RepC protein of the octopine-type Ti plasmid binds to the probable origin of replication within repC and functions only in cis

Molecular Microbiology

Volumn 81, Issue 6, 2011, Pages 1593-1606

  Pinto, Uelinton M ^b   Flores Mireles, Ana L ^a   Costa, Esther D ^a   Winans, Stephen C ^a  

^a Cornell University ^*  (United States)

^b FEDERAL UNIVERSITY OF OURO PRETO   (Brazil)

Author keywords

[No Author keywords available]

Indexed keywords

OCTOPINE; PROTEIN; REPA PROTEIN; REPB PROTEIN; REPC PROTEIN; TRANSCRIPTION FACTOR; UNCLASSIFIED DRUG;

ALPHAPROTEOBACTERIA; ARTICLE; AT RICH SEQUENCE; BACTERIAL CHROMOSOME; BACTERIAL GENE; BINDING AFFINITY; BINDING SITE; DAUGHTER CELL; DNA BINDING; GENE DOSAGE; NONHUMAN; OPERON; PLASMID; PRIORITY JOURNAL; PROTEIN EXPRESSION; PROTEIN FUNCTION; PROTEIN PURIFICATION; REPLICON; RHIZOBIUM RADIOBACTER; STRUCTURAL HOMOLOGY; TI PLASMID;

AGROBACTERIUM TUMEFACIENS; BINDING SITES; DNA HELICASES; DNA MUTATIONAL ANALYSIS; DNA REPLICATION; DNA-BINDING PROTEINS; MODELS, MOLECULAR; PLANT TUMOR-INDUCING PLASMIDS; PROTEIN BINDING; PROTEIN STRUCTURE, TERTIARY; REPLICATION ORIGIN; SEQUENCE DELETION; TRANS-ACTIVATORS;

AGROBACTERIUM TUMEFACIENS; ALPHAPROTEOBACTERIA;

EID: 80052747783     PISSN: 0950382X     EISSN: 13652958     Source Type: Journal    
DOI: 10.1111/j.1365-2958.2011.07789.x     Document Type: Article

References (60)

