The methylomes of six bacteria

Nucleic Acids Research

Volumn 40, Issue 22, 2012, Pages 11450-11462

  Murray, Iain A ^a   Clark, Tyson A ^b   Morgan, Richard D ^a   Boitano, Matthew ^b   Anton, Brian P ^a   Luong, Khai ^b   Fomenkov, Alexey ^a   Turner, Stephen W ^b   Korlach, Jonas ^b   Roberts, Richard J ^a  

^a NEW ENGLAND BIOLABS   (United States)

^b PACIFIC BIOSCIENCES   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

5 METHYLCYTOSINE; 6 N METHYLADENINE; CYTOSINE DERIVATIVE; DNA METHYLTRANSFERASE; N4 METHYLCYTOSINE; TYPE I SITE SPECIFIC DEOXYRIBONUCLEASE; UNCLASSIFIED DRUG;

ARTICLE; BACILLUS CEREUS; BACTERIAL GENOME; BACTERIAL STRAIN; BACTERIAL VIABILITY; CAMPYLOBACTER JEJUNI; CHROMOHALOBACTER; CHROMOHALOBACTER SALEXIGENS; GENE EXPRESSION; GENE SEQUENCE; GENOME; GEOBACTER METALLIREDUCENS; METHYLATION; METHYLOME; MOLECULAR CLONING; NONHUMAN; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; SIGNAL PROCESSING; SUBSPECIES; VIBRIO; VIBRIO BREOGANI;

ADENINE; BACILLUS CEREUS; CAMPYLOBACTER JEJUNI; CHROMOHALOBACTER; CYTOSINE; DNA METHYLATION; DNA MODIFICATION METHYLASES; DNA, BACTERIAL; GENOME, BACTERIAL; GEOBACTER; SEQUENCE ANALYSIS, DNA; VIBRIO;

BACILLUS CEREUS ATCC 10987; BACTERIA (MICROORGANISMS); CAMPYLOBACTER JEJUNI; CAMPYLOBACTER JEJUNI SUBSP. JEJUNI 81-176; CHROMOHALOBACTER SALEXIGENS; GEOBACTER METALLIREDUCENS GS-15; VIBRIO;

EID: 84871222928     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gks891     Document Type: Article

References (42)

