Rolling-Circle Replication

Saleem A. Khan

doi:10.1128/9781555817732.ch4

Chapter 4 : Rolling-Circle Replication

VIEW AFFILIATIONS HIDE AFFILIATIONS

Affiliations: 1: Department of Molecular Genetics and Biochemistry, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261

Content Type: Monograph

Publication Year: 2004

Category: Microbial Genetics and Molecular Biology

Book DOI: 10.1128/9781555817732

Chapter DOI: 10.1128/9781555817732.ch4

MyBook is a cheap paperback edition of the original book and will be sold at uniform, low price.

Preview this chapter:

Rolling-Circle Replication, Page 1 of 2

< Previous page | Next page > /docserver/preview/fulltext/10.1128/9781555817732/9781555812652_Chap04-1.gif /docserver/preview/fulltext/10.1128/9781555817732/9781555812652_Chap04-2.gif

Abstract:

Plasmids that replicate by a rolling-circle (RC) mechanism are ubiquitous in gram-positive bacteria and are also found in gram-negative bacteria as well as in Archaea. This chapter discusses the general anatomy of rolling-circle replicating (RCR) plasmids, architecture of the double-strand origin (dso), the single-strand origin (sso), the initiator proteins and their structure-function relationship, key events during the initiation and termination process, and the role of host proteins in plasmid RC replication. It highlights the gaps in the current understanding of the replication of RCR plasmids and possible future lines of research that may uncover these gaps. The first of the RCR plasmids to be identified were native to the gram-positive bacterium, Staphylococcus aureus. The Rep proteins of the pT181 family act as dimers and utilize Tyr-191 of the two monomers in the initiation and termination events. Biochemical analyses using heterodimers of the pT181 RepC protein have provided insights into the role of individual monomers in plasmid RC replication. Elucidation of the three-dimensional structure of plasmid Rep proteins should considerably increase the understanding of the mechanistic aspects of plasmid RC replication. The availability of crystal structures of the initiators of various plasmid families should provide major insights into the mechanisms of initiation and termination of plasmid RC replication.

Citation: Khan S. 2004. Rolling-Circle Replication, p 63-78. In Funnell B, Phillips G (ed), Plasmid Biology. ASM Press, Washington, DC. doi: 10.1128/9781555817732.ch4

Key Concept Ranking

Tomato yellow leaf curl virus: 0.43214157

0.43214157

Highlighted Text: Show | Hide

Full text loading...

Figures

Rolling-Circle Replication

[com.pub2web.rdf.cci.facet.ContentItem[id=http://asm.metastore.ingenta.com/content/author/10.1128/9781555817732.chap4-1,webId=/content/author/10.1128/9781555817732.chap4-1,properties={foaf_givenname=Saleem A., foaf_name=Saleem A. Khan, foaf_surname=Khan, pub_isAffiliatedWith=[com.pub2web.rdf.cci.facet.ContentItem[id=http://asm.metastore.ingenta.com/content/affiliation/10.1128/9781555817732.chap4-aff1]]}]]

Citation: Khan S. 2004. Rolling-Circle Replication, p 63-78. In Funnell B, Phillips G (ed), Plasmid Biology. ASM Press, Washington, DC. doi: 10.1128/9781555817732.ch4

/content/10.1128/9781555817732.chap4.fig4-1

Figure 1

Functional organization of RCR plasmids. Four plasmid families represented by pT181, pMV158 (parent of pLS1), pC194, and pSN2 are shown. Arrows indicate the direction of transcription of the various genes or the direction of leading-strand replication from the dso, rep, initiator gene; cop, copy-control gene(s); dso, double-strand origin; sso, single-strand origin; cat and tet, chloramphenicol and tetracycline resistance genes; pre, recombinase gene; mob, mobilization gene.

10.1128/9781555817732/fig4-1_thmb.gif

10.1128/9781555817732/fig4-1.gif

Figure 1

Citation: Khan S. 2004. Rolling-Circle Replication, p 63-78. In Funnell B, Phillips G (ed), Plasmid Biology. ASM Press, Washington, DC. doi: 10.1128/9781555817732.ch4

/content/10.1128/9781555817732.chap4.fig4-2

Figure 2

A model for plasmid RCR replication. See text for details.

