Interactions between the RepB initiator protein of plasmid pMV158 and two distant DNA regions within the origin of replication

Nucleic Acids Research

Volumn 35, Issue 4, 2007, Pages 1230-1244

  Ruiz Masó, José A ^a   Lurz, Rudi ^b   Espinosa, Manuel ^a   del Solar, Gloria ^a  

^a CENTRO DE INVESTIGACIONES BIOLÓGICAS   (Spain)

^b MAX PLANCK INSTITUTE FOR MOLECULAR GENETICS   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

DNA; REPLICATION INITIATOR PROTEIN DNAA;

ARTICLE; BINDING AFFINITY; BINDING SITE; CONFORMATION; CONTROLLED STUDY; DNA SUPERCOILING; GENE LOCUS; GENE REPLICATION; NONHUMAN; NUCLEOTIDE SEQUENCE; PLASMID; PRIORITY JOURNAL; PROTEIN DNA BINDING; PROTEIN DNA INTERACTION;

BACTERIAL PROTEINS; BINDING SITES; DNA, BACTERIAL; DNA, SUPERHELICAL; NUCLEIC ACID CONFORMATION; PLASMIDS; REPLICATION ORIGIN;

EID: 34047146480     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkl1099     Document Type: Article

References (50)

1. del Solar,G., Giraldo,R., Ruiz-Echevarría,M.J., Espinosa,M. and Díaz-Orejas,R. (1998) Replication and control of circular bacterial plasmids. Microbiol. Mol. Biol. Rev., 62, 434-464.
2. Khan,S.A. (2000) Plasmid rolling-circle replication: Recent developments. Mol. Microbiol., 37, 477-484.
3. Novick,R.P. (1998) Contrasting lifestyles of rolling-circle phages and plasmids. Trends Biochem. Sci., 23, 434-438.
4. Osborn,M. (2002) Database of plasmid replicons: http://www.essex.ac.uk/ bs/staff/osborn/DPR_home.htm.
5. Khan,S.A. (2005) Plasmid rolling-circle replication: Highlights of two decades of research. Plasmid, 53, 126-136.
6. Thomas,C.D., Balson,D.F. and Shaw,W. (1990) In vitro studies of the initiation of staphylococcal plasmid replication. Specificity of RepD for its origin (oriD) and characterization of the Rep-ori tyrosil ester. J. Biol. Chem., 265, 5519-5530.
7. Noirot-Gross,M.F., Bidnenko,V. and Ehrlich,S.D. (1994) Active site of the replication protein in the rolling circle plasmid pC194. EMBO J., 13, 4412-4420.
8. Chang,T.-L., Naqvi,A., Anand,S.P., Kramer,M.G., Munshi,R. and Khan,S.A. (2002) Biochemical characterization of the Staphylococcus aureus PcrA helicase and its role in plasmid rolling circle replication. J. Biol. Chem., 277, 45880-45886.
9. Khan,S.A. (2003) DNA-protein interactions during the initiation and termination of plasmid pT181 rolling-circle replication. Prog. Nucleic Acid Res. Mol. Biol., 75, 113-137.
10. Rasooly,A., Wang,P. and Novick,R. (1994) Replication-specific conversion of the Staphylococcus aureus pT181 initiator protein from an active homodimer to an inactive heterodimer. EMBO J., 13, 5245-5251.
11. Zhao,A.C. and Khan,S.A. (1997) Sequence requirements for the termination of rolling-circle replication of plasmid pT181. Mol. Microbiol., 24, 535-544.
12. del Solar,G., Moscoso,M. and Espinosa,M. (1993) In vivo definition of the functional origin of replication (ori(+)) of the promiscuous plasmid pLS1. Mol. Gen. Genet., 237, 65-72.
13. Thomas,C.D., Nikiforov,T.T., Connolly,B.A. and Shaw,W.V. (1995) Determination of sequence specificity between a plasmid replication initiator protein and the origin of replication. J. Mol. Biol., 254, 381-391.
14. Dempsey,L., Birch,P. and Khan,S. (1992) Uncoupling of the DNA topoisomerase and replication activities of an initiator protein. Proc. Natl. Acad. Sci. USA, 89, 3083-3087.
15. Moscoso,M., del Solar,G. and Espinosa,M. (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.
16. Zock,J.M., Birch,P. and Khan,S.A. (1990) Specificity of RepC protein in plasmid pT181 DNA replication. J. Biol. Chem., 265, 3484-3488.
17. Jin,R. and Novick,R.P. (2001) Role of the double-strand origin cruciform in pT181 replication. Plasmid, 46, 95-105.
18. de la Campa,A.G., del Solar,G. and Espinosa,M. (1990) Initiation of replication of plsmid pLS1. The initiator protein RepB acts on two distant regions. J. Mol. Biol., 213, 247-262.
19. Puyet,A., del Solar,G. and Espinosa,M. (1988) Identification of the origin and direction of replication of the broad-host-range plasmid pLS1. Nucl. Acids Res., 16, 115-133.
20. Moscoso,M., del Solar,G. and Espinosa,M. (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.
21. Ruiz-Maso,J.A., Lopez-Zumel,C., Menendez,M., Espinosa,M. and del Solar,G. (2004) Structural features of the initiator of replication protein RepB encoded by the promiscuous plasmid pMV158. Biochimica et Biophysica Acta (BBA) - Proteins & Proteomics, 1696, 113-119.
