DNA-Protein Interactions during the Initiation and Termination of Plasmid pT181 Rolling-Circle Replication

Progress in Nucleic Acid Research and Molecular Biology

Volumn 75, Issue , 2003, Pages 113-137

  Khan, Saleem A ^a  

^a UNIVERSITY OF PITTSBURGH SCHOOL OF MEDICINE   (United States)

Author keywords

DNA helicase; DNA protein interactions; Initiator proteins; Origins of replication; Plasmids; Rolling circle replication

Indexed keywords

DNA BINDING PROTEIN;

AMINO ACID SEQUENCE; BIOSYNTHESIS; CHEMISTRY; DNA REPLICATION; DNA REPLICATION ORIGIN; GENETICS; METABOLISM; NUCLEOTIDE SEQUENCE; PHYSIOLOGY; PLASMID; REVIEW;

AMINO ACID SEQUENCE; BASE SEQUENCE; DNA REPLICATION; DNA-BINDING PROTEINS; PLASMIDS; REPLICATION ORIGIN;

EID: 1542675416     PISSN: 00796603     EISSN: None     Source Type: Book Series    
DOI: 10.1016/S0079-6603(03)75004-1     Document Type: Review

References (74)

1. G.H. del Solar M. Moscoso M. Espinosa Rolling-circle replicating plasmids from Gram-positive and Gram-negative bacteria: a wall falls Mol. Microbiol. 8 1993 789 796
2. G. del Solar R. Giraldo M.J. Ruiz-Echevarria M. Espinosa R. Diaz-Orejas Replication and control of circular bacterial plasmids Microbiol. Mol. Biol. Rev. 62 1998 434 464
3. A. Gruss S.D. Ehrlich The family of highly interrelated single-stranded deoxyribonucleic acid plasmids Microbiol. Rev. 53 1989 231 241
4. S.A. Khan Mechanism of replication and copy number control of plasmids in Gram-positive bacteria J.K. Setlow Genetic Engineering 18 1996 Plenum Press New York 183 201
5. S.A. Khan Rolling-circle replication of bacterial plasmids Microbiol. Mol. Biol. Rev. 61 1997 442 455
6. S.A. Khan Plasmid rolling-circle replication: recent developments Mol. Microbiol. 37 2000 477 484
7. R.P. Novick Staphylococcal plasmids and their replication Annu. Rev. Microbiol. 43 1989 537 565
8. R.P. Novick Contrasting lifestyles of rolling-circle phages and plasmids TIBS 23 1998 434 438
9. S.J. Projan R.P. Novick Comparative analysis of five related staphylococcal plasmids Plasmid 19 1988 203 221
10. T.V. Ilyina E.V. Koonin 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 1992 3279 3285
11. L.A. Dempsey P. Birch S.A. Khan Uncoupling of the DNA topoisomerase and replication activities of an initiator protein Proc. Natl. Acad. Sci. USA 89 1992 3083 3087
12. C.D. Thomas D.F. Balson W.V. Shaw Identification of the tyrosine residue involved in bond formation between replication origin and the initiator protein of plasmid pC221 Biochem. Soc. Trans. 16 1988 758 759
13. P. Noirot J. Bargonetti R.P. Novick Initiation of rolling-circle replication in pT181 plasmid: initiator protein enhances cruciform extrusion at the origin Proc. Natl. Acad. Sci. USA 87 1990 8560 8564
14. R. Jin R.P. Novick Role of the double-strand origin cruciform in pT181 replication Plasmid 46 2001 95 105
15. R. Jin M.-E. Fernandez-Beros R.P. Novick Why is the initiation nick site of an AT-rich rolling circle plasmid at the tip of a GC-rich cruciform? EMBO J. 16 1997 4456 4466
16. J.M. Zock P. Birch S.A. Khan Specificity of RepC protein in plasmid pT181 DNA replication J. Biol. Chem. 265 1990 3484 3488
17. C.D. Thomas T.T. Nikiforov B.A. Connolly W.V. Shaw Determination of sequence specificity between a plasmid replication initiator protein and the origin of replication J. Mol. Biol. 254 1995 381 391
18. C.D. Thomas D.F. Balson W.V. Shaw In vitro studies of the initiation of staphylococcal plasmid replication J. Biol. Chem. 265 1990 5519 5530
19. S.A. Khan R.P. Novick Complete nucleotide sequence of pT181, a tetracycline-resistance plasmid from Staphylococcus aureus Plasmid 10 1983 251 259
20. S.A. Khan G.K. Adler R.P. Novick Functional origin of replication of pT181 plasmid DNA is contained within a 168 base-pair segment Proc. Natl. Acad. Sci. USA 79 1982 4580 4584
21. M.L. Gennaro S. Iordanescu R.P. Novick R.W. Murray T.R. Steck S.A. Khan Functional organization of the plasmid pT181 replication origin J. Mol. Biol. 205 1989 355 362
22. R.R. Koepsel R.W. Murray S.A. Khan Sequence-specific interaction between the replication initiator protein of plasmid pT181 and its origin of replication Proc. Natl. Acad. Sci. USA 83 1986 5484 5488