10.1128/9781555817732/fig4-2_thmb.gif

10.1128/9781555817732/fig4-2.gif

Figure 2

A model for plasmid RCR replication. See text for details.

Citation: Khan S. 2004. Rolling-Circle Replication, p 63-78. In Funnell B, Phillips G (ed), Plasmid Biology. ASM Press, Washington, DC. doi: 10.1128/9781555817732.ch4

/content/10.1128/9781555817732.chap4.fig4-3

Figure 3

Folded structures of ssoA's and ssoU. The structures of the pLS1 and pE194 ssoA's are predicted from their sequence while that of the pUB110/pMV158 ssoU has been deduced from the results of nuclease P1 and DNase I mapping experiments. The −10 and −35 regions are indicated, along with the conserved RSB and CS-6 sequences. The initiation sites of primer RNA (pRNA) synthesis are indicated.

10.1128/9781555817732/fig4-3b_thmb.gif

10.1128/9781555817732/fig4-3b.gif

Figure 3

Citation: Khan S. 2004. Rolling-Circle Replication, p 63-78. In Funnell B, Phillips G (ed), Plasmid Biology. ASM Press, Washington, DC. doi: 10.1128/9781555817732.ch4

/content/10.1128/9781555817732.chap4.fig4-4

Figure 4

An alignment of ssoA, ssoW, ssoT, and ssoU sequences found in various RCR plasmids. Shaded areas indicate nucleotides that are conserved in at least four of the five sso's shown. The −10 and −35 sequences and the conserved RSB sequences are shown. Boxed regions correspond to the conserved CS-6 sequences found in ssoA's and their homologues in other sso types.

10.1128/9781555817732/fig4-4_thmb.gif

10.1128/9781555817732/fig4-4.gif

Figure 4

Citation: Khan S. 2004. Rolling-Circle Replication, p 63-78. In Funnell B, Phillips G (ed), Plasmid Biology. ASM Press, Washington, DC. doi: 10.1128/9781555817732.ch4

References

/content/book/10.1128/9781555817732.chap4

1. Alonso, J. C.,, C. A. Stiege,, R. H. Tailor,, and J.-F. Viret, 1988. Functional analysis of dna (Ts) mutants of Bacillus subtilis: plasmid pUB110 replication as a model system. Mol. Gen. Genet. 214: 482– 489.

2. Andrup, L.,, J. Damgaard,, K. Wasserman,, L. Boe,, S. M. Madsen,, and F. G. Hansen. 1994. Complete nucleotide sequence of the Bacillus thuringiensis subsp. israelensis plasmid pTX14-3 and its correlation with biological properties. Plasmid 31: 72– 88.

3. Andrup, L.,, G. B. Jenseb,, A. Wilcks,, L. Smidt,, L. Hoflack,, and J . Mahillon. 2003. The patchwork nature of rolling-circle plasmids: comparison of six plasmids from distinct Bacillus thuringiensis serotypes. Plasmid 49: 205– 232.

4. Baas, P. D. 1985. DNA replication of single-stranded Escherichia coli DNA phages. Biochim. Biophys. Acta 825: 111– 139.

5. Backcrt, S.,, K. MciBner,, and T. Borner. 1997. Unique features of the mitochondrial rolling circle-plasmid mp1 from the higher plant Chenopodium album (L.). Nucleic Acids Res. 25: 582– 589.

6. Berns, K. 1990. Parvovirus replication. Microbiol. Rev. 54: 316– 329.

7. Bidnenko, V. E.,, A. Gruss,, and S. D. Ehrlich. 1993. Mutation in the plasmid pUB110 Rep protein affects termination of rolling circle replication. J. Bacteriol. 175: 5611– 5616.

8. Birch, P.,, and S. A. Khan. 1992. Replication of single-stranded plasmid pT181 DNA in vitro. Proc. Natl. Acad. Sci. USA 89: 290– 294.

9. Bird, L. E.,, J. A. Brannigan,, H. S. Subramanya,, and D. B. Wigley. 1998. Characterization of Bacillus stearothermophilus PcrA helicase: evidence against an active rolling mechanism. Nucleic Acids Res. 26: 2686– 2693.

10. Bird, L. E.,, S. Subramanya,, and D. B. Wigley. 1998. Hclicases: a unifying structural theme? Curr. Opin. Struct. Biol. 8: 14– 18.

