Plasmid replication control by antisense RNAs

Microbiology Spectrum

Volumn 2, Issue 4, 2014, Pages

  Brantl, Sabine ^a  

^a FRIEDRICH SCHILLER UNIVERSITY JENA   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

COMPLEMENTARY RNA;

BACTERIUM; DNA REPLICATION; GENE EXPRESSION REGULATION; GENETICS; METABOLISM; PLASMID;

BACTERIA; DNA REPLICATION; GENE EXPRESSION REGULATION, BACTERIAL; PLASMIDS; RNA, ANTISENSE;

EID: 84940111502     PISSN: None     EISSN: 21650497     Source Type: Journal    
DOI: 10.1128/microbiolspec.PLAS-0001-2013     Document Type: Article

References (189)

1. Argaman L, Herschberg R, Vogel J, Bejerano G, Wagner EGH, Margalit H, Altuvia S. 2001. Novel small RNA-encoding genes in the intergenic regions of Escherichia coli. Curr Biol 11:941-950.
2. Wassarman KM, Repoila F, Rosenow C, Storz G, Gottesman S. 2001. Identification of novel small RNAs using comparative genomics and microarrays. Genes Dev 15:1637-1651.
3. Brantl S. 2009. Bacterial chromosome-encoded regulatory RNAs. Future Microbiol 4:85-103.
4. Brantl S. 2012. Acting antisense-plasmid-and chromosome-encoded small regulatory RNAs (sRNAs) from Gram-positive bacteria. Future Microbiol 7:853-871.
5. Nordström K, Molin S, Light J. 1984. Control of replication of bacterial plasmids: genetics, molecular biology, and physiology of the plasmid R1 system. Plasmid 12:71-90.
6. Wagner EG, Altuvia S, Romby P. 2002. Antisense RNAs in bacteria and their genetic elements. Adv Genet 46:361-398.
7. Uhlin BE, Nordström K. 1978. A runaway-replication mutant of plasmid R1drd-19: temperature-dependent loss of copy number control. Mol Gen Genet 165:167-179.
8. Summers D. 1996. The Biology of Plasmids. Blackwell Science, Oxford, United Kingdom.
9. Novick RP, Iordanescu S, Projan SJ, Kornblum J, Edelman I. 1989. pT181 plasmid replication is regulated by a countertranscript-driven transcriptional attenuator. Cell 59:395-404.
10. Projan S, Novick RP. 1988. Comparative analysis of five related staphylococcal plasmids. Plasmid 19:203-221.
11. Brantl S, Behnke D, Alonso JC. 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 18:4783-4790.
12. Bruand C, Ehrlich SD, Jannière L. 1991. Unidirectional theta replication of the structurally stable Enterococcus faecalis plasmid pAMβ1. EMBO J 10:2171-2177.
13. Ceglowski P, Lurz R, Alonso JC. 1993. Functional analysis of pSM19035 derived replicons in Bacillus subtilis. FEMS Microbiol Lett 109:145-150.
14. Le Chatelier E, Ehrlich SD, Jannière L. 1993. Biochemical and genetic analysis of the unidirectional theta replication of the S. agalactiae plasmid pIP501. Plasmid 29:50-56.
15. Brantl S, Birch-Hirschfeld E, Behnke D. 1993. RepR protein expression on plasmid pIP501 is controlled by an antisense RNA-mediated transcription attenuation mechanism. J Bacteriol 175:4052-4061.
16. Le Chatelier E, Ehrlich SD, Jannière L. 1996. Countertranscript-driven attenuation system of the pAMβ1 repE gene. Mol Microbiol 20:1099-1112.
17. Pouwels PH, van Luijk N, Leer RJ, Posno M. 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 242:614-622.
18. Duan K, Liu CQ, Supple S, Dunn NW. 1998. Involvement of antisense RNA in replication control of the lactococcal plasmid pND324. FEMS Microbiol Lett 164:419-426.
19. Brantl S, Behnke D. 1992. Characterization of the minimal origin required for replication of the streptococcal plasmid pIP501 in Bacillus subtilis. Mol Microbiol 6:3501-3510.
20. Brantl S, Behnke D. 1992. The amount of the RepR protein determines the copy number of plasmid pIP501 in B. subtilis. J Bacteriol 174:5475-5478.
21. Manch-Citron, JN, Gennaro ML, Majumder S, Novick RP. 1986. RepC is rate limiting for pT181 plasmid replication. Plasmid 16:108-115.
22. Bruand C., Ehrlich SD. 1998. Transcription-driven DNA replication of plasmid pAMβ1 in Bacillus subtilis. Mol Microbiol 30:135-145.
23. Kumar CC, Novick RP. 1985. Plasmid pT181 replication is regulated by two countertranscripts. Proc Natl Acad Sci USA 82:638-642.
