Bringing them together: Plasmid pMV158 rolling circle replication and conjugation under an evolutionary perspective

Plasmid

Volumn 74, Issue , 2014, Pages 15-31

  Lorenzo Díaz, Fabián ^a   Fernández López, Cris ^b   Garcillán Barcia, M Pilar ^c   Espinosa, Manuel ^b  

^a HOSPITAL UNIVERSITARIO NUESTRA SEÑORA DE CANDELARIA   (Spain)

^b CENTRO DE INVESTIGACIONES BIOLÓGICAS   (Spain)

^c UNIVERSITY OF CANTABRIA   (Spain)

Author keywords

Conjugative transfer; Firmicutes; Origins of transfer; Relaxases; Rolling circle replicating plasmids

Indexed keywords

BACTERIAL ENZYME; DNA TOPOISOMERASE; ENDONUCLEASE; RELAXASE; UNCLASSIFIED DRUG; BACTERIAL DNA; BACTERIAL PROTEIN;

ARTICLE; BACILLALES; BACTERIAL GENE; BACTERIUM CONJUGATION; DNA REPLICATION ORIGIN; DNA SUPERCOILING; ENZYME ACTIVITY; GENETIC PARAMETERS; LACTOBACILLALES; MOBM GENE; NONHUMAN; NUCLEOTIDE SEQUENCE; PLASMID; PLASMID MOBV1; PLASMID P1414; PLASMID PMV158; PLASMID PT181; SEQUENCE ANALYSIS; SINGLE STRAND ORIGIN A; SINGLE STRAND ORIGIN T; SINGLE STRAND ORIGIN U; SINGLE STRAND ORIGIN W; UNINDEXED SEQUENCE; CONFORMATION; DNA REPLICATION; GENETICS; ISOLATION AND PURIFICATION; METABOLISM; MOLECULAR EVOLUTION; MOLECULAR GENETICS; STREPTOCOCCUS;

BACTERIAL PROTEINS; BASE SEQUENCE; DNA REPLICATION; DNA TOPOISOMERASES; DNA, BACTERIAL; ENDONUCLEASES; EVOLUTION, MOLECULAR; LACTOBACILLALES; MOLECULAR SEQUENCE DATA; NUCLEIC ACID CONFORMATION; PLASMIDS; REPLICATION ORIGIN; STREPTOCOCCUS;

EID: 84904659449     PISSN: 0147619X     EISSN: 10959890     Source Type: Journal    
DOI: 10.1016/j.plasmid.2014.05.004     Document Type: Article

References (160)

