A robust platform for chemical genomics in bacterial systems

Molecular Biology of the Cell

Volumn 27, Issue 6, 2016, Pages 1015-1025

  French, Shawn ^a   Mangat, Chand ^a   Bharat, Amrita ^a   Cté, Jean Philippe ^a   Mori, Hirotada ^b   Brown, Eric D ^a  

^a MCMASTER UNIVERSITY   (Canada)

^b NARA INSTITUTE OF SCIENCE AND TECHNOLOGY   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

ANTIBIOTIC AGENT; CHLORAMPHENICOL; CIPROFLOXACIN; DOXYCYCLINE; ERYTHROMYCIN; NALIDIXIC ACID; NORFLOXACIN; RIFAMPICIN; SPECTINOMYCIN; STREPTOMYCIN; TETRACYCLINE; ANTIINFECTIVE AGENT;

ANIMAL CELL; ARTICLE; BACTERIAL CELL WALL; BACTERIAL GENOME; BACTERIAL GROWTH; BACTERIAL STRAIN; BACTERIUM; BACTERIUM COLONY; BIOGENESIS; BIOMASS; CHEMICAL GENETICS; CONTROLLED STUDY; DRUG DESIGN; GENE DELETION; GENE EXPRESSION PROFILING; GENE MAPPING; GENETIC SELECTION; GENOMICS; GROWTH RATE; IN VITRO STUDY; MEASUREMENT; MINIMUM INHIBITORY CONCENTRATION; NONHUMAN; PRIORITY JOURNAL; DRUG EFFECTS; ESCHERICHIA COLI; GENETICS; GENOTYPE ENVIRONMENT INTERACTION; METABOLISM; MULTIDRUG RESISTANCE; PROCEDURES;

ANTI-BACTERIAL AGENTS; DRUG RESISTANCE, MULTIPLE, BACTERIAL; ESCHERICHIA COLI; GENE DELETION; GENE-ENVIRONMENT INTERACTION; GENOMICS; METABOLIC NETWORKS AND PATHWAYS;

EID: 84960911814     PISSN: 10591524     EISSN: 19394586     Source Type: Journal    
DOI: 10.1091/mbc.E15-08-0573     Document Type: Article

References (51)

1. Baba T, Ara T, Hasegawa M, Takai Y, Okumura Y, Baba M, Datsenko KA, Tomita M, Wanner BL, Mori H (2006). Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection. Mol Syst Biol 2, 2006.0008.
2. Baryshnikova A, Costanzo M, Kim Y, Ding H, Koh J, Toufighi K, Youn J-Y, Ou J, Luis B-JS, Bandyopadhyay S, et al. (2010). Quantitative analysis of fitness and genetic interactions in yeast on a genome scale. Nat Methods 7, 1017-1024.
3. Bianchi AA, Baneyx F (1999). Hyperosmotic shock induces the sigma32 and sigmaE stress regulons of Escherichia coli. Mol Microbiol 34, 1029-1038.
4. Brideau C, Gunter B, Pikounis B, Liaw A (2003). Improved statistical methods for hit selection in high-Throughput screening. J Biomol Screen 8, 634-647.
5. Brochado AR, Typas A (2013). High-Throughput approaches to understanding gene function and mapping network architecture in bacteria. Curr Opin Microbiol 16, 199-206.
6. Cascales E, Gavioli M, Sturgis JN, Lloubes R (2000). Proton motive force drives the interaction of the inner membrane TolA and outer membrane pal proteins in Escherichia coli. Mol Microbiol 38, 904-915.
7. Chase JW, Richardson CC (1977). Escherichia coli mutants deficient in exonuclease VII. J Bacteriol 129, 934-947.
8. Delcour AH (2009). Outer membrane permeability and antibiotic resistance. Biochim Biophys Acta 1794, 808-816.
9. Dixon SJ, Costanzo M, Baryshnikova A, Andrews B, Boone C (2009). Systematic mapping of genetic interaction networks. Annu Rev Genet 43, 601-625.
10. Ejim L, Farha MA, Falconer SB, Wildenhain J, Coombes BK, Tyers M, Brown ED, Wright GD (2011). Combinations of antibiotics and nonantibiotic drugs enhance antimicrobial efficacy. Nat Chem Biol 7, 348-350.
11. Grishin AM, Ajamian E, Tao L, Zhang L, Menard R, Cygler M (2011). Structural and functional studies of the Escherichia coli phenylacetyl-CoA monooxygenase complex. J Biol Chem 286, 10735-10743.
12. Harrison JJ, Wade WD, Akierman S, Vacchi-Suzzi C, Stremick CA, Turner RJ, Ceri H (2009). The chromosomal toxin gene yafQ is a determinant of multidrug tolerance for Escherichia coli growing in a biofilm. Antimicrob Agents Chemother 53, 2253-2258.
13. Hibbing ME, Fuqua C, Parsek MR, Peterson SB (2010). Bacterial competition: surviving and thriving in the microbial jungle. Nat Rev Microbiol 8, 15-25.
14. Hirai K, Aoyama H, Irikura T, Iyobe S, Mitsuhashi S (1986). Differences in susceptibility to quinolones of outer membrane mutants of Salmonella typhimurium and Escherichia coli. Antimicrob Agents Chemother 29, 535-538.
15. Ihaka R, Gentleman R (1996). R: a language for data analysis and graphics. J Comput Graph Stat 5, 299-314.
16. Kahm M Hasenbrink G (2010). grofit: fitting biological growth curves with R. J Stat Softw 33.
17. Keseler IM, Mackie A, Peralta-Gil M, