Characterization of the 5-hydroxymethylcytosine-specific DNA restriction endonucleases

Nucleic Acids Research

Volumn 41, Issue 7, 2013, Pages 4198-4206

  Borgaro, Janine G ^a   Zhu, Zhenyu ^a  

^a NEW ENGLAND BIOLABS   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

5 HYDROXYMETHYLCYTOSINE; CYTOSINE; DNA RESTRICTION ENDONUCLEASE; PVURTS1I PROTEIN; RESTRICTION ENDONUCLEASE; UNCLASSIFIED DRUG;

ARTICLE; BACTERIOPHAGE T4; CONTROLLED STUDY; DOUBLE STRANDED DNA BREAK; ENZYME INHIBITION; ENZYME SPECIFICITY; ENZYME SUBSTRATE; GLYCOSYLATION; NONHUMAN; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL;

BACTERIOPHAGE T4; CYTOSINE; DNA CLEAVAGE; DNA RESTRICTION ENZYMES; DNA, VIRAL; GLUCOSYLTRANSFERASES; SEQUENCE HOMOLOGY, AMINO ACID; SUBSTRATE SPECIFICITY;

BACTERIOPHAGE 5;

EID: 84876532947     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkt102     Document Type: Article

References (31)

1. Warren, R.A. (1980) Modified bases in bacteriophage DNAs. Annu. Rev. Microbiol., 34, 137-158.
2. Kornberg, S.R., Zimmerman, S.B. and Kornberg, A. (1961) Glucosylation of deoxyribonucleic acid by enzymes from bacteriophage-infected Escherichia coli. J. Biol. Chem., 236, 1487-1493.
3. Mulligan, E.A. and Dunn, J.J. (2008) Cloning, purification and initial characterization of E. coli McrA, a putative 5-methylcytosine-specific nuclease. Protein Expr. Purif., 62, 98-103.
4. Sutherland, E., Coe, L. and Raleigh, E.A. (1992) McrBC: a multisubunit GTP-dependent restriction endonuclease. J. Mol. Biol., 225, 327-348.
5. Xu, S.Y., Corvaglia, A.R., Chan, S.H., Zheng, Y. and Linder, P. (2011) A type IV modification-dependent restriction enzyme SauUSI from Staphylococcus aureus subsp. aureus USA300. Nucleic Acids Res., 39, 5597-5610.
6. Janosi, L., Yonemitsu, H., Hong, H. and Kaji, A. (1994) Molecular cloning and expression of a novel hydroxymethylcytosine-specific restriction enzyme (PvuRts1I) modulated by glucosylation of DNA. J. Mol. Biol., 242, 45-61.
7. Rifat, D., Wright, N.T., Varney, K.M., Weber, D.J. and Black, L.W. (2008) Restriction endonuclease inhibitor IPI* of bacteriophage T4: a novel structure for a dedicated target. J. Mol. Biol., 375, 720-734. (Pubitemid 350297286)
8. Lehman, I.R. and Pratt, E.A. (1960) On the structure of the glucosylated hydroxymethylcytosine nucleotides of coliphages T2, T4, and T6. J. Biol. Chem., 235, 3254-3259.
9. Rottach, A., Leonhardt, H. and Spada, F. (2009) DNA methylation-mediated epigenetic control. J. Cell Biochem., 108, 43-51.
10. 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 TET1. Science, 324, 930-935.
11. Kriaucionis, S. and Heintz, N. (2009) The nuclear DNA base 5-hydroxymethylcytosine is present in Purkinje neurons and the brain. Science, 324, 929-930.
12. Ito, S., D'Alessio, A.C., Taranova, O.V., Hong, K., Sowers, L.C. and Zhang, Y. (2010) Role of Tet proteins in 5mC to 5hmC conversion, ES-cell self-renewal and inner cell mass specification. Nature, 466, 1129-1133.
13. Meyer, C., Kowarz, E., Hofmann, J., Renneville, A., Zuna, J., Trka, J., Ben Abdelali, R., Macintyre, E., De Braekeleer, E., De Braekeleer, M. et al. (2009) New insights to the MLL recombinome of acute leukemias. Leukemia, 23, 1490-1499.
14. Cortellino, S., Xu, J., Sannai, M., Moore, R., Caretti, E., Cigliano, A., Le Coz, M., Devarajan, K., Wessels, A., Soprano, D. et al. (2011) Thymine DNA glycosylase is essential for active DNA demethylation by linked deamination-base excision repair. Cell, 146, 67-79.
