Isolation and quantitation of topoisomerase complexes accumulated on Escherichia coli chromosomal DNA

Antimicrobial Agents and Chemotherapy

Volumn 56, Issue 11, 2012, Pages 5458-5464

  Aedo, Sandra ^a   Tse Dinh, Yuk Ching ^a,b  

^a NEW YORK MEDICAL COLLEGE   (United States)

^b FLORIDA INTERNATIONAL UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL DNA; CESIUM CHLORIDE; DNA TOPOISOMERASE (ATP HYDROLYSING); DNA TOPOISOMERASE (ATP HYDROLYSING) A; DNA TOPOISOMERASE IV; NALIDIXIC ACID; NORFLOXACIN; PROTEIN PARC;

ANTIBIOTIC RESISTANCE; ANTIBODY DETECTION; ARTICLE; BACTERIOSTASIS; CELL DEATH; CELL LYSATE; CONTROLLED STUDY; CULTURE MEDIUM; DENSITY GRADIENT CENTRIFUGATION; DNA DRUG COMPLEX; DNA REPLICATION; DRUG TARGETING; ENZYME ASSAY; ESCHERICHIA COLI; GENE MUTATION; IN VIVO STUDY; MINIMUM INHIBITORY CONCENTRATION; NONHUMAN; PRIORITY JOURNAL; QUANTITATIVE ANALYSIS; SLOT BLOT HYBRIDIZATION;

ANTI-BACTERIAL AGENTS; CELL FRACTIONATION; CESIUM; CHLORIDES; CHROMOSOMES, BACTERIAL; DNA GYRASE; DNA TOPOISOMERASE IV; DNA, BACTERIAL; DNA-BINDING PROTEINS; ESCHERICHIA COLI; MICROBIAL SENSITIVITY TESTS; MICROBIAL VIABILITY; MUTATION; NORFLOXACIN; PROTEIN BINDING; ULTRACENTRIFUGATION;

EID: 84868015367     PISSN: 00664804     EISSN: 10986596     Source Type: Journal    
DOI: 10.1128/AAC.01182-12     Document Type: Article

References (43)

