A conformational switch between transcriptional repression and replication initiation in the RepA dimerization domain

Nature Structural Biology

Volumn 10, Issue 7, 2003, Pages 565-571

  Giraldol, Rafael ^a   Fernández Tornero, Carlos ^a   Evans, Philip R ^b   Díaz Orejas, Ramón ^a   Romero, Antonio ^a  

^a CENTRO DE INVESTIGACIONES BIOLÓGICAS   (Spain)

^b MRC LABORATORY OF MOLECULAR BIOLOGY   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

HELICASE; PLASMID DNA; PROTEIN REPA; PROTEIN REPE; UNCLASSIFIED DRUG;

ALPHA HELIX; ARTICLE; BETA SHEET; CONFORMATIONAL TRANSITION; CONTROLLED STUDY; CRYSTAL STRUCTURE; DIMERIZATION; DNA REPLICATION; DNA TRANSCRIPTION; GENE REPRESSION; GRAM NEGATIVE BACTERIUM; HYDROPHOBICITY; NONHUMAN; PHYLOGENY; PLASMID; PRIORITY JOURNAL; PROTEIN DNA BINDING; PROTEIN DOMAIN; PSEUDOMONAS SYRINGAE;

AMINO ACID SEQUENCE; DIMERIZATION; DNA HELICASES; DNA-BINDING PROTEINS; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; OPERATOR REGIONS (GENETICS); PROTEIN CONFORMATION; PROTEINS; SEQUENCE HOMOLOGY, AMINO ACID; TRANS-ACTIVATORS; TRANSCRIPTION, GENETIC;

ARCHAEA; BACTERIA (MICROORGANISMS); EUKARYOTA; NEGIBACTERIA; PSEUDOMONAS; PSEUDOMONAS SYRINGAE;

EID: 0038392686     PISSN: 10728368     EISSN: None     Source Type: Journal    
DOI: 10.1038/nsb937     Document Type: Article

References (43)