11. Boe, L.,, M. F. Gros,, H. te Riele,, S. D. Ehrlich,, and A. Gruss. 1989. Replication origins of single-stranded-DNA plasmid pUB110 J. Bacteriol. 171: 3366– 3372.

12. Brito, L.,, G. Vieira,, M. A. Santos,, and H. Paveia. 1996. Nucleotide sequence analysis of pOg32, a cryptic plasmid from Leuconostoc oenos. Plasmid 36: 49– 54.

13. Bron, S.,, P. Bosma,, M. Van Belkum,, and E. Luxen. 1987. Stability function in the Bacillus subtilis plasmid pTA1060. Plasmid 18: 8– 15.

14. Brown, D. R.,, M. J. Roth,, D. Reinberg,, and J . Hurwitz. 1984. Analysis of bacteriophage ϕX174 gene A protein-mediated termination and reinitiation of (ϕX174 DNA synthesis. I. Characterization of the termination and reinitiation reactions. J. Biol. Chem. 259: 10545– 10555.

15. Bruand, C.,, and S. D. Ehrlich. 2000. UvrD-dependent replication of rolling-circle plasmids in Escherichia coli. Mol. Microbiol. 35: 204– 210.

16. Chang, T.-L.,, M. G. Kramer,, R. A. Ansari,, and S. A. Khan. 2000. Role of individual monomers of a dimeric initiator protein in the initiation and termination of plasmid rolling circle replication. J. Biol. Chem. 275: 13529– 13534.

17. Chang, T.-L.,, A. Naqvi,, S. P. Anand,, M. G. Kramer,, R. Munshi,, and S. A. Khan. 2002. Biochemical characterization of the Staphylococcus aureus PcrA helicase and its role in plasmid rolling-circle replication. J. Biol. Chem. 277: 45880– 45886.

17.a. Campos-Olivas, R.,, J. M. Louis,, D. Clerot,, B. Gronenborn,, and A. M. Gronenborn. 2002. The structure of a replication initiator unites diverse aspects of nucleic acid metabolism. Proc. Natl. Acad. Sci. USA 99: 10310– 10315.

18. dela Campa, A. G.,, G. del Solar,, and M. Espinosa. 1990. Initiation of replication of plasmid pLS1. The initiator protein RepB acts on two distant DNA regions. J. Mol. Biol. 213: 247– 262.

19. del Solar, G.,, G. Kramer,, S. Ballester,, and M. Espinosa. 1993. Replication of the promiscuous plasmid pLSl: a region encompassing the minus origin of replication is associated with stable plasmid inheritance Mol. Gen. Genet. 241: 97– 105.

20. del Solar, G.,, R. Giraldo,, M. J. Ruiz-Echevarria,, M. Espinosa,, and R. Diaz-Orejas. 1998. Replication and control of circular bacterial plasmids. Microbiol. Mol. Biol. Rev. 62: 434– 464.

21. del Solar, G. H.,, M. Moscoso,, and M. Espinosa. 1993. Rolling-circle replicating plasmids from gram-positive and gram-negative bacteria: a wall falls. Mol. Microbiol. 8: 789– 796.

22. Dempsey, L. A.,, P. Birch,, and S. A. Khan. 1992. Six amino acids determine the sequence-specific DNA binding and replication specificity of the initiator proteins of the pT181 family. J. Biol. Chem. 267: 24538– 24543.

23. Dempsey, L. A.,, P. Birch,, and S. A. Khan. 1992. Uncoupling of the DNA topoisomerase and replication activities of an initiator protein. Proc. Natl. Acad. Sci. USA 89: 3083– 3087.

24. Dempsey, L. A.,, A. C Zhao,, and S. A. Khan. 1995. Localization of the start sites of lagging-strand replication of rolling-circle plasmids from gram-positive bacteria. Mol. Microbiol. 15: 679– 687.

25. Dervyn, E.,, C. Suski,, R. Daniel,, C. Bruand,, J. Chapuis,, J. Errington,, L. Janniere,, and S. Dusko Ehrlich. 2001. Two essential DNA polymerases at the bacterial replication fork. Science 294: 1716– 1719.

26. Devine, K.,, S. Hogan,, D. Higgins,, and D. McConnell. 1989. Replication and segregational stability of Bacillus plasmid pBAA1. J. Bacteriol. 171: 1166– 1172.