15. He, Y.F., Li, B.Z., Li, Z., Liu, P., Wang, Y., Tang, Q., Ding, J., Jia, Y., Chen, Z., Li, L. et al. (2011) Tet-mediated formation of 5-carboxylcytosine and its excision by TDG in mammalian DNA. Science, 333, 1303-1307.
16. Maiti, A. and Drohat, A.C. (2011) Thymine DNA glycosylase can rapidly excise 5-formylcytosine and 5-carboxylcytosine: potential implications for active demethylation of CpG sites. J. Biol. Chem., 286, 35334-35338.
17. Valinluck, V. and Sowers, L.C. (2007) Endogenous cytosine damage products alter the site selectivity of human DNA maintenance methyltransferase DNMT1. Cancer Res., 67, 946-950.
18. Valinluck, V., Tsai, H.H., Rogstad, D.K., Burdzy, A., Bird, A. and Sowers, L.C. (2004) Oxidative damage to methyl-CpG sequences inhibits the binding of the methyl-CpG binding domain (MBD) of methyl-CpG binding protein 2 (MeCP2). Nucleic Acids Res., 32, 4100-4108. (Pubitemid 39232282)
19. Booth, M.J., Branco, M.R., Ficz, G., Oxley, D., Krueger, F., Reik, W. and Balasubramanian, S. (2012) Quantitative sequencing of 5-methylcytosine and 5-hydroxymethylcytosine at single-base resolution. Science, 336, 934-937.
20. Yu, M., Hon, G.C., Szulwach, K.E., Song, C.X., Zhang, L., Kim, A., Li, X., Dai, Q., Shen, Y., Park, B. et al. (2012) Base-resolution analysis of 5-hydroxymethylcytosine in the mammalian genome. Cell, 149, 1368-1380.
21. Huang, Y., Pastor, W.A., Shen, Y., Tahiliani, M., Liu, D.R. and Rao, A. (2010) The behaviour of 5-hydroxymethylcytosine in bisulfite sequencing. PLoS One, 5, e8888.
22. Wang, H., Guan, S., Quimby, A., Cohen-Karni, D., Pradhan, S., Wilson, G., Roberts, R.J., Zhu, Z. and Zheng, Y. (2011) Comparative characterization of the PvuRts1I family of restriction enzymes and their application in mapping genomic 5-hydroxymethylcytosine. Nucleic Acids Res., 39, 9294-9305.
23. Sun, Z., Terragni, J., Borgaro, J.G., Liu, Y., Yu, L., Guan, S., Wang, H., Sun, D., Cheng, X., Zhu, Z. et al. (2012) High resolution enymatic mapping of genomic 5-hydroxymethylcytosine in mouse embrionic stem cells. Cell Rep., 3, 1-10.
24. Puigbo, P., Guzman, E., Romeu, A. and Garcia-Vallve, S. (2007) OPTIMIZER: a web server for optimizing the codon usage of DNA sequences. Nucleic Acids Res., 35, W126-W131.
25. Kuo, T.T., Huang, T.C. and Teng, M.H. (1968) 5-Methylcytosine replacing cytosine in the deoxyribonucleic acid of a bacteriophage for Xanthomonas oryzae. J. Mol. Biol., 34, 373-375.
26. 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. (Pubitemid 27359211)
27. Georgopoulos, C.P. and Revel, H.R. (1971) Studies with glucosyl transferase mutants of the T-even bacteriophages. Virology, 44, 271-285.
28. Song, C.X., Szulwach, K.E., Fu, Y., Dai, Q., Yi, C., Li, X., Li, Y., Chen, C.H., Zhang, W., Jian, X. et al. (2011) Selective chemical labeling reveals the genome-wide distribution of 5-hydroxymethylcytosine. Nat. Biotechnol., 29, 68-72.
29. Shi, D., Yu, X., Cabrera-Luque, J., Chen, T.Y., Roth, L., Morizono, H., Allewell, N.M. and Tuchman, M. (2007) A single mutation in the active site swaps the substrate specificity of N-acetyl-L-ornithine transcarbamylase and N-succinyl-L-ornithine transcarbamylase. Protein Sci., 16, 1689-1699. (Pubitemid 47195695)
30. Todd, A.E., Orengo, C.A. and Thornton, J.M. (2001) Evolution of function in protein superfamilies, from a structural perspective. J. Mol. Biol., 307, 1113-1143. (Pubitemid 33029957)
31. Gruber, T.D., Borrok, M.J., Westler, W.M., Forest, K.T. and Kiessling, L.L. (2009) Ligand binding and substrate discrimination by UDP-galactopyranose mutase. J. Mol. Biol., 391, 327-340.