1. Alonso J.C., et al. Functional analysis of the leading strand replication origin of plasmid pUB110 in Bacillus subtilis. Nucleic Acids Res. 1988, 16:9127-9145.
2. Alonso, J.C., Tomalsky, M., 2014. Plasmids: biology and impact in biotechnology and discovery. In: A. Press, (Ed.).
3. Altschul S.F., et al. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 1997, 25:3389-3402.
4. Anand S.P., et al. The PcrA3 mutant binds DNA and interacts with the RepC initiator protein of plasmid pT181 but is defective in its DNA helicase and unwinding activities. Plasmid 2005, 54:104-113.
5. Anand S.P., Khan S.A. Structure-specific DNA binding and bipolar helicase activities of PcrA. Nucleic Acids Res. 2004, 32:3190-3197.
6. Anderson M.T., Seifert H.S. Opportunity and means: horizontal gene transfer from the human host to a bacterial pathogen. MBio 2011, 2:e00005-e00011.
7. Arends K., et al. TraG encoded by the pIP501 type IV secretion system is a two-domain peptidoglycan-degrading enzyme essential for conjugative transfer. J. Bacteriol. 2013, 195:4436-4444.
8. Ballester S., et al. Comparative expression of the pC194-cat gene in Streptococcus pneumoniae, Bacillus subtilis and Escherichia coli. Gene 1990, 86:71-79.
9. Bannam T.L., Rood J.I. Relationship between the Clostridium perfringens catQ gene product and chloramphenicol acetyltransferases from other bacteria. Antimicrob. Agents Chemother. 1991, 35:471-476.
10. Baquero F. From pieces to patterns: evolutionary engineering in bacterial pathogens. Nat. Rev. Microbiol. 2004, 2:510-518.
11. Baquero F. Environmental stress and evolvability in microbial systems. Clin. Microbiol. Infect. 2009, 15:5-10.
12. Baron C., et al. Bacterial secrets of secretion: EuroConference on the biology of type IV secretion processes. Mol. Microbiol. 2002, 43:1359-1365.
13. Bates S., et al. Expression of leading region genes on IncI 1 plasmid ColIb-P9: genetic evidence for single-stranded DNA transcription. Microbiology 1999, 145:2665-2672.
14. Bergemann A.D., et al. Homology of mycoplasma plasmid pADB201 and staphylococcal plasmid pE194. J. Bacteriol. 1989, 171:593-595.
15. Bhatty M., et al. The expanding bacterial type IV secretion lexicon. Res. Microbiol. 2013, 164:620-639.
16. Breton M., et al. Distribution and diversity of mycoplasma plasmids: lessons from cryptic genetic elements. BMC Microbiol. 2012, 12:257.
17. Burdett V. Identification of tetracycline-resistant R-plasmids in Streptococcus agalactiae (group B). Antimicrob. Agents Chemother. 1980, 18:753-760.
18. Caryl J.A., et al. Reconstitution of a staphylococcal plasmid-protein relaxation complex in vitro. J. Bacteriol. 2004, 186:3374-3383.
19. Caryl J.A., Thomas C.D. Investigating the basis of substrate recognition in the pC221 relaxosome. Mol. Microbiol. 2006, 60:1302-1318.
20. Cascales E., et al. DNA substrate-induced activation of the Agrobacterium VirB/VirD4 type IV secretion system. J. Bacteriol. 2013, 195:2691-2704.
21. Clewell D.B., et al. Extrachromosomal and mobile elements in enterococci: transmission, maintenance, and epidemiology. Enterococci: From Commensals to Leading Causes of Drug Resistant Infection 2014, Massachusetts Eye and Ear Infirmary, Boston.
22. Coffey A., et al. Nucleotide sequence and structural organization of the small broad-host-range plasmid pCI411 from Leuconostoc lactis. Microbiology 1994, 140:2263-2269.
23. Crooks G.E., et al. WebLogo: a sequence logo generator. Genome Res. 2004, 14:1188-1190.
24. Chandler M., et al. Breaking and joining single-stranded DNA: the HUH endonuclease superfamily. Nat. Rev. Microbiol. 2013, 11:625-638.
25. Chang T.-L., et al. Role of individual monomers of a dimeric initiator protein in the initiation and termination of plasmid rolling circle replication. J. Biol. Chem. 2000, 275:13529-13534.
26. Chen I., et al. The ins and outs of DNA transfer in bacteria. Science 2005, 310:1456-1460.
27. de Antonio C., et al. Features of the plasmid pMV158-encoded MobM, a protein involved in its mobilization. J. Mol. Biol. 2004, 335:733-743.
28. de la Campa A.G., et al. Initiation of replication of plasmid pLS1. The initiator protein RepB acts on two distant DNA regions. J. Mol. Biol. 1990, 213:247-262.
29. de la Cruz F., et al. Conjugative DNA metabolism in gram-negative bacteria. FEMS Microbiol. Rev. 2010, 34:18-40.
30. de las Rivas B., et al. Complete nucleotide sequence and structural organization of pPB1, a small Lactobacillus plantarum cryptic plasmid that originated by modular exchange. Plasmid 2004, 52:203-211.
31. de Paz H.D., et al. Functional interactions between type IV secretion systems involved in DNA transfer and virulence. Microbiology 2005, 151:3505-3516.
32. del Solar G., Espinosa M. Plasmid copy number control: an ever-growing story. Mol. Microbiol. 2000, 37:492-500.
33. del Solar G., et al. Replication and control of circular bacterial plasmids. Microbiol. Mol. Biol. Rev. 1998, 62:434-464.
34. del Solar G., et al. A genetically economical family of plasmid-encoded transcriptional repressors in control of plasmid copy number. J. Bacteriol. 2002, 184:4943-4951.
35. del Solar G., et al. Rolling circle-replicating plasmids from gram-positive and gram-negative bacteria: a wall falls. Mol. Microbiol. 1993, 8:789-796.
36. del Solar G., et al. Initiation signals for the conversion of single stranded to double stranded DNA forms in the streptococcal plasmid pLS1. Nucleic Acids Res. 1987, 15:5561-5580.
37. Dempsey L.A., Dubnau D.A. Identification of plasmid and Bacillus subtilis chromosomal recombination sites used for pE194 integration. J. Bacteriol. 1989, 171:2856-2865.
38. Dempsey L.A., et al. Localization of the start sites of lagging-strand replication of rolling circle plasmids from gram-positive bacteria. Mol. Microbiol. 1995, 15:679-687.
39. Díaz A., et al. Multiple roles for DNA polymerase I in establishment and replication of the promiscuous plasmid pLS1. Mol. Microbiol. 1994, 14:773-783.
40. Draper O., et al. Site-specific recombinase and integrase activities of a conjugative relaxase in recipient cells. Proc. Natl. Acad. Sci. U.S.A. 2005, 102:16385-16390.
41. Edgar R.C. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 2004, 32:1792-1797.
42. Espinosa M. Plasmids as models to study macromolecular interactions: the pMV158 paradigm. Res. Microbiol. 2013, 164:199-204.
43. Espinosa M., et al. Plasmid rolling circle replication and its control. FEMS Microbiol. Lett. 1995, 130:111-120.
44. Farías M.E., Espinosa M. Conjugal transfer of plasmid pMV158: uncoupling of the pMV158 origin of transfer from the mobilization gene mobM, and modulation of pMV158 transfer in Escherichia coli mediated by IncP plasmids. Microbiology 2000, 146:2259-2265.
45. Fernández-López, C. et al., 2014. Mobilizable rolling-circle replicating plasmids from Gram-positive bacteria: a low-cost conjugative transfer. In: Alonso, J.C., Tomalsky, M. (Eds.). vol. ASM Press, in press.
46. Fernández-López C., et al. Nicking activity of the pMV158 MobM relaxase on cognate and heterologous origins of transfer. Plasmid 2013, 120-130.
47. Fernández-López C., et al. Functional properties and structural requirements of the plasmid pMV158-encoded MobM relaxase domain. J. Bacteriol. 2013, 195:3000-3008.
48. Francia M.V., et al. A classification scheme for mobilization regions of bacterial plasmids. FEMS Microbiol. Rev. 2004, 28:79-100.
49. Frost L., et al. Mobile genetic elements: the agents of open source evolution. Nat. Rev. Microbiol. 2005, 3:722-732.
50. Plasmid Biology 2004, ASM Press, Washington, DC. B.E. Funnell, G.J. Phillips (Eds.).
51. Garcillán-Barcia M.P., et al. Identification of bacterial plasmids based on mobility and plasmid population biology. FEMS Microbiol. Rev. 2011, 35:936-956.
52. Garcillán-Barcia M.P., et al. The diversity of conjugative relaxases and its application in plasmid classification. FEMS Microbiol. Rev. 2009, 33:657-687.
53. Garcillán-Barcia M.P., et al. Conjugative transfer can be inhibited by blocking relaxase activity within recipient cells with intrabodies. Mol. Microbiol. 2007, 63:404-416.
54. Gennaro M.L., et al. A site-specific recombination function in Staphylococcus aureus plasmids. J. Bacteriol. 1987, 169:2601-2610.