27. Diaz, A.,, S. A. Lacks,, and P. Lopez. 1994. Multiple roles for DNA polymerase I in establishment and replication of the promiscuous plasmid pLS1. Mol. Microbiol. 14: 773– 783.

28. Dillingham, M. S.,, P. Soultanas,, and D. B. Wigley. 1999. Site-directed mutagenesis of motif 111 in PcrA helicase reveals a role in coupling ATP hydrolysis to strand separation. Nucleic Acids Res. 27: 3310– 3317.

29. Dillingham, M. S.,, P. Soultanas,, P. Wiley,, M. R. Webb,, and D. B. Wigley. 2001. Defining the roles of individual residues in the single-stranded DNA binding site of PcrA helicase. Proc. Natl. Acad. Sci. USA 98: 8381– 8387.

30. Eisenberg, S.,, J. F. Scott,, and A. Kornberg. 1979. Enzymatic replication of ϕX174 duplex circles: continuous synthesis. Cold Spring Harbor Symp. Quant. Biol. 43: 295– 302.

31. Gennaro, M. L.,, S. Iordanescu,, R. P. Novick,, R. W. Murray,, T. R. Steck,, and S. A. Khan. 1989. Functional organization of the plasmid pT181 replication origin. J. Mol. Biol. 205: 355– 362.

32. Goetz, G. S.,, S. Englard,, T. Schmidt-Glenewinkel,, A. Aoyama,, M. Hayashi,, and J . Hurwitz. 1988. Effect of ϕX C protein on leading strand DNA synthesis in the ϕX174 replication pathway. J. Biol. Chem. 263: 16452– 16460.

33. Gros, M.-F.,, H. te Riele,, and S. D. Ehrlich. 1987. Rolling circle replication of single-stranded DNA plasmid pCl94. EMBO J. 6: 3863– 3869.

34. Gros, M.-F.,, H. te Riele,, and S. D. Ehrlich. 1989. Replication origin of a single-stranded DNA plasmid pC194. EMBO J. 8: 2711– 2716.

35. Gruss, A.,, and S. D. Ehrlich. 1989. The family of highly interrelated single-stranded deoxyribonucleic acid plasmids. Microbiol. Rev. 53: 231– 241.

36. Gruss, A.,, H. F. Ross,, and R. P. Novick. 1987. Functional analysis of a palindromic sequence required for normal replication of several staphylococcal plasmids. Proc. Natl. Acad. Sci. USA 84: 2165– 2169.

37. Ilyina, T. V.,, and E. V. Koonin. 1992. Conserved sequence motifs in the initiator proteins for rolling circle DNA replication encoded by diverse replicons from eubacteria, eucaryotes and archaebacteria. Nucleic Acids Res. 20: 3279– 3285.

37.a. Inoue, R.,, C. Kaito,, M. Tanabe,, K. Kamura,, N. Akimitsu,, and K. Sekimizu. 2001. Genetic identification of two distinct DNA polymerases, DnaE and PolC, that are essential for chromosomal DNA replication in Staphylococcus aureus. Mol. Gen. Genom. 266: 564– 571.

38. Iordanescu, S. 1989. Specificity of the interaction between the Rep proteins and the origin of replication of Staphylococcus aureus plasmids pTl81 and pC221. Mol. Gen. Genet. 217: 481– 487.

39. Iordanescu, S. 1993. Identification and characterization of Staphylococcus aureus chromosomal gene pcrA, identified by mutations affecting plasmid pT181 replication. Mol. Gen. Genet. 241: 185– 192.

40. Iordanescu, S. 1993. Plasmid pT181-linked suppressors of the Staphylococcus aureus pcrA3 chromosomal mutation. J. Bacteriol. 175: 3916– 3917.

41. Iordanescu, S.,, and R. Basheer. 1991. The Staphylococcus aureus mutation pcrA3 leads to the accumulation of pT181 replication initiation complexes. J. Mol. Biol. 221: 1183– 1189.

42. Iordanescu, S.,, and S. J. Projan. 1988. Replication terminus for staphylococcal plasmids: plasmids pTl81 and pC22l cross-react in the termination process. J. Bacteriol. 170: 3427– 3434.

