Cleavage of phosphorothioated DNA and methylated DNA by the type IV restriction endonuclease ScoMcrA

PLoS Genetics

Volumn 6, Issue 12, 2010, Pages 1-13

  Liu, Guang ^a   Ou, Hong Yu ^a   Wang, Tao ^a   Li, Li ^a   Tan, Huarong ^b   Zhou, Xiufen ^a   Rajakumar, Kumar ^c,d   Deng, Zixin ^a   He, Xinyi ^a  

^a SHANGHAI JIAO TONG UNIVERSITY   (China)

^b INSTITUTE OF MICROBIOLOGY   (China)

^c UNIVERSITY OF LEICESTER   (United Kingdom)

^d UNIVERSITY HOSPITALS OF LEICESTER NHS TRUST   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

DEOXYRIBONUCLEASE I; DNA DEGRADATION A GENE; DNA DEGRADATION B GENE; DNA DEGRADATION C GENE; DNA DEGRADATION D GENE; DNA DEGRADATION E GENE; DOUBLE STRANDED DNA; HISTIDINE; PHOSPHOROTHIOIC ACID; RESTRICTION ENDONUCLEASE; SECRETORY LEUKOCYTE PROTEINASE INHIBITOR; STREPTOMYCES COELICOLOR PROTEIN 4631; UNCLASSIFIED DRUG; BACTERIAL DNA; BACTERIAL PROTEIN; PHOSPHATE; SULFUR;

ARTICLE; BACTERIAL STRAIN; CELL DEATH; DNA DEGRADATION; DNA FOOTPRINTING; DNA METHYLATION; DNA MODIFICATION; ENZYME ACTIVITY; FRAMESHIFT MUTATION; GENE CLUSTER; GENE IDENTIFICATION; GENOMIC ISLAND; MOLECULAR CLONING; NONHUMAN; NUCLEOTIDE SEQUENCE; PROTEIN BINDING; PROTEIN CLEAVAGE; PROTEIN EXPRESSION; PROTEIN FUNCTION; STREPTOMYCES COELICOLOR; STREPTOMYCES LIVIDANS; ENZYMOLOGY; GENE EXPRESSION; GENETICS; METABOLISM; MOLECULAR GENETICS;

PROKARYOTA; STREPTOMYCES COELICOLOR; STREPTOMYCES LIVIDANS;

BACTERIAL PROTEINS; BASE SEQUENCE; DNA METHYLATION; DNA RESTRICTION ENZYMES; DNA, BACTERIAL; GENE EXPRESSION; MOLECULAR SEQUENCE DATA; PHOSPHATES; STREPTOMYCES COELICOLOR; STREPTOMYCES LIVIDANS; SULFUR;

EID: 78650694154     PISSN: 15537390     EISSN: 15537404     Source Type: Journal    
DOI: 10.1371/journal.pgen.1001253     Document Type: Article

References (52)

