A dichotomous epigenetic mechanism governs expression of the LlaJI restriction/modification system

Molecular Microbiology

Volumn 57, Issue 6, 2005, Pages 1532-1544

  O'Driscoll, Jonathan ^a   Fitzgerald, Gerald F ^a,b   Van Sinderen, Douwe ^a,b  

^a UNIVERSITY COLLEGE CORK   (Ireland)

^b UNIVERSITY COLLEGE CORK   (Ireland)

Author keywords

[No Author keywords available]

Indexed keywords

CYTOSINE;

ARTICLE; BINDING AFFINITY; CONTROLLED STUDY; DNA BINDING; DNA MODIFICATION; DNA RESTRICTION; EPIGENETICS; GENE EXPRESSION; GENE EXPRESSION REGULATION; GENE LOCATION; GENE REPRESSION; IN VIVO STUDY; METHYLATION; MOLECULAR RECOGNITION; MUTATIONAL ANALYSIS; NONHUMAN; NUCLEOTIDE SEQUENCE; OPERON; PRIORITY JOURNAL; PROMOTER REGION; TRANSCRIPTION REGULATION;

BASE SEQUENCE; CYTOSINE; DNA RESTRICTION-MODIFICATION ENZYMES; DNA, BACTERIAL; GENE EXPRESSION REGULATION, BACTERIAL; LACTOCOCCUS LACTIS; MOLECULAR SEQUENCE DATA; MUTATION; PROMOTER REGIONS (GENETICS); SITE-SPECIFIC DNA METHYLTRANSFERASE (CYTOSINE-SPECIFIC); TRANSCRIPTION, GENETIC;

EID: 25144440957     PISSN: 0950382X     EISSN: None     Source Type: Journal    
DOI: 10.1111/j.1365-2958.2005.04769.x     Document Type: Article

References (58)

