High-frequency transposition for determining antibacterial mode of action

Nature Chemical Biology

Volumn 7, Issue 10, 2011, Pages 720-729

  Wang, Hao ^a   Claveau, David ^a   Vaillancourt, John P ^a   Roemer, Terry ^a   Meredith, Timothy C ^a,b  

^a MERCK FROSST CENTRE FOR THERAPEUTIC RESEARCH   (Canada)

^b NOVARTIS INSTITUTES FOR BIOMEDICAL RESEARCH   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

METICILLIN;

ARTICLE; BACTERIOPHAGE; GENE EXPRESSION; GENE INSERTION; GENOME; GENOTYPE; METHICILLIN RESISTANT STAPHYLOCOCCUS AUREUS; METHICILLIN SUSCEPTIBLE STAPHYLOCOCCUS AUREUS; NONHUMAN; PHENOTYPE; PRIORITY JOURNAL; ROOM TEMPERATURE; STAPHYLOCOCCUS AUREUS; TRANSPOSON;

BACTERIA (MICROORGANISMS); STAPHYLOCOCCUS AUREUS;

EID: 80052961113     PISSN: 15524450     EISSN: 15524469     Source Type: Journal    
DOI: 10.1038/nchembio.643     Document Type: Article

References (50)

1. Theuretzbacher, U. Future antibiotics scenarios: is the tide starting to turn? Int. J. Antimicrob. Agents 34, 15-20 (2009).
2. Rice, L. B. The clinical consequences of antimicrobial resistance. Curr. Opin. Microbiol. 12, 476-481 (2009).
3. Brötz-Oesterhelt, H. & Sass, P. Postgenomic strategies in antibacterial drug discovery. Future Microbiol. 5, 1553-1579 (2010).
4. Boucher, H. W. et al. Bad bugs, no drugs: no ESKAPE! An update from the Infectious Diseases Society of America. Clin. Infect. Dis. 48, 1-12 (2009).
5. Mills, S. D. When will the genomics investment pay off for antibacterial discovery? Biochem. Pharmacol. 71, 1096-1102 (2006).
6. Alekshun, M. N. & Levy, S. B. Molecular mechanisms of antibacterial multidrug resistance. Cell 128, 1037-1050 (2007). (Pubitemid 46427883)
7. Bockstael, K. & Van Aerschot, A. Antimicrobial resistance in bacteria. Cent. Eur. J. Med. 4, 141-155 (2009).
8. Lange, R. P., Locher, H. H., Wyss, P. C. & Then, R. L. The targets of currently used antibacterial agents: lessons for drug discovery. Curr. Pharm. Des. 13, 3140-3154 (2007). (Pubitemid 350130963)
9. Silver, L. L. Challenges of antibacterial discovery. Clin. Microbiol. Rev. 24, 71-109 (2011).
10. Payne, D. J., Gwynn, M. N., Holmes, D. J. & Pompliano, D. L. Drugs for bad bugs: confronting the challenges of antibacterial discovery. Nat. Rev. Drug Discov. 6, 29-40 (2007). (Pubitemid 46020284)
11. Breithaupt, H. The new antibiotics. Nat. Biotechnol. 17, 1165-1169 (1999).
12. Miesel, L., Greene, J. & Black, T. A. Genetic strategies for antibacterial drug discovery. Nat. Rev. Genet. 4, 442-456 (2003). (Pubitemid 36648144)
13. Payne, D. J., Gwynn, M. N., Holmes, D. J. & Rosenberg, M. Genomic approaches to antibacterial discovery. Methods Mol. Biol. 266, 231-259 (2004).
14. Bordi, C. et al. In vitro mutagenesis of Bacillus subtilis by using a modified Tn7 transposon with an outward-facing inducible promoter. Appl. Environ. Microbiol. 74, 3419-3425 (2008). (Pubitemid 351812796)
15. Salipante, S. J., Barlow, M. & Hall, B. G. GeneHunter, a transposon tool for identification and isolation of cryptic antibiotic resistance genes. Antimicrob. Agents Chemother. 47, 3840-3845 (2003). (Pubitemid 37484998)
16. Carleton, S., Projan, S. J., Highlander, S. K., Moghazeh, S. M. & Novick, R. P. Control of pT181 replication II. Mutational analysis. EMBO J. 3, 2407-2414 (1984).