23. R. Jin X. Zhou R.P. Novick The inactive pT181 initiator heterodimer, RepC/C∗, binds but fails to induce melting of the plasmid replication origin J. Biol. Chem. 271 1996 31086 31091
24. P.-Z. Wang S.J. Projan V. Henriquez R.P. Novick Origin recognition specificity in pT181 plasmids is determined by a functionally asymmetric palindromic DNA element EMBO J. 12 1993 45 52
25. S. Iordanescu Specificity of the interaction between the Rep proteins and the origin of replication of Staphylococcus aureus plasmids pT181 and pC221 Mol. Gen. Genet. 217 1989 481 487
26. R.R. Koepsel S.A. Khan Static and initiator protein-enhanced bending of DNA at a replication origin Science 233 1986 1316 1318
27. R. R. Koepsel, R. W. Murray, W. D. Rosenblum and S. A. Khan, The replication initiator protein of plasmid pT181 has sequence-specific endonuclease and topoisomerase-like activities, Proc. Natl. Acad. Sci. USA 82 , 6845–6849 (1985)
28. A.C. Zhao S.A. Khan An 18-bp sequence is sufficient for termination of rolling-circle replication of plasmid pT181 J. Bacteriol. 24 1996 5222 5228
29. A.C. Zhao S.A. Khan Sequence requirements for the termination of rolling-circle replication of plasmid pT181 Mol. Microbiol. 24 1997 535 544
30. S. Iordanescu S.J. Projan Replication terminus for staphylococcal plasmids: plasmids pT181 and pC221 cross-react in the termination process J. Bacteriol. 170 1988 3427 3434
31. A.C. Zhao R.A. Ansari M.C. Schmidt S.A. Khan An oligonucleotide inhibits oligomerization of a rolling-circle initiator protein at the pT181 origin of replication J. Biol. Chem. 273 1998 16082 16089
32. R.W. Murray R.R. Koepsel S.A. Khan Synthesis of single-stranded plasmid pT181 DNA in vitro: initiation and termination of DNA replication J. Biol. Chem. 264 1989 1051 1057
33. A. Rasooly R.P. Novick Replication-specific inactivation of the pT181 plasmid initiator protein Science 262 1993 1048 1050
34. M.L. Gennaro Genetic evidence for replication enhancement from a distance Proc. Natl. Acad. Sci. USA 90 1993 5529 5533
35. M.L. Gennaro R.P. Novick cmp , a cis -acting plasmid locus that increases interaction between replication origin and initiator protein J. Bacteriol. 168 1986 160 166
36. V. Henriquez V. Milisavljevic J.D. Kahn M.L. Gennaro Sequence and structure of cmp , the replication enhancer of the Staphylococcus aureus plasmid pT181 Gene 134 1993 93 98
37. D. Colombo S. Iordanescu M.L. Gennaro Replication enhancer requirement for recognition of heterologous replication origin by an initiator protein Plasmid 33 1995 232 234
38. Q. Zhang S.S. De Olivera R. Colangeli M.L. Gennaro Binding of a novel host factor to the pT181 plasmid replication enhancer J. Bacteriol. 179 1997 684 688
39. R.R. Koepsel R.W. Murray W.D. Rosenblum S.A. Khan Purification of pT181-encoded RepC protein required for the initiation of plasmid replication J. Biol. Chem. 260 1985 8571 8577
40. S.A. Khan S.M. Carleton R.P. Novick Replication of plasmid pT181 DNA in vitro : requirement for a plasmid-encoded product Proc. Natl. Acad. Sci. USA 78 1981 4902 4906
41. L.A. Dempsey P. Birch S.A. Khan Six amino acids determine the sequence-specific DNA binding and replication specificity of the initiator proteins of the pT181 family J. Biol. Chem. 267 1992 24538 24543
42. P.-Z. Wang S.J. Projan V. Henriquez R.P. Novick 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 1992 145 158
43. T.-L. Chang M.G. Kramer R.A. Ansari S.A. Khan Role of individual monomers of a dimeric initiator protein in the initiation and termination of plasmid rolling circle replication J. Biol. Chem. 275 2000 13529 13534
44. R.R. Koepsel S.A. Khan Cleavage of single-stranded DNA by plasmid pT181-encoded RepC protein Nucleic Acids Res. 15 1987 4085 4097
45. C.D. Thomas L.J. Jennings RepD/D∗: a protein-DNA adduct arising during plasmid replication Biochem. Soc. Trans. 23 1995 442S
46. R. Jin A. Rasooly R.P. Novick In vitro inhibitory activity of RepC/C∗, the inactivated form of the pT181 plasmid initiation protein, RepC J. Bacteriol. 179 1997 141 147
47. A. Rasooly S.J. Projan R.P. Novick Plasmids of the pT181 family show replication-specific initiator protein modification J. Bacteriol. 176 1994 2450 2453
48. A. Rasooly P.-Z. Wang R.P. Novick Replication-specific conversion of the Staphylococcus aureus pT181 initiator protein from an active homodimer to an inactive heterodimer EMBO J. 13 1994 5245 5251
