Use of genomics to select antibacterial targets

Biochemical Pharmacology

Volumn 71, Issue 7, 2006, Pages 1066-1072

  Pucci, Michael J ^a  

^a Achillion Pharmaceuticals Inc   (United States)

Author keywords

Antibacterial; Antibiotic; Bioinformatics; Essentiality; Genomics; Mutagenesis

Indexed keywords

ANTIBIOTIC AGENT; BACTERIAL VACCINE; GENE PRODUCT;

ANTIBIOTIC RESISTANCE; BACTERIAL GENETICS; BIOINFORMATICS; DNA SEQUENCE; DRUG EFFICACY; DRUG RESEARCH; DRUG TARGETING; GENE DISRUPTION; GENE IDENTIFICATION; GRAM NEGATIVE BACTERIUM; HUMAN; IN VIVO STUDY; METHICILLIN RESISTANT STAPHYLOCOCCUS AUREUS; MUTAGENESIS; NONHUMAN; PATHOGENESIS; PRIORITY JOURNAL; REVIEW;

EID: 33644514658     PISSN: 00062952     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.bcp.2005.12.004     Document Type: Article

References (49)

1. S.B. Levy, and B. Marshall Antibacterial resistance worldwide: causes, challenges and responses Nat Med 10 Suppl 2004 S122 S129
2. D.M. Livermore Bacterial resistance: origins, epidemiology, and impact Clin Infect Dis 36 Suppl 2003 S11 S23
3. C.T. Barrett, and J.F. Barrett Antibacterials: are the new entries enough to deal with the emerging resistance problems? Curr Opin Biotechnol 14 2003 621 625
4. IDSA Report: Bad bugs, no drugs as antibiotic discovery stagnates, a public health crisis brews; July 2004. http://www.idsociety.org.
5. R.D. Fleischmann, M.D. Adams, O. White, R.A. Clayton, E.F. Kirkness, and A.R. Kerlavage Whole-genome random sequencing and assembly of Haemophilus influenzae Rd Science 269 1995 496 512
6. T.J. Dougherty, J.F. Barrett, and M.J. Pucci Genomics-based approaches to novel antimicrobial target discovery T.J. Dougherty S.J. Projan Microbial genomics and drug discovery 2003 Marcel Dekker New York 71 96
7. D. McDevitt, and M. Rosenberg Exploiting genomics to discover new antibiotics Trends Microbiol 9 2001 611 617
8. S.A. Haney, L.E. Alkane, P.M. Dunman, E. Murphy, and S.J. Projan Genomics in anti-infective drug discovery-getting to endgame Curr Pharmaceut Des 8 2002 1099 1118
9. C. Freiberg, and H. Brotz-Oesterhelt Functional genomics in antibacterial drug discovery Drug Discov Today 10 2005 927 935
10. R.E. Bruccoleri, TJ. Dougherty, and D.B. Davison Concordance analysis of microbial genomes Nucl Acids Res 26 1998 4482 4486
11. M.S. Lee, B.A. Dougherty, A.C. Madeo, and D.A. Morrison Construction and analysis of a library for random insertional mutagenesis in Streptococcus pneumoniae: use for recovery of mutants defective in genetic transformation and for identification of essential genes Appl Environ Microbiol 65 1999 1883 1890
12. C.D. Herring, and F.R. Blattner Conditional lethal amber mutations in essential Escherichia coli genes J Bacteriol 186 2004 2673 2681
13. M.B. Schmid, N. Kapur, D.R. Isaacson, P. Lindroos, and C. Sharpe Genetic analysis of temperature-sensitive lethal mutants of Salmonella typhimurium Genetics 123 1989 625 633
14. S.Y. Gerdes, M.D. Scholle, J.W. Campbell, G. Balazzi, E. Ravasz, and M.D. Daugherty Experimental determination and system level analysis of essential genes in Escherichia coli MG1655 J Bacteriol 185 2003 5673 5684