17. Xia, M., Lunsford, R. D., McDevitt, D. & Iordanescu, S. Rapid method for the identification of essential genes in Staphylococcus aureus. Plasmid 42, 144-149 (1999). (Pubitemid 29440095)
18. Novick, R. P., Edelman, I. & Lofdahl, S. Small Staphylococcus aureus plasmids are transduced as linear multimers that are formed and resolved by replicative processes. J. Mol. Biol. 192, 209-220 (1986). (Pubitemid 17203053)
19. Yansura, D. G. & Henner, D. J. Use of the Escherichia coli lac repressor and operator to control gene expression in Bacillus subtilis. Proc. Natl. Acad. Sci. USA 81, 439-443 (1984). (Pubitemid 14185745)
20. Luong, T. T., Ouyang, S., Bush, K. & Lee, C. Y. Type 1 capsule genes of Staphylococcus aureus are carried in a staphylococcal cassette chromosome genetic element. J. Bacteriol. 184, 3623-3629 (2002). (Pubitemid 34625671)
21. Anthony, R. M., Schuitema, A. R., Oskam, L. & Klatser, P. R. Direct detection of Staphylococcus aureus mRNA using a flow through microarray. J. Microbiol. Methods 60, 47-54 (2005). (Pubitemid 39573336)
22. Heath, R. J., Li, J., Roland, G. E. & Rock, C. O. Inhibition of the Staphylococcus aureus NADPH-dependent enoyl-acyl carrier protein reductase by triclosan and hexachlorophene. J. Biol. Chem. 275, 4654-4659 (2000). (Pubitemid 30108851)
23. Huber, J. et al. Chemical genetic identification of peptidoglycan inhibitors potentiating carbapenem activity against methicillin-resistant Staphylococcus aureus. Chem. Biol. 16, 837-848 (2009).
24. Ruiz, N. Bioinformatics identification of MurJ (MviN) as the peptidoglycan lipid II flippase in Escherichia coli. Proc. Natl. Acad. Sci. USA 105, 15553-15557 (2008).
25. Champoux, J. J. DNA topoisomerases: structure, function, and mechanism. Annu. Rev. Biochem. 70, 369-413 (2001). (Pubitemid 32662215)
26. Ng, E. Y., Trucksis, M. & Hooper, D. C. Quinolone resistance mutations in topoisomerase IV: relationship to the flqA locus and genetic evidence that topoisomerase IV is the primary target and DNA gyrase is the secondary target of fluoroquinolones in Staphylococcus aureus. Antimicrob. Agents Chemother. 40, 1881-1888 (1996). (Pubitemid 26277810)
27. Ng, E. Y., Trucksis, M. & Hooper, D. C. Quinolone resistance mediated by norA: physiologic characterization and relationship to flqB, a quinolone resistance locus on the Staphylococcus aureus chromosome. Antimicrob. Agents Chemother. 38, 1345-1355 (1994). (Pubitemid 24170718)
28. Ince, D. & Hooper, D. C. Quinolone resistance due to reduced target enzyme expression. J. Bacteriol. 185, 6883-6892 (2003). (Pubitemid 37444490)
29. Donald, R. G. et al. A Staphylococcus aureus fitness test platform for mechanism-based profiling of antibacterial compounds. Chem. Biol. 16, 826-836 (2009).
30. Hurdle, J. G., O'Neill, A. J. & Chopra, I. Anti-staphylococcal activity of indolmycin, a potential topical agent for control of staphylococcal infections. J. Antimicrob. Chemother. 54, 549-552 (2004). (Pubitemid 39177486)
31. Werner, R. G., Thorpe, L. F., Reuter, W. & Nierhaus, K. H. Indolmycin inhibits prokaryotic tryptophanyl-tRNA ligase. Eur. J. Biochem. 68, 1-3 (1976).
32. Cassels, R., Oliva, B. & Knowles, D. Occurrence of the regulatory nucleotides ppGpp and pppGpp following induction of the stringent response in staphylococci. J. Bacteriol. 177, 5161-5165 (1995).
33. Wolz, C., Geiger, T. & Goerke, C. The synthesis and function of the alarmone (p) ppGpp in firmicutes. Int. J. Med. Microbiol. 300, 142-147 (2010).