55. Glucksmann-Kuis M.A., et al. Specific sequences and a hairpin structure in the template strand are required for N4 virion RNA polymerase promoter recognition. Cell 1992, 70:491-500.
56. Goessweiner-Mohr N., et al. Conjugative type IV secretion systems in gram-positive bacteria. Plasmid 2013, 70:289-302.
57. Gomis-Rüth F.X., Coll M. Cut and move: protein machinery for DNA processing in bacterial conjugation. Curr. Opin. Struct. Biol. 2006, 16:744-752.
58. Gomis-Ruth F.X., et al. Coupling factors in macromolecular type-IV secretion machineries. Curr. Pharm. Des. 2004, 10:1551-1565.
59. Goursot R., et al. Plasmids from Staphylococcus aureus replicate in yeast Saccharomyces cerevisiae. Nature 1982, 298:488-490.
60. Grohmann E., et al. Mobilisation of the streptococcal plasmid pMV158: interactions of MobM protein with its cognate oriT DNA region. Mol. Gen. Genet. 1999, 261:707-715.
61. Grohmann E., et al. Conjugative plasmid transfer in gram-positive bacteria. Microbiol. Mol. Biol. Rev. 2003, 67:277-301.
62. Grohmann E., et al. Determination of specific DNA strand discontinuities with nucleotide resolution in exponentially growing bacteria harbouring rolling circle-replicating plasmids. FEMS Microbiol. Lett. 1997, 152:363-369.
63. Gruss A.D., Ehrlich S.D. The family of highly interrelated single-stranded deoxyribonucleic avid plasmids. Microbiol. Rev. 1989, 53:231-241.
64. Gruss A.D., et al. Functional analysis of a palindromic sequence required for normal replication of several staphylococcal plasmids. Proc. Natl. Acad. Sci. U.S.A. 1987, 84:2165-2169.
65. Guasch A., et al. Recognition and processing of the origin of transfer DNA by conjugative relaxase TrwC. Nat. Struct. Biol. 2003, 10:1002-1010.
66. Guglielmini J., et al. The repertoire of ICE in prokaryotes underscores the unity, diversity, and ubiquity of conjugation. PLoS Genet. 2011, 7:e1002222.
67. Guzmán L., Espinosa M. The mobilization protein, MobM, of the streptococcal plasmid pMV158 specifically cleaves supercoiled DNA at the plasmid oriT. J. Mol. Biol. 1997, 266:688-702.
68. Halbedel S., Stülke J. Tools for the genetic analysis of Mycoplasma. Int. J. Med. Microbiol. 2007, 297:37-44.
69. Hamilton C.M., et al. TraG from RP4 and TraG and VirD4 from Ti plasmids confer relaxosome specificity to the conjugal transfer system of pTiC58. J. Bacteriol. 2000, 182:1541-1574.
70. Harwood C.R., et al. Nucleotide sequence of a Bacillus pumilus gene specifying chloramphenicol acetyltransferase. Gene 1983, 24:163-169.
71. Hernández-Arriaga A.M., et al. A functional lagging strand origin does not stabilize plasmid pMV158 inheritance in Escherichia coli. Plasmid 2000, 43:49-58.
72. Horinouchi S., Weisblum B. Nucleotide sequence and functional map of pC194, a plasmid that specifies inducible chloramphenicol resistance. J. Bacteriol. 1982, 815-825.
73. Inamine J.M., et al. Evidence that UGA is read as a tryptophan codon rather than as a stop codon by Mycoplasma pneumoniae, Mycoplasma genitalium, and Mycoplasma gallisepticum. J. Bacteriol. 1990, 172:504-506.
74. Jin R., Novick R.P. Role of the double-strand origin cruciform in pT181 replication. Plasmid 2001, 46:95-105.
75. Jones R.N. Resistance patterns among nosocomial pathogens: trends over the past few years. Chest 2001, 119(2 Suppl.):397S-404S.
76. Kent B.N., et al. Development of a novel plasmid as a shuttle vector for heterologous gene expression in Mycoplasma yeatsii. J. Microbiol. Methods 2012, 91:121-127.
77. Khan S.A. Mechanism of replication and copy number control of plasmids in gram-positive bacteria. Genetic Engineering 1996, vol. 18. Plenum Press, New York.
78. Khan S.A. Rolling-circle replication of bacterial plasmids. Microbiol. Mol. Biol. Rev. 1997, 61:442-455.
79. Khan S.A. Plasmid rolling-circle replication: recent developments. Mol. Microbiol. 2000, 37:477-484.
80. Khan S.A. DNA-protein interactions during the initiation and termination of plasmid pT181 rolling-circle replication. Prog. Nucleic Acid Res. Mol. Biol. 2003, 75:113-137.
81. Khan S.A. Plasmid rolling-circle replication: highlights of two decades of research. Plasmid 2005, 53:126-136.
