Identification and characterization of an inhibitor specific to bacterial NAD+-dependent DNA ligases

FEBS Journal

Volumn 275, Issue 21, 2008, Pages 5258-5271

  Meier, Timothy I ^a   Yan, Dalai ^a   Peery, Robert B ^a   McAllister, Kelly A ^a   Zook, Chris ^a   Peng, Sheng Bin ^a   Zhao, Genshi ^a  

^a ELI LILLY AND COMPANY   (United States)

Author keywords

Antibiotics; DNA ligase; DNA replication; Ligase inhibitor; Streptococcus pneumoniae

Indexed keywords

2,4 DIAMINO 7 DIMETHYLAMINO PYRIMIDO[4,5 D]PYRIMIDINE; ADENOSINE PHOSPHATE; ADENOSINE TRIPHOSPHATE; ANTIINFECTIVE AGENT; DNA; DNA FRAGMENT; METHOTREXATE; NICOTINAMIDE ADENINE DINUCLEOTIDE; NOVOBIOCIN; POLYDEOXYRIBONUCLEOTIDE SYNTHASE; PYRIMIDINE DERIVATIVE; RIFAMPICIN; TETRACYCLINE; THYMIDINE; TRIMETHOPRIM; UNCLASSIFIED DRUG;

ADENYLATION; ANTIBACTERIAL ACTIVITY; ARTICLE; BACTERIAL GENOME; BACTERIAL GROWTH; BACTERIAL PNEUMONIA; BACTERIAL STRAIN; CHEMICAL ANALYSIS; CONTROLLED STUDY; DNA REPAIR; DNA REPLICATION; DNA SYNTHESIS; DRUG IDENTIFICATION; DRUG STRUCTURE; ENZYME ACTIVITY; ENZYME ANALYSIS; ENZYME INHIBITION; GENE EXPRESSION; GENE IDENTIFICATION; GENE LIBRARY; GENE OVEREXPRESSION; GENETIC SCREENING; MICROBIOLOGY; MOLECULAR CLONING; NONHUMAN; PRIORITY JOURNAL; PROTEIN EXPRESSION; PROTEIN PURIFICATION; STREPTOCOCCUS PNEUMONIAE;

ANTI-BACTERIAL AGENTS; BACTERIAL PROTEINS; BASE SEQUENCE; DNA LIGASES; ENZYME INHIBITORS; HUMANS; KINETICS; PYRIMIDINES; SMALL MOLECULE LIBRARIES; STREPTOCOCCUS PNEUMONIAE;

BACTERIA (MICROORGANISMS); EUKARYOTA; LIGA; STREPTOCOCCUS PNEUMONIAE;

EID: 53849127859     PISSN: 1742464X     EISSN: 17424658     Source Type: Journal    
DOI: 10.1111/j.1742-4658.2008.06652.x     Document Type: Article

References (46)