24. Brantl S, Nuez B, Behnke D. 1992. In vitro and in vivo analysis of transcription within the replication region of plasmid pIP501. Mol Gen Genet 234:105-112.
25. Brantl S, Wagner EG. 1994. Antisense-RNA-mediated transcriptional attenuation occurs faster than stable antisense/target RNA pairing: an in vitro study of plasmid pIP501. EMBO J 13:3599-3607.
26. Brantl S, Wagner EG. 2000. Antisense RNA-mediated transcriptional attenuation: an in vitro study of plasmid pT181. Mol Microbiol 35:1469-1482.
27. Wagner EG, Brantl S. 1998. Kissing and RNA stability in antisense control of plasmid replication. Trends Biochem Sci 23:451-454.
28. Brantl S, Wagner EG. 1996. An unusually long-lived antisense RNA in plasmid copy number control: in vivo RNAs encoded by the streptococcal plasmid pIP501. J Mol Biol 255:275-288.
29. Brantl S, Behnke D. 1992. Copy number control of the streptococcal plasmid pIP501 occurs at three levels. Nucleic Acids Res 20:395-400.
30. Brantl S. 1994. The copR gene product of plasmid pIP501 acts as a transcriptional repressor at the essential repR promoter. Mol Microbiol 14:473-483.
31. Brantl S, Wagner EG. 1997. Dual function of the copR gene product of plasmid pIP501. J Bacteriol 179:7016-7024.
32. Le Chatelier E, Ehrlich SD, Jannière L. 1994. The pAMβ1 CopF repressor regulates plasmid copy number by controlling transcription of the repE gene. Mol Microbiol 14:463-471.
33. Swinfield TJ, Oultram JD, Thompson DE, Brehm JK, Minton NP. 1990. Physical characterisation of the replication region of the plasmid pAMβ1. Gene 87:79-90.
34. Ceglowski P, Alonso JC. 1994. Gene organization of the Streptococcus pyogenes plasmid pDB101: sequence analysis of the orf eta-copS region. Gene 145:33-39.
35. Steinmetzer K, Brantl S. 1997. Plasmid pIP501 encoded transcriptional repressor CopR binds asymmetrically at two consecutive major grooves of the DNA. J Mol Biol 269:684-693.
36. Steinmetzer K., Behlke J, Brantl S. 1998. Plasmid pIP501 encoded transcriptional repressor CopR binds to its target DNA as a dimer. J. Mol. Biol. 283:595-603.
37. Steinmetzer K, Behlke J, Brantl S, Lorenz M. 2002. CopR binds and bends its target DNA: A footprinting and fluorescence resonance energy transfer study. Nucleic Acids Res 30:2052-2060.
38. Freede P, Brantl S. 2004. Transcriptional repressor CopR: use of SELEX to study the copR operator indicates that evolution was directed at maximal binding affinity. J Bacteriol 186:6254-6264.
39. Licht A, Freede P, Brantl S. 2011. Transcriptional repressor CopR acts by inhibiting RNA polymerase binding. Microbiology 157:1000-1008.
40. Steinmetzer K, Hillisch A, Behlke J, Brantl S. 2000. Transcriptional repressor CopR: Structure model based localization of the DNA binding motif. Proteins 38:393-406.
41. Steinmetzer K, Hillisch A, Behlke J, Brantl S. 2000. Transcriptional repressor CopR: amino acids involved in forming the dimeric interface. Proteins 39:408-416.
42. Steinmetzer K, Kuhn K, Behlke J, Golbik R, Brantl S. 2002. Plasmid pIP501 encoded transcriptional repressor CopR: Single amino acids involved in dimerization are also important for folding of the monomer. Plasmid 47:201-209.
43. Kuhn K, Steinmetzer K, Brantl S. 2000. Transcriptional repressor CopR: the structured acidic C terminus is important for protein stability. J Mol Biol 300:1021-1031.
44. Kuhn K, Steinmetzer K, Brantl S. 2001. Transcriptional repressor CopR: dissection of stabilizing motifs within the C terminus. Microbiology 14:3387-3392.
45. Heidrich N, Brantl S. 2007. Antisense-RNA mediated transcriptional attenuation: the simultaneous interaction between two complementary loop pairs is required for efficient inhibition by the antisense RNA. Microbiology 153:420-427.
46. Franch T, Petersen M, Wagner EG, Jacobsen JP, Gerdes K. 1999. Antisense RNA regulation in prokaryotes: Rapid RNA/RNA interaction facilitated by a general U-turn loop structure. J Mol Biol 294:1115-1125.
47. Franch T, Gerdes K. 2000. U-turns and regulatory RNAs. Curr Opin Microbiol 3:159-164.
48. Heidrich N, Brantl S. 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 333:917-929.
49. Brantl S, Wagner EG. 2002. An antisense RNA-mediated transcription attenuation mechanism functions in Eschericha coli. J Bacteriol 184:2740-2747.