82. Khan S.A., et al. Replication of plasmid pT181 in vitro: requirement for a plasmid-encoded product. Proc. Natl. Acad. Sci. U.S.A. 1981, 78:4902-4906.
83. King K.W., Dybvig K. Nucleotide sequence of Mycoplasma mycoides subspecies mycoides plasmid pKMK1. Plasmid 1992, 86-91.
84. Koehler T.M., Thorne C.B. Bacillus subtilis (natto) plasmid pLS20 mediates interspecies plasmid transfer. J. Bacteriol. 1987, 169:5271-5278.
85. Koepsel R.R., et al. Sequence-specific interaction between the replication initiator protein of plasmid pT181 and its origin of replication. Proc. Natl. Acad. Sci. U.S.A. 1986, 83:5484-5488.
86. Koepsel R.R., et al. The replication initiator protein of plasmid pT181 has sequence-specific endonuclease and topoisomerase-like activities. Proc. Natl. Acad. Sci. U.S.A. 1985, 82:6845-6849.
87. Kornberg A., Baker T. DNA Replication 1992, Freeman and Co., New York.
88. Kramer M.G., et al. Lagging-strand origins of the promiscuous plasmid pMV158: physical and functional characterization. Microbiology 1995, 141:655-662.
89. Kramer M.G., et al. Lagging strand replication of rolling-circle plasmids: specific recognition of the ssoA-type origins in different gram-positive bacteria. Proc. Natl. Acad. Sci. U.S.A. 1998, 95:10505-10510.
90. Kramer M.G., et al. Characterization of a single-strand origin, ssoU, required for broad host range replication of rolling-circle plasmids. Mol. Microbiol. 1999, 33:466-475.
91. Kramer M.G., et al. Plasmid rolling circle replication: identification of the RNA polymerase-directed primer RNA and requirement of DNA polymerase I for lagging strand initiation. EMBO J. 1997, 16:5784-5795.
92. Kramer M.G., et al. Lagging-strand replication from the ssoA origin of plasmid pMV158 in Streptococcus pneumoniae: in vivo and in vitro influences of mutations in two conserved ssoA regions. J. Bacteriol. 1998, 180:83-89.
93. Lacks S.A., et al. Identification and analysis of genes for tetracycline resistance and replication functions in the broad-host-range plasmid pLS1. J. Mol. Biol. 1986, 192:753-765.
94. Lanka E., Wilkins B.M. DNA processing reactions in bacterial conjugation. Annu. Rev. Biochem. 1995, 64:141-169.
95. Lederberg J., Tatum E. Gene recombination in E. coli. Nature 1946, 158:558.
96. Lederberg J., Tatum E. Sex in bacteria; genetic studies, 1945-1952. Science 1953, 118:169-175.
97. Lee C.A., et al. The Bacillus subtilis conjugative transposon ICEBs1 mobilizes plasmids lacking dedicated mobilization functions. J. Bacteriol. 2012, 194:3165-3172.
98. 2+ and DNA specific-binding. Nucleic Acids Res. 2011, 39:4315-4329.
99. Lorenzo-Díaz F., Espinosa M. Lagging strand DNA replication origins are required for conjugal transfer of the promiscuous plasmid pMV158. J. Bacteriol. 2009, 191:720-727.
100. Lorenzo-Díaz F., et al. Autoregulation of the synthesis of the MobM relaxase encoded by the promiscuous plasmid pMV158. J. Bacteriol. 2012, 194:1789-1799.
101. Lucas M., et al. Relaxase DNA binding and cleavage are two distinguishable steps in conjugative DNA processing that involve different sequence elements of the nic site. J. Biol. Chem. 2010, 285:8918-8926.
102. Llosa M., et al. Bacterial conjugation: a two-step mechanism for DNA transport. Mol. Microbiol. 2002, 45:1-8.
103. Llosa M., et al. Bacterial type IV secretion systems in human disease. Mol. Microbiol. 2009, 73:141-151.
104. Machón C., et al. RepD-mediated recruitment of PcrA helicase at the Staphylococcus aureus pC221 plasmid replication origin, oriD. Nucleic Acids Res. 2010, 38:1874-1888.
105. Masai H., Arai K. Frpo: a novel single-stranded DNA promoter for transcription and for primer RNA synthesis of DNA replication. Cell 1997, 89:897-907.
106. Matilla I., et al. The conjugative DNA translocase TrwB is a structure-specific DNA-binding protein. J. Biol. Chem. 2010, 285:17537-17544.
107. McKenzie T., et al. The nucleotide sequence of pUB110: some salient features in relation to replication and its regulation. Plasmid 1986, 15:93-103.
