Antisense-RNA mediated control of plasmid replication – pIP501 revisited

Plasmid - Tập 78 - Trang 4-16 - 2015
Sabine Brantl1
1Friedrich-Schiller-Universität Jena, Lehrstuhl für Genetik, AG Bakteriengenetik, Philosophenweg 12, D-07743 Jena, Germany

Tài liệu tham khảo

André, 2008, S-box and T-box riboswitches and antisense RNA control a sulfur metabolic operon of Clostridium acetobutylicum, Nucleic Acids Res, 36, 10.1093/nar/gkn601 Asano, 1991, An induced mRNA secondary structure enhances repZ translation in plasmid ColIb-P9, J. Biol. Chem, 266, 24549, 10.1016/S0021-9258(18)54264-2 Behnke, 1979, Post-transformational rearrangement of an in vitro reconstructed group A-streptococcal erythromycin resistance plasmid, Plasmid, 2, 605, 10.1016/0147-619X(79)90058-1 Beisel, 2010, Base pairing small RNAs and their roles in global regulatory networks, FEMS Microbiol. Rev, 34, 866, 10.1111/j.1574-6976.2010.00241.x Bidnenko, 1998, In vivo relations between pAMβ1-encoded type I topoisomerase and plasmid replication, Mol. Microbiol, 28, 1005, 10.1046/j.1365-2958.1998.00862.x Brantl, 1994, The copR gene product of plasmid pIP501 acts as a transcriptional repressor at the essential repR promoter, Mol. Microbiol, 14, 473, 10.1111/j.1365-2958.1994.tb02182.x Brantl, 2002, Antisense RNAs in plasmids: control of replication and maintenance, Plasmid, 48, 165, 10.1016/S0147-619X(02)00108-7 Brantl, 2004, Bacterial gene regulation: from transcription attenuation to riboswitches and ribozymes, Trends Microbiol, 12, 473, 10.1016/j.tim.2004.09.008 Brantl, 2007, Regulatory mechanisms employed by cis-encoded antisense RNAs, Curr. Opin. Microbiol, 10, 102, 10.1016/j.mib.2007.03.012 Brantl, 2009, Bacterial chromosome-encoded small regulatory RNAs, Future Microbiol, 4, 85, 10.2217/17460913.4.1.85 Brantl, 2012, Acting antisense: plasmid- and chromosome-encoded sRNAs from Gram-positive bacteria, Future Microbiol, 7, 853, 10.2217/fmb.12.59 Brantl, 2013, Plasmid replication control by antisense RNAs, Microbiol. Spectrum, 2 Brantl, 1992, Copy number control of the streptococcal plasmid pIP501 occurs at three levels, Nucleic Acids Res, 20, 395, 10.1093/nar/20.3.395 Brantl, 1992, The amount of RepR protein determines the copy number of plasmid pIP501 in Bacillus subtilis, J. Bacteriol, 174, 5475, 10.1128/JB.174.16.5475-5478.1992 Brantl, 1992, Characterization of the minimal origin required for replication of the streptococcal plasmid pIP501 in Bacillus subtilis, Mol. Microbiol, 6, 3501, 10.1111/j.1365-2958.1992.tb01785.x Brantl, 2014, Small regulatory RNAs from low-GC Gram-positive bacteria, RNA Biol, 11, 1, 10.4161/rna.28036 Brantl, 1994, Antisense RNA-mediated transcriptional attenuation occurs faster than stable antisense/target RNA pairing: an in vitro-study of plasmid pIP501, EMBO J., 13, 3599, 10.1002/j.1460-2075.1994.tb06667.x Brantl, 1996, An unusually long-lived antisense RNA in plasmid copy number control: in vivo RNAs encoded by the streptococcal plasmid pIP501, J. Mol. Biol, 255, 275, 10.1006/jmbi.1996.0023 Brantl, 1997, Dual function of the copR gene product of plasmid pIP501, J. Bacteriol, 179, 7016, 10.1128/JB.179.22.7016-7024.1997 Brantl, 2000, Antisense RNA-mediated transcriptional attenuation: an in vitro study of plasmid pT181, Mol. Microbiol, 35, 1469, 10.1046/j.1365-2958.2000.01813.x Brantl, 2002, An antisense RNA-mediated transcriptional attenuation mechanism functions in Escherichia coli, J. Bacteriol, 