50. de la Hoz AB, Ayora S, Sitkiewicz I, Fernández S, Pankiewicz R, Alonso JC, Ceglowski P. 2000. Plasmid copy-number control and betterthan random segregation genes of pSM19035 share a common regulator. Proc Natl Acad Sci USA 97:728-733.
51. De LaHoz AB, Pratto F, Misselwitz R, Speck C, Weihofen W, Welfle K, Saenger W, Welfle H, Alonso JC. 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 32:3136-3147.
52. Welfle K, Pratto F, Misselwitz R, Behlke J, Alonso JC, Welfle H. 2005. Role of the N-terminal region and of β-sheet residue Thr29 on the activity of the omega2 global regulator form the broad-host range Streptococcus pyogenes plasmid pSM19035. Biol Chem 386:881-894.
53. Murayama K, Orth P, del la Hoz AB, Alonso JC, Saenger W. 2001. Crystal Structure of ω transcriptional repressor encoded by Streptococcus pyogenes plasmid pSM19035 at 1.5 Å resolution. J Mol Biol 314:789-796.
54. Bruand C, Le Chatelier E, Ehrlich SD, Jannière L. 1993. A fourth class of theta replicating plasmids. The pAMβ1 family from gram-positive bacteria. Proc Natl Acad Sci USA 90:11668-11672.
55. Bruand C, Farache M, McGovern S, Ehrlich SD, Polard P. 2001. DnaB, DnaD and DnaI proteins are components of the Bacillus subtilis replication restart primosome. Mol Microbiol 42:245-255.
56. Bidnenko V, Ehrlich SD, Jannière L. 1998. In vivo relations between pAMβ1-encoded type I topoisomerase and plasmid replication. Mol Microbiol 28:1005-1016.
57. Jannière L, Bidnenko V, McGovern S, Ehrlich SD, Petit MA. 1997. Replication terminus for DNA polymerase I during initiation of pAMβ1 replication: role of the plasmid encoded resolution system. Mol Microbiol 23:525-535.
58. Marsin S, McGovern S, Ehrlich SD, Bruand C, Polard P. 2001. Early steps of Bacillus subtilis primosome assembly. J Biol Chem 276:45818-45825.
59. Polard P, Marsin S, McGovern S, Velten M, Wigley DB, Ehrlich SD, Bruand C. 2002. Restart of DNA replication in Gram-positive bacteria: functional characterisation of the Bacillus subtilis PriA initiator. Nucleic Acids Res 30:1593-1605.
60. Dervyn E, Suski C, Daniel R, Chapuis J, Errington J, Jannière L, Ehrlich SD. 2001. Two essential DNA polymerases at the bacterial replication fork. Science 294:1716-1719.
61. Bruand C, Ehrlich SD, Jannière L. 1995. Primosome assembly site in Bacillus subtilis. EMBO J 14:2642-2650.
62. Le Chatelier E, Jannière L, Ehrlich SD, Canceill C. 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 276:10234-10246.
63. Masukata H, Tomizawa J. 1984. Effects of point mutations on formation and structure of the RNA primer for ColE1 DNA replication. Cell 36:513-522.
64. Masukata H, Tomizawa J. 1986. Control of primer formation for ColE1 plasmid replication: conformational change of the primer transcript. Cell 44:125-136.
65. Polisky B, TammJ, Fitzwater T. 1985. Construction of ColE1 RNA I mutants and analysis of their function in vivo. Basic Life Sci 30:321-333.
66. Polisky B, Zhang XY, Fitzwater T. 1990. Mutations affecting primer RNA interaction with the replication repressor RNA I in plasmid ColE1: potential RNA folding pathway mutants. EMBO J 9:295-304.
67. Masukata H, Tomizawa J. 1990. A mechanism of formation of a persistent hybrid between elongating RNA and template DNA. Cell 62: 331-338.
68. Itoh T, Tomizawa J. 1980. Formation of an RNA primer for initiation of replication of ColE1 DNA by ribonuclease H. Proc Natl Acad Sci USA 77:2450-2454.
69. Itoh T, Tomizawa J. 1982. Purification of ribonuclease H as a factor required for initiation of in vitro ColE1 DNA replication. Nucleic Acids Res 10:5949-5965.
70. Itoh T, Tomizawa J. 1978. Initiation of replication of plasmid ColE1 DNA by RNA polymerase, ribonuclease H and DNA polymerase I. Cold Spring Harbor Symp Quant Biol 43:409-417.
71. Ma D, Campbell JL. 1988. The effect of dnaA protein and n' sites on the replication of plasmid ColE1. J Biol Chem 263:15008-15015.
72. Lacatena RM, Cesareni G. 1981. Base pairing of RNA I with its complementary sequence in the primer precursor inhibits ColE1 replication. Nature 294:623-626.
