Role and mechanism of action of C · PvuII, a regulatory protein conserved among restriction-modification systems

Journal of Bacteriology

Volumn 182, Issue 2, 2000, Pages 477-487

  Vijesurier, Roy M ^a,c   Carlock, Leon ^a   Blumenthal, Robert M ^b   Dunbar, Joan C ^a  

^a WAYNE STATE UNIVERSITY SCHOOL OF MEDICINE   (United States)

^b MEDICAL COLLEGE OF OHIO   (United States)

^c CHILDREN'S HOSPITAL OF MICHIGAN   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

METHYLTRANSFERASE; REGULATOR PROTEIN; RESTRICTION ENDONUCLEASE;

ARTICLE; DNA HYBRIDIZATION; ENZYME ACTIVITY; GENE ACTIVATION; GENE EXPRESSION REGULATION; GENETIC TRANSCRIPTION; NONHUMAN; PLASMID; PRIORITY JOURNAL;

BASE SEQUENCE; DEOXYRIBONUCLEASES, TYPE II SITE-SPECIFIC; DNA-BINDING PROTEINS; MOLECULAR SEQUENCE DATA; NUCLEIC ACID CONFORMATION; PROMOTER REGIONS (GENETICS); PROTEUS VULGARIS; SITE-SPECIFIC DNA METHYLTRANSFERASE (CYTOSINE-SPECIFIC); TIME FACTORS; TRANS-ACTIVATION (GENETICS); TRANSCRIPTION, GENETIC;

EID: 0033988985     PISSN: 00219193     EISSN: None     Source Type: Journal    
DOI: 10.1128/JB.182.2.477-487.2000     Document Type: Article

References (68)