15. N.R. Salama, B. Shepherd, and S. Falkow Global transposon mutagenesis and essential gene analysis of Helicobacter pylori J Bacteriol 186 2004 7926 7935
16. C.A. Hutchinson, S.N. Peterson, S.R. Gill, R.T. Cline, O. White, and C.M. Fraser Global transposon mutagenesis and a minimal Mycoplasma genome Science 286 1999 2165 2169
17. R.A. Forsyth, R.J. Hasselbeck, K.L. Ohlsen, R.T. Yamamoto, H. Xu, and J.D. Trawic A genome-wide strategy for the identification of essential genes in Staphylococus aureus Mol Microbiol 43 2002 1387 1400
18. B.A. Dougherty, and H.O. Smith Identification of Haemophilus influenzae Rd transformation genes using cassette mutagenesis Microbiology 145 1999 401 409
19. C. Freiberg, B. Wieland, F. Splatmann, K. Ehlert, H. Brotz, and H. Labischinski Identification of novel essential Escherichia coli genes conserved among pathogenic bacteria J Mol Biotechnol 3 2001 483 489
20. J.A. Thanassi, S.L. Hartman-Neumann, T.J. Dougherty, B.A. Dougherty, and M.J. Pucci Identification of 113 conserved essential genes using a high-throughput gene disruption system in Streptococcus pneumoniae Nucl Acids Res 30 2002 3152 3162
21. A.F. Chalker, H.W. Minehart, N.J. Hughes, K.K. Koretke, M.A. Lonetto, and K.K. Brinkman Systematic identification of selective essential genes in Helicobacter pylori by genome prioritization and allelic replacement mutagenesis J Bacteriol 183 2001 1259 1268
22. A.J. Link, D. Phillips, and G.M. Church Methods for generating precise deletions and insertions in the genome of wild-type Escherichia coli: application to open reading frame characterization J Bacteriol 179 1997 6228 6237
23. M. Jana, T.T. Luong, H. Komatsuzawa, M. Shigeta, and C.Y. Lee A method for demonstrating gene essentiality in Staphylococcus aureus Plasmid 44 2000 100 104
24. M. Hensel, J.E. Shea, C. Gleeson, M.D. Jones, E. Dalton, and D.W. Holden Simultaneous identification of bacterial virulence genes by negative selection Science 269 1995 400 403
25. M.J. Mahan, J.W. Tobias, J.M. Slauch, P.C. Hanna, R.J. Collier, and J. Mekalanos Antibiotic-based selection for bacterial genes that are specifically induced during infection of a host Proc Natl Acad Sci USA 92 1995 669 673
26. R.H. Valdivia, and S. Falkow Bacterial genetics by flow cytometry: rapid isolation of Salmonella typhimurium acid-inducible promoters by differential fluorescence induction Mol Microbiol 22 1996 367 378
27. K. Kobayashi, S.D. Ehrlich, A. Albertini, A. Amati, K.K. Andersen, and M. Arnaud Essential Bacillus subtilis genes Proc Natl Acad Sci USA 100 2003 4678 4683
28. B.J. Akerley, E.J. Rubin, A. Camilli, D.J. Lampe, H.M. Robertson, and J.J. Mekalanos Systematic identification of essential genes by in vitro mariner mutagenesis Proc Natl Acad Sci USA 95 1998 8927 8932
29. A.F. Chalker, and R.D. Lunsford Rational identification of new antibacterial drug targets that are essential for viability using a genomics-based approach Pharmacol Therapeut 95 2002 1 20
30. Vilar S J.M.G., C.C. Guet, and S. Liebler Modeling network dynamics: the lac operon, a case study J Cell Biol 161 2003 471 476
31. M.B. Schmid Novel approaches to the discovery of antimicrobial agents Curr Opin Chem Biol 2 1998 529 534