43. Janniere, L.,, A. Gruss,, and S. D. Ehrlich,. 1993. Plasmids, p. 625– 644. In A. L. Sonenshein,, J. A. Hoch,, and R. Losick (ed.), Bacillus subtilis and Other Gram-Positive Bacteria: Biochemistry, Physiology, and Molecular Genetics. American Society for Microbiology, Washington, D.C.

44. Jin, R.,, M.-E. Fernandes-Beros,, and R. P. Novick. 1997. Why is the initiation nick site of an AT-rich rolling circle plasmid at the tip of a GC-rich cruciform? EMBO J. 16: 4456– 4466.

45. Jin, R.,, and R. P. Novick. 2001. Role of the double-strand origin cruciform in pT181 replication. Plasmid 46: 95– 105.

46. Jin, R.,, A. Rasooly,, and R. P. Novick. 1997. In vitro inhibitory activity of RepC/C*, the inactivated form of the pT181 plasmid initiation protein, RepC. J. Bacteriol, 179: 141– 147.

47. Josson, K.,, T. Scheirlinck,, F. Michiels, C Platteeuw, P. Stanssens, H. Joos, P. Dhaese, M. Zabeau, and J. Mahillon. 1989. Characterization of a gram-positive broad-host-range plasmid isolated from Lactobacillus hilgardii. Plasmid 21: 9– 20.

48. Kaul, S.,, B. K. Mohanty,, T. Sahoo,, I. Patel,, S. A. Khan,, and D. Bastia. 1994. The replication terminator protein of the gram-positive bacterium B. subtilis functions as a polar contrahelicase in gram-negative E. coli. Proc. Natl. Acad. Sci. USA 91: 11143– 11147.

49. Khan, S. A., 1996. Mechanism of replication and copy number control of plasmids in gram-positive bacteria, p. 183– 201. In J. K. Setlow (ed.), Genetic Engineering, vol. 18. Plenum Press, New York, N.Y.

50. Khan, S. A, 1997. Rolling-circle replication of bacterial plasmids. Microbiol. Mol. Biol. Rev. 61: 442– 455.

51. Khan, S. A. 2000. Plasmid rolling-circle replication: recent developments. Mol. Microbiol. 37: 477– 484.

52. Khan, S. A.,, G. K. Adler,, and R. P. Novick. 1982. Functional origin of replication of pT181 plasmid DNA is contained within a 168 base-pair segment. Proc. Natl. Acad. Sci. USA 79: 4580– 4584.

53. Khan, S. A.,, S. M. Carleton,, and R. P. Novick. 1981. Replication of plasmid pT181 DNA in vitro: requirement for a plasmid-encoded product. Proc. Natl. Acad. Sci. USA 78: 4902– 4906.

54. Khan, S. A.,, and R. P. Novick. 1982. Structural analysis of plasmid pSN2 in Staphylococcus aureus: no involvement in enterotoxin B production. J. Bacteriol. 149: 642– 649.

55. Kocpscl, R. R.,, and S. A. Khan. 1987. Cleavage of single-stranded DNA by plasmid pT181-encoded RepC protein. Nucleic Acids Res. 15: 4085– 4097.

56. Kocpscl, R. R.,, and S. A. Khan. 1986. Static and initiator protein-enhanced bending of DNA at a replication origin. Science 233: 1316– 1318.

57. Koepsel, R. R.,, R. W. Murray,, and S. A. Khan. 1986. Sequence-specific interaction between the replication initiator protein of plasmid pT181 and its origin of replication. Proc. Natl. Acad. Sci. USA 83: 5484– 5488.

58. Koepsel, R. R.,, R. W. Murray,, W. D. Rosenblum,, and S. A. Khan. 1985. Purification of pT181-encoded RepC protein required for the initiation of plasmid replication. J. Biol. Chem. 260: 8571– 8577.

59. Koepsel, R. R.,, R. W. Murray,, W. D. Rosenblum,, and S. A. Khan. 1985. The replication initiator protein of plasmid pT181 has sequence-specific endonuclease and topoisomerase-like activities. Proc. Natl. Acad. Sci. USA 82: 6845– 6849.

60. Kramer, M. G.,, G. del Solar,, and M. Espinosa. 1995. Lagging-strand origins of the promiscuous plasmid pMV158: physical and functional characterization. Microbiology 141: 655– 662.