1. Adams, G. M., and R. M. Blumenthal. 1995. Gene pvuIIW: a possible modulator of PvuII endonuclease subunit association. Gene 157:193-199.
2. Anderson, J., S. A. Forst, K. Zhao, M. Inouye, and N. Delihas. 1989. The function of micF RNA. micF RNA is a major factor in the thermal regulation of OmpF protein in Escherichia coli. J. Biol. Chem. 264:17961-17970.
3. Anderson, J. E. 1993. Restriction endonucleases and modification methylases. Curr. Opin. Struct. Biol. 3:24-30.
4. Ansari, A. Z., J. E. Bradner, and T. V. O'Halloran. 1995. DNA-bend modulation in a repressor-to-activator switching mechanism. Nature 374:371-375.
5. Anton, B. P., D. F. Heiter, J. S. Benner, E. J. Hess, L. Greenough, L. S. Moran, B. E. Slatko, and J. E. Brooks. 1997. Cloning and characterization of the BglII restriction-modification system reveal a possible evolutionary footprint. Gene 187:19-27.
6. Aoyama, T., and M. Takanami. 1988. Supercoiling response of E. coli promoters with different spacer lengths. Biochim. Biophys. Acta 949:311-317.
7. Athanasiadis, A., M. Gregoriu, D. Thanos, M. Kokkinidis, and J. Papamatheakis. 1990. Complete nucleotide sequence of the PvuII restriction enzyme gene from Proteus vulgaris. Nucleic Acids Res. 18:6434.
8. Athanasiadis, A., M. Vlassi, D. Kotsifaki, P. A. Tucker, K. S. Wilson, and M. Kokkinidis. 1994. Crystal structure of PvuII endonuclease reveals extensive structural homologies to EcoRV. Struct. Biol. 1:469-475.
9. Baumberg, S., and M. Roberts. 1984. Anomalous expression of the E. coli lac operon in Proteus mirabilis. II. Effects of lacI and lacP mutations. Mol. Gen. Genet. 198:166-71.
10. Beach, M. B., and R. Osuna. 1998. Identification and characterization of the fis operon in enteric bacteria. J. Bacteriol. 180:5932-5946.
11. Blumenthal, R. M., S. A. Gregory, and J. S. Cooperider. 1985. Cloning of a restriction-modification system from Proteus vulgaris and its use in analyzing a methylase-sensitive phenotype in Escherichia coli. J. Bacteriol. 164:501-509.
12. Brizzard, B. L., R. G. Chubet, and D. L. Vizard. 1994. Immunoaffinity purification of FLAG epitope-tagged bacterial alkaline phosphatase using a novel monoclonal antibody and peptide elution. BioTechniques 16:730-735.
13. Brooks, J. E., P. D. Nathan, D. Landry, L. A. Sznyter, P. Waite-Rees, C. L. Ives, L. S. Moran, B. E. Slatko, and J. S. Benner. 1991. Characterization of the cloned BamH1 restriction modification system: its nucleotide sequence, properties of the methylase, and expression in heterologous hosts. Nucleic Acids Res. 19:841-850.
14. Brosius, J. 1984. Plasmid vectors for the selection of promoters. Gene 27:151-160.
15. Butkus, V., S. Klimasauskas, L. Petrauskiene, Z. Maneliene, A. Lebionka, and A. A. Janulaitis. 1987. Interaction of AluI, Cfr6I and PvuII restriction-modification enzymes with substrates containing either N4-methylcytosine or 5-methylcytosine. Biochim. Biophys. Acta 909:201-207.
16. Calvin-Koons, M. D., and R. M. Blumenthal. 1995. Characterization of pPvu1, the autonomous plasmid from Proteus vulgaris that carries the genes of the PvuII restriction-modification system. Gene 157:73-79.
17. Chang, A. C., and S. N. Cohen. 1978. Construction and characterization of amplifiable multicopy DNA cloning vehicles derived from the P15A cryptic miniplasmid. J. Bacteriol. 134:1141-1156.
18. Cheng, X. 1995. Structure and function of DNA methyltransferases. Annu. Rev. Biophys. Biomol. Struct. 24:293-318.
19. Cheng, X., K. Balendiran, I. Schildkraut, and J. E. Anderson. 1995. Crystal stucture of the PvuII restriction endonuclease. Gene 157:139-140.
20. Chomczynski, P., and N. Sacchi. 1987. Single-step method of RNA isolation by acid guanidinium thiocyanate-phenol-chloroform extraction. Anal. Biochem. 162:156-159.
21. Cui, Y., Q. Wang, G. D. Stormo, and J. M. Calvo. 1995. A consensus sequence for binding of Lrp to DNA. J. Bacteriol. 177:4872-4880.
22. De Backer, O., and C. Colson. 1991. Transfer of the genes for the StyLTI restriction-modification system of Salmonella typhimurium to strains lacking modification ability results in death of the recipient cells and degradation of their DNA. J. Bacteriol. 173:1328-1330.