34. Brandenberger, M., Tschierske, M., Giachino, P., Wada, A. & Berger-Bachi, B. Inactivation of a novel three-cistronic operon tcaR-tcaA-tcaB increases teicoplanin resistance in Staphylococcus aureus. Biochim. Biophys. Acta 1523, 135-139 (2000).
35. Law, C. J., Maloney, P. C. & Wang, D. N. Ins and outs of major facilitator superfamily antiporters. Annu. Rev. Microbiol. 62, 289-305 (2008).
36. De Crécy-Lagard, V., El, Y. B., de la Garza, R. D., Noiriel, A. & Hanson, A. D. Comparative genomics of bacterial and plant folate synthesis and salvage: predictions and validations. BMC Genomics 8, 245 (2007).
37. Bermingham, A. & Derrick, J. P. The folic acid biosynthesis pathway in bacteria: evaluation of potential for antibacterial drug discovery. Bioessays 24, 637-648 (2002). (Pubitemid 34780351)
38. Hawser, S., Lociuro, S. & Islam, K. Dihydrofolate reductase inhibitors as antibacterial agents. Biochem. Pharmacol. 71, 941-948 (2006).
39. Sammes, P. G. Sulfonamides and sulfones in Comprehensive Medicinal Chemistry (eds. Sammes, P. G. & Taylor, J. B.) 255-270 (Pergamon Press, Oxford, 1990).
40. Saxild, H. H., Brunstedt, K., Nielsen, K. I., Jarmer, H. & Nygaard, P. Definition of the Bacillus subtilis PurR operator using genetic and bioinformatic tools and expansion of the PurR regulon with glyA, guaC, pbuG, xpt-pbuX, yqhZ-folD, and pbuO. J. Bacteriol. 183, 6175-6183 (2001). (Pubitemid 34059389)
41. Freiberg, C., Brunner, N., Macko, L. & Fischer, H. P. Discovering antibiotic efficacy biomarkers: toward mechanism-specific high content compound screening. Mol. Cell. Proteomics 5, 2326-2335 (2006). (Pubitemid 46040637)
42. Swedberg, G., Castensson, S. & Skold, O. Characterization of mutationally altered dihydropteroate synthase and its ability to form a sulfonamidecontaining dihydrofolate analog. J. Bacteriol. 137, 129-136 (1979). (Pubitemid 9093926)
43. Lampe, D. J., Churchill, M. E. & Robertson, H. M. A purified mariner transposase is sufficient to mediate transposition in vitro. EMBO J. 15, 5470-5479 (1996). (Pubitemid 26336228)
44. Bae, T. et al. Staphylococcus aureus virulence genes identified by Bursa aurealis mutagenesis and nematode killing. Proc. Natl. Acad. Sci. USA 101, 12312-12317 (2004). (Pubitemid 39145440)
45. Chaudhuri, R. R. et al. Comprehensive identification of essential Staphylococcus aureus genes using transposon-mediated differential hybridisation (TMDH). BMC Genomics 10, 291 (2009).
46. Wright, G. D. The antibiotic resistome: the nexus of chemical and genetic diversity. Nat. Rev. Microbiol. 5, 175-186 (2007). (Pubitemid 46291277)
47. Meredith, T. C., Swoboda, J. G. & Walker, S. Late-stage polyribitol phosphate wall teichoic acid biosynthesis in Staphylococcus aureus. J. Bacteriol. 190, 3046-3056 (2008). (Pubitemid 351508205)
48. Pitcher, D. G., Saunders, N. A. & Owen, R. J. Rapid extraction of bacterial genomic DNA with guanidium thiocyanate. Lett. Appl. Microbiol. 8, 151-156 (1989). (Pubitemid 19126878)
49. Ralser, M. et al. An efficient and economic enhancer mix for PCR. Biochem. Biophys. Res. Commun. 347, 747-751 (2006). (Pubitemid 44092646)
50. Livak, K. J. & Schmittgen, T. D. Analysis of relative gene expression data using real-time quantitative PCR and the 2 (-Delta Delta C (T)) Method. Methods 25, 402-408 (2001). (Pubitemid 34164012)