61. Kramer, M. G.,, M. Espinosa,, T. K. Misra,, and S. A. Khan, 1998. Lagging strand replication of rolling-circle plasmids: specific recognition of the ssoA-type origins in different gram-positive bacteria. Proc. Natl. Acad. Sci. USA 95: 10505– 10562.

62. Kramer, M. G.,, M. Espinosa,, T. K. Misra,, and S. A. Khan. 1999. Characterization of a single-strand origin, ssoU, required for broad host range replication of rolling-circle plasmids. Mol. Microbiol. 33: 466– 475.

63. Kramer, M. G.,, S. A. Khan,, and M. Espinosa. 1997. Plasmid rolling circle replication: identification of the RNA polymerase-directed primer RNA and requirement of DNA polymerase I for lagging strand synthesis. EMBO J. 16: 5784– 5795.

64. Kramer, M. G.,, S. A. Khan,, and M. Espinosa. 1998. Lagging strand replication from ssoA origin of plasmid pMV158 in Streptococcus pneumoniae: in vivo and in vitro influences of mutations in two conserved ssoA regions. J. Bacteriol 180: 83– 89.

65. Madsen, S. M.,, L. Andrup,, and L. Boe. 1993. Fine mapping and DNA sequence of replication functions of Bacillus thuringiensis plasmid pTX14-3. Plasmid 30: 119– 130.

66. Marsin, S.,, and P. Forterre. 1999. The active site of the rolling circle replication protein Rep75 is involved in site-specific nuclease, ligase and nucleotidyl transferase activities. Mol. Microbiol. 33: 537– 545.

67. Meijer, W. J. J.,, G. Venema,, and S. Bron. 1995. Characterization of single strand origins of cryptic rolling-circle plasmids from Bacillus subtilis. Nucleic Acids Res. 23: 612– 619.

68. Meijer, W. J.,, G. B. Wisman,, P. Terpstra,, P. B. Thorsted,, C. M. Thomas,, S. Holsappel,, G. Venema,, and S. Bron. 1998. Rolling-circle plasmids from Bacillus subtilis: complete nucleotide sequences and analyses of genes of pTA1015, pTA1040, pTA1050 and pTA1060, and comparisons with related plasmids from gram-positive bacteria. FEMS Microbiol. Rev. 21: 337– 368.

69. Moscoso, M.,, G. del Solar,, and M. Espinosa. 1995. In vitro recognition of the replication origin of pLS1 and of plasmids of the pLS1 family by the RepB initiator protein. J. Bacteriol. 177: 7041– 7049.

70. Moscoso, M.,, G. del Solar,, and M. Espinosa. 1995. Specific nicking-closing activity of the initiator of replication protein RepB of plasmid pMV158 on supercoiled or single-stranded DNA. J. Biol. Chem. 270: 3772– 3779.

71. Moscoso, M.,, R. Eritja,, and M. Espinosa. 1997. Initiation of replication of plasmid pMV158: mechanisms of DNA strand-transfer reactions mediated by the initiator RepB protein. J. Mol. Biol. 268: 840– 856.

72. Murray, R. W.,, R. R. Koepsel,, and S. A. Khan. 1989. Synthesis of single-stranded plasmid pT181 DNA in vitro: initiation and termination of DNA replication. J. Biol. Chem. 264: 1051– 1057.

73. Noirot, P.,, J. Bargonetti,, and R. P. Novick. 1990. Initiation of rolling-circle replication in pT181 plasmid: initiator protein enhances cruciform extrusion at the origin. Proc. Natl. Acad. Sci. USA 87: 8560– 8564.

74. Noirot-Gros, M. F.,, V. Bidnenko,, and S. D. Ehrlich. 1994. Active site of the replication protein of the rolling circle plasmid pC194. EMBO J. 13: 4412– 4420.

75. Noirot-Gros, M.-F.,, and S. D. Ehrlich. 1996. Change of a catalytic reaction carried out by a DNA replication protein. Science 274: 777– 780.

76. Novick, R. P. 1989. Staphylococcal plasmids and their replication. Annu. Rev. Microbiol. 43: 537– 565.

77. Novick, R. P. 1998. Contrasting lifestyles of rolling-circle phages and plasmids. Trends Biochem. Sci. 23: 434– 438.

78. Perez-Martin, J.,, G. H. del Solar,, A. G. de la Campa,, and M. Espinosa. 1988. Three regions in the DNA of plasmid pLS1 show sequence-directed static bending. Nucleic Acids Res. 16: 9113– 9126.