49. S. Iordanescu Identification and characterization of Staphylococcus aureus chromosomal gene pcrA , identified by mutations affecting plasmid pT181 replication Mol. Gen. Genet. 241 1993 185 192
50. S. Iordanescu Plasmid pT181-linked suppressors of the Staphylococcus aureus pcrA3 chromosomal mutation J. Bacteriol. 175 1993 3916 3917
51. S. Iordanescu R. Basheer The Staphylococcus aureus mutation pcrA3 leads to the accumulation of pT181 replication initiation complexes J. Mol. Biol. 221 1991 1183 1189
52. M.C. Hall S.W. Matson Helicase motifs: the engine that powers DNA unwinding Mol. Microbiol. 34 1989 867 877
53. L.E. Bird S. Subramanya D.B. Wigley Helicases: a unifying structural theme? Curr. Opin. Struct. Biol. 8 1998 14 18
54. H.S. Subramanya L.E. Bird J.A. Branningan D.B. Wigley Crystal structure of a DExx box DNA helicase Nature 384 1996 379 383
55. S.S. Velankar P. Soultanas M.S. Dillingham S. Subramanya D.B. Wigley Crystal structures of complexes of PcrA DNA helicase with a DNA substrate indicate an inchworm mechanism Cell 97 1999 75 84
56. P. Soultanas M.S. Dillingham P. Wiley M.R. Webb D.B. Wigley Uncoupling DNA translocation and helicase activity in PcrA: direct evidence for an active mechanism EMBO J. 19 2000 3799 3810
57. M.-A. Petit E. Dervyn M. Rose K.-D. Entian S. McGovern S.D. Ehrlich C. Bruand PcrA is an essential DNA helicase of Bacillus subtilis fulfilling functions both in repair and rolling-circle replication Mol. Microbiol. 29 1998 261 273
58. C. Bruand S.D. Ehrlich UvrD-dependent replication of rolling-circle plasmids in Escherichia coli Mol. Microbiol. 35 2000 204 210
59. M.S. Dillingham P. Soultanas D.B. Wigley Site-directed mutagenesis of motif III in PcrA helicase reveals a role in coupling ATP hydrolysis to strand separation Nucleic Acids Res. 27 1999 3310 3317
60. P. Soultanas M.S. Dillingham F. Papadopoulos S.E.V. Phillips C.D. Thomas D.B. Wigley Plasmid replication initiator protein RepD increases the processivity of PcrA DNA helicase Nucleic Acids Res. 27 1999 1421 1428
61. T.-L. Chang A. Naqvi S.P. Anand M.G. Kramer R. Munshi S.A. Khan Biochemical characterization of the Staphylococcus aureus PcrA helicase and its role in plasmid rolling-circle replication J. Biol. Chem. 277 2002 45880 45886
62. D.E. Bussiere D. Bastia Termination of DNA replication of bacterial and plasmid chromosomes Mol. Microbiol. 31 1999 1611 1618
63. S. Kaul B.K. Mohanty T. Sahoo I. Patel S.A. Khan D. Bastia 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 1994 11143 11147
64. S. Majumder R.P. Novick Intermediates in plasmid pT181 DNA replication Nucleic Acids Res. 16 1988 2897 2912
65. R. Inoue C. Kaito M. Tanabe K. Kamura N. Akimitsu K. Sekimizu Genetic identification of two distinct DNA polymerases, DnaE and PolC, that are essential for chromosomal DNA replication in Staphylococcus aureus Mol. Gen. Genomics 266 2001 564 571
66. E. Dervyn C. Suski R. Daniel C. Bruand J. Chapuis J. Errington L. Janniere S. Dusko Ehrlich Two essential DNA polymerases at the bacterial replication fork Science 294 2001 1716 1719
67. I. Bruck M. O'Donnell The DNA replication machine of a Gram-positive organism J. Biol. Chem. 275 2000 28971 28983
68. P. Birch S.A. Khan Replication of single-stranded plasmid pT181 DNA in vitro Proc. Natl. Acad. Sci. USA 89 1992 290 294
69. L.A. Dempsey A.C. Zhao S.A. Khan Localization of the start sites of lagging-strand replication of rolling-circle plasmids from Gram-positive bacteria Mol. Microbiol. 15 1995 679 687
70. A. Gruss H.F. Ross R.P. Novick Functional analysis of a palindromic sequence required for normal replication of several staphylococcal plasmids Proc. Natl. Acad. Sci. USA 84 1987 2165 2169
71. M.G. Kramer S.A. Khan M. Espinosa 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 1998 83 89
72. M.G. Kramer S.A. Khan M. Espinosa 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 1997 5784 5795
73. M.G. Kramer M. Espinosa T.K. Misra S.A. Khan 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 1998 10505 10562
74. A. Diaz S.A. Lacks P. Lopez Multiple roles for DNA polymerase I in establishment and replication of the promiscuous plasmid pLS1 Mol. Microbiol. 14 1994 773 783