73. Tomizawa J, Itoh T. 1981. Inhibition of ColE1 RNA primer formation by a plasmid-specified small RNA. Proc Natl Acad Sci USA 78:1421-1425.
74. Tamm J, Polisky B. 1983. Structural analysis of RNA molecules involved in plasmid copy number control. Nucleic Acids Res 11:6381-6397.
75. Tomizawa J. 1986. Control of ColE1 plasmid replication: binding of RNA I to RNA II and inhibition of primer formation. Cell 47:89-97.
76. Lacatena RM, Cesareni G. 1983. Interaction between RNA I and the primer precursor in the regulation of ColE1 replication. J Mol Biol 170: 635-650.
77. Muesing M, Tamm J, Shepard HM, Polisky B. 1981. A single basepair alteration is responsible for the DNA overproduction phenotype of a plasmid-copy-number mutant. Cell 24:235-242.
78. Eguchi Y, Itoh T, Tomizawa J. 1991. Antisense RNA. Annu Rev Biochem 60:631-652.
79. Eguchi Y, Tomizawa J. 1990. Complex formed by complementary RNA stem-loops and its stabilization by a protein: function of ColE1 Rom protein. Cell 60:199-209.
80. Tomizawa J. 1985. Control of ColE1 plasmid replication: initial interaction of RNA I and the primer transcript is reversible. Cell 40:527-535.
81. Tomizawa J. 1990. Control of ColE1 plasmid replication. Interaction of Rom protein with an unstable complex formed by RNA I and RNA II. J Mol Biol 212:695-708.
82. Tomizawa, J. 1990.Control ofColE1 plasmid replication. Intermediates in the binding of RNA I and RNA II. J Mol Biol 212:683-694.
83. Tomizawa J. 1984. Control of ColE1 plasmid replication: the process of binding of RNAI to the primer transcript. Cell 38:861-870.
84. Tomizawa J, Som T. 1984. Control of ColE1 plasmid replication. Enhancement of binding of RNA I to primer transcript by the Rom protein. Cell 38:871-878.
85. Lee AJ, Crothers DM. 1998. The solution structure of an RNA loop-loop complex: the ColE1 inverted loop sequence. Structure 6:993-1005.
86. Marino JP, Gregorian RSJ, Csankovszki G, Crothers DM. 1995. Bent helix formation between RNA hairpins with complementary loops. Science 268:1448-1454.
87. Lin-Chao S, Cohen SN. 1991. The rate of processing and degradation of antisense RNA I regulates the replication of ColE1-type plasmids in vivo. Cell 65:1233-1242.
88. He L, Söderbom F, Wagner EG, Binnie U, Binns N, Masters M. 1993. PcnB is required for the rapid degradation of RNAI, the antisense RNA that controls the copy number of ColE1-related plasmids. Mol Microbiol 9:1131-1142.
89. Cesareni G, Muesing MA, Polisky B. 1982. Control of ColE1 DNA replication. The rop gene product negatively affects transcription from the replication primer promoter. Proc Natl Acad Sci USA 79:6313-6317.
90. Som T, Tomizawa J. 1983. Regulatory regions of ColE1 that are involved in determination of plasmid copy number. Proc Natl Acad Sci USA 80:3232-3236.
91. Atlung T, Christensen BB, Hansen FG. 1999. Role of the Rom protein in copy number control of plasmid pBR322 at different growth rates in Escherichia coli K-12. Plasmid 41:110-119.
92. Banner DW, Kokkinidis M, Tsernoglou D. 1987. Structure of the ColE1 Rop protein at 1.7 Å resolution. J Mol Biol 5:657-675.
93. Castagnoli L, Scarpa M, Kokkinidis M, Banner DW, Tsernoglou D, Cesareni G. 1989. Genetic and structural analysis of the ColE1 Rop (Rom) protein. EMBO J 8:621-629.
94. Predki PF, Nayak LM, Gottlieb MBC, Regan L. 1995. Dissecting RNA-protein interactions: RNA-RNA recognition by Rop. Cell 80:41-50.
95. Lin-Chao S, Chen WT, Wong TT. 1992. High copy number of the pUC plasmid results from a Rom/Rop-suppressible point mutation in RNAII. Mol Microbiol 6:3385-3393.
96. Brenner M, Tomizawa J. 1991. Quantitation of ColE1-encoded replication elements. Proc Natl Acad Sci USA 88:405-409.
97. Brendel V, Perelson AS. 1993. Quantitative model of ColE1 plasmid copy number control. J Mol Biol 229:860-872.
98. Paulson J, Nordström K, Ehrenberg M. 1998. Requirements for rapid plasmid ColE1 copy number adjustments: a mathematical model of inhibition modes and RNA turnover rates. Plasmid 39:215-234.
99. Hama C, Takizawa T, Moriwaki H, Urasaki Y, Mizobuchi K. 1990. Organization of the replication control region of plasmid ColIb-P9. J Bacteriol 172:1983-1991.