1. Kumar, S., Cheng, X., Klimasauskas, S., Mi, S., Posfai, J., Roberts, R. J. and Wilson, G. G. (1994) The DNA (cytosine-5) methyltransferases. Nucleic Acids Res., 22, 1-10.
2. Tahiliani, M., Koh, K. P., Shen, Y., Pastor, W. A., Bandukwala, H., Brudno, Y., Agarwal, S., Iyer, L. M., Liu, D. R., Aravind, L. et al. (2009) Conversion of 5-methylcytosine to 5-hydroxymethylcytosine in mammalian DNA by MLL partner TETI. Science, 324, 930-935.
3. Kriaucionis, S. and Heintz, N. (2009) The nuclear DNA base 5-hydroxymethylcytosine is present in Purkinje neurons and the brain. Science, 324, 929-930.
4. Ito, S., Shen, L., Dai, Q., Wu, S. C., Collins, L. B., Swenberg, J. A., He, C. and Zhang, Y. (2011) Tet proteins can convert 5-methylcytosine to 5-formylcytosine and 5-carboxylcytosine. Science, 333, 1300-1303.
5. Roberts, R. J., Vincze, T., Posfai, J. and Macelis, D. (2010) REBASE-a database for DNA restriction and modification: enzymes, genes and genomes. Nucleic Acids Res., 38, D234-D236.
6. Eid, J., Fehr, A., Gray, J., Luong, K., Lyle, J., Otto, G., Peluso, P., Rank, D., Baybayan, P., Bettman, B. et al. (2009) Real-time DNA sequencing from single polymerase molecules. Science, 323, 133-138.
7. Flusberg, B. A., Webster, D. R., Lee, J. H., Travers, K. J., Olivares, E. C., Clark, T. A., Korlach, J. and Turner, S. W. (2010) Direct detection of DNA methylation during single-molecule, real-time sequencing. Nat. Methods, 7, 461-465.
8. Korlach, J. and Turner, S. W. (2012) Going beyond five bases in DNA sequencing. Curr. Opin. Struct. Biol., 22, 251-261.
9. Roberts, R. J. and Halford, S. E. (1993) Type II restriction enzymes. In: Linn, S. M., Lloyd, R. S. and Roberts, R. J. (eds), Nucleases. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, pp. 35-88.
10. Marinus, M. G. and Casadesus, J. (2009) Roles of DNA adenine methylation in host-pathogen interactions: mismatch repair, transcriptional regulation, and more. FEMS Microbiol. Rev., 33, 488-503.
11. Srikhanta, Y. N., Fox, K. L. and Jennings, M. P. (2010) The phasevarion: phase variation of type III DNA methyltransferases controls coordinated switching in multiple genes. Nat. Rev. Microbiol., 8, 196-206.
12. Casadesú s, J. and Low, D. (2006) Epigenetic gene regulation in the bacterial world. Microbiol. Mol. Biol. Rev., 70, 830-856.
13. Bhagwat, A. S. and McClelland, M. (1992) DNA mismatch correction by very short patch repair may have altered the abundance of oligonucleotides in the E. coli genome. Nucleic Acids Res., 20, 1663-1668.
14. Reisenauer, A., Kahng, L. S., McCollum, S. and Shapiro, L. (1999) Bacterial DNA methylation: a cell cycle regulator? J. Bacteriol., 181, 5135-5139.
15. Clark, T. A., Murray, I. A., Morgan, R. D., Kislyuk, A. O., Spittle, K. E., Boitano, M., Fomenkov, A., Roberts, R. J. and Korlach, J. (2012) Characterization of DNA methyltransferase specificities using single-molecule, real-time DNA sequencing. Nucleic Acids Res., 40, e29.
16. Bickle, T. A. (1993) The ATP-dependent restriction enzymes. In: Linn, S. M., Lloyd, R. S. and Roberts, R. J. (eds), Nucleases. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, pp. 89-109.
17. Travers, K. J., Chin, C. S., Rank, D. R., Eid, J. S. and Turner, S. W. (2010) A flexible and efficient template format for circular consensus sequencing and SNP detection. Nucleic Acids Res., 38, e159.
18. Machanick, P. and Bailey, T. L. (2011) MEME-ChIP: motif analysis of large DNA datasets. Bioinformatics, 27, 1696-1697.
19. Sayers, E. W., Barrett, T., Benson, D. A., Bolton, E., Bryant, S. H., Canese, K., Chetvernin, V., Church, D. M., Dicuccio, M., Federhen, S. et al. (2012) Database resources of the National Center for Biotechnology Information. Nucleic Acids Res., 40, D13-D25.
20. Posfai, J., Bhagwat, A. S., Posfai, G. and Roberts, R. J. (1989) Predictive motifs derived from cytosine methyltransferases. Nucleic Acids Res., 17, 2421-2435.
21. Klimasauskas, S., Timinskas, A., Menkevicius, S., Butkiene, D., Butkus, V. and Janulaitis, A. (1989) Sequence motifs characteristic of DNA[cytosine-N4]methylases: similarity to adenine and cytosine-C5 DNA-methylases. Nucleic Acids Res., 17, 9823-9832.
22. Kong, H., Lin, L. F., Porter, N., Stickel, S., Byrd, D., Posfai, J. and Roberts, R. J. (2000) Functional analysis of putative restriction-modification system genes in the Helicobacter pylori J99 genome. Nucleic Acids Res., 28, 3216-3223.
23. Sibley, M. H. and Raleigh, E. A. (2004) Cassette-like variation of restriction enzyme genes in Escherichia coli C and relatives. Nucleic Acids Res., 32, 522-534.