1. Robertson KD (2005) DNA Methylation and human disease. Nat Rev Genet 6: 597-610.
2. Bickle TA, Kruger DH (1993) Biology of DNA restriction. Microbiol Rev 57: 434-450.
3. Dryden DT, Murray NE, Rao DN (2001) Nucleoside triphosphate-dependent restriction enzymes. Nucleic Acids Res 29: 3728-3741.
4. Roberts RJ, Vincze T, Posfai J, Macelis D (2010) REBASE-a database for DNA restriction and modification: enzymes, genes and genomes. Nucleic Acids Res 38: D234-236.
5. Bair CL, Black LW (2007) A type IV modification dependent restriction nuclease that targets glucosylated hydroxymethyl cytosine modified DNAs. J Mol Biol 366: 768-778.
6. Zhou X, He X, Liang J, Li A, Xu T, et al. (2005) A novel DNA modification by sulphur. Mol Microbiol 57: 1428-1438.
7. Zhou X, Deng Z, Firmin JL, Hopwood DA, Kieser T (1988) Site-specific degradation of Streptomyces lividans DNA during electrophoresis in buffers contaminated with ferrous iron. Nucleic Acids Res 16: 4341-4352.
8. Bentley SD, Chater KF, Cerdeno-Tarraga AM, Challis GL, Thomson NR, et al. (2002) Complete genome sequence of the model actinomycete Streptomyces coelicolor A3(2). Nature 417: 141-147.
9. Gonzalez-Ceron G, Miranda-Olivares OJ, Servin-Gonzalez L (2009) Characterization of the methyl-specific restriction system of Streptomyces coelicolor A3(2) and of the role played by laterally acquired nucleases. FEMS Microbiol Lett 301: 35-43.
10. Flett F, Mersinias V, Smith CP (1997) High efficiency intergeneric conjugal transfer of plasmid DNA from Escherichia coli to methyl DNA-restricting streptomycetes. FEMS Microbiol Lett 155: 223-229.
11. Kieser T, Bibb MJ, Chater KF, Butter MJ, Hopwood DA (2000) Practical Streptomyces genetics. A laboratory manual. Norwich: John Innes Foundation, United Kingdom.
12. Jayapal KP, Lian W, Glod F, Sherman DH, Hu WS (2007) Comparative genomic hybridizations reveal absence of large Streptomyces coelicolor genomic islands in Streptomyces lividans. BMC Genomics 8: 229.
13. He X, Ou HY, Yu Q, Zhou X, Wu J, et al. (2007) Analysis of a genomic island housing genes for DNA S-modification system in Streptomyces lividans 66 and its counterparts in other distantly related bacteria. Mol Microbiol 65: 1034-1048.
14. Bibb MJ, Ward JM, Kieser T, Cohen SN, Hopwood DA (1981) Excision of chromosomal DNA sequences from Streptomyces coelicolor forms a novel family of plasmids detectable in Streptomyces lividans. Mol Gen Genet 184: 230-240.
15. Raleigh EA, Wilson G (1986) Escherichia coli K-12 restricts DNA containing 5- methylcytosine. Proc Natl Acad Sci U S A 83: 9070-9074.
16. Mulligan EA, Dunn JJ (2008) Cloning, purification and initial characterization of E. coli McrA, a putative 5-methylcytosine-specific nuclease. Protein Expr Purif 62: 98-103.
17. Mulligan EA, Hatchwell E, McCorkle SR, Dunn JJ (2010) Differential binding of Escherichia coli McrA protein to DNA sequences that contain the dinucleotide m5CpG. Nucleic Acids Res 38: 1997-2005.
18. Wang L, Chen S, Xu T, Taghizadeh K, Wishnok JS, et al. (2007) Phosphorothioation of DNA in bacteria by dnd genes. Nat Chem Biol 3: 709-710.
19. Ray T, Mills A, Dyson P (1995) Tris-dependent oxidative DNA strand scission during electrophoresis. Electrophoresis 16: 888-894.
20. Ou HY, He X, Shao Y, Tai C, Rajakumar K, et al. (2009) DndDB: a database focused on phosphorothioation of the DNA backbone. PLoS ONE 4: e5132. doi:10.1371/journal.pone.0005132.
21. Liang J, Wang Z, He X, Li J, Zhou X, et al. (2007) DNA modification by sulfur: analysis of the sequence recognition specificity surrounding the modification sites. Nucleic Acids Res 35: 2944-2954.
22. Sun Y, He X, Liang J, Zhou X, Deng Z (2009) Analysis of functions in plasmid pHZ1358 influencing its genetic and structural stability in Streptomyces lividans 1326. Appl Microbiol Biotechnol 82: 303-310.
23. Evans M, Kaczmarek FS, Stutzman-Engwall K, Dyson P (1994) Characterization of a Streptomyces-lividans-type site-specific DNA modification system in the avermectin-producer Streptomyces avermitilis permits investigation of two novel giant linear plasmids, pSA1 and pSA2. Microbiology 140(Pt 6): 1367-1371.
24. Hsu M, Berg P (1978) Altering the specificity of restriction endonuclease: effect of replacing Mg2+ with Mn2+. Biochemistry 17: 131-138.
25. Thielking V, Selent U, Kohler E, Landgraf A, Wolfes H, et al. (1992) Mg2+ confers DNA binding specificity to the EcoRV restriction endonuclease. Biochemistry 31: 3727-3732.