100. Praszkier J, Wei T, Siemering K, Pittard AJ. 1991. Comparative analysis of the replication regions of IncB, IncK and IncZ plasmids. J Bacteriol 173:2393-2397.
101. Asano K, Moriwaki H, Mizobuchi K. 1991. An induced mRNA secondary structure enhances repZ translation in plasmid ColIb-P9. J Biol Chem 266:24549-24556.
102. Asano K, Kato A, Moriwaki H, Hama C, Shiba K, Mizobuchi K. 1991. Positive and negative regulations of plasmid ColIb-P9-repZ gene expression at the translational level. J Biol Chem 266:3774-3781.
103. Wilson IW, Praszkier J, Pittard AJ. 1993. Mutations affecting pseudoknot control of the replication of B group plasmids. J Bacteriol 175:6476-6483.
104. Hama C, Takizawa T, Moriwaki H, Mizobuchi K. 1990. Role of leader peptide synthesis in repZ gene expression of the ColIb-P9 plasmid. J Biol Chem 265:10666-10673.
105. Praszkier J, Wilson IW, Pittard AJ. 1992. Mutations affecting translation coupling between the rep genes of an IncB miniplasmid. J Bacteriol 174:2376-2383.
106. Asano K, Mizobuchi K. 1998. An RNA pseudoknot as the molecular switch for translation of the repZ gene encoding the replication initiator of IncIa plasmid ColIb-P9. J Biol Chem 273:11815-11825.
107. Praszkier J, Bird P, Nikoletti S, Pittard AJ. 1989. Role of countertranscript RNA in the copy number control system of an IncB miniplasmid. J Bacteriol 171:5056-5064.
108. Shiba K, Mizobuchi K. 1990. Posttranscriptional control of plasmid ColIb-P9 repZ gene expression by a small RNA. J Bacteriol 172:1992-1997.
109. Asano K, Mizobuchi K. 1998. Copy number control of IncIa plasmid ColIb-P9 by competition between pseudoknot formation and antisense RNA binding at a specific RNA site. EMBO J 17:5201-5213.
110. Wilson IW, Siemering KR, Praszkier J, Pittard AJ. 1997. Importance of structural differences between complementary RNA molecules to control of replication of an IncB plasmid. J Bacteriol 179:742-753.
111. Asano K, Mizobuchi K. 2000. Structural analysis of late intermediate complex formed between plasmid ColIb-P9 Inc RNA and its target RNA. How does a single antisense RNA repress translation of two genes at different rates? J Biol Chem 275:1269-1274.
112. Siemering KR, Praszkier J, Pittard AJ. 1993. Interaction between the antisense and target RNAs involved in the regulation of IncB plasmid replication. J Bacteriol 175:2895-2906.
113. Wilson IW, Praszkier J, Pittard AJ. 1994. Molecular analysis of RNAI control of repB translation in IncB plasmids. J Bacteriol 176:6497-6508.
114. Athanasopoulos V, Praszkier J, Pittard AJ. 1999. Analysis of elements involved in pseudoknot-dependent expression and regulation of the repA gene of an IncL/M plasmid. J Bacteriol 181:1811-1819.
115. Siemering KR, Praszkier J, Pittard AJ. 1994. Mechanism of binding of the antisense and target RNAs involved in the regulation of IncB plasmid replication. J Bacteriol 176:2677-2688.
116. Kolb FA, Westhof E, Ehresmann B, Ehresmann C, Wagner EG, Romby P. 2001. Four-way junctions in antisense RNA-mRNA complexes involved in plasmid replication control: a common theme? J Mol Biol 309:605-614.
117. Praszkier J, Pittard AJ. 1999. Role of CIS in replication of an IncB plasmid. J Bacteriol 181: 2765-2772.
118. Praszkier J, Murthy S, Pittard AJ. 2000. Effect of CIS on activity in trans of the replication initiator protein of an IncB plasmid. J Bacteriol 182:3972-3980.
119. del Solar G, Espinosa M. 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 6:83-94.
120. del Solar G, Acebo P, Espinosa M. 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 18:913-924.
121. del Solar G, Espinosa M. 2000. Plasmid copy number control: an ever-growing story. Mol Microbiol 37:492-500.
122. López-Aguilar C, del Solar G. 2013. Probing the sequence and structure of in vitro synthesized antisense and target RNAs from the replication control system of plasmid pMV158. Plasmid 70:94-103.
123. López-Aguilar C, Ruiz-Masó JA, Rubio-Lepe TS, Sanz M, del Solar G. 2013. Translation initiation of the replication initiator repB gene of promiscuous plasmid pMV158 is led by an extended non-SD sequence. Plasmid 70:69-77.
124. del Solar G, Acebo P, Espinosa M. 1997. Replication control of plasmid pLS1: the antisense RNA II and the compact rnaII region are involved in translational regulation of the initiator RepB synthesis. Mol Microbiol 23:95-108.