24. Gibson, D. G., Young, L., Chuang, R. Y., Venter, J. C., Hutchison, C. A. III and Smith, H. O. (2009) Enzymatic assembly of DNA molecules up to several hundred kilobases. Nat. Methods, 6, 343-345.
25. Xu, S. Y., Nugent, R. L., Kasamkattil, J., Fomenkov, A., Gupta, Y., Aggarwal, A., Wang, X., Li, Z., Zheng, Y. and Morgan, R. (2012) Characterization of Type II and III restriction-modification systems from Bacillus cereus strains ATCC10987 and ATCC14579. J. Bacteriol., 194, 49-60.
26. Takata, T., Wassenaar, T. M., Xu, Q. and Blaser, M. J. (2002) The gene product of Campylobacter jejuni gene Cj0208 is a DNA methyltransferase with specificity for GAATTC. Abstr. Gen. Meet. Am. Soc. Microbiol., 102, 164.
27. Kim, J. S., Li, J. Q., Barnes, I. H. A., Baltzegar, D. A., Pajaniappan, M., Cullen, T. W., Trent, M. S., Burns, C. M. and Thompson, S. A. (2008) Role of the Campylobacter jejuni cj1461 DNA methyltransferase in regulating virulence characteristics. J. Bacteriol., 190, 6524-6529.
28. Kan, N. C., Lautenberger, J. A., Edgell, M. H. and Hutchison, C. A. III (1979) The nucleotide sequence recognized by the Escherichia coli K12 restriction and modification enzymes. J. Mol. Biol., 130, 191-209.
29. Lovley, D. R. and Phillips, E. J. P. (1988) Novel mode of microbial energy-metabolism-organic-carbon oxidation coupled to dissimilatory reduction of iron or manganese. (1988). Appl. Environ. Microbiol., 54, 1472-1480.
30. Graentzdoerffer, A., Lindenstrauss, U., Pich, A. and Andreesen, J. R. (2002) New DNA-methyltransferase M. EacI, useful for protecting double stranded DNA against cleavage by restriction enzymes, derived from Eubacterium acidaminophilum, German Patent Office DE 10060526.
31. Copeland, A., Lucas, S., Copeland, A., Lucas, S., Lapidus, A., Barry, K., Detter, J. C., Glavina del Rio, T., Hammon, N., Israni, S. et al. (2011) Complete genome sequence of the halophilic and highly halotolerant Chromohalobacter salexigens type strain (1H11T). Stand. Genomic Sci., 5, 379-388.
32. Ventura, M., Canchaya, C., Bernini, V., Altermann, E., Barrangou, R., McGrath, S., Claesson, M. J., Li, Y., Leahy, S., Walker, C. D. et al. (2006) Comparative genomics and transcriptional analysis of prophages identified in the genomes of Lactobacillus gasseri, Lactobacillus salivarius and Lactobacillus casei. Appl. Environ. Microbiol., 72, 3130-3146.
33. Hunt, D. E., David, L. A., Gevers, D., Preheim, S. P., Alm, E. J. and Polz, M. F. (2008) Resource partitioning and sympatric differentiation among closely related bacterioplankton. Science, 320, 1081-1085.
34. Preheim, S. P., Timberlake, S. and Polz, M. F. (2011) Merging taxonomy with ecological population prediction in a case study of Vibrionaceae. Appl. Environ. Microbiol., 77, 7195-7206.
35. Brooks, J. E., Blumenthal, R. M. and Gingeras, T. R. (1983) The isolation and characterization of the Escherichia coli DNA adenine methylase (dam) gene. Nucleic Acids Res., 11, 837-851.
36. Wang, L., Chen, S. and Deng, Z. (2012) Phosphorothioation: an unusual post-replicative modification on the dna backbone. In: Seligmann, H. (ed. ), DNA Replication-Current Advances, New York: InTech, Chapter 3. pp. 57-74.
37. Parkhill, J., Wren, B. W., Mungall, K., Ketley, J. M., Churcher, C., Basham, D., Chillingworth, T., Davies, R. M., Feltwell, T. and Holroyd, S. (2000) The genome sequence of the food-borne pathogen Campylobacter jejuni reveals hypervariable sequences. Nature, 403, 665-668.
38. Rasko, D. A., Ravel, J., Økstad, O. A., Helgason, E., Cer, R. Z., Jiang, L., Shores, K. A., Fouts, D. E., Tourasse, N. J. and Angiuoli, S. V. (2004) The genome sequence of Bacillus cereus ATCC 10987 reveals metabolic adaptations and a large plasmid related to Bacillus anthracis pXO1. Nucleic Acids Res., 32, 977-988.
39. Morgan, R. D. and Luyten, Y. A. (2009) Rational engineering of type II restriction endonuclease DNA binding and cleavage specificity. Nucleic Acids Res., 37, 5222-5233.
40. Roberts, R. J., Chang, Y. C., Hu, Z., Rachlin, J. N., Anton, B. P., Pokrzywa, R. M., Choi, H. P., Faller, L. L., Guleria, J. and Housman, G. (2011) COMBREX: a project to accelerate the functional annotation of prokaryotic genomes. Nucleic Acids Res., 39, D11-D14.
41. Donahue, J. P., Israel, D. A., Peek, R. M., Blaser, M. J. and Miller, G. G. (2000) Overcoming the restriction barrier to plasmid transformation of Helicobacter pylori. Mol. Microbiol., 37, 1066-1074.
42. Dong, H., Zhang, Y., Dai, Z. and Li, Y. (2010) Engineering Clostridium strain to accept unmethylated DNA. PLoS One, 5, e9038.