26. Janulaitis A, Petrusyte M, Maneliene Z, Klimasauskas S, Butkus V (1992) Purification and properties of the Eco57I restriction endonuclease and methylase-prototypes of a new class (type IV). Nucleic Acids Res 20: 6043-6049.
27. Stewart FJ, Raleigh EA (1998) Dependence of McrBC cleavage on distance between recognition elements. Biol Chem 379: 611-616.
28. Jurenaite-Urbanaviciene S, Kazlauskiene R, Urbelyte V, Maneliene Z, Petrusyte M, et al. (2001) Characterization of BseMII, a new type IV restriction-modification system, which recognizes the pentanucleotide sequence 59-CTCAG(N)(10/8). Nucleic Acids Res 29: 895-903.
29. Stewart FJ, Panne D, Bickle TA, Raleigh EA (2000) Methyl-specific DNA binding by McrBC, a modification-dependent restriction enzyme. J Mol Biol 298: 611-622.
30. Chan SH, Opitz L, Higgins L, O'Loane D, Xu SY (2010) Cofactor requirement of HpyAV restriction endonuclease. PLoS ONE 5: e9071. doi:10.1371/ journal.pone.0009071.
31. Zheng Y, Cohen-Karni D, Xu D, Chin HG, Wilson G, et al. (2010) A unique family of Mrr-like modification-dependent restriction endonucleases. Nucleic Acids Res.
32. Roberts RJ, Belfort M, Bestor T, Bhagwat AS, Bickle TA, et al. (2003) A nomenclature for restriction enzymes, DNA methyltransferases, homing endonucleases and their genes. Nucleic Acids Res 31: 1805-1812.
33. Dyson P, Evans M (1998) Novel post-replicative DNA modification in Streptomyces: analysis of the preferred modification site of plasmid pIJ101. Nucleic Acids Res 26: 1248-1253.
34. Sutherland E, Coe L, Raleigh EA (1992) McrBC: a multisubunit GTPdependent restriction endonuclease. J Mol Biol 225: 327-348.
35. Raleigh EA, Trimarchi R, Revel H (1989) Genetic and physical mapping of the mcrA (rglA) and mcrB (rglB) loci of Escherichia coli K-12. Genetics 122: 279-296.
36. Raleigh EA, Benner J, Bloom F, Braymer HD, DeCruz E, et al. (1991) Nomenclature relating to restriction of modified DNA in Escherichia coli. J Bacteriol 173: 2707-2709.
37. Gorbalenya AE (1994) Self-splicing group I and group II introns encode homologous (putative) DNA endonucleases of a new family. Protein Sci 3: 1117-1120.
38. Dalgaard JZ, Klar AJ, Moser MJ, Holley WR, Chatterjee A, et al. (1997) Statistical modeling and analysis of the LAGLIDADG family of site-specific endonucleases and identification of an intein that encodes a site-specific endonuclease of the HNH family. Nucleic Acids Res 25: 4626-4638.
39. Fukuda E, Kaminska KH, Bujnicki JM, Kobayashi I (2008) Cell death upon epigenetic genome methylation: a novel function of methyl-specific deoxyribonucleases. Genome Biol 9: R163.
40. MacNeil DJ (1988) Characterization of a unique methyl-specific restriction system in Streptomyces avermitilis. J Bacteriol 170: 5607-5612.
41. Thompson CJ, Ward JM, Hopwood DA (1982) Cloning of antibiotic resistance and nutritional genes in streptomycetes. J Bacteriol 151: 668-677.
42. Omer CA, Cohen SN (1984) Plasmid formation in Streptomyces: excision and integration of the SLP1 replicon at a specific chromosomal site. Mol Gen Genet 196: 429-438.
43. Thompson CJ, Kieser T, Ward JM, Hopwood DA (1982) Physical analysis of antibiotic-resistance genes from Streptomyces and their use in vector construction. Gene 20: 51-62.
44. Bahl MI, Hansen LH, Sorensen SJ (2009) Persistence mechanisms of conjugative plasmids. Methods Mol Biol 532: 73-102.
45. Furuta Y, Abe K, Kobayashi I (2010) Genome comparison and context analysis reveals putative mobile forms of restriction-modification systems and related rearrangements. Nucleic Acids Res 38: 2428-2443.
46. Asakura Y, Kobayashi I (2009) From damaged genome to cell surface: transcriptome changes during bacterial cell death triggered by loss of a restriction-modification gene complex. Nucleic Acids Res 37: 3021-3031.
47. Collier J (2009) Epigenetic regulation of the bacterial cell cycle. Curr Opin Microbiol 12: 722-729.
48. Marinus MG, Casadesus J (2009) Roles of DNA adenine methylation in hostpathogen interactions: mismatch repair, transcriptional regulation, and more. FEMS Microbiol Rev 33: 488-503.
49. Modrich P (1987) DNA mismatch correction. Annu Rev Biochem 56: 435-466.
50. Lee SC, Omer CA, Brasch MA, Cohen SN (1988) Analysis of recombination occurring at SLP1 att sites. J Bacteriol 170: 5806-5813.
51. Xu T, Yao F, Zhou X, Deng Z, You D (2010) A novel host-specific restriction system associated with DNA backbone S-modification in Salmonella. Nucleic Acids Res.
52. Sambrook J, Fritsch EF, Maniatis T (1989) Molecular cloning: a laboratory manual, 2nd ed. Cold Spring Harbor, N.Y: Cold Spring Harbor Laboratory.