125. del Solar G, Perez-Martin J, Espinosa M. 1990. Plasmid-encoded RepA protein regulates transcription from repAB promoter by binding to a DNA sequence containing a 13 base pair symmetric element. J Biol Chem 265:12569-12575.
126. Gomis-Rüth FX, Sola M, Acebo P, Parraga A, Guasch A, Eritja R, Gonzalez A, Espinosa M, del Solar G, Coll M. 1998. The structure of plasmid encoded transcriptional repressor CopG unliganded and bound to its operator. EMBO J 17:7404-7415.
127. Hernández-Arriaga AM, Rubio-Lepe TS, Espinosa M, del Solar G. 2009. Repressor CopG prevents access of RNA polymerase to promoter and actively dissociates open complexes. Nucleic Acids Res 37:4799-4811.
128. Kwak JH, Weisblum B. 1994. Regulation of plasmid pE194 replication: control of cop-repF operon transcription by Cop and of repF translation by countertranscript RNA. J Bacteriol 176:5044-5051.
129. Kwak JH, Kim J, Kim M-Y, Choi E-C. 1998. Purification and characterization of Cop, a protein involved in the copy number control of plasmid pE194. Arch Pharm Res 3:291-297.
130. Alonso JC, Tailor RM. 1987. Initiation of plasmid pC194 replication and its control in Bacillus subtilis. Mol Gen Genet 210:476-484.
131. Okibe N, Suzuki N, Inui M, Yukawa H. 2010. Antisense-RNAmediated plasmid copy number control in pCG1-family plasmids, pCGR2 and pCG1, in Corynebacterium glutamicum. Microbiology 156:3609-3623.
132. Okibe N, Suzuki N, Inui M, Yukawa H. 2013. pCGR2 copy number depends on the par locus that forms a ParC-ParB-DNA partition complex in Corynebacterium glutamicum. J Appl Microbiol 115:495-508.
133. Masai H, Arai K. 1988. R1 plasmid replication in vitro. RepA and dnaA-dependent initiation at oriR, p 113-121 In Moses RE, Summers KC (ed), DNA Replication and Mutagenesis. ASM Press, Washington, DC.
134. Ortega-Jiménez R, Giraldo-Suárez ME, Fernández-Tresguerres ME, Berzal-Herranz A, Díaz-Orejas R. 1992. DnaA dependent replication of plasmid R1 occurs in the presence of point mutations that disrupt the dnaA box of oriR. Nucleic Acids Res 20:2547-2551.
135. Giraldo R, Diaz R. 1992. Differential binding of wild-type and a mutant RepA protein to oriR sequence suggests a model for the initiation of plasmid R1 replication. J Mol Biol 228:787-802.
136. Krabbe M, Zabielski J, Bernander R, Nordström K. 1997. Inactivation of the replication-termination system affects the replication mode and causes unstable maintenance of plasmid R1. Mol Microbiol 24:723-735.
137. Söderbom F, Binnie U, Masters M, Wagner EG. 1997. Regulation of plasmid R1 replication: PcnB and RNase E expedite the decay of the antisense RNA, CopA. Mol Microbiol 26:493-504.
138. Light J, Molin S. 1982. The sites of action of the two copy number control functions of plasmid R1. Mol Gen Genet 187:486-493.
139. Malmgren C, Engdahl HM, Romby P, Wagner EG. 1996. An antisense/target RNA duplex or a strong intramolecular RNA structure 5' of a translation initiation signal blocks ribosome binding: the case of plasmid R1. RNA 2:1022-1032.
140. Blomberg P, Wagner EG, Nordström K. 1990. Replication control of plasmid R1: the duplex between the antisense RNA, CopA, and its target, CopT, is processed specifically in vivo and in vitro by RNase III. EMBO J 9:2331-2340.
141. Blomberg P, Nordström K, Wagner EG. 1992. Replication control of plasmid R1: RepA synthesis is regulated by CopA RNA through inhibition of leader peptide translation. EMBO J 11:2675-2683.
142. Blomberg P, Engdahl HM, Malmgren C, Romby P, Wagner EG. 1994. Replication control of plasmid R1: disruption of an inhibitory RNA structure that sequesters the repA ribosome-binding site permits tapindependent RepA synthesis. Mol Microbiol 12:49-60.
143. Wu RP, Wang X, Womble DD, Rownd RH. 1992. Expression of the repA1 gene of IncFII plasmid NR1 is translationally coupled to expression of an overlapping leader peptide. J Bacteriol 174:7620-7628.
144. Brady G, Frey J, Danbara H, Timmis KN. 1983. Replication control mutations of plasmid R6-5 and their effects on interactions of the RNA-I control element with its target. J Bacteriol 154:429-436.