1. Altschul, S.F., Madden, T.L., Schaffer, A.A., Zhang, J., Zhang, Z., Miller, W., and Lipman, D.J. (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25: 3389-3402.
2. Au, K.G., Welsh, K., and Modrich, P. (1992) Initiation of methyl-directed mismatch repair. J Biol Chem 267: 12142-12148.
3. Bandaru, B., Gopal, J., and Bhagwat, A.S. (1996) Overproduction of DNA cytosine methyltransferases causes methylation and C → T mutations at non-canonical sites. J Biol Chem 271: 7851-7859.
4. Beletskaya, I.V., Zakharova, M.V., Shlyapnikov, M.G., Semenova, L.M., and Solonin, A.S. (2000) DNA methylation at the CfrBl site is involved in expression control in the CfrBl restriction-modification system. Nucleic Acids Res 28:3817-3822.
5. Boye, E., and Lobner-Olesen, A. (1990) The role of dam methyltransferase in the control of DNA replication in E. coli. Cell 62: 981-989.
6. Braaten, B.A., Nou, X., Kaltenbach, L.S., and Low, D.A. (1994) Methylation patterns in pap regulatory DNA control pyelonephritis-associated pili phase variation in E. coli. Cell 76: 577-588.
7. Braun, R.E., and Wright, A. (1986) DNA methylation differentially enhances the expression of one of the two E. coli dnaA promoters in vivo and in vitro. Mol Gen Genet 202: 246-250.
8. Brooks, J.E., Nathan, P.D., Landry, D., Sznyter, L.A., Waite-Rees, P., Ives, C.L., et al. (1991) Characterization of the cloned BamHI restriction modification system: its nucleotide sequence, properties of the methylase, and expression in heterologous hosts. Nucleic Acids Res 19: 841-850.
9. Butler, D., and Fitzgerald, G.F. (2001) Transcriptional analysis and regulation of expression of the ScrFI restriction-modification system of Lactococcus lactis subsp. cremoris UC503. J Bacteriol 183: 4668-4673.
10. Campbell, J.L., and Kleckner, N. (1990) E. coli oriC and the dnaA gene promoter are sequestered from dam methyltransferase following the passage of the chromosomal replication fork. Cell 62: 967-979.
11. Cesnaviciene, E., Mitkaite, G., Stankevicius, K., Janulaitis, A., and Lubys, A. (2003) Esp1396I restriction-modification system: structural organization and mode of regulation. Nucleic Acids Res 31: 743-749.
12. Christensen, L.L., and Josephsen, J. (2004) The methyltransferase from the LlaDII restriction-modification system influences the level of expression of Its own gene. J Bacteriol 186: 287-295.
13. Dodd, I.B., and Egan, J.B. (1990) Improved detection of helix-turn-helix DNA-binding motifs in protein sequences. Nucleic Acids Res 18: 5019-5026.
14. Frommer, M., McDonald, L.E., Millar, D.S., Collis, C.M., Watt, F., Grigg, G.W., et al. (1992) A genomic sequencing protocol that yields a positive display of 5-methylcytosine residues in individual DNA strands. Proc Natl Acad Sci USA 89: 1827-1831.
15. Gasson, M.J. (1983) Plasmid complements of Streptococcus lactis NCDO 712 and other lactic streptococci after protoplast-induced curing. J Bacteriol 154: 1-9.
16. Hattman, S., Brooks, J.E., and Masurekar, M. (1978) Sequence specificity of the P1 modification methylase (M.Eco P1) and the DNA methylase (M.Eco dam) controlled by the Escherichia coli dam gene. J Mol Biol 126: 367-380.
17. Horton, P.M., Cai, Z.L, Ho, S.N., and Pease, L.R. (1990) Gene splicing by overlap extension: tailor-made genes using the polymerase chain reaction. Biotechniques 8: 528-535.
18. Israelsen, H., Madsen, S.M., Vrang, A., Hansen, E.B., and Johansen, E. (1995) Cloning and partial characterization of regulated promoters from Lactococcus lactis Tn917-lacZ integrants with the new promoter probe vector, pAK80. Appl Environ Microbiol 61: 2540-2547.
19. Ives, C.L., Nathan, P.D., and Brooks, J.E. (1992) Regulation of the BamHI restriction-modification system by a small intergenic open reading frame, bamHIC, in both Escherichia coli and Bacillus subtilis. J Bacteriol 174: 7194-7201.
20. Kaltenbach, L.S., Braaten, B.A., and Low, D.A. (1995) Specific binding of Papl to Lrp-pap DNA complexes. J Bacteriol 177: 6449-6455.
21. Karyagina, A., Shilov, I., Tashlitskii, V., Khodoun, M., Vasil'ev, S., Lau, P.C., and Nikolskaya, I. (1997) Specific binding of sso II DNA methyltransferase to its promoter region provides the regulation of sso II restriction-modification gene expression. Nucleic Acids Res 25: 2114-2120.
22. Keatch, S.A., Su, T.J., and Dryden, D.T. (2004) Alleviation of restriction by DNA condensation and non-specific DNA binding ligands. Nucleic Acids Res 32: 5841-5850.
23. Kita, K., Tsuda, J., and Nakai, S.Y. (2002) C.EcoO109I, a regulatory protein for production of EcoO109I restriction endonuclease, specifically binds to and bends DNA upstream of its translational start site. Nucleic Acids Res 30:3558-3565.
24. Kobayashi, I. (2001) Behavior of restriction-modification systems as selfish mobile elements and their impact on genome evolution. Nucleic Acids Res 29: 3742-3756.
25. Kuipers, O.P., de Ruyter, P.G.G.A., Kleerebezem, M., and de Vos, W.M. (1998) Quorum sensing-controlled gene expression in lactic acid bacteria. J Biotechnol 64: 15-21.
26. Laemmli, U.K. (1970) Cleavage of structural proteins during the assembly of the head of bacteriophage T4. Nature 227: 680-685.
27. Law, J., Buist, G., Haandrikman, A., Kok, J., Venema, G., and Leenhouts, K. (1995) A system to generate chromosomal mutations in Lactococcus lactis which allows fast analysis of targeted genes. J Bacteriol 177: 7011-7018.
28. Lubys, A., Jurenaite, S., and Janulaitis, A. (1999) Structural organization and regulation of the plasmid-borne type II restriction- modification system Kpn2l from Klebsiella pneumoniae RFL2. Nucleic Acids Res 27: 4228-4234.