23. Estrem, S. T., T. Gaal, W. Ross, and R. L. Gourse. 1998. Identification of an UP element consensus sequence for bacterial promoters. Proc. Natl. Acad. Sci. USA 95:9761-9766.
24. Gingeras, T. R., L. Greenough, I. Schildkraut, and R. J. Roberts. 1981. Two new restriction endonucleases from Proteus vulgaris. Nucleic Acids Res. 9:4525-4536.
25. Gong, W., M. O'Gara, R. M. Blumenthal, and X. Cheng. 1997 Structure of PvuII DNA-(cytosine N4) methyltransferase, an example of domain permutation and protein fold assignment. Nucleic Acids Res. 25:2702-2715.
26. Heidmann, S., W. Seifert, C. Kessler, and H. Domdey. 1989. Cloning, characterization and heterologous expression of the SmaI restriction-modification system. Nucleic Acids Res. 17:9783-9796.
27. Hidalgo, E., and B. Demple. 1997. Spacing of promoter elements regulates the basal expression of the soxS gene and converts SoxR from a transcriptional activator into a repressor. EMBO J. 16:1056-1065.
28. Hopp, T. P., B. Gallis, and K. S. Prickett. 1996. Metal-binding properties of a calcium-dependent monoclonal antibody. Mol. Immunol. 33:601-608.
29. Horowitz, H., and T. Platt. 1982. Regulation of transcription from tandem and convergent promoters. Nucleic Acids Res. 10:5447-5465.
30. Horton, J. R., J. Bonventre, and X. Cheng. 1998. How is modification of the DNA substrate recognized by the PvuII restriction endonuclease? Biol. Chem. 379:451-458.
31. Ives, C. L., A. Sohail, and J. E. Brooks. 1995. The regulatory C proteins from different restriction-modification systems can cross-complement. J. Bacteriol. 177:6313-6315.
32. Klotsky, R. A., and I. Schwartz. 1987. Measurement of cat expression from growth-rate-regulated promoters employing beta-lactamase activity as an indicator of plasmid copy number. Gene 55:141-146.
33. Liebig, B., and R. Wagner. 1995. Effects of different growth conditions on the in vivo activity of the tandem Escherichia coli ribosomal RNA promoters P1 and P2. Mol. Gen. Genet. 249:328-335.
34. Lin-Chao, S., and H. Bremer. 1986. Effect of the bacterial growth rate on replication control of plasmid pBR322 in Escherichia coli. Mol. Gen. Genet. 203:143-149.
35. Liu, W., Y. Qi, and F. M. Hulett. 1998. Sites internal to the coding regions of phoA and pstS bind PhoP and are required for full promoter activity. Mol. Microbiol. 28:119-130.
36. Nakayama, Y., and I. Kobayashi. 1998. Restriction-modification gene complexes as selfish gene entities: roles of a regulatory system in their establishment, maintenance, and apoptotic mutual exclusion. Proc. Natl. Acad. Sci. USA 95:6442-6447.
37. Noel, R. J., Jr., and W. S. Reznikoff. 1998. CAP, the -45 region, and RNA polymerase: three partners in transcription initiation at lacP1 in Escherichia coli. J. Mol. Biol. 282:495-504.
38. O'Callaghan, C. H., A. Morris, S. M. Kirby, and A. H. Shingler. 1972. Novel method for detection of β-lactamases by using a chromogenic cephalosporin substrate. Antimicrob. Agents Chemother. 1:283-288.
39. O'Connor, C. D., and G. O. Humphreys. 1982. Expression of the EcoRI restriction-modification system and the construction of positive-selection cloning vectors. Gene 20:219-229.
40. O'Neill, M. C. 1989. Escherichia coli promoters. I. Consensus as it relates to spacing class, specificity, repeat substructure, and three-dimensional organization. J. Biol. Chem. 264:5522-5530.
41. Perez-Rueda, E., J. D. Gralla, and J. Collado-Vides. 1998. Genomic position analyses and the transcription machinery. J. Mol. Biol. 275:165-170.
42. Ponnambalam, S., and S. Busby. 1987. RNA polymerase molecules initiating transcription at tandem promoters can collide and cause premature transcription termination. FEBS Lett. 212:21-27.
43. K genes after conjugate transfer. Mol. Gen. Genet. 241: 491-496.
44. K (restriction-modification) genes. J. Bacteriol. 175:4905-4906.
45. Raleigh, E. A., and J. E. Brooks. 1998. Restriction modification systems: where they are and what they do, p. 78-92. In F. J. De Bruijn, J. R. Lupski, and G. M. Weinstock (ed.), Bacterial genomes. Chapman & Hall, New York, N.Y.