145. Giskov M, Molin S. 1984. Copy mutants of plasmid R1: effects of base pair substitutions in the copA gene on the replication control system. Mol Gen Genet 194:286-292.
146. Persson C, Wagner EG, Nordström K. 1988. Control of replication of plasmid R1: kinetics of in vitro interaction between the antisense RNA, CopA, and its target, CopT. EMBO J 7:3279-3288.
147. Persson C, Wagner EG, Nordström K. 1990. Control of replication of plasmid R1: structures and sequences of the antisense RNA, CopA, required for its binding to the target RNA, CopT. EMBO J 9:3767-3775.
148. Persson C, Wagner EG, Nordström K. 1990. Control of replication of plasmid R1: formation of an initial transient complex is rate-limiting for antisense RNA-target RNA pairing. EMBO J 9:3777-3785.
149. Hjalt TA, Wagner EG. 1992. The effect of loop size in antisense and target RNAs on the efficiency of antisense RNA control. Nucleic Acids Res 20:6723-6732.
150. Hjalt TA, Wagner EG. 1995. Bulged-out nucleotides in an antisense RNA are required for rapid target RNA binding in vitro and inhibition in vivo. Nucleic Acids Res 23:580-587.
151. Kolb FA, Engdahl HM, Slagter-Jäger JG, Ehresmann B, Ehresmann C, Westhof E, Wagner EG, Romby P. 2000. Progression of a loop-loop complex to a four-way junction is crucial for the activity of a regulatory antisense RNA. EMBO J 19:5905-5915.
152. Kolb FA, Malmgren C, Westhof E, Ehresmann C, Ehresmann B, Wagner EG, Romby P. 2000. An unusual structure formed by antisensetarget RNA binding involves an extended kissing complex with a four-way junction and a side-by-side helical alignment. RNA 6:311-324.
153. Malmgren C, Wagner EG, Ehresmann C, Ehresmann B, Romby P. 1997. Antisense RNA control of plasmid R1 replication. The dominant product of the antisense RNA-mRNA binding is not a full RNA duplex. J Biol Chem 272:12508-12512.
154. Brantl S. 2007. Regulatory mechanisms employed by cis-encoded antisense RNAs. Curr Opin Microbiol 10:102-109.
155. Söderbom F, Wagner EG. 1998. Degradation pathway of CopA, the antisense RNA that controls replication of plasmid R1. Microbiology 144:1907-1917.
156. Riise E, Stougaard P, Bindslev B, Nordström K, Molin S. 1982. Molecular cloning and functional characterization of a copy number control gene (copB) of plasmid R1. J Bacteriol 151:1136-1145.
157. Riise E, Molin S. 1986. Purification and characterization of the CopB replication control protein, and precise mapping of its target site in the R1 plasmid. Plasmid 15:163-171.
158. Stougaard P, Light J, Molin S. 1982. Convergent transcription interferes with expression of the copy number control gene, copA, from plasmid R1. EMBO J 1:323-328.
159. Light J, Riise E, Molin S. 1985. Transcription and its regulation in the basic replicon region of plasmid R1. Mol Gen Genet 198:503-508.
160. Kwong SM, Skurray, RA, Firth N. 2004. Staphylococcus aureus multiresistance plasmid pSK41: analysis of the replication region, initiator protein binding and antisense RNA regulation. Mol Microbiol 51:497-509.
161. Kwong SM, Skurray, RA, Firth N. 2006. Replication control of staphylococcal multiresistance plasmid pSK41: an antisense RNA mediates dual-level regulation of Rep expression. J Bacteriol 188:4404-4412.
162. Kwong, SM, Lim R, LeBard RJ, Skurray RA, Firth N. 2008. Analysis of the pSK1 replicon, a prototype from the staphylococcal multiresistance plasmid family. Microbiology 154:3084-3094.
163. Cevallos MA, Cervantes-Rivera R, Gutiérrez-Ríos RM. 2008. The repABC plasmid family. Plasmid 60:19-37.
164. Izquierdo J, Venkova-Canova T, Ramírez-Romero MA, Téllez-Sosa J, Hernández-Lucas I, Sanjuan J, Cevallos MA. 2005. An antisense RNA plays a central role in the replication control of a repC plasmid. Plasmid 54:259-277.
165. Venkova-Canova T, Soberón NE, Ramírez-Romero MA, Cevallos MA. 2004. Two discrete elements are required for the replication of a repABC plasmid: an antisense RNA and a stem-loop structure. Mol Microbiol 54:1431-1444.
166. Cervantes-Rivera R, Romero-López C, Berzal-Herranz A, Cevallos MA. 2010. Analysis of the mechanism of action of the antisense RNA that controls the replication of the repABC plasmid p42d. J Bacteriol 192: 3268-3278.
167. MacLellan SR, Smallbone LA, Sibley CD, Finan TM. 2005. The expression of a novel antisense gene mediates incompatibility within the large repABC family of a-proteobacterial plasmids. Mol Microbiol 55:611-623.