184, 2740, 10.1128/JB.184.10.2740-2747.2002 Brantl, 1990, Molecular analysis of the replication region of the conjugative Streptococcus agalactiae plasmid pIP501 in Bacillus subtilis. Comparison with plasmids pAMβ1 and pSM19035, Nucleic Acids Res, 18, 4783, 10.1093/nar/18.16.4783 Brantl, 1992, In vitro and in vivo analysis of transcription within the replication region of plasmid pIP501, Mol. Gen. Genet, 234, 105, 10.1007/BF00272351 Brantl, 1993, RepR protein expression on plasmid pIP501 is controlled by an antisense RNA-mediated transcription attenuation mechanism, J. Bacteriol, 175, 4052, 10.1128/JB.175.13.4052-4061.1993 Breaker, 2012, Riboswitches and the RNA world, Cold Spring Harb. Perspect. Biol, 4, a003566, 10.1101/cshperspect.a003566 Brenner, 1991, Quantitation of ColE1-eoncoded replication elements, Proc. Natl. Acad. Sci. U.S.A., 88, 405, 10.1073/pnas.88.2.405 Bruand, 1991, Unidirectional theta replication of the structurally stable Enterococcus faecalis plasmid pAMβ1, EMBO J., 10, 2171, 10.1002/j.1460-2075.1991.tb07752.x Bruand, 1993, A fourth class of theta replicating plasmids. The pAMβ1 family from grampositive bacteria, Proc. Natl. Acad. Sci. U.S.A., 90, 11668, 10.1073/pnas.90.24.11668 Bruand, 1995, Primosome assembly site in Bacillus subtilis, EMBO J., 14, 2642, 10.1002/j.1460-2075.1995.tb07262.x Ceglowski, 1994, Gene organization of the Streptococcus pyogenes plasmid pDB101: sequence analysis of the orf eta-copS region, Gene, 145, 33, 10.1016/0378-1119(94)90319-0 Cervantes-Rivera, 2010, Analysis of the mechanism of action of the antisense RNA that controls the replication of the repABC plasmid p42d, J. Bacteriol, 192, 3268, 10.1128/JB.00118-10 Chattoraj, 2000, Control of plasmid DNA replication by iterons: no longer paradoxical, Mol. Microbiol, 37, 467, 10.1046/j.1365-2958.2000.01986.x Clewell, 1974, Characterization of three plasmid deoxyribonucleic acid molecules in a strain of Streptococcus faecalis: identification of a plasmid determining erythromycin resistance, J. Bacteriol, 117, 283, 10.1128/JB.117.1.283-289.1974 Commichau, 2009, Novel activities of glycolytic enzymes in Bacillus subtilis: interactions with essential proteins involved in mRNA processing, Mol. Cell. Proteomics, 8, 1350, 10.1074/mcp.M800546-MCP200 Cromie, 2006, An RNA sensor for intracellular Mg2+, Cell, 125, 71, 10.1016/j.cell.2006.01.043 de la Hoz, 2000, Plasmid copy-number control and better-than random segregation genes of pSM19035 share a common regulator, Proc. Natl. Acad. Sci. U.S.A., 97, 728, 10.1073/pnas.97.2.728 de la Hoz, 2004, Recognition of DNA by omega protein from the broad-host range Streptococcus pyogenes plasmid pSM19035: analysis of binding to operator DNA with one to four heptad repeats, Nucleic Acids Res, 32, 3136, 10.1093/nar/gkh633 del Solar, 1992, The copy number of plasmid pLS1 is regulated by two trans-acting plasmid products: the antisense RNA II and the repressor protein, RepA, Mol. Microbiol, 6, 83, 10.1111/j.1365-2958.1992.tb00840.x del Solar, 1995, Replication control of plasmid pLS1: efficient regulation of plasmid copy number is exerted by the combined action of two plasmid components, CopG and RNAII, Mol. Microbiol, 18, 913, 10.1111/j.1365-2958.1995.18050913.x del Solar, 1997, Replication control of plasmid pLS1:the antisense RNA II and the compact region are involved in translational regulation of the initiator RepB synthesis, Mol. Microbiol, 23, 95, 