1. Kornberg A Baker TA (1992) DNA ligased. In DNA Replication, 2nd edn (Kornberg A Baker TA, eds pp. 307 322. W. H. Freeman, New York, NY.
2. Lindahl T Barnes DE (1992) Mammalian DNA ligases. Annu Rev Biochem 61, 251 281.
3. Tomkinson AE, Vijayakumar S, Pascal JM Ellenberger T (2006) DNA ligases: structure, reaction mechanisms, and function. Chem Rev 106, 687 699.
4. Feldberg RS, Young H, Morrice LAF Keir HM (1972) Some observations on the cofactor requirement for partially purified DNA ligase from Escherichia coli. FEBS Lett 27, 345 349.
5. Konard EB, Mordrich P Lehman IR (1973) Genetic and enzymatic characterization of a conditional lethal mutant of Escherichia coli K12 with a temperature-sensitive DNA ligase. J Mol Biol 77, 519 529.
6. Modrich P Lehman IR (1971) Enzymatic characterization of a mutant of Escherichia coli with an altered DNA ligase. Proc Natl Acad Sci USA 68, 1002 1005.
7. Dermody JJ, Robinson GT Sternglanz R (1979) Conditional-lethal deoxyribonucleic acid ligase mutant of Escherichia coli. J Bacteriol 139, 701 704.
8. Gellert M Bullock ML (1970) DNA ligase mutants of Escherichia coli. Proc Natl Acad Sci USA 67, 1580 1587.
9. Gottsman MM, Hicks ML Gellert M (1973) Genetics and function of DNA ligase in Escherichia coli. J Mol Biol 77, 531 547.
10. Horiuchi T, Sato T Nagata T (1975) DNA degradation in an amber mutant of Escherichia coli K12 affecting DNA ligase and viability. J Mol Biol 95, 271 287.
11. Sato T, Horiuchi T Nagata T (1975) Genetic analysis of an amber mutation in Escherichia coli K-12, affecting deoxyribonucleic acid ligase and viability. J Bacteriol 124, 1089 1096.
12. Morse LS, Beck LA Pauling C (1976) Effect of chloramphenicol and the recB gene product on DNA metabolism in Escherichia coli K12 strains defective in DNA ligase. Mol Gen Genet 147, 79 82.
13. Morse LS Pauling C (1975) Induction of error-prone repair as a consequence of DNA ligase deficiency in Escherichia coli. Proc Natl Acad Sci USA 72, 4645 4649.
14. Pauling C, Beck LA Wilczynski SP (1976) Properties of a DNA ligase mutant of Escherichia coli: introduction of strand breaks in DNA. J Gen Microbiol 94, 297 304.
15. Gong C, Martins A, Bongiorno P, Glickman M Shuman S (2004) Biochemical and genetic analysis of the four DNA ligases of mycobacteria. J Biol Chem 279, 20594 20606.
16. +-dependent DNA ligase from Staphylococcus aureus. J Bacteriol 183, 3016 3024.
17. Park UE, Olivera BM, Hughes KT, Roth JR Hillyard DR (1989) DNA ligase and the pyridine nucleotide cycle in Salmonella typhimurium. J Bacteriol 171, 2173 2180.
18. +-dependent ligase encoded by yerG is an essential gene of Bacillus subtilis. Nucleic Acids Res 28, 4642 4648.
19. Wilkinson A, Day J Bowater R (2001) Bacterial DNA ligases. Mol Microbiol 40, 1241 1248.
20. Ishino Y, Shinagawa H, Makino K, Tsunasawa S, Saklyama F Nakata A (1986) Nucleotide sequence of the lig gene and primary structure of DNA ligase of Escherichia coli. Mol Gen Genet 204, 1 7.
21. Shark KB Conway T (1992) Cloning and molecular characterization of the DNA ligase gene (lig) from Zymomonas mobilis. FEMS Microbiol Lett 96, 19 26.
22. +-dependent DNA ligase. Structure 7, 35 42.
23. Takahasi M, Yamaguchi E Uchida T (1984) Thermophilic DNA ligase: purification and properties of the enzyme from Thermus thermophilus HB8. J Biol Chem 259, 10041 10047.
24. Thorbjarnardottir SH, Jonsson ZO, Andresson OS, Kristjansson JK, Eggertsson G Palsdottir A (1995) Cloning and sequence analysis of the DNA ligase-encoding gene of Rhodothermus marinus, and overproduction, purification, and characterization of two thermophilic DNA ligases. Gene 161, 1 6.
25. Doherty AJ Wigley DB (1999) Functional domains of an ATP-dependent DNA ligase. J Mol Biol 285, 63 71.