79. Petit, M.-A.,, E. Dervyn,, M. Rose,, K.-D. Entian,, S. McGovern,, S. D. Ehrlich,, and C. Bruand. 1998. PcrA is an essential DNA helicase of Bacillus subtilis fulfilling functions both in repair and rolling-circle replication. Mol. Microbiol. 29: 261– 273.

80. Pigac, J.,, D. Vujaklija,, Z. Toman,, V. Gamulin,, and H. Schrempf. 1988. Structural instability of a bifunctional plasmid pZG1 and single-stranded DNA formation in Streptomyces. Plasmid 19: 222– 230.

81. Projan, S.J.,, and R. P. Novick. 1988. Comparative analysis of five related staphylococcal plasmids. Plasmid 19: 203– 221.

82. Rasooly, A.,, and R. P. Novick. 1993. Replication-specific inactivation of the pT181 plasmid initiator protein. Science 262: 1048– 1050.

83. Rasooly, A.,, S. J . Projan,, and R. P. Novick. 1994. Plasmids of the pT18l family show replication-specific initiator protein modification. J. Bacteriol. 176: 2450– 2453.

84. Rasooly, A.,, P.-Z. Wang,, and R. P. Novick. 1994. Replication-specific conversion of the Staphylococcus aureus pT181 initiator protein from an active homodimcr to an inactive heterodimer. EMBO J. 13: 5245– 5251.

85. Reinberg, D.,, S. L. Zipurski,, P. Weisbeck,, D. Brown,, and J . Hurwitz, 1983. Studies on the ϕX174 gene A protein-mediated termination of leading strand DNA synthesis. J. Biol Chem. 258: 529– 537.

86. Seegers, J. F. M. L.,, A. C. Zhao,, S. A. Khan,, L. E. Pearcc,, W. J . J . Meijer. G. Venema, and S. Bron. 1995. Structural and functional analysis of the single-strand origin of replication from the lactococcal plasmid pWVO1. Mol. Gen. Genet. 249: 43– 50.

87. Seery, L. T.,, N. C Nolan,, P. M. Sharp,, and K. M. Devine. 1993. Comparative analysis of the pC194 group of rolling circle plasmids. Plasmid 30: 185– 196.

88. Servin-Gonzalcz, L.,, A. Sampieri,, J. Cabello,, L. Galvan,, V. Juarez,, and C. Castro. 1995. Sequence and functional analysis of the Streptomyces phaeochromogenes plasmid pJV1 reveals a modular organization of Streptomyces plasmids that replicate by rolling circle. Microbiology 141: 2499– 2510.

89. Sims, J.,, S. Koths,, and D. Dressler. 1979. Single-stranded phage replication: positive- and negative-strand DNA synthesis. Cold Spring Harbor Symp. Quant. Biol. 43: 349– 365.

90. Soultanas, P.,, M. S. Dillingham,, F. Papadopoulos,, S. E. V. Phillips,, C. D. Thomas,, and D. B. Wiglcy. 1999. Plasmid replication initiator protein RepD increases the processivity of PcrA DNA helicase. Nucleic Acids Res. 27: 1421– 1428.

91. Soultanas, P.,, M. S. Dillingham,, P. Wiley,, M. R. Webb,, and D. B. Wigley. 2000. Uncoupling DNA translocation and helicase activity in PcrA: direct evidence for an active mechanism, EMBO J. 19: 3799– 3810.

92. Sozhamannan, S.,, P. Dabert,, V. Moretto,, S. D. Ehrlich,, and A. Gruss. 1990. Plus-origin mapping of single-stranded DNA plasmid pE194 and nick site homologies with other plasmids. J. Bacteriol. 172: 4543– 4548.

93. Subramanya, H. S.,, L. E. Bird,, J . A. Branningan,, and D. B. Wigley. 1996. Crystal structure of a DExx box DNA helicase. Nature 384: 379– 383.

94.Suzuki, L, M. Kataoka, T. Seki, and Y. Yoshida. 1997. Three single-strand origins located on both strands of the Streptomyces rolling circle plasmid pSN22. Plasmid 37: 51– 64.

