Early Events in the Binding of the pPS10 Replication Protein RepA to Single Iteron and Operator DNA Sequences

Journal of Molecular Biology

Volumn 364, Issue 5, 2006, Pages 909-920

  Díaz López, Teresa ^a   Dávila Fajardo, Cristina ^a   Blaesing, Franca ^b   Lillo, M Pilar ^c   Giraldo, Rafael ^a  

^a CENTRO DE INVESTIGACIONES BIOLÓGICAS   (Spain)

^b MAX PLANCK INSTITUTE FOR MOLECULAR GENETICS   (Germany)

^c INSTITUTO DE QUÍMICA FÍSICA ROCASOLANO   (Spain)

Author keywords

conformational intermediate; DNA replication; DNA binding steps; pPS10; RepA

Indexed keywords

BOVINE SERUM ALBUMIN; DNA; OVALBUMIN; REPLICATION PROTEIN A;

ANISOTROPY; ARTICLE; CIRCULAR DICHROISM; DNA BINDING; DNA SEQUENCE; GEL MOBILITY SHIFT ASSAY; HYDRODYNAMICS; MOLECULAR INTERACTION; PRIORITY JOURNAL; PROTEIN BINDING; PROTEIN CONFORMATION; PROTEIN DNA INTERACTION; PROTEIN DOMAIN; PROTEIN MODIFICATION; SURFACE PLASMON RESONANCE; X RAY CRYSTALLOGRAPHY;

BOS TAURUS; PSEUDOMONAS;

EID: 33751090123     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jmb.2006.09.013     Document Type: Article

References (42)