108. Meijer W.J.J., et al. Effects of the generation of single-stranded DNA on the maintenance of plasmid pMV158 and derivatives in different Bacillus subtilis strains. Plasmid 1995, 33:79-89.
109. Meijer W.J.J., et al. Effects of the generation of single-stranded DNA on the maintenance of plasmid pMV158 and derivatives in Lactococcus lactis. Plasmid 1995, 33:91-99.
110. Moscoso M., et al. Initiation of replication of plasmid pMV158: mechanisms of DNA strand transfer reactions mediated by the initiator RepB protein. J. Mol. Biol. 1997, 268:840-856.
111. Murray R.W., Koepsel R.R., Khan S.A. Synthesis of single-stranded plasmid pT181 DNA in vitro. J. Biol. Chem. 1989, 264:1051-1057.
112. Naglich J.G., Andrews R.E.J. Tn916-dependent conjugal transfer of pC194 and pUB110 from Bacillus subtilis into Bacillus thuringiensis subsp. israelensis. Plasmid 1988, 20:113-126.
113. Nasim M.T., et al. The activity of a single-stranded promoter of plasmid ColIb-P9 depends on its secondary structure. Mol. Microbiol. 2004, 53:405-417.
114. Noirot P., et al. Initiation of rolling circle replication in pT181 plasmid: initiator protein enhances cruciform extrusion at the origin. Proc. Natl. Acad. Sci. U.S.A. 1990, 87:8560-8564.
115. Nordström K., et al. Control of replication of bacterial plasmids: genetics, molecular biology, and physiology of the plasmid R1 system. Plasmid 1984, 12:71-90.
116. Novick R.P. Staphylococcal plasmids and their replication. Annu. Rev. Microbiol. 1989, 43:537-565.
117. Novick R.P. Contrasting lifestyles of rolling-circle phages and plasmids. Trends Biochem. Sci. 1998, 23:434-438.
118. Novick R.P., et al. Staphylococcal plasmid cointegrates are formed by host- and phage-mediated general rec systems that act on short regions of homology. Mol. Gen. Genet. 1984, 195:374-377.
119. Ochman H., et al. Lateral gene transfer and the nature of bacterial innovation. Nature 2000, 405:229-304.
120. Osborn M., et al. The evolution of bacterial plasmids. The Horizontal Gene Pool 2000, Harwood Academic Publishers, Amsterdam.
121. Oskam L., et al. The large Bacillus plasmid pTB19 contains two integrated rolling-circle plasmids carrying mobilization functions. Plasmid 1991, 26:30-39.
122. Pansegrau W., Lanka E. Enzymology of DNA strand transfer by conjugative mechanisms. Prog. Nucleic Acid Res. Mol. Biol. 1996, 54:197-251.
123. Pansegrau W., Lanka E. Mechanisms of initiation and termination reactions in conjugative DNA processing: independence of tight substrate binding and catalytic activity of relaxase (TraI) of IncPα plasmid RP4. J. Biol. Chem. 1996, 271:13068-13076.
124. Paulson J., Ehrenberg M. Trade-off between segregational stability and metabolic burden: a mathematical model of plasmid ColE1 replication control. J. Mol. Biol. 1998, 279:73-88.
125. Pepper K., et al. Heterogeneity of chromosomal genes encoding chloramphenicol resistance in streptococci. Plasmid 1988, 19:71-74.
126. Priebe S.D., Lacks S.A. Region of the streptococcal plasmid pMV158 required for conjugative mobilization. J. Bacteriol. 1989, 171:4778-4784.
127. Projan S.J., Novick R.P. Comparative analysis of five related staphylococcal plasmids. Plasmid 1988, 19:203-221.
128. Puyet A., et al. Identification of the origin and direction of replication of the broad-host-range plasmid pLS1. Nucleic Acids Res. 1988, 16:115-133.
129. Reyes-Lamothe R., et al. High-copy bacterial plasmids diffuse in the nucleoid-free space, replicate stochastically and are randomly partitioned at cell division. Nucleic Acids Res. 2014, 42:1042-1051.
130. Ruiz-Masó J.A., et al. Genetic and biochemical characterization of the Streptococcus pneumoniae PcrA helicase and its role in plasmid rolling circle replication. J. Bacteriol. 2006, 188:7416-7425.
131. Ruiz-Masó J.A., et al. Interactions between the RepB initiator protein of plasmid pMV158 and two distant DNA regions within the origin of replication. Nucleic Acids Res. 2007, 35:1230-1244.
132. Seegers J.F.M.L., et al. Structural and functional analysis of the single-strand origin of replication from the lactococcal plasmid pWV01. Mol. Gen. Genet. 1995, 249:43-50.