46. Raleigh, E. A., N. E. Murray, H. Revel, R. M. Blumenthal, D. Westaway, A. D. Reith, P. W. J. Rigby, J. Elhai, and D. Hanahan. 1988. McrA and McrB restriction phenotypes of some E. coli strains and implications for gene cloning. Nucleic Acids Res. 15:1563-1575.
47. Rhee, K. Y., D. F. Senear, and G. W. Hatfield. 1998. Activation of gene expression by a ligand-induced conformational change of a protein-DNA complex. J. Biol. Chem. 273:11257-11266.
48. Rimseliene, R., R. Vaisvila, and A. Janulaitis. 1995 The eco72IC gene specifies a trans-acting factor which influences expression of both DNA methyltransferase and endonuclease from the Eco721 restriction-modification system. Gene 157:217-219.
49. Roberts, M., and S. Baumberg. 1984. Anomalous expression of the E. coli lac operon in Proteus mirabilis. I. Effects of L8 and L8 UV5. Mol. Gen. Genet. 198:159-165.
50. Roberts, R. J., and X. Cheng. 1998. Base flipping. Annu. Rev. Biochem. 67:181-198.
51. Robison, K., A. M. McGuire, and G. M. Church. 1998. A comprehensive library of DNA-binding site matrices for 55 proteins applied to the complete Escherichia coli K-12 genome. J. Mol. Biol. 284:241-254.
52. Rodicio, M. R., and K. F. Chater. 1988. Cloning and expression of the SalI restriction-modification genes of Streptomyces albus G. Mol. Gen. Genet. 213:346-353.
53. Rodicio, M. R., T. Quinton-Jager, L. S. Moran, B. E. Slatko, and G. G. Wilson. 1994. Organization and sequence of the SalI restriction-modification system. Gene 151:167-172.
54. Ross, W., K. K. Gosink, J. Salomon, K. Igarashi, C. Zou, A. Ishihama, K. Severinov, and R. L. Gourse. 1993. A third recognition element in bacterial promoters: DNA binding by the alpha subunit of RNA polymerase. Science 262:1407-1413.
55. Sheehan, B. J., and C. J. Dorman. 1998. In vivo analysis of the interactions of the LysR-like regulator SpvR with the operator sequences of the spvA and spvR virulence genes of Salmonella typhimurium. Mol. Microbiol. 30:91-105.
56. Shultzaberger, R. K., and T. D. Schneider. 1999. Using sequence logos and information analysis of Lrp DNA binding sites to investigate discrepancies between natural selection and SELEX. Nucleic Acids Res. 27:882-887.
57. Tao, T. 1992. Doctoral dissertation, Medical College of Ohio, Toledo.
58. Tao, T., and R. M. Blumenthal. 1992. Sequence and characterization of pvuIIR, the PvuII endonuclease gene, and of pvuIIC, its regulatory gene. J. Bacteriol. 174:3395-3398.
59. Tao, T., J. C. Bourne, and R. M. Blumenthal. 1991. A family of regulatory genes associated with type II restriction-modification systems. J. Bacteriol. 173:1367-1375.
60. Tao, T., J. Walter, K. J. Brennan, M. M. Cotterman, and R. M. Blumenthal. 1989. Sequence, internal homology and high-level expression of the gene for a DNA-(cytosine N4)-methyltransferase, M · PvuII. Nucleic Acids Res. 17: 4161-4175.
61. Vijesurier, R. M. 1996. Doctoral dissertation, Wayne State University, Detroit, Mich.
62. Wang, Q., M. Sacco, E. Ricca, C. T. Lago, M. DeFelice, and J. M. Calvo. 1993. Organization of Lrp-binding sites upstream of ilvIH in Salmonella typhimurium. Mol. Microbiol. 7:883-891.
63. Ward, D. F., and N. E. Murray. 1979. Convergent transcription in bacteriophage lambda: interference with gene expression. J. Mol. Biol. 133:249-266.
64. Wiese, D. E., II, B. R. Ernsting, R. M. Blumenthal, and R. G. Matthews. 1997. A nucleoprotein activation complex between the leucine-responsive regulatory protein and DNA upstream of the gltBDF operon in Escherichia coli. J. Mol. Biol. 270:152-168.
65. Wilson, G. G., and N. E. Murray. 1991. Restriction and modification systems. Annu. Rev. Genet. 25:585-627.
66. Winkler, F. K. 1992. Structure and function of restriction endonucleases. Curr. Opin. Struct. Biol. 2:93-99.
67. Wintjens, R., and M. Rooman. 1996. Structural classification of HTH DNA-binding domains and protein-DNA interaction modes. J. Mol. Biol. 262:294-313.
68. Withers, B. E., and J. C. Dunbar. 1995. Sequence-specific DNA recognition by the Sma1 endonuclease. J. Biol. Chem. 270:6496-6504.