1. del Solar G., Giraldo R., Ruíz-Echevarría M.J., Espinosa M., and Díaz R. Replication and control of circular bacterial plasmids. Microbiol. Mol. Biol. Rev. 62 (1998) 434-464
2. Krüger R., Rakowski S.A., and Filutowicz M. Participating elements in the replication of iteron containing plasmids. In: Funnell B.E., and Phillips G.J. (Eds). Plasmid Biology (2004), ASM Press, Washington, DC 25-45
3. Chattoraj D.K. Control of plasmid DNA replication by iterons: no longer paradoxical. Mol. Microbiol. 37 (2000) 467-476
4. Giraldo R., and Fernández-Tresguerres M.E. 20 years of the pPS10 replicon: insights on the molecular mechanism for the activation of DNA replication in iteron-containing bacterial plasmids. Plasmid 52 (2004) 69-83
5. Nieto C., Giraldo R., Fernández-Tresguerres E., and Díaz R. Genetic and functional analysis of the basic replicon of pPS10, a plasmid specific of Pseudomonas isolated from Pseudomonas syringae pv. savastanoi. J. Mol. Biol. 223 (1992) 415-426
6. Giraldo R., Andreu J.M., and Díaz-Orejas R. Protein domains and conformational changes in the activation of RepA, a DNA replication initiator. EMBO J. 17 (1998) 4511-4526
7. Komori H., Matsunaga F., Higuchi Y., Ishiai M., Wada C., and Miki K. Crystal structure of a prokaryotic replication initiator protein bound to DNA at 2.6 Å resolution. EMBO J. 18 (1999) 4597-4607
8. Sharma S., Sathyanarayana K., Bird J.G., Hoskins J.R., Lee B., and Wickner S. Plasmid P1 RepA is homologous to the F plasmid RepE class of initiators. J. Biol. Chem. 279 (2004) 6027-6034
9. Abhyankar M.M., Reddy J.M., Sharma R., Büllesbach E., and Bastia D. Biochemical investigations of control of replication of plasmid R6K. J. Biol. Chem. 279 (2004) 6711-6719
10. Kunnimalaiyaan S., Krüger R., Ross W., Rakowski S.A., and Filutowicz M. Binding modes of the initiator and inhibitor forms of the replication protein π to the gamma ori iteron of plasmid R6K. J. Biol. Chem. 279 (2004) 41058-41066
11. Giraldo R., Fernández-Tornero C., Evans P.R., Díaz-Orejas R., and Romero A. A conformational switch between transcriptional repression and replication initiation in the RepA dimerization domain. Nature Struct. Biol. 10 (2003) 565-571
12. Díaz-López T., Lages-Gonzalo M., Serrano-López A., Alfonso C., Rivas G., Díaz-Orejas R., and Giraldo R. Structural changes in RepA, a plasmid replication initiator, upon binding to origin DNA. J. Biol. Chem. 278 (2003) 18606-18616
13. Beckett D. Functional switches in transcription regulation; molecular mimicry and plasticity in protein-protein interactions. Biochemistry 43 (2004) 7983-7991
14. Cunningham E.L., and Berger J.M. Unraveling the early steps of prokaryotic replication. Curr. Opin. Struct. Biol. 15 (2005) 68-76
15. Marianayagam N.J., Sunde M., and Matthews J.M. The power of two: protein dimerization in biology. Trends Biochem. Sci. 29 (2004) 618-625
16. Zzaman S., and Bastia D. Oligomeric initiator protein-mediated DNA looping negatively regulates plasmid replication in vitro by preventing origin melting. Mol. Cell 20 (2005) 833-843
17. Minton A.P. The influence of macromolecular crowding and macromolecular confinement on biochemical reactions in physiological media. J. Biol. Chem. 276 (2001) 10577-10580
18. García de Viedma D., Giraldo R., Ruíz-Echevarría M.J., Lurz R., and Díaz-Orejas R. Transcription of repA, the gene of the initiation protein of the Pseudomonas plasmid pPS10, is autoregulated by sequential interactions of the RepA protein at a symmetrical operator. J. Mol. Biol. 247 (1995) 211-223
19. García de Viedma D., Giraldo R., Rivas G., Fernández-Tresguerres E., and Díaz-Orejas R. A Leucine-Zipper motif determines different functions in a DNA replication protein. EMBO J. 15 (1996) 925-934
20. Lakowicz J.R. Principles of Fluorescence Spectroscopy. 2nd. edit. (1999), Kluwer Academic-Plenum Publishers, New York
21. Maestro B., Sanz J.M., Díaz-Orejas R., and Fernández-Tresguerres E. Modulation of pPS10 host range by plasmid-encoded RepA initiator protein. J. Bacteriol. 185 (2003) 1367-1375
22. Kunnimalaiyaan S., Inman R.B., Rakowski S.A., and Filutowicz M. Role of π dimers in coupling ("handcuffing") of plasmid R6K's γ ori iterons. J. Bacteriol. 187 (2005) 3779-3785
23. Speck C., Weigel C., and Messer W. ATP- and ADP-DnaA protein, a molecular switch in gene regulation. EMBO J. 18 (1999) 6169-6176
24. Blaesing F., Weigel C., Welzeck M., and Messer W. Analysis of the DNA-binding domain of Escherichia coli DnaA protein. Mol. Microbiol. 36 (2000) 557-569
25. Jiang Y., Pacek M., Helinski D.R., Konieczny I., and Toukdarian A. A multifunctional plasmid-encoded replication initiation protein both recruits and positions an active helicase at the replication origin. Proc. Natl Acad. Sci. USA 100 (2003) 8692-8697
26. Das N., Valjavec-Gratian M., Basuray A.N., Fekete R.A., Papp P.P., Paulsson J., and Chattoraj D.K. Multiple homeostatic mechanisms in the control of P1 plasmid replication. Proc. Natl Acad. Sci. USA 102 (2004) 2856-2861
27. Minton A.P. Influence of macromolecular crowding upon the stability and state of association of proteins: predictions and observations. J. Pharm. Sci. 94 (2005) 1668-1675
28. Zhou H.X. Protein folding and binding in confined spaces and in crowded solutions. J. Mol. Recogn. 17 (2004) 368-375
29. Das N., and Chattoraj D.K. Origin pairing ('handcuffing') and unpairing in the control of P1 plasmid replication. Mol. Microbiol. 54 (2004) 836-849
30. Norman D.G., Grainger J., Uhrin D., and Lilley D.M. Location of cyanine-3 on double-stranded DNA: importance for fluorescence resonance energy transfer studies. Biochemistry 39 (2000) 6317-6324
31. Mukhopadhyay G., and Chattoraj D.K. Conformation of the origin of P1 plasmid replication. Initiator protein induced wrapping and intrinsic unstacking. J. Mol. Biol. 231 (1993) 19-28
32. Kawasaki Y., Matsunaga F., Kano Y., Yura T., and Wada C. The localized melting of mini-F origin by the combined action of the mini-F initiator protein (RepE) and HU and DnaA of Escherichia coli. Mol. Gen. Genet. 253 (1996) 42-49
33. Murakami A., Sugiura S., and Yamaguchi K. DNA bending of pSC101 ori induced by Rep, a replication initiator protein and IHF. J. Gen. Appl. Microbiol. 43 (1997) 189-197
34. Krüger R., Rakowski S.A., and Filutowicz M. Isomerization and apparent DNA bending by π, the replication protein of plasmid R6K. Biochem. Biophys. Res. Commun. 313 (2004) 834-840
35. Kim J., Zwieb C., Wu C., and Adhya S. Bending of DNA by gene-regulatory proteins: construction and use of a DNA bending vector. Gene 85 (1989) 15-23
36. Thompson J.F., and Landy A. Empirical estimation of protein-induced DNA bending angles: applications to lambda site-specific recombination complexes. Nucl. Acids Res. 16 (1988) 9687-9705
37. Zorrilla S., Rivas G., and Lillo M.P. Fluorescence anisotropy as a probe to study tracer proteins in crowded solutions. J. Mol. Recogn. 17 (2004) 408-416
38. Urh M., Wu J., Wu J., Forest K., Inman R.B., and Filutowicz M. Assemblies of replication initiation protein on symmetric and asymmetric DNA sequences depend on multiple protein oligomerization surfaces. J. Mol. Biol. 283 (1998) 619-631
39. Paulsson J., and Chattoraj D.K. Origin inactivation in bacterial DNA replication control. Mol. Microbiol. 61 (2006) 9-15
40. Yguerabide J., and Yguerabide E.E. Nanosecond fluorescence spectroscopy. In: Rousseau D.L. (Ed). Optical Techniques in Biological Research (1984) chapt. 4
41. Lillo M.P., Cañadas O., Dale R.E., and Acuña A.U. Location and properties of the taxol binding center in microtubules: a picosecond laser study with fluorescent taxoids. Biochemistry 41 (2002) 12436-12439
42. Beechem J.M., Gratton E., Ameloot M., Knutson J.R., and Brand L. In: Lakowicz J.R. (Ed). Topics in Fluorescence Spectroscopy vol. 2 (1991), Plenum Press, New York 241-305