133. Selinger L.B., et al. Mobilization of closely related plasmids pUB110 and pBC16 by Bacillus plasmid pXO503 requires trans-acting open reading frame beta. J. Bacteriol. 1990, 172:3290-3297.
134. Seufert W., et al. A novel replicon occurring naturally in Escherichia coli is a phage-plasmid hybrid. EMBO J. 1988, 7:4005-4010.
135. Showsh S.A., Andrews R.E. Analysis of the requirement for a pUB110 mob region during Tn916-dependent mobilization. Plasmid 1999, 41:179-186.
136. Smillie C., et al. Mobility of plasmids. Microbiol. Mol. Biol. Rev. 2010, 74:434-452.
137. Smith M.C.A., Thomas C.D. An accessory protein is required for relaxosome formation by small staphylococcal plasmids. J. Bacteriol. 2004, 186:3363-3373.
138. Soultanas P., et al. Plasmid replication initiator protein RepD increases the processivity of PcrA DNA helicase. Nucleic Acids Res. 1999, 27:1421-1428.
139. Stamatakis A. RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics 2006, 22:2688-2690.
140. Szpirer C.Y., et al. Mobilization function of the pBHR1 plasmid, a derivative of the broad-host-range plasmid pBBR1. J. Bacteriol. 2001, 183:2101-2110.
141. te Riele H., et al. Are single-stranded circles intermediates in plasmid DNA replication?. EMBO J. 1986, 5:631-637.
142. te Riele H., et al. Single-stranded plasmid DNA in Bacillus subtilis and Staphylococcus aureus. Proc. Natl. Acad. Sci. U.S.A. 1986, 83:2541-2545.
143. Thomas C.M. The Horizontal Gene Pool 2000, Harwood Academic Publishers, Amsterdam, p. 419.
144. Thomas C.M., Nielsen K.M. Mechanisms of, and barriers to, horizontal gene transfer between bacteria. Nat. Rev. Microbiol. 2005, 3:711-721.
145. Thomas J., et al. A conserved helicase processivity factor is needed for conjugation and replication of an integrative and conjugative element. PLoS Genet. 2013, 9:e1003198.
146. Turgeon N., Moineau S. Isolation and characterization of a Streptococcus thermophilus plasmid closely related to the pMV158 family. Plasmid 2001, 45:171-183.
147. van der Lelie D., et al. Similarity of minus origins of replication and flanking open reading frames of plasmids pUB110, pTB913 and pMV158. Nucleic Acids Res. 1989, 17:7283-7294.
148. van der Lelie D., et al. Conjugal mobilization of streptococcal plasmid pMV158 between strains of Lactococcus lactis subsp. lactis. J. Bacteriol. 1990, 172:47-52.
149. Walker A. Welcome to the plasmidome. Nat. Rev. Microbiol. 2012, 10:379.
150. Waters V.L., Guiney D.G. Processes at the nick region link conjugation, T-DNA transfer and rolling-circle replication. Mol. Microbiol. 1993, 9:1123-1130.
151. Wellington E.M., et al. The role of the natural environment in the emergence of antibiotic resistance in gram-negative bacteria. Lancet Infect. Dis. 2013, 13:155-165.
152. Wilkins B., Lanka E. DNA Processing and Replication During Plasmid Transfer Between Gram-Negative Bacteria 1993, Plenum Press, New York.
153. Woodbury R.L., et al. Plasmid-borne erm(T) from invasive, macrolide-resistant Streptococcus pyogenes strains. Antimicrob. Agents Chemother. 2008, 52:1140-1143.
154. Yamao F., et al. UGA is read as tryptophan in Mycoplasma capricolum. Proc. Natl. Acad. Sci. U.S.A. 1985, 82:2306-2309.
155. Yasukawa H., et al. Rolling-circle replication of the plasmid pKYM isolated from a gram-negative bacterium. Proc. Natl. Acad. Sci. U.S.A. 1991, 88:10282-10286.
156. Yin S., et al. Functional analysis of the plasmid pM4 replicon from Lactobacillus plantarum M4: determination of the minimal replicon and functionality identification of the putative sso. Plasmid 2009, 62:166-171.
157. Zechner E.L., et al. Conjugative-DNA transfer processes. The Horizontal Gene Pool 2000, Harwood Academic publishers, Amsterdam. C.M. Thomas (Ed.).
158. Zhai Z., et al. Characterization of a novel rolling-circle replication plasmid pYSI8 from Lactobacillus sakei YSI8. Plasmid 2009, 62:30-34.
159. Zhang W., et al. Type-IVC secretion system: a novel subclass of type IV secretion system (T4SS) common existing in gram-positive genus Streptococcus. PLoS ONE 2012, 7:e46390.
160. Zhou H., et al. Characterization of a rolling-circle replication plasmid pXY3 from Lactobacillus plantarum XY3. Plasmid 2010, 64:36-40.