1. Alvarez-Martinez, C.E., and Christie, P.J. (2009) Biological diversity of prokaryotic type IV secretion systems. Microbiol Mol Biol Rev 73: 775-808.
2. Bartosik, D., Baj, J., and Wlodarczyk, M. (1998) Molecular and functional analysis of pTAV320, a repABC-type replicon of the Paracoccus versutus composite plasmid pTAV1. Microbiology 144: 3149-3157.
3. Bingle, L.E., and Thomas, C.M. (2001) Regulatory circuits for plasmid survival. Curr Opin Microbiol 4: 194-200.
4. Bruand, C., and Ehrlich, S.D. (1998) Transcription-driven DNA replication of plasmid pAMbeta1 in Bacillus subtilis. Mol Microbiol 30: 135-145.
5. Cangelosi, G.A., Best, E.A., Martinetti, G., and Nester, E.W. (1991) Genetic analysis of Agrobacterium. Methods Enzymol 204: 384-397.
6. Castillo-Ramirez, S., Vazquez-Castellanos, J.F., Gonzalez, V., and Cevallos, M.A. (2009) Horizontal gene transfer and diverse functional constrains within a common replication-partitioning system in Alphaproteobacteria: the repABC operon. BMC Genomics 10: 536.
7. Cervantes-Rivera, R., Romero-Lopez, C., Berzal-Herranz, A., and Cevallos, M.A. (2010) Analysis of the mechanism of action of the antisense RNA that controls the replication of the repABC plasmid p42d. J Bacteriol 192: 3268-3278.
8. Cevallos, M.A., Cervantes-Rivera, R., and Gutierrez-Rios, R.M. (2008) The repABC plasmid family. Plasmid 60: 19-37.
9. Chai, Y., and Winans, S.C. (2005a) RepB protein of an Agrobacterium tumefaciens Ti plasmid binds to two adjacent sites between repA and repB for plasmid partitioning and autorepression. Mol Microbiol 58: 1114-1129.
10. Chai, Y., and Winans, S.C. (2005b) A small antisense RNA downregulates expression of an essential replicase protein of an Agrobacterium tumefaciens Ti plasmid. Mol Microbiol 56: 1574-1585.
11. Chattoraj, D.K. (2000) Control of plasmid DNA replication by iterons: no longer paradoxical. Mol Microbiol 37: 467-476.
12. Chen, C.Y., and Winans, S.C. (1991) Controlled expression of the transcriptional activator gene virG in Agrobacterium tumefaciens by using the Escherichia coli lac promoter. J Bacteriol 173: 1139-1144.
13. Cho, H., and Winans, S.C. (2005) VirA and VirG activate the Ti plasmid repABC operon, elevating plasmid copy number in response to wound-released chemical signals. Proc Natl Acad Sci USA 102: 14843-14848.
14. Cho, H., and Winans, S.C. (2007) TraA, TraC and TraD autorepress two divergent quorum-regulated promoters near the transfer origin of the Ti plasmid of Agrobacterium tumefaciens. Mol Microbiol 63: 1769-1782.
15. Cho, H., Pinto, U.M., and Winans, S.C. (2009) Transsexuality in the rhizosphere: quorum sensing reversibly converts Agrobacterium tumefaciens from phenotypically female to male. J Bacteriol 191: 3375-3383.
16. Collier, J., McAdams, H.H., and Shapiro, L. (2007) A DNA methylation ratchet governs progression through a bacterial cell cycle. Proc Natl Acad Sci USA 104: 17111-17116.
17. Collins, M., and Myers, R.M. (1987) Alterations in DNA helix stability due to base modifications can be evaluated using denaturing gradient gel electrophoresis. J Mol Biol 198: 737-744.
18. Crossman, L.C. (2005) Plasmid replicons of Rhizobium. Biochem Soc Trans 33: 157-158.
19. Das, N., and Chattoraj, D.K. (2004) Origin pairing ('handcuffing') and unpairing in the control of P1 plasmid replication. Mol Microbiol 54: 836-849.
20. Derbyshire, K.M., and Grindley, N.D. (1996) Cis preference of the IS903 transposase is mediated by a combination of transposase instability and inefficient translation. Mol Microbiol 21: 1261-1272.
21. Farrand, S.K., O'Morchoe, S.P., and McCutchan, J. (1989) Construction of an Agrobacterium tumefaciens C58 recA mutant. J Bacteriol 171: 5314-5321.
22. Francia, M.V., Fujimoto, S., Tille, P., Weaver, K.E., and Clewell, D.B. (2004) Replication of Enterococcus faecalis pheromone-responding plasmid pAD1: location of the minimal replicon and oriV site and RepA involvement in initiation of replication. J Bacteriol 186: 5003-5016.
23. Fuangthong, M., Atichartpongkul, S., Mongkolsuk, S., and Helmann, J.D. (2001) OhrR is a repressor of ohrA, a key organic hydroperoxide resistance determinant in Bacillus subtilis. J Bacteriol 183: 4134-4141.
24. Funnell, B.E. (2005) Partition-mediated plasmid pairing. Plasmid 53: 119-125.
25. Gering, M., Gotz, F., and Bruckner, R. (1996) Sequence and analysis of the replication region of the Staphylococcus xylosus plasmid pSX267. Gene 182: 117-122.
26. Hong, M., Fuangthong, M., Helmann, J.D., and Brennan, R.G. (2005) Structure of an OhrR-ohrA operator complex reveals the DNA binding mechanism of the MarR family. Mol Cell 20: 131-141.
27. Izquierdo, J., Venkova-Canova, T., Ramirez-Romero, M.A., Tellez-Sosa, J., Hernandez-Lucas, I., Sanjuan, J., and Cevallos, M.A. (2005) An antisense RNA plays a central role in the replication control of a repC plasmid. Plasmid 54: 259-277.
28. Johnson, T.J., and Nolan, L.K. (2009) Pathogenomics of the virulence plasmids of Escherichia coli. Microbiol Mol Biol Rev 73: 750-774.
29. Katayama, T., Ozaki, S., Keyamura, K., and Fujimitsu, K. (2010) Regulation of the replication cycle: conserved and diverse regulatory systems for DnaA and oriC. Nat Rev Microbiol 8: 163-170.