10.1046/j.1365-2958.1997.1981561.x Dervyn, 2001, Two essential DNA polymerases at the bacterial replication fork, Science, 294, 1716, 10.1126/science.1066351 Duan, 1998, Involvement of antisense RNA in replication control of the lactococcal plasmid pN324, FEMS Microbiol. Lett, 164, 419, 10.1111/j.1574-6968.1998.tb13118.x Eguchi, 1990, Complex formed by complementary RNA stem-loops and its stabilization by a protein: function of ColE1 Rom protein, Cell, 60, 199, 10.1016/0092-8674(90)90736-X Franch, 1999, Antisense RNA regulation in prokaryotes: rapid RNA/RNA interaction facilitated by a general U-turn loop structure, J. Mol. Biol, 294, 1115, 10.1006/jmbi.1999.3306 Freede, 2004, Transcriptional repressor CopR: use of SELEX to study the copR operator indicates that evolution was directed at maximal binding affinity, J. Bacteriol, 186, 6254, 10.1128/JB.186.18.6254-6264.2004 Giangrossi, 2010, A novel antisense RNA regulates at transcriptional level the virulence gene icsA of Shigella flexneri, Nucleic Acids Res, 38, 2275, 10.1093/nar/gkq025 Gimpel, 2010, A dual-function sRNA from B. subtilis: SR1 acts as a peptide encoding mRNA on the gapA operon, Mol. Microbiol, 76, 990, 10.1111/j.1365-2958.2010.07158.x Gimpel, 2012, SR1 – a small RNA with two remarkably conserved functions, Nucleic Acids Res, 40, 11659, 10.1093/nar/gks895 Gollnick, 2001, Posttranscription initiation control of tryptophan metabolism in Bacillus subtilis by the trp RNA-binding attenuation protein (TRAP), anti-TRAP, and RNA structure, J. Bacteriol, 183, 5795, 10.1128/JB.183.20.5795-5802.2001 Gomis-Rüth, 1998, The structure of plasmid-encoded transcriptional repressor CopG unliganded and bound to its operator, EMBO J., 17, 7404, 10.1093/emboj/17.24.7404 Grundy, 1994, Conservation of a transcription antitermination mechanism in aminoacyl-tRNA synthetase and amino acid biosynthesis genes in gram-positive bacteria, J. Mol. Biol, 235, 798, 10.1006/jmbi.1994.1038 Heidrich, 2003, Antisense-RNA mediated transcriptional attenuation: importance of a U-turn loop structure in the target RNA of plasmid pIP501 for efficient inhibition by the antisense RNA, J. Mol. Biol, 333, 917, 10.1016/j.jmb.2003.09.020 Heidrich, 2007, Antisense RNA-mediated transcriptional attenuation in plasmid pP501: the simultaneous interaction between two complementary loop pairs is required for efficient inhibition by the antisense RNA, Microbiology, 153, 420, 10.1099/mic.0.2006/002329-0 Heidrich, 2007, In vitro analysis of the interaction between the small RNA SR1 and its primary target ahrC mRNA, Nucleic Acids Res, 35, 4331, 10.1093/nar/gkm439 Hernández-Arriaga, 2009, Repressor CopG prevents access of RNA polymerase to promoter and actively dissociates open complexes, Nucleic Acids Res, 37, 4799, 10.1093/nar/gkp503 Horodniceanu, 1976, R plasmids in Streptococcus agalactiae (group B), Antimicrob. Agents Chemother, 10, 795, 10.1128/AAC.10.5.795 Houman, 1990, Transcriptional antitermination in the bgl operon of E. coli is modulated by a specific RNA binding protein, Cell, 62, 1153, 10.1016/0092-8674(90)90392-R Huntzinger, 2005, Staphylococcus aureus RNAIII and the endoribonuclease III coordinately regulate spa gene expression, EMBO J., 24, 824, 10.1038/sj.emboj.7600572 Jahn, 2013, One antitoxin – two functions: SR4 controls toxin mRNA decay and translation, Nucleic Acids Res, 41, 9870, 10.1093/nar/gkt735 Jahn, 2012, BsrG/SR4 from Bacillus subtilis – the first