Direct comparison of nick-joining activity of the nucleic acid ligases from bacteriophage T4

Biochemical Journal

Volumn 398, Issue 1, 2006, Pages 135-144

  Bullard, Desmond R ^a   Bowater, Richard P ^a  

^a UNIVERSITY OF EAST ANGLIA   (United Kingdom)

Author keywords

Bacteriophage T4; DNA ligase; Ligation; Rate of nick joining; RNA ligase; RNA DNA hybrid

Indexed keywords

BACTERIOPHAGES; BIOCHEMISTRY; ENZYMES; NUCLEIC ACID SEQUENCES; PHYSIOLOGY; SUBSTRATES;

BACTERIOPHAGE T4; DNA LIGASE; LIGATION; RATE OF NICK JOINING; RNA LIGASE; RNA-DNA HYBRID;

GENETIC ENGINEERING;

DNA; OLIGONUCLEOTIDE; POLYDEOXYRIBONUCLEOTIDE SYNTHASE; RECOMBINANT PROTEIN; RNA; RNA LIGASE;

ARTICLE; BACTERIOPHAGE; CHEMICAL ANALYSIS; CONTROLLED STUDY; DNA REPAIR; DNA STRAND BREAKAGE; ENZYME ACTIVATION; ENZYME SPECIFICITY; NONHUMAN; PRIORITY JOURNAL;

BACTERIOPHAGE T4; CLONING, MOLECULAR; DNA; DNA LIGASES; DNA REPAIR; ESCHERICHIA COLI; HYDROGEN-ION CONCENTRATION; RNA LIGASE (ATP); SUBSTRATE SPECIFICITY; TEMPERATURE;

EID: 33747177904     PISSN: 02646021     EISSN: None     Source Type: Journal    
DOI: 10.1042/BJ20060313     Document Type: Article

References (60)