32. J.A. DeVito, J.A. Mills, V.G. Liu, A. Agarwal, C.F. Sizemore, and Z. Yao An array of target-specific screening strains for antibacterial discovery Nat Biotechnol 20 2002 478 483
33. C.M. Berg, D.E. Berg, and E.A. Groisman Transposable elements and the genetic engineering of bacteria D.E. Berg M. Howe Mobile DNA 1989 American Society for Microbiology Washington, DC 879 925
34. I. Hamer, T.M. DeZwaan, M.V. Montenegro-Chamorro, S.A. Frank, and J.E. Hame Recent advances in large-scale transposon mutagenesis Curr Opin Chem Biol 5 2001 67 73
35. B.J. Akerley, E.J. Rubin, A. Camilli, D.J. Lampe, H.M. Robertson, and J.J. Mekalanos Systematic identification of essential genes by in vitro mariner mutagenesis Proc Natl Acad Sci USA 95 1998 8927 8932
36. S.M. Wong, and J.J. Mekalanos Genetic footprinting with mariner-based transposition in Pseudomonas aeruginosa Proc Natl Acad Sci USA 97 2000 10191 10196
37. B.P. Guo, and J.J. Mekalanos Helicobacter pylori mutagenesis by mariner in vitro transposition FEMS Immumol Med Microbiol 30 2001 87 93
38. D. Yin, and Y. Ji Genomic analysis using conditional phenotypes generated by antisense RNA Curr Opin Microbiol 5 2002 330 333
39. J.-M. Reyrat, V. Pelicic, B. Gicquel, and R. Rappuoli Counterselectable markers: untapped tools for bacterial genetics and pathogenesis Infect Immun 66 1998 4011 4017
40. S. Ramanathan-Girish, J. McColm, J.M. Clements, P. Taupin, S. Barrowcliffe, and J. Hevizi Pharmacokinetics in animals and humans of a first-in-class peptide deformylase inhibitor Antimicrob Agents Chemother 48 2004 4835 4842
41. J.M. Clements, A. Ayscough, K. Keavey, and S.P. East Peptide deformylase inhibitors, potential for a new class of broad spectrum antibacterials Curr Med Chem 1 2002 239 249
42. S.Y. Gerdes, M.D. Scholle, M. D'Souza, A. Bernal, M.V. Baev, and M. Farrell From genetic footprinting to antimicrobial drug targets: examples in cofactor biosynthetic pathways J Bacteriol 184 2002 4555 4572
43. S.R. Gill, D.E. Fouts, G.L. Archer, E.F. Mongodin, R.T. DeBoy, and J. Ravel Insights on evolution of virulence and resistance from the complete genome analysis of an early meticicllin-resistant Staphylococcus aureus strain and a biofilm-producing methicillin-resistant Staphylococcus epidermidis strain J Bacteriol 187 2005 2426 2438
44. M.B. Schmid Seeing is believing: the impact of structural genomics on antimicrobial drug discovery Nat Rev Microbiol 2 2004 739 746
45. J. Liu, M. Dehbi, G. Moeck, F. Arhin, P. Bauda, and D. Bergeron Antimicrobial drug discovery through bacteriophage genomics Nat Biotechnol 22 2004 185 191
46. A. Meinke, T. Henics, and E. Nagy Bacterial genomes pave the way to novel vaccines Curr Opin Microbiol 7 2004 314 320
47. J. Adu-Bobie, B. Capecchi, D. Serruto, R. Rappuoli, and M. Pizza Two years into reverse vaccinology Vaccine 21 2003 605 610
48. M.A. Barry, W.C. Lai, and S.A. Johnston Protection against mycoplasma infection using expression-library immunization Nature 377 1995 632 635
49. K. Stemke-Hale, B. Kaltenboeck, F.J. DeGraves, K.F. Sykes, J. Huang, and C.H. Bu Screening the whole genome of a pathogen in vivo for individual protective antigens Vaccine 23 2005 3016 3025