22. Lacks,S.A., López,P., Greenberg,B. and Espinosa,M. (1986) Identification and analysis of genes for tetracycline resistance and replication functions in the broad-host-range plasmid pLS1. J. Mol. Biol., 192, 753-765.
23. Sambrook,J., Fritsch,E.F. and Maniatis,T. (1989) ed. Molecular Cloning. A Laboratory Manual, 2nd edn, Cold Spring Harbor Laboratory Press, New York.
24. Kim,K., Zwieb,C., Wu,C. and Adhya,S. (1989) Bending of DNA by gene-regulatory proteins: Construction and use of a DNA bending vector. Gene, 85, 15-23.
25. Man,T.-K. and Stormo,G.D. (2001) Non-independence of Mnt repressor-operator interaction determined by a new quantitative multiple fluorescence relative affinity (QuMFRA) assay. Nucl. Acids Res., 29, 2471-2478.
26. Thompson,J.F. and Landy,A. (1988) Empirical estimation of protein-induced DNA bending angles: Applications to 1 site-specific recombination complexes. Nucl. Acids Res., 16, 9687-9705.
27. Spiess,E. and Lurz,R. (1988) Electron microscopic analysis of nucleic acids and nucleic acid-protein complexes. Methods Microbiol, 20, 293-323.
28. del Solar,G.H., Perez-Martin,J. and Espinosa,M. (1990) Plasmid pLS1-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.
29. Maxam,A.H. and Gilbert,W. (1980) Sequencing end-labelled DNA with base-specific chemical cleavages. Methods Enzymol., 65.
30. Papavassiliou,A.G. (1993) Localisation of DNA-protein contact points by DMS resistance of complexes resolved in gel retardation assays. Nucl. Acids Res., 21, 757-758.
31. Sasse-Dwight,S. and Gralla,J.D. (1991) Footprinting Protein-DNA Complexes in Vivo. Methods Enzymol, 208, 146-168.
32. Shaw,P.E. and Stewart,F. (1994). Kneale,G.G. (ed.), DNA-Protein Interactions: Principles and Protocols. Vol. 30. Humana Press Inc., Totowa, NJ, pp. 79-87.
33. Wu,H.M. and Crothers,D.M. (1984) The locus of sequence-directed and protein-induced DNA bending. Nature, 308, 509-513.
34. Krüger,R., Rakowski,A.A. and Filutowicz,M. (2004) Isomerization and apparent DNA bending by Pi, the replication protein of plasmid R6K. Biochem. Biophys. Res. Comm., 313, 834-840.
35. Beerens,N., Hoeijmakers,J.H.J., Kanaar,R., Vermeulen,W. and Wyman,C. (2005) The CSB Protein Actively Wraps DNA. J. Biol. Chem., 280, 4722-4729.
36. Schlax,P.J., Capp,M.W. and Record,M.T. (1995) Inhibition of transcription initiation by lac repressor. J. Mol. Biol., 245, 331-350.
37. Díaz,A., Lacks,S.A. and López,P. (1994) Multiple roles for DNA polymerase I in establishment and replication of the promiscuous plasmid pLS1. Mol. Microbiol., 14, 773-783.
38. Koepsel,R.R., Murray,R.W. and Khan,S.A. (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.
39. Thomas,C.D., Balson,D.F. and Shaw,W. (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.
40. Jin,R., Fernandez-Beros,M.-E. and Novick,R.P. (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.
41. Schleif,R. (1992) DNA looping. Annu. Rev. Biochem., 61, 199-223.
42. Swigon,D., Coleman,B.D. and Olson,W.K. (2006) Modeling the Lac repressor-operator assembly: The influence of DNA looping on Lac repressor conformation. Proc. Natl. Acad. Sci. USA, 103, 9879-9884.
43. Swinger,K.K. and Rice,P.A. (2004) IHF and HU: Flexible architects of bent DNA. Curr. Opin. Struct. Biol., 14, 28.
44. Noirot-Gros,M.-F., Bidnenko,V. and Ehrlich,S.D. (1994) Active site of the replication protein of the rolling circle plasmid pC194. EMBO J., 13, 4412-4420.
45. Hickman,A.B., Ronning,D.R., Perez,Z.N., Kotin,R.M. and Dyda,F. (2004) The nuclease domain of adeno-associated virus Rep coordinates replication initiation using two distinct DNA recognition interfaces. Molecular Cell, 13, 403.
46. Enemark,E.J. and Joshua-Tor,L. (2006) Mechanism of DNA translocation in a replicative hexameric helicase. Nature, 442, 270.
47. Senear,D.F. and Brenowitz,M. (1991) Determination of binding constants for cooperative site-specific protein-DNA interactions using the gel mobility-shift assay. J. Biol. Chem., 266, 13661-13671.
48. Moscoso,M., del Solar,G. and Espinosa,M. (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.
49. Kim,S.W., Jeong,E.J., Kang,H.S., Tak,J.I., Bang,W.Y., Heo,J.B., Jeong,J.Y., Yoon,G.M., Kang,H.Y. and Bahk,J.D. (2006) Role of RepB in the replication of plasmid pJB01 isolated from Enterococcus faecium JC1. Plasmid, 55, 99-113.
50. de la Campa,A.G., del Solar,G. and Espinosa,M. (1990) Initiation of replication of plsmid pLS1. The initiator protein RepB acts on two distant regions. J. Mol. Biol., 213, 247-262.