168. Chai Y, Winans SC. 2005. A small antisense RNA downregulates expression of an essential replicase protein of an Agrobacterium tumefaciens Ti plasmid. Mol Microbiol 56:1574-1585.
169. Pinto UM, Pappas KM, Winans SC. 2012. The ABCs of plasmid replication and segregation. Nat Rev Microbiol 10:755-765.
170. Hollands K, Proshkin S, Sklyarova S, Epshtein V, Mironov A, Nudler E, Groisman EA. 2012. Riboswitch control of Rho-dependent transcription termination. Proc Natl Acad Sci USA 109:5376-5381.
171. Takechi S, Matsui H, Itoh T. 1995. Primer RNA synthesis by plasmid-specified Rep protein for initiation of ColE2 DNA replication. EMBO J 14:5141-5147.
172. Takechi S, Itoh T. 1995. Initiation of unidirectional ColE2 DNA replication by a unique priming mechanism. Nucleic Acids Res 23:4196-4201.
173. Takechi S, Yasueda H, Itoh T. 1994. Control of ColE2 plasmid replication: regulation of Rep expression by a plasmid-coded antisense RNA. Mol Gen Genet 244:49-56.
174. Sugiyama T, Itoh T. 1993. Control of ColE2 DNA replication: in vitro binding of the antisense RNA to the rep mRNA. Nucleic Acids Res 21:5972-5977.
175. Yasueda H, Takechi S, Sugiyama T, Itoh T. 1994. Control of ColE2 plasmid replication: negative regulation of the expression of the plasmidspecified initiator protein, Rep, at a posttranscriptional step. Mol Gen Genet 244:41-48.
176. Nagase T, Nishio S-Y, Itoh T. 2007. Importance of the leader region of mRNA for translation initiation of ColE2 Rep protein. Plasmid 58:249-260.
177. Shinora M, Itoh T. 1996. Specificity determinants in interaction of the initiator (Rep) proteins with the origins in the plasmids ColE2-P9 and ColE3-CA38 identified by chimera analysis. J Mol Biol 257:290-300.
178. Nishio SY, Itoh T. 2008. Replication initiator protein mRNA of ColE2 plasmid and its antisense regulator RNA are under the control of different degradation pathways. Plasmid 59:102-110.
179. Nishio SY, Itoh T. 2008. The effects of RNA degradation enzymes on antisense RNAI controlling ColE2 plasmid copy number. Plasmid 60: 174-180.
180. André G, Even S, Putzer H, Burguière P, Croux C, Danchin A, Martin-Verstraete I, Soutourina O. 2008. S-box and T-box riboswithces and antisense RNA control a sulphur metabolic operon of Clostridium acetobutylicum. Nucleic Acids Res 36:5955-5969.
181. Sayed N, Jousselin A, Felden B. 2011. A cis-antisense RNA acts in trans in Staphylococcus aureus to control translation of a human cytolytic peptide. Nat Struct Mol Biol 19:105-112.
182. Jäger D, Pernitzsch SR, Richter AS, Backofen R, Sharma CM, Schmitz RA. 2012. An archeaeal sRNA targeting cis-and trans-encoded mRNAs via two distinct domains. Nucleic Acids Res 40:10964-10979.
183. Gimpel M, Heidrich N, Mäder U, Krügel H, Brantl S. 2010. A dualfunction sRNA from B. subtilis: SR1 acts as a peptide encoding mRNA on the gapA operon. Mol Microbiol 76:990-1009.
184. Vanderpool CK, Balasubramanian D, Lloyd CR. 2011. Dualfunction RNA regulators in bacteria. Biochimie 93:1943-1949.
185. Beisel CL, Storz G. 2010. Base pairing small RNAs and their roles in global regulatory networks. FEMS Microbiol Rev 34:866-882.
186. Eiamphungporn W, Helmann JD. 2009. Extracytoplasmic function sigma factors regulate expression of the Bacillus subtilis yabE gene via a cis-acting antisense RNA. J Bacteriol 191:1101-1105.
187. Lee EJ, Groisman EA. 2010. An antisense RNA that governs the expression kinetics of a multifunctional virulence gene. Mol Microbiol 76:1020-1033.
188. Konieczny I, Bury K, Wawrzycka A, Wegrzyn K. Iteron plasmids. In Tolmasky ME, Alonso JC (ed), Plasmids: Biology and Impact in Biotechnology and Discovery. ASM Press, Washington, DC, in press.
189. Ruiz-Masó JA, Machón C, Bordanaba L, Espinosa M, Coll M, Del Solar G. 2014. Plasmid rolling-circle replication. In Tolmasky ME, Alonso JC (ed), Plasmids: Biology and Impact in Biotechnology and Discovery. ASM Press, Washington, DC, in press.