1. Adachi N, So S, Koyama H. 2004. Loss of nonhomologous end joining confers camptothecin resistance in DT40 cells. Implications for the repair of topoisomerase I-mediated DNA damage. J. Biol. Chem. 279:37343-37348. doi:10.1074/jbc.M313910200.
2. Bau JT, Kurz EU. 2011. Sodium salicylate is a novel catalytic inhibitor of human DNA topoisomerase II alpha. Biochem. Pharmacol. 81:345-354. doi:10.1016/j.bcp.2010.10.009.
3. Collin F, Karkare S, Maxwell A. 2011. Exploiting bacterial DNA gyrase as a drug target: current state and perspectives. Appl. Microbiol. Biotechnol. 92:479-497. doi:10.1007/s00253-011-3557-z.
4. Cowell IG, Tilby MJ, Austin CA. 2011. An overview of the visualisation and quantitation of low and high MW DNA adducts using the trapped in agarose DNA immunostaining (TARDIS) assay. Mutagenesis 26:253-260. doi:10.1093/mutage/ geq094.
5. Desai SD, Li TK, Rodriguez-Bauman A, Rubin EH, Liu LF. 2001. Ubiquitin/26S proteasome-mediated degradation of topoisomerase I as a resistance mechanism to camptothecin in tumor cells. Cancer Res. 61: 5926-5932.
6. Deweese JE, Osheroff N. 2009. The DNA cleavage reaction of topoisom-erase II: wolf in sheep's clothing. Nucleic Acids Res. 37:738-748. doi: 10.1093/nar/gkn937.
7. Drlica K, Engle EC, Manes SH. 1980. DNA gyrase on the bacterial chromosome: possibility of two levels of action. Proc. Natl. Acad. Sci. U. S. A. 77:6879-6883.
8. Drlica K, Malik M, Kerns RJ, Zhao X. 2008. Quinolone-mediated bacterial death. Antimicrob. Agents Chemother. 52:385-392. doi: 10.1128/AAC.01617-06.
9. Drolet M. 2006. Growth inhibition mediated by excess negative super-coiling: the interplay between transcription elongation, R-loop formation and DNA topology. Mol. Microbiol. 59:723-730. doi:10.1111/j.1365-2958.2005. 05006.x.
10. Dwyer DJ, Kohanski MA, Hayete B, Collins JJ. 2007. Gyrase inhibitors induce an oxidative damage cellular death pathway in Escherichia coli. Mol. Syst. Biol. 3:91. doi:10.1038/msb4100135.
11. Hartsuiker E. 2011. Detection of covalent DNA-bound Spo11 and topo-isomerase complexes. Methods Mol. Biol. 745:65-77. doi:10.1007/978-1-61779- 129-1-5.
12. Hartsuiker E, Neale MJ, Carr AM. 2009. Distinct requirements for the Rad32(Mre11) nuclease and Ctp1(CtIP) in the removal of covalently bound topoisomerase I and II from DNA. Mol. Cell 33:117-123. doi: 10.1016/j.molcel. 2008.11.021.
13. Interthal H, Champoux JJ. 2011. Effects of DNA and protein size on substrate cleavage by human tyrosyl-DNA phosphodiesterase1. Biochem. J. 436:559-566. doi:10.1042/BJ20101841.
14. Kaufmann SH, Svingen PA. 1999. Immunoblot analysis and band depletion assays. Methods Mol. Biol. 94:253-268. doi:10.1385/1-59259-259-7: 253.
15. Keeney S, Giroux CN, Kleckner N. 1997. Meiosis-specific DNA doublestrand breaks are catalyzed by Spo11, a member of a widely conserved protein family. Cell 88:375-384.
16. Khlebnikov A, Datsenko KA, Skaug T, Wanner BL, Keasling JD. 2001. Homogeneous expression of the P(BAD) promoter in Escherichia coli by constitutive expression of the low-affinity high-capacity AraE transporter. Microbiology 147:3241-3247.
17. Khodursky AB, Cozzarelli NR. 1998. The mechanism of inhibition of topoisomerase IV by quinolone antibacterials. J. Biol. Chem. 273:27668-27677.
18. Khodursky AB, et al. 2000. Analysis of topoisomerase function in bacterial replication fork movement: use of DNA microarrays. Proc. Natl. Acad. Sci. U. S. A. 97:9419-9424.
19. Khodursky AB, Zechiedrich EL, Cozzarelli NR. 1995. Topoisomerase IV is a target of quinolones in Escherichia coli. Proc. Natl. Acad. Sci. U. S. A. 92:11801-11805.
20. Kohn KW. 1991. Principles and practice of DNA filter elution. Pharmacol. Ther. 49:55-77.
21. Liao ZY, et al. 2005. A novel polypyrimidine antitumor agent FdUMP[10] induces thymineless death with topoisomerase I-DNA complexes. Cancer Res. 65:4844 - 4851. doi:10.1158/0008-5472.CAN-04-1302.
22. Liu LF. 1989. DNA topoisomerase poisons as antitumor drugs. Annu. Rev. Biochem. 58:351-375. doi:10.1146/annurev.bi.58.070189.002031.
23. Malik M, Zhao X, Drlica K. 2006. Lethal fragmentation of bacterial chromosomes mediated by DNA gyrase and quinolones. Mol. Microbiol. 61:810-825. doi:10.1111/j.1365-2958.2006.05275.x.
24. Nitiss JL. 2009. Targeting DNA topoisomerase IIin cancer chemotherapy. Nat. Rev. Cancer 9:338-350. doi:10.1038/nrc2607.
25. Peters KB, Brown JM. 2002. Tirapazamine: a hypoxia-activated topo-isomerase II poison. Cancer Res. 62:5248-5253.
26. Pommier Y. 2009. DNA topoisomerase I inhibitors: chemistry, biology, and interfacial inhibition. Chem. Rev. 109:2894-2902. doi:10.1021/cr900097c.
27. Pommier Y, Leo E, Zhang H, Marchand C. 2010. DNA topoisomerases and their poisoning by anticancer and antibacterial drugs. Chem. Biol. 17:421-433. doi:10.1016/j.chembiol.2010.04.012.
28. Rowe TC, Grabowski D, Ganapathi R. 2001. Isolation of covalent enzyme-DNA complexes. Methods Mol. Biol. 95:129-135.
29. Snyder M, Drlica K. 1979. DNA gyrase on the bacterial chromosome: DNA cleavage induced by oxolinic acid. J. Mol. Biol. 131:287-302.
30. Subramanian D, Furbee CS, Muller MT. 2001. ICE bioassay. Isolating in vivo complexes of enzyme to DNA. Methods Mol. Biol. 95:137-147.
31. Tavío MM, et al. 1999. Mechanisms involved in the development of resistance to fluoroquinolones in Escherichia coli isolates. J. Antimicrob. Chemother. 44:735-742.
32. Trask DK, DiDonato JA, Muller MT. 1984. Rapid detection and isolation of covalent DNA/protein complexes: application to topoisomerase I and II. EMBO J. 3:671-676.
33. Trask DK, Muller MT. 1988. Stabilization of type I topoisomerase-DNA covalent complexes by actinomycin D. Proc. Natl. Acad. Sci. U. S. A. 85:1417-1421.
34. Tse-Dinh YC. 2007. Exploring DNA topoisomerases as targets of novel therapeutic agents in the treatment of infectious diseases. Infect. Disord. Drug Targets 7:3-9.
35. Tse-Dinh YC. 2009. Bacterial topoisomerase I as a target for discovery of antibacterial compounds. Nucleic Acids Res. 37:731-737. doi:10.1093/nar/gkn936.
36. Wang JC. 2002. Cellular roles of DNA topoisomerases: a molecular perspective. Nat. Rev. Mol. Cell Biol. 3:430-440. doi:10.1038/nrm831.
37. Wang X, Zhao X, Malik M, Drlica K. 2010. Contribution of reactive oxygen species to pathways of quinolone-mediated bacterial cell death. J. Antimicrob. Chemother. 65:520-524. doi:10.1093/jac/dkp486.
38. Willmott CJ, Maxwell A. 1993. A single point mutation in the DNA gyrase A protein greatly reduces binding of fluoroquinolones to the gyrase-DNA complex. Antimicrob. Agents Chemother. 37:126-127.
39. Yoshida H, et al. 1993. Mechanism of action of quinolones against Esch-erichia coli DNA gyrase. Antimicrob. Agents Chemother. 37:839-845.
40. Zechiedrich EL, et al. 2000. Roles of topoisomerases in maintaining steady-state DNA supercoiling in Escherichia coli. J. Biol. Chem. 275: 8103-8113.
41. Zhang A, et al. 2006. A protease pathway for the repair of topoisomerase II-DNA covalent complexes. J. Biol. Chem. 281:35997-36003. doi: 10.1074/jbc.M604149200.
42. Zhang HF, et al. 2004. Cullin 3 promotes proteasomal degradation of the topoisomerase I-DNA covalent complex. Cancer Res. 64:1114-1121.
43. Zhang YW, et al. 2011. Poly(ADP-ribose) polymerase and XPF-ERCC1 participate in distinct pathways for the repair of topoisomerase I-induced DNA damage in mammalian cells. Nucleic Acids Res. 39:3607-3620. doi: 10.1093/nar/gkq1304.