30. Kelley, L.A., and Sternberg, M.J. (2009) Protein structure prediction on the Web: a case study using the Phyre server. Nat Protoc 4: 363-371.
31. Khan, S.R., Gaines, J., Roop, R.M., II, and Farrand, S.K. (2008) Broad-host-range expression vectors with tightly regulated promoters and their use to examine the influence of TraR and TraM expression on Ti plasmid quorum sensing. Appl Environ Microbiol 74: 5053-5062.
32. Kwong, S.M., Skurray, R.A., and Firth, N. (2004) Staphylococcus aureus multiresistance plasmid pSK41: analysis of the replication region, initiator protein binding and antisense RNA regulation. Mol Microbiol 51: 497-509.
33. Li, P.L., and Farrand, S.K. (2000) The replicator of the nopaline-type Ti plasmid pTiC58 is a member of the repABC family and is influenced by the TraR-dependent quorum-sensing regulatory system. J Bacteriol 182: 179-188.
34. Lindahl, G. (1970) Bacteriophage P2: replication of the chromosome requires a protein which acts only on the genome that coded for it. Virology 42: 522-533.
35. McAdams, H.H., and Shapiro, L. (2003) A bacterial cell-cycle regulatory network operating in time and space. Science 301: 1874-1877.
36. McFall, E. (1986) cis-acting proteins. J Bacteriol 167: 429-432.
37. Messer, W. (2002) The bacterial replication initiator DnaA. DnaA and oriC, the bacterial mode to initiate DNA replication. FEMS Microbiol Rev 26: 355-374.
38. Miller, J. (1972) Experiments in Molecular Genetics. Cold Spring Harbor, NY: Cold Spring Harbor Laboratory Press.
39. Nikaido, H. (2009) Multidrug resistance in bacteria. Annu Rev Biochem 78: 119-146.
40. Ozaki, S., and Katayama, T. (2009) DnaA structure, function, and dynamics in the initiation at the chromosomal origin. Plasmid 62: 71-82.
41. Pappas, K.M. (2008) Cell-cell signaling and the Agrobacterium tumefaciens Ti plasmid copy number fluctuations. Plasmid 60: 89-107.
42. Pappas, K.M., and Winans, S.C. (2003a) The RepA and RepB autorepressors and TraR play opposing roles in the regulation of a Ti plasmid repABC operon. Mol Microbiol 49: 441-455.
43. Pappas, K.M., and Winans, S.C. (2003b) A LuxR-type regulator from Agrobacterium tumefaciens elevates Ti plasmid copy number by activating transcription of plasmid replication genes. Mol Microbiol 48: 1059-1073.
44. Paulsson, J., and Chattoraj, D.K. (2006) Origin inactivation in bacterial DNA replication control. Mol Microbiol 61: 9-15.
45. Petersen, J., Brinkmann, H., and Pradella, S. (2009) Diversity and evolution of repABC type plasmids in Rhodobacterales. Environ Microbiol 11: 2627-2638.
46. Phale, P.S., Basu, A., Majhi, P.D., Deveryshetty, J., Vamsee-Krishna, C., and Shrivastava, R. (2007) Metabolic diversity in bacterial degradation of aromatic compounds. OMICS 11: 252-279.
47. Pinto, U.M., and Winans, S.C. (2009) Dimerization of the quorum-sensing transcription factor TraR enhances resistance to cytoplasmic proteolysis. Mol Microbiol 73: 32-42.
48. Ravin, N.V., Kuprianov, V.V., Gilcrease, E.B., and Casjens, S.R. (2003) Bidirectional replication from an internal ori site of the linear N15 plasmid prophage. Nucleic Acids Res 31: 6552-6560.
49. Sambrook, J., and Russel, D.W. (2001) Molecular Cloning - A Laboratory Manual. Cold Spring Harbor, NY: Cold Spring Harbor Laboratory Press.
50. Scherer, G. (1978) Nucleotide sequence of the O gene and of the origin of replication in bacteriophage lambda DNA. Nucleic Acids Res 5: 3141-3156.
51. Slater, S.C., Goldman, B.S., Goodner, B., Setubal, J.C., Farrand, S.K., Nester, E.W., etal. (2009) Genome sequences of three Agrobacterium biovars help elucidate the evolution of multichromosome genomes in bacteria. J Bacteriol 191: 2501-2511.
52. Smith, E.F., and Townsend, C.O. (1907) A plant-tumor of bacterial origin. Science 25: 671-673.
53. del Solar, G., Giraldo, R., Ruiz-Echevarria, M.J., Espinosa, M., and Diaz-Orejas, R. (1998) Replication and control of circular bacterial plasmids. Microbiol Mol Biol Rev 62: 434-464.
54. Tanaka, T., Ishida, H., and Maehara, T. (2005) Characterization of the replication region of plasmid pLS32 from the Natto strain of Bacillus subtilis. J Bacteriol 187: 4315-4326.
55. Thomas, C.M. (2000) Paradigms of plasmid organization. Mol Microbiol 37: 485-491.
56. Wagner-Dobler, I., Ballhausen, B., Berger, M., Brinkhoff, T., Buchholz, I., Bunk, B., etal. (2010) The complete genome sequence of the algal symbiont Dinoroseobacter shibae: a hitchhiker's guide to life in the sea. ISME J 4: 61-77.
57. Waldminghaus, T., and Skarstad, K. (2009) The Escherichia coli SeqA protein. Plasmid 61: 141-150.
58. Wood, D.W., Setubal, J.C., Kaul, R., Monks, D.E., Kitajima, J.P., Okura, V.K., etal. (2001) The genome of the natural genetic engineer Agrobacterium tumefaciens C58. Science 294: 2317-2323.
59. Zianni, M., Tessanne, K., Merighi, M., Laguna, R., and Tabita, F.R. (2006) Identification of the DNA bases of a DNase I footprint by the use of dye primer sequencing on an automated capillary DNA analysis instrument. J Biomol Tech 17: 103-113.
60. Zzaman, S., and Bastia, D. (2005) Oligomeric initiator protein-mediated DNA looping negatively regulates plasmid replication in vitro by preventing origin melting. Mol Cell 20: 833-843.