95. te Riele, H.,, B. Michel,, and S. D. Ehrlich. 1986. Are single-stranded circles intermediate in plasmid DNA replication? EMBO J. 5: 631– 637.

96. te Riele, H.,, B. Michel,, and S. D. Ehrlich. 1986. Single-stranded plasmid DNA in Bacillus subtilis and Staphylococcus aureus. Proc. Natl. Acad. Sci. USA 83: 2541– 2545.

97. Thomas, C. D.,, D. F. Balson,, and W. V. Shaw. 1988. Identification of the tyrosine residue involved in bond formation between replication origin and the initiator protein of plasmid pC221. Biochem. Soc. Trans. 16: 758– 759.

98. Thomas, C. D.,, D. F. Balson,, and W. V. Shaw. 1990. In vitro studies of the initiation of staphylococcal plasmid replication. J. Biol. Chem. 265: 5519– 5530.

99. Thomas, C. D.,, and L. J. Jennings. 1995. RepD/D*: a protein-DNA adduce arising during plasmid replication. Biochem. Soc. Trans. 23: 442S

100. Thomas, C. D.,, T. T. Nikiforov,, B. A. Connolly,, and W. V. Shaw. 1995. Determination of sequence specificity between a plasmid replication initiator protein and the origin of replication. J. Mol. Biol. 254: 381– 391.

101. Van Mansfeld, A. D. M.,, H. A. A. M. van Teefelen,, P. D. Baas,, and H. S. Jansz. 1986. Two juxtaposed tyrosyl-OH groups participate in ϕX174 gene A protein catalyzed cleavage and ligation of DNA. Nucleic Acids Res. 14: 4229– 4238.

102. Velankar, S. S.,, P. Souhanas,, M. S. Dillingham,, S. Subramanya,, and D. B. Wigley, 1999. Crystal structures of complexes of PcrA DNA helicase with a DNA substrate indicate an inchworm mechanism. Cell 97: 75– 84.

103. Wang, P.-Z.,, S. J . Projan,, V. Henriquez,, and R. P. Novick. 1992. Specificity of origin recognition by replication initiator protein in plasmids of the pT181 family is determined by a six amino acid residue element. J. Mol. Biol. 223: 145– 158.

104. Wang, P.-Z.,, S. J . Projan,, V. Henriquez,, and R. P. Novick. 1993. Origin recognition specificity in pTl81 plasmids is determined by a functionally asymmetric palindromic DNA element. EMBO J. 12: 45– 52.

105. Yasukawa, H.,, T. Hase,, and Y. Masamune. 1993. The mutational analysis of the plus origin and the identification of the minus origin of the plasmid pKYM which replicates via a rolling-circle mechanism. J. Gen. Appl. Microbiol. 39: 237– 245.

106. Yasukawa, H.,, T. Hase,, A. Sakai,, and Y. Masamune. 1991. Rolling-circle replication of the plasmid pKYM isolated from a gram-negative bacterium. Proc. Natl. Acad. Sci. USA 88: 10282– 10286.

107. Zaman, S.,, L. Radnedge,, H. Richards,, and J. M. Ward. 1993. Analysis of the site for second-strand initiation during replication of the Streptomyces plasmid plJ101. J. Gen. Microbiol. 139: 669– 676.

108. Zhao, A. C., R A. Ansari, M. C. Schmidt, and S. A. Khan. 1998. An oligonucleotide inhibits oligomerization of a rolling-circle initiator protein at the pT181 origin of replication. J. Biol. Chem. 273: 16082– 16089.

109. Zhao, A. C.,, and S. A. Khan, 1996. An 18-bp sequence is sufficient for termination of rolling-circle replication of plasmid pT181 J. Bacteriol. 24: 5222– 5228.

110. Zhao, A. C.,, and S. A. Khan. 1997. Sequence requirements for the termination of rolling-circle replication of plasmid pT181. Mol. Microbiol. 24: 535– 544.

111. Zinder, N. D.,, and K. Horiuchi. 1985. Multiregulatory element of filamentous bacteriophages. Microbiol. Rev. 49: 101– 106.

112. Zock, J. M.,, P. Birch,, and S. A. Khan, 1990. Specificity of RepC protein in plasmid pT181 DNA replication. J. Biol. Chem. 265: 3484– 3488.