1. del Solar, G., Giraldo, R., Ruíz-Echevarría, M.J., Espinosa, M. & Díaz, R. Replication and control of circular bacterial plasmids. Microbiol. Mol. Biol. Rev. 62, 434-464 (1998).
2. Giraldo, R. Common domains in the initiators of DNA replication in Bacteria, Archaea and Eukarya: combined structural, functional and phylogenetic perspectives. FEMS Microbiol. Rev. 26, 533-554 (2003).
3. Manen, D., Upegui, G.L. & Caro, L. Monomers and dimers of the RepA protein in plasmid pSC101 replication: domains in RepA. Proc. Natl. Acad. Sci. USA 89, 8923-8927 (1992).
4. Ishiai, M., Wada, C., Kawasaki, Y. & Yura, T. Replication initiator protein RepE of mini-F plasmid: functional differentiation between monomers (initiator) and dimers (autogenous repressor). Proc. Natl. Acad. Sci. USA 91, 3839-3843 (1994).
5. García de Viedma, D., Giraldo, R., Ruíz-Echevarría, M.J., Lurz, R. & 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, 211-223 (1995).
6. Wickner, S., Skowyra, D., Hoskins, J. & McKenney, K. DnaJ, DnaK, and GrpE heat shock proteins are required in oriP1 DNA replication solely at the RepA monomerization step. Proc. Natl. Acad. Sci. USA 89, 10345-10349 (1992).
7. Sozhamannan, S. & Chattoraj, D.K. Heat shock proteins DnaJ, DnaK and GrpE stimulate P1 plasmid replication by promoting initiator binding to the origin. J. Bacteriol. 175, 3546-3555 (1993).
8. DasGupta, S., Mukhopadhyay, G., Papp, P.P., Lewis, M.S. & Chattoraj, D.K. Activation of DNA binding by the monomeric form of the P1 replication initiator RepA by heat shock proteins DnaJ and DnaK. J. Mol. Biol. 232, 23-34 (1993).
9. Wickner, S. et al. A molecular chaperone, ClpA, functions like DnaK and DnaJ. Proc. Natl. Acad. Sci. USA 91, 12218-12222 (1994).
10. Dibbens, J.A., Muraiso, K. & Chattoraj, D.K. Chaperone-mediated reduction of RepA dimerization is associated with RepA conformational change. Mol. Microbiol. 26, 185-195 (1997).
11. Konieczny, I. & Helinski, D.R. The replication initiator protein of the broad-host-range plasmid RK2 is activated by the ClpX chaperone. Proc. Natl. Acad. Sci. USA 94, 14378-14382 (1997).
12. Díaz-López, T. et al. Structural changes in RepA, a plasmid replication initiator, upon binding to origin DNA. J. Biol. Chem. 278, 18606-18616 (2003).
13. García de Viedma, D., Giraldo, R., Rivas, G., Fernández-Tresguerres, E. & DíazOrejas, R. A leucine-zipper motif determines different functions in a DNA replication protein. EMBO J. 15, 925-934 (1996).
14. Giraldo, R., Andreu, J.M. & Díaz-Orejas, R. Protein domains and conformational changes in the activation of RepA, a DNA replication initiator. EMBO J. 17, 4511-4526 (1998).
15. Nieto, C., Giraldo, R., Fernández-Tresguerres, E. & 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, 415-426 (1992).
16. Komori, H. et al. Crystal structure of a prokaryotic replication initiator protein bound to DNA at 2.6 Å resolution. EMBO J. 18, 4597-4607 (1999).
17. Gajiwala, K.S. & Burley, S.K. Winged helix proteins. Curr. Op. Struct. Biol. 10, 110-116 (2000).
18. Holm, L. & Sander, C. Protein structure comparison by alignment of distance matrices. J. Mol. Biol. 233, 123-138 (1993).
19. Giraldo, R., Nieto, C., Fernández-Tresguerres, M.E. & Díaz, R. Bacterial zipper. Nature 342, 866 (1989).
20. García de Viedma, D., Serrano-López, A. & Díaz-Orejas, R. Specific binding of the replication protein of plasmid pPS10 to direct and inverted repeats is mediated by an HTH motif. Nucleic Acids Res. 23, 5048-5054 (1995).
21. Liu, J. et al. Structure and function of Cdc6/Cdc18: implications for origin recognition and checkpoint control. Mol. Cell 6, 637-648 (2000).
22. Giraldo, R. & Díaz-Orejas, R. Similarities between the DNA replication initiators of Gram-negative bacteria plasmids (RepA) and eukaryotes (Orc4p)/archaea (Cdc6p). Proc. Natl. Acad. Sci. USA 98, 4938-4943 (2001).
23. Maestro, B., Sanz, J.M., Díaz-Orejas, R. & Fernández-Tresguerres, E. Modulation of pPS10 host range by plasmid-encoded RepA initiator protein. J. Bacteriol. 185, 1367-1375 (2003).
24. Matsunaga, F. et al. The central region of RepE initiator protein of mini-F plasmid plays a crucial role in dimerization required for negative replication control. J. Mol. Biol. 274, 27-38 (1997).
25. Xia, G., Manen, D., Yu, Y. & Caro, L. In vivo and in vitro studies of a copy number mutation of the RepA replication protein of plasmid pSC101. J. Bacteriol. 175, 4165-4175 (1993).
26. Miron, A., Patel, I. & Bastia, D. Multiple pathways of copy control of y replicon of R6K: mechanisms both dependent on and independent of cooperativity of interaction of π protein with DNA affect the copy number. Proc. Natl. Acad. Sci. USA 91, 6438-6442 (1994).
27. Chattoraj, D.K. Control of plasmid DNA replication by iterons: no longer paradoxical. Mol. Microbiol. 37, 467-476 (2000).
28. Blasina, A., Kittell, B.L., Toukdarian, A.E. & Helinski, D.R. Copy-up mutants of the plasmid RK2 replication initiation protein are defective in coupling RK2 replication origins. Proc. Natl. Acad. Sci. USA 93, 3559-3564 (1996).
29. Urh, M. et al. Assemblies of replication initiation protein on symmetric and asymmetric DNA sequences depend on multiple protein oligomerization surfaces. J. Mol. Biol. 283, 619-631 (1998).
30. Uga, H., Matsunaga, F. & Wada, C. Regulation of DNA replication by iterons: an interaction between the ori2 and incC regions mediated by RepE-bound iterons inhibits DNA replication of mini-F plasmid in Escherichia coli. EMBO J. 18, 3856-3867 (1999).
31. Park, K., Han, E., Paulsson, J. & Chattoraj, D.K. Origin pairing ('handcuffing') as a mode of negative control of P1 plasmid copy number. EMBO J. 20, 7323-7332 (2001).
32. Spolar, R.S. & Record, T.M. Jr. Coupling of local folding to site-specific binding of proteins to DNA. Science 263, 777-784 (1994).
33. Jen-Jacobson, L., Engler, L.E. & Jacobson, L.A. Structural and thermodynamic strategies for site-specific DNA binding proteins. Structure 8, 1015-1023 (2000).
34. Leslie, A.G.W. Recent changes to the MOSFLM package for processing film and image plate data. Joint CCP4 ESF-EAMCB Newslett. Protein Crystallogr. 26 (1992).
35. Collaborative Computational Project, Number 4. The CCP4 suite: programs for protein crystallography. Acta Crystallogr. D 50, 760-763 (1994).
36. Brunger, A.T. et al. Crystallography & NMR system: a new software suite for macromolecular structure determination. Acta Crystallogr. D 54, 905-921 (1998).
37. de La Fortelle, E. & Bricogne, G. Maximum-likelihood heavy-atom parameter refinement for multiple isomorphous replacement and multiwavelength anomalous diffraction methods. Methods Enzymol. 276, 472-494 (1997).
38. Jones, T.A., Zou, J.-Y., Cowan, S.W. & Kjeldgaard, M. Improved methods for building protein models in electron density maps and the location of errors in these models. Acta Crystallogr. A 47, 110-119 (1991).
39. Murshudov, G.N., Vagin, A.A. & Dodson, E.J. Refinement of macromolecular structures by the maximum-likelihood method. Acta Crystallogr. D 53, 240-255 (1997).
40. Laskowski, R.A., MacArthur, M.W., Moss, D.S. & Thornton, J.M. PROCHECK: a program to check the stereochemical quality of protein structure. J. Appl. Crystallogr. 26, 283-291 (1993).
41. Kraulis, P.J. MOLSCRIPT - a program to produce both detailed and schematic plots of protein structures. Appl. Crystallogr. 24, 946-950 (1996).
42. Merritt, E.A. & Bacon, D.J. Raster 3D: photorealistic molecular graphics. Methods Enzymol. 277, 505-524 (1997).
43. Nicholls, A., Sharp, K.A. & Honig, B. Protein folding and association: insights from the interfacial and thermodynamic properties of hydrocarbons. Proteins 11, 281-296 (1991).