclic di-GMP, Science, 321, 411, 10.1126/science.1159519

Sukhodolets, 2003, Interaction of Escherichia coli RNA polymerase with the ribosomal protein S1 and the Sm-like ATPase Hfq, Biochemistry, 42, 8022, 10.1021/bi020638i

Suzuki, 2006, Identification of a novel regulatory protein (CsrD) that targets the global regulatory RNAs CsrB and CsrC for degradation by RNase E, Genes Dev., 20, 2605, 10.1101/gad.1461606

Svenningsen, 2008, A negative feedback loop involving small RNAs accelerates Vibrio cholerae's transition out of quorum-sensing mode, Genes Dev., 22, 226, 10.1101/gad.1629908

Svenningsen, 2009, Gene dosage compensation calibrates four regulatory RNAs to control Vibrio cholerae quorum sensing, EMBO J., 10.1038/emboj.2008.300

Tang, 2002, Identification of 86 candidates for small non-messenger RNAs from the archaeon Archaeoglobus fulgidus, Proc. Natl. Acad. Sci. USA, 99, 7536, 10.1073/pnas.112047299

Tang, 2005, Identification of novel non-coding RNAs as potential antisense regulators in the archaeon Sulfolobus solfataricus, Mol. Microbiol., 55, 469, 10.1111/j.1365-2958.2004.04428.x

Thompson, 2007, σE regulates and is regulated by a small RNA in Escherichia coli, J. Bacteriol., 189, 4243, 10.1128/JB.00020-07

Tjaden, 2008, TargetRNA: A tool for predicting targets of small RNA action in bacteria, Nucleic Acids Res., 36, W109, 10.1093/nar/gkn264

Tjaden, 2006, Target prediction for small, noncoding RNAs in bacteria, Nucleic Acids Res., 34, 2791, 10.1093/nar/gkl356

Toledo-Arana, 2007, Small noncoding RNAs controlling pathogenesis, Curr. Opin. Microbiol., 10, 182, 10.1016/j.mib.2007.03.004

Tomizawa, 1981, Inhibition of ColE1 RNA primer formation by a plasmid-specified small RNA, Proc. Natl. Acad. Sci. USA, 78, 1421, 10.1073/pnas.78.3.1421

Tramonti, 2008, GadX/GadW-dependent regulation of the Escherichia coli acid fitness island: Transcriptional control at the gadY-gadW divergent promoters and identification of four novel 42-bp GadX/GadW-specific binding sites, Mol. Microbiol., 70, 965, 10.1111/j.1365-2958.2008.06458.x

Trotochaud, 2005, A highly conserved 6S RNA structure is required for regulation of transcription, Nat. Struct. Mol. Biol., 12, 313, 10.1038/nsmb917

Tu, 2007, Multiple small RNAs act additively to integrate sensory information and control quorum sensing in Vibrio harveyi, Genes Dev., 21, 221, 10.1101/gad.1502407

Tu, 2008, A small-RNA-mediated negative feedback loop controls quorum-sensing dynamics in Vibrio harveyi, Mol. Microbiol., 70, 896, 10.1111/j.1365-2958.2008.06452.x

Unoson, 2008, A small SOS-induced toxin is targeted against the inner membrane in Escherichia coli, Mol. Microbiol., 70, 258, 10.1111/j.1365-2958.2008.06416.x

Updegrove, 2008, Effect of Hfq on RprA-rpoS mRNA pairing: Hfq-RNA binding and the influence of the 5′ rpoS mRNA leader region, Biochemistry, 47, 11184, 10.1021/bi800479p

Urban, 2008, Two seemingly homologous noncoding RNAs act hierarchically to activate glmS mRNA translation, PLoS Biol., 6, e64, 10.1371/journal.pbio.0060064

Urbanowski, 2000, The gcvB gene encodes a small untranslated RNA involved in expression of the dipeptide and oligopeptide transport systems in Escherichia coli, Mol. Microbiol., 37, 856, 10.1046/j.1365-2958.2000.02051.x

Valentin-Hansen, 2004, The bacterial Sm-like protein Hfq: A key player in RNA transactions, Mol. Microbiol., 51, 1525, 10.1111/j.1365-2958.2003.03935.x

Valentin-Hansen, 2007, Small RNAs controlling outer membrane porins, Curr. Opin. Microbiol., 10, 152, 10.1016/j.mib.2007.03.001

Vecerek, 2007, Control of Fur synthesis by the non-coding RNA RyhB and iron-responsive decoding, EMBO J., 26, 965, 10.1038/sj.emboj.7601553

Viegas, 2007, Characterization of the role of ribonucleases in Salmonella small RNA decay, Nucleic Acids Res., 35, 7651, 10.1093/nar/gkm916

Vogel, 2007, Target identification of small noncoding RNAs in bacteria, Curr. Opin. Microbiol., 10, 262, 10.1016/j.mib.2007.06.001

Wadler, 2007, A dual function for a bacterial small RNA: SgrS performs base pairing-dependent regulation and encodes a functional polypeptide, Proc. Natl. Acad. Sci. USA, 104, 20454, 10.1073/pnas.0708102104

Wagner, 2002, Antisense RNAs in bacteria and their genetic elements, Adv. Genet., 46, 361, 10.1016/S0065-2660(02)46013-0

Wassarman, 2007, 6S RNA: A small RNA regulator of transcription, Curr. Opin. Microbiol., 10, 164, 10.1016/j.mib.2007.03.008

Wassarman, 2006, Synthesis-mediated release of a small RNA inhibitor of RNA polymerase, Science, 314, 1601, 10.1126/science.1134830

Wassarman, 1999, Small RNAs in Escherichia coli, Trends Microbiol., 7, 37, 10.1016/S0966-842X(98)01379-1

Weinberg, 2007, Identification of 22 candidate structured RNAs in bacteria using the CMfinder comparative genomics pipeline, Nucleic Acids Res., 35, 4809, 10.1093/nar/gkm487

Wilderman, 2004, Identification of tandem duplicate regulatory small RNAs in Pseudomonas aeruginosa involved in iron homeostasis, Proc. Natl. Acad. Sci. USA, 101, 9792, 10.1073/pnas.0403423101

Windbichler, 2008, Isolation of small RNA-binding proteins from E. coli: Evidence for frequent interaction of RNAs with RNA polymerase, RNA Biol., 5, 30, 10.4161/rna.5.1.5694

Zhang, 2003, Global analysis of small RNA and mRNA targets of Hfq, Mol. Microbiol., 50, 1111, 10.1046/j.1365-2958.2003.03734.x