temperature-dependent type I toxin-antitoxin system, Mol. Microbiol, 83, 579, 10.1111/j.1365-2958.2011.07952.x Kuhn, 2000, Transcriptional repressor CopR. The structured acidic C terminus is important for protein stability, J. Mol. Biol, 300, 1021, 10.1006/jmbi.2000.3929 Kuhn, 2001, Transcriptional repressor CopR. Dissection of stabilizing motifs within the C terminus, Microbiology, 147, 3387, 10.1099/00221287-147-12-3387 Kumar, 1985, Plasmid pT181 replication is regulated by two countertranscripts, Proc. Natl. Acad. Sci. U.S.A., 82, 638, 10.1073/pnas.82.3.638 Kwak, 1994, Regulation of plasmid pE194 replication: control of cop-repF operon transcription by Cop and of repF translation by countertranscript RNA, J. Bacteriol, 176, 5044, 10.1128/JB.176.16.5044-5051.1994 Kwong, 2004, Staphylococcus areus multiresistance plasmid pSK41: analysis of the replication region, initiator protein binding and antisense RNA regulation, Mol. Microbiol, 51, 497, 10.1046/j.1365-2958.2003.03843.x Le Chatelier, 1994, The pAMβ1 CopF repressor regulates plasmid copy number by controlling transcription of the repE gene, Mol. Microbiol, 14, 463, 10.1111/j.1365-2958.1994.tb02181.x Le Chatelier, 1996, Countertranscript-driven attenuation system of the pAMβ1 repE gene, Mol. Microbiol, 20, 1099, 10.1111/j.1365-2958.1996.tb02550.x Le Chatelier, 2001, The RepE initiator is a double-stranded and single-stranded DNA-binding protein that forms an atypical open complex at the onset of replication of plasmid pAMβ1 from Gram-positive bacteria, J. Biol. Chem, 276, 10234, 10.1074/jbc.M010118200 Licht, 2005, Implication of CcpN in the regulation of a novel untranslated RNA (SR1) in Bacillus subtilis, Mol. Microbiol, 58, 189, 10.1111/j.1365-2958.2005.04810.x Licht, 2011, Transcriptional repressor CopR acts by inhibiting RNA polymerase binding, Microbiology, 157, 1000, 10.1099/mic.0.047209-0 Loh, 2009, A trans-acting riboswitch controls expression of the virulence regulator PrfA in Listeria monocytogenes, Cell, 139, 770, 10.1016/j.cell.2009.08.046 Mangold, 2004, Synthesis of group A streptococcal virulence factors is controlled by a regulatory RNA molecule, Mol. Microbiol, 53, 1515, 10.1111/j.1365-2958.2004.04222.x Masukata, 1986, Control of primer formation for ColE1 plasmid replication: conformational change of the primer transcript, Cell, 44, 125, 10.1016/0092-8674(86)90491-5 Mironov, 2002, Sensing small molecules by nascent RNA: a mechanism to control transcription in bacteria, Cell, 111, 747, 10.1016/S0092-8674(02)01134-0 Morfeldt, 1995, Activation of alpha-toxin translation in Staphylococcus aureus by the trans-encoded antisense RNA, RNAIII, EMBO J., 14, 4569, 10.1002/j.1460-2075.1995.tb00136.x Nielsen, 2009, Defining a role for Hfq in Gram-positive bacteria: evidence for Hfq-dependent antisense regulation in Listeria monocytogenes, Nucleic Acids Res, 38, 907, 10.1093/nar/gkp1081 Nordström, 1984, Control of replication of bacterial plasmids: genetics, molecular biology, and physiology of the plasmid R1 system, Plasmid, 12, 71, 10.1016/0147-619X(84)90054-4 Novick, 1989, PT181 plasmid replication is regulated by a countertranscript-driven transcriptional attenuator, Cell, 59, 395, 10.1016/0092-8674(89)90300-0 Pouwels, 1994, Control of replication of the Lactobacillus pentosus plasmid p353-2: evidence for a mechanism involving transcriptional attenuation of the gene coding for the replication protein, Mol. Gen. Genet, 