26. +)-dependent DNA ligase: modular architecture and functional implications. EMBO J 19, 1119 1129.
27. Luo J Barany F (1996) Identification of essential residues in Thermus thermophilus DNA ligase. Nucleic Acids Res 24, 3079 3085.
28. Timson DJ Wigley DB (1999) Functional domains of an NAD+-dependent DNA ligase. J Mol Biol 285, 73 83.
29. + synthesis within a bacterial DNA ligase crystal. Structure 12, 1449 1459.
30. Nandakumar J, Nair PA Shuman S (2007) Last stop on the road to repair: structure of E. coli DNA ligase bound to nicked DNA-adenylate. Mol Cell 26, 257 271.
31. Pascal JM, O'Brien PJ, Tomkinson AE Ellenberger T (2004) Human DNA ligase I completely encircles and partially unwinds nicked DNA. Nature 432, 473 478.
32. +-dependent DNA ligase is selectively inhibited by glycosylamines compared with human DNA ligase I. Nucleic Acids Res 33, 7090 7094.
33. +- dependent DNA ligase (Rv3014c) from Mycobacterium tuberculosis: crystal structure of the adenylation domain and identification of novel inhibitors. J Biol Chem 280, 30273 30281.
34. Subramanya HS, Doherty AJ, Ashford SR Wigley DB (1996) Crystal structure of an ATP-dependent DNA ligase from bacteriophage T7. Cell 85, 607 615.
35. +-dependent DNA ligase by pyridochromanones. J Biol Chem 278, 39435 39442.
36. Ciarrocchi G, Macphee DG, Deady LW Tilley L (1999) Specific inhibition of the eubacterial DNA ligase by arylamino compounds. Antimicrob Agents Chemother 43, 2766 2772.
37. Chen XC, Hentz NG, Hubbard F, Meier TI, Sittampalam S Zhao G (2002) Development of a fluorescence resonance energy transfer assay for measuring the activity of Streptococcus pneumoniae DNA ligase, an enzyme essential for DNA replication, repair, and recombination. Anal Biochem 309, 232 240.
38. Hoskins JA, Alborn WE Jr., Arnold J, Blaszczak LC, Burgett S, DeHoff BS, Estrem ST, Fritz L, Fu DJ, Fuller W et al. (2001) The genome of the bacterium Streptococcus pneumoniae strain R6. J Bacteriol 183, 5709 5717.
39. Hoskins J, Matsushima P, Tang J, Mullen DL, Zhao G, Meier TI, Nicas T Jaskunas SR (1999) Gene disruption studies of penicillin-binding protein 1a, 1b, and 2a in Streptococcus pneumoniae. J Bacteriol 181, 6552 6555.
40. Barnes DE, Johnston LH, Kodama K, Tomkinson AE, Lasko DD Lindahl T (1990) Human DNA ligase I cDNA: cloning and functional expression in Saccharomyces cerevisiae. Proc Natl Acad Sci USA 87, 6679 6683.
41. Teraoka H, Minami H, Iijima S, Tsukada K, Koiwai O Date T (1993) Expression of active human DNA ligase I in Escherichia coli cells that harbor a full-length DNA ligase I cDNA construct. J Biol Chem 268, 24156 24162.
42. Yang SW Chan JYH (1992) Analysis of the formation of AMP-DNA intermediate and the successive reaction by human DNA ligase I and II. J Biol Chem 267, 8117 8122.
43. Acebo P, Nieto C, Corrales MA, Espinosa M Lopez P (2000) Quantitative detection of Streptococcus pneumoniae cells harboring single or multiple copies of the gene encoding the green fluorescent protein. Microbiology 146, 1267 1273.
44. Clancy J, Petipas J, Dib-Hajj F, Yuan W, Cronan M, Kamath AV, Bergeron J Retsema JA (1996) Molecular cloning and functional analysis of a novel macrolide-resistance determinant, mefA, from Streptococcus pyogenes. Mol Microbiol 22, 867 879.
45. Zhao G, Meier TI, Peery RB, Matsushima P Skatrud PL (1999) Biochemical and molecular analysis of the C-terminal domain of Era GTPase from Streptococcus pneumoniae. Microbiology 145, 791 800.
46. Ma L Kovacs J (2000) Expression and characterization of recombinant human-derived Pneumocystis carinii dihydrofolate reductase. Antimicrob Agents Chemother 44, 3092 3096.