1. Miller, E. S., Kutter, E., Mosig, G., Arisaka, F., Kunisawa, T. and Ruger, W. (2003) Bacteriophage T4 genome. Microbiol. Mol. Biol. Rev. 67, 86-156
2. Lehman, I. R. (1974) DNA ligase: structure, mechanism, and function. Science 186, 790-797
3. Shuman, S. and Schwer, B. (1995) RNA capping enzyme and DNA ligase: a superfamily of covalent nucleotidyl transferases. Mol. Microbiol. 17, 405-110
4. Wilkinson, A., Day, J. and Bowater, R. (2001) Bacterial DNA ligases. Mol. Microbiol. 40, 1241-1248
5. Doherty, A. J. and Sun, S. W. (2000) Structural and mechanistic conservation in DNA ligases. Nucleic Acids Res. 28, 4051-4058
6. Shuman, S. and Lima, C. D. (2004) The polynucleotide ligase and RNA capping enzyme superfamily of covalent nucleotidyltransferases. Curr. Opin. Struct. Biol. 14, 757-764
7. Tomkinson, A. E., Vijayakumar, S., Pascal, J. M. and Ellenberger, T. (2006) DNA ligases: structure, reaction mechanism, and function. Chem. Rev. 106, 687-699
8. Weiss, B. and Richardson, C. C. (1967) Enzymatic breakage and joining of deoxyribonucleic acid, I. Repair of single-strand breaks in DNA by an enzyme system from Escherichia coli infected with T4 bacteriophage. Proc. Natl. Acad. Sci. U.S.A. 57, 1021-1028
9. Fareed, G. C. and Richardson, C. C. (1967) Enzymatic breakage and joining of deoxyribonucleic acid. II. The structural gene for polynucleotide ligase in bacteriophage T4. Proc. Natl. Acad. Sci. U.S.A. 58, 665-672
10. Wood, W. B. and Henninger, M. (1969) Attachment of tail fibers in bacteriophage T4 assembly: some properties of the reaction in vitro and its genetic control. J. Mol. Biol. 39, 603-618
11. Wood, W. B., Conley, M. P., Lyle, H. L. and Dickson, R. C. (1978) Attachment of tail fibers in bacteriophage T4 assembly. Purification, properties, and site of action of the accessory protein coded by gene 63. J. Biol. Chem. 253, 2437-2445
12. Snopek, T. J., Wood, W. B., Conley, M. P., Chen, P. and Cozzarelli, N. R. (1977) Bacteriophage T4 RNA ligase is gene 63 product, the protein that promotes tail fiber attachment to the baseplate. Proc. Natl. Acad. Sci. U.S.A. 74, 3355-3359
13. Runnels, J. M., Soltis, D., Hey, T. and Snyder, L. (1982) Genetic and physiological studies of the role of the RNA ligase of bacteriophage T4. J. Mol. Biol. 154, 273-286
14. Amitsur, M., Levitz, R. and Kaufmann, G. (1987) Bacteriophage T4 anticodon nuclease, polynucleotide kinase and RNA ligase reprocess the host lysine tRNA. EMBO J. 6, 2499-2503
15. Ho, C. K. and Shuman, S. (2002) Bacteriophage T4 RNA ligase 2 (gp24.1) exemplifies a family of RNA ligases found in all phylogenetic domains. Proc. Natl. Acad. Sci. U.S.A. 99, 12709-12714
16. Yin, S., Kiong Ho, C., Miller, E. S. and Shuman, S. (2004) Characterization of bacteriophage KVP40 and T4 RNA ligase 2. Virology 319, 141-151
17. Cherepanov, A. V. and De Vries, S. (2002) Dynamic mechanism of nick recognition by DNA ligase. Eur. J. Biochem. 269, 5993-5999
18. Wang, L. K., Ho, C. K., Pei, Y. and Shuman, S. (2003) Mutational analysis of bacteriophage T4 RNA ligase 1. Different functional groups are required for the nucleotidyl transfer and phosphodiester bond formation steps of the ligation reaction. J. Biol. Chem. 278, 29454-29462
19. Martins, A. and Shuman, S. (2004) An RNA ligase from Deinococcus radiodurans. J. Biol. Chem. 279, 50654-50661
20. Martins, A. and Shuman, S. (2004) Characterization of a baculovirus enzyme with RNA ligase, polynucleotide 5′ kinase and polynucleotide 3′ phosphatase activities. J. Biol. Chem. 279, 18220-18231
21. Worthey, E. A., Schnaufer, A., Mian, I. S., Stuart, K. and Salavati, R. (2003) Comparative analysis of editosome proteins in trypanosomatids. Nucleic Acids Res. 31, 6392-6408
22. Stuart, K. D., Schnaufer, A., Ernst, N. L. and Panigrahi, A. K. (2005) Complex management: RNA editing in trypanosomes. Trends Biochem. Sci. 30, 97-105
23. Timson, D. J., Singleton, M. R. and Wigley, D. B. (2000) DNA ligases in the repair and replication of DNA. Mutat. Res. 460, 301-318
24. Ho, C. K., Wang, L. K., Lima, C. D. and Shuman, S. (2004) Structure and mechanism of RNA ligase. Structure 12, 327-339
25. Omari, K. E., Ren, J., Bird, L. E., Bona, M. K., Klarmann, G., LeGrice, S. F. J. and Stammers, D. K. (2006) Molecular architecture and ligand recognition determinants for T4 RNA ligase. J. Biol. Chem. 281, 1573-1579
26. Pascal, J. M., O'Brien, P. J., Tomkinson, A. E. and Ellenberger, T. (2004) Human DNA ligase I completely encircles and partially unwinds nicked DNA. Nature (London) 432, 473-478
27. Sriskanda, V. and Shuman, S. (1998) Specificity and fidelity of strand joining by Chlorella virus DNA ligase. Nucleic Acids Res. 26, 3536-3541
28. Sekiguchi, J. and Shuman, S. (1997) Ligation of RNA-containing duplexes by vaccinia DNA ligase. Biochemistry 36, 9073-9079
29. Nandakumar, J. and Shuman, S. (2004) How an RNA ligase discriminates RNA versus DNA damage. Mol. Cell 16, 211-221
30. Nandakumar, J., Ho, C. K., Lima, C. D. and Shuman, S. (2004) RNA substrate specificity and structure-guided mutational analysis of bacteriophage T4 RNA ligase 2. J. Biol. Chem. 279, 31337-31347