242, 614, 10.1007/BF00285285 Praszkier, 1992, Mutations affecting translational coupling between the rep genes of an IncB miniplasmid, J. Bacteriol, 174, 2376, 10.1128/JB.174.7.2376-2383.1992 Riise, 1986, Purification and characterization of the CopB replication control protein, a precise mapping of its target site in the R1 plasmid, Plasmid, 15, 163, 10.1016/0147-619X(86)90034-X Romby, 2010, An overview of RNAs with regulatory functions in gram-positive bacteria, Cell. Mol. Life Sci, 67, 217, 10.1007/s00018-009-0162-8 Shababian, 2009, RNase Y, a novel endoribonuclease, initiates riboswitch turnover in Bacillus subtilis, EMBO J., 28, 3523, 10.1038/emboj.2009.283 Silvaggi, 2005, Small RNA antitoxin in Bacillus subtilis, J. Bacteriol, 187, 6641, 10.1128/JB.187.19.6641-6650.2005 Smaldone, 2012, The FsrA sRNA and FbpB protein mediate the iron-dependent induction of the Bacillus subtilis lutABC iron-sulfur-containing oxidases, J. Bacteriol, 194, 2586, 10.1128/JB.05567-11 Steinmetzer, 1997, Plasmid pIP501-encoded transcriptional repressor CopR binds asymmetrically at two consecutive major grooves of the DNA, J. Mol. Biol, 269, 693, 10.1006/jmbi.1997.1083 Steinmetzer, 1998, Plasmid pIP501 encoded transcription repressor copR binds to its target DNA as a dimer, J. Mol. Biol, 283, 595, 10.1006/jmbi.1998.2122 Steinmetzer, 2000, Transcriptional repressor CopR: structure model-based localization of the deoxyribonucleic acid binding motif, Proteins, 38, 393, 10.1002/(SICI)1097-0134(20000301)38:4<393::AID-PROT5>3.0.CO;2-H Steinmetzer, 2000, Transcriptional repressor CopR: amino acids involved in forming of the dimeric interface, Proteins, 39, 408, 10.1002/(SICI)1097-0134(20000601)39:4<408::AID-PROT130>3.0.CO;2-0 Steinmetzer, 2002, CopR binds and bends its target DNA: a footprinting and fluorescence resonance energy transfer study, Nucleic Acids Res, 30, 2052, 10.1093/nar/30.9.2052 Steinmetzer, 2002, Plasmid pIP501 encoded transcriptional repressor CopR: single amino acids involved in dimerization are also important for folding of the monomer, Plasmid, 47, 201, 10.1016/S0147-619X(02)00002-1 Tran, 2011, A multifactor regulatory circuit involving H-NS, VirF and an antisense RNA modulates transcription of the virulence gene icsA of Shigella flexneri, Nucleic Acids Res, 39, 8122, 10.1093/nar/gkr521 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 Venkova-Canova, 2004, Two discrete elements are required for the replication of a repABC plasmid: an antisense RNA and a stem-loop structure, Mol. Microbiol, 54, 1431, 10.1111/j.1365-2958.2004.04366.x 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. U.S.A., 104, 20454, 10.1073/pnas.0708102104 Wagner, 1998, Kissing and stability in antisense control of plasmid replication, Trends Biochem. Sci, 23, 451, 10.1016/S0968-0004(98)01322-X Wagner, 1994, Antisense RNA control in bacteria, phages, and plasmids, Annu. Rev. Microbiol, 48, 713, 10.1146/annurev.mi.48.100194.003433 Wagner, 1987, Control of replication of plasmid R1: translation of the 7k reading frame in the RepA mRNA leader region counteracts the interaction between CopA RNA and CopT RNA, EMBO J., 6, 515, 10.1002/j.1460-2075.1987.tb04783.x Winkler, 2002, Thiamine derivatives bind messenger RNAs directly to regulate bacterial gene expression, Nature, 419, 952, 10.1038/nature01145 Yanovsky, 1981, Attenuation in the control of expression of bacterial operons, Nature, 289, 751, 10.1038/289751a0