29. McKay, L.L., and Baldwin, K.A. (1984) Conjugative 40-megadalton plasmid in Streptococcus lactis subsp. diacetylactis DRC3 is associated with resistance to nisin and bacteriophage. Appl Environ Microbiol 47: 68-74.
30. Makovets, S., Doronina, V.A., and Murray, N.E. (1999) Regulation of endonuclease activity by proteolysis prevents breakage of unmodified bacterial chromosomes by type I restriction enzymes. Proc Natl Acad Sci USA 96: 9757-9762.
31. Makovets, S., Powell, L.M., Titheradge, A.J., Blakely, G.W., and Murray, N.E. (2004) Is modification sufficient to protect a bacterial chromosome from a resident restriction endonuclease? Mol Microbiol 51: 135-147.
32. Marinus, M.G. (1987) DNA methylation in Escherichia coli. Annu Rev Genet 21: 113-131.
33. Marinus, M.G. (1996) Methylation of DNA. In Escherichia coli and Salmonella: Cellular and Molecular Biology. Umbarger, H.E. (ed.). Washington, DC: American Society for Microbiology Press, pp. 782-791.
34. O'Driscoll, J., Glynn, F., Cahalane, O., O'Connell-Motherway, M., Fitzgerald, G.F., and Van Sinderen, D. (2004) Lactococcal plasmid pNP40 encodes a novel, temperature-sensitive restriction-modification system. Appl Environ Microbiol 70: 5546-5556.
35. O'Sullivan, D., and Klaenhammer, T. (1993) Rapid mini-prep isolation of high-quality plasmid DNA from lactococcus and lactobacillus spp. Appl Environ Microbiol 59: 2730-2733.
36. O'Sullivan, D.J., and Klaenhammer, T.R. (1998) Control of expression of LlaI restriction in Lactococcus lactis. Mol Microbiol 27: 1009-1020.
37. Peterson, K.R., Wertman, K.F., Mount, D.W., and Marinus, M.G. (1985) Viability of Escherichia coli K-12 DNA adenine methylase (dam) mutants requires increased expression of specific genes in the SOS regulon. Mol Gen Genet 201: 14-19.
38. Rimseliene, R., Vaisvila, R., and Janulaitis, A. (1995) The eco72IC gene specifies a trans-acting factor which influences expression of both DNA methyltransferase and endonuclease from the Eco72I restriction-modification system. Gene 157: 217-219.
39. Roberts, R.J., and Macelis, D. (1993) REBASE - restriction enzymes and methylases. Nucleic Acids Res 21: 3125-3137.
40. Roberts, R.J., Belfort, M., Bestor, T., Bhagwat, A.S., Bickle, T.A., Bitinaite, J., et al. (2003) A nomenclature for restriction enzymes, DNA methyltransferases, homing endonucleases and their genes. Nucleic Acids Res 31: 1805-1812.
41. Roberts, R.J., Vincze, T., Posfai, J., and Macelis, D. (2005) REBASE - restriction enzymes and DNA methyltransferases. Nucleic Acids Res 33 Database Issue: D230-232.
42. de Ruyter, P.G., Kuipers, O.P., and de Vos, W.M. (1996) Controlled gene expression systems for Lactococcus lactis with the food-grade inducer nisin. Appl Environ Microbiol 62: 3662-3667.
43. Sambrook, J., Fritsch, E.F., and Maniatis, T. (1989) Molecular Cloning: A Laboratory Manual. Cold Spring Harbor, New York: Cold Spring Harbor Laboratory.
44. Sethmann, S., Ceglowski, P., Willert, J., Iwanicka-Nowicka, R., Trautner, T.A., and Walter, J. (1999) M. (phi) BssHII, a novel cytosine-C5-DNA- methyltransferase with target-recognizing domains at separated locations of the enzyme. EMBO J 18: 3502-3508.
45. Som, S., and Friedman, S. (1994) Regulation of EcoRII methyltransferase: effect of mutations on gene expression and in vitro binding to the promoter region. Nucleic Acids Res 22: 5347-5353.
46. Som, S., and Friedman, S. (1997) Characterization of the intergenic region which regulates the MspI restriction-modification system. J Bacteriol 179: 964-967.
47. Sugisaki, H. (1978) Recognition sequence of a restriction endonuclease from Haemophilus gallinarum. Gene 3: 17-28.
48. Sugisaki, H., Yamamoto, K., and Takanami, M. (1991) The Hgal restriction-modification system contains two cytosine methylase genes responsible for modification of different DNA strands. J Biol Chem 266: 13952-13957.
49. Tao, T., and Blumenthal, R.M. (1992) Sequence and characterization of pvuIIR, the PvuII endonuclease gene, and of pvuIIC, its regulatory gene. J Bacteriol 174: 3395-3398.
50. Tao, T., Bourne, J.C., and Blumenthal, R.M. (1991) A family of regulatory genes associated with type II restriction-modification systems. J Bacteriol 173: 1367-1375.
51. Trotter, M., Mills, S., Ross, R.P., Fitzgerald, G.F., and Coffey, A. (2001) The use of cadmium resistance on the phage-resistance plasmid pNP40 facilitates selection for its horizontal transfer to industrial dairy starter lactococci. Lett Appl Microbiol 33: 409-414.
52. Vijesurier, R.M., Carlock, L., Blumenthal, R.M., and Dunbar, J.C. (2000) Role and mechanism of action of C. PvuII, a regulatory protein conserved among restriction-modification systems. J Bacteriol 182: 477-487.
53. Wallecha, A., Munster, V., Correnti, J., Chan, T., and van der Woude, M. (2002) Dam- and OxyR-dependent phase variation of agn43: essential elements and evidence for a new role of DNA methylation. J Bacteriol 184: 3338-3347.
54. Wells, J.M., Wilson, P.W., and Le Page, R.W. (1993) Improved cloning vectors and transformation procedure for Lactococcus lactis. J Appl Bacteriol 74: 629-636.
55. Weyand, N.J., and Low, D.A. (2000) Regulation of Pap phase variation. Lrp is sufficient for the establishment of the phase off pap DNA methylation pattern and repression of pap transcription in vitro. J Biol Chem 275: 3192-3200.
56. van der Woude, M., Braaten, B., and Low, D. (1996) Epigenetic phase variation of the pap operon in Escherichia coli. Trends Microbiol 4: 5-9.
57. Zakharova, M., Minakhin, L., Solonin, A., and Severinov, K. (2004) Regulation of RNA polymerase promoter selectivity by covalent modification of DNA. J Mol Biol 335: 103-111.
58. Zheleznaya, L.A., Kainov, D.E., Yunusova, A.K., and Matvienko, N.I. (2003) Regulatory C protein of the EcoRV modification-restriction system. Biochemistry (Mosc) 68: 105-110.