31. Nandakumar, J. and Shuman, S. (2005) Dual mechanisms whereby a broken RNA end assists the catalysis of its repair by T4 RNA ligase 2. J. Biol. Chem. 280, 23484-23489
32. Higgins, N. P. and Cozzarelli, N. R. (1979) DNA-joining enzymes: a review. Methods Enzymol. 68, 50-71
33. Engler, M. J. and Richardson, C. C. (1982) DNA ligases. In The Enzymes, vol. XV (Boyer, P. D., ed.), pp. 3-29, Academic Press, New York
34. Moore, M. J. and Query, C. C. (2000) Joining of RNAs by splinted ligation. Methods Enzymol. 317, 109-123
35. Clepet, C., Le Clainche, I. and Caboche, M. (2004) Improved full-length cDNA production based on RNA tagging by T4 DNA ligase. Nucleic Acids Res. 32, e6
36. Kuhn, H. and Frank-Kamenetskii, M. D. (2005) Template-independent ligation of single-stranded DNA by T4 DNA ligase. FEBS J. 272, 5991-6000
37. Yin, S., Ho, C. K. and Shuman, S. (2003) Structure-function analysis of T4 RNA ligase 2. J. Biol. Chem. 278, 17601-17608
38. +-dependent DNA ligases of Mycobscterium tuberculosis and Streptomyces coelicolor. Proteins Struct. Fund. Genet. 51, 321-326
39. Lavesa-Curto, M., Sayer, H., Bullard, D., MacDonald, A., Wilkinson, A., Smith, A., Bowater, L., Hemmings, A. and Bowater, R. (2004) Characterisation of a temperature-sensitive DNA ligase from Escherichia coli. Microbiology 150, 4171-4180
40. Wilkinson, A., Smith, A., Bullard, D., Lavesa-Curto, M., Sayer, H., Bonner, A., Hemmings, A. M. and Bowater, R. (2005) Analysis of ligation and DNA binding by Escherichia coli DNA ligase (LigA). Biochim. Biophys. Acta 1749, 113-122
41. Sambrook, J. and Russell, D. W. (2001) Molecular Cloning: A Laboratory Manual, 3rd edn., Cold Spring Harbor Laboratory Press, Plainview, NY
42. Wang, Q. S. and Unrau, P. J. (2002) Purification of histidine-tagged T4 RNA ligase from E. coli. BioTechniques 33, 1256-1260
43. Cherepanov, A. V. and de Vries, S. (2003) Kinetics and thermodynamics of nick sealing by T4 DNA ligase. Eur. J. Biochem. 270, 4315-4325
44. Blondal, T., Hjorleifsdottir, S. H., Fridjonsson, O. F., Aevarsson, A., Skirnisdottir, S., Hermannsdottir, A. G., Hreggvidsson, G. O., Smith, A. V. and Kristjansson, J. K. (2003) Discovery and characterization of a thermostable bacteriophage RNA ligase homologous to T4 RNA ligase 1. Nucleic Acids Res. 31, 7247-7254
45. Blondal, T., Thorisdottir, A., Unnsteinsdottir, U., Hjorleifsdottir, S., Aevarsson, A., Ernstsson, S., Fridjonsson, O. H., Skirnisdottir, S., Wheat, J. O., Hermannsdottir, A. G. et al. (2005) Isolation and characterization of a thermostable RNA ligase 1 from a Thermus scotoductus bacteriophage TS2126 with good single-stranded DNA ligation properties. Nucleic Acids Res. 33, 135-142
46. a of lysine 159. J. Biol. Chem. 274, 8586-8588
47. Keppetipola, N. and Shuman, S. (2005) Characterization of a thermophilic ATP-dependent DNA ligase from the euryarchaeon Pyrococcus horikoshii. J. Bacteriol. 187, 6902-6908
48. Markham, N. R. and Zuker, M. (2005) DINAMelt web server for nucleic acid melting prediction. Nucleic Acids Res. 33, W577-W581
49. Bellacosa, A. and Moss, E. G. (2003) RNA repair: damage control. Curr. Biol. 13, R482-R484
50. Begley, T. J. and Samson, L. D. (2003) Molecular biology: a fix for RNA. Nature (London) 421, 795-796
51. Kaufmann, G. (2000) Anticodon nucleases. Trends Biochem. Sci. 25, 70-74
52. Rossi, R., Montecucco, A., Ciarrocchi, G. and Biamonti, G. (1997) Functional characterization of the T4 DNA ligase: a new insight into the mechanism of action. Nucleic Acids Res. 25, 2106-2113
53. Nick McElhinny, S. A. and Ramsden, D. A. (2003) Polymerase mu is a DNA-directed DNA/RNA polymerase. Mol. Cell. Biol. 23, 2309-2315
54. Ruiz, J. F., Juarez, R., Garcia-Diaz, M., Terrados, G., Picher, A. J., Gonzalez-Barrera, S., Fernandez de Henestrosa, A. R. and Blanco, L. (2003) Lack of sugar discrimination by human Pol mu requires a single glycine residue. Nucleic Acids Res. 31, 4441-4449
55. Della, M., Palmbos, P. L., Tseng, H. M., Tonkin, L. M., Daley, J. M., Topper, L. M., Pitcher, R. S., Tomkinson, A. E., Wilson, T. E. and Doherty, A. J. (2004) Mycobacterial Ku and ligase proteins constitute a two-component NHEJ repair machine. Science 306, 683-685
56. Pitcher, R. S., Tonkin, L. M., Green, A. J. and Doherty, A. J. (2005) Domain structure of a NHEJ DNA repair ligase from Mycobacterium tuberculosis. J. Mol. Biol. 351, 531-544
57. Bebenek, K., Garcia-Diaz, M., Patishall, S. R. and Kunkel, T. A. (2005) Biochemical properties of Saccharomyces cerevisiae DNA polymerase IV. J. Biol. Chem. 280, 20051-20058
58. Kornberg, A. and Baker, T. A. (1992) DNA Replication, Freeman, New York
59. Rydberg, B. and Game, J. (2002) Excision of misincorporated ribonucleotides in DNA by RNase H (type 2) and FEN-1 in cell-free extracts. Proc. Natl. Acad. Sci. U.S.A. 99, 16654-16659
60. Pitcher, R. S., Wilson, T. E. and Doherty, A. J. (2005) New insights into NHEJ repair processes in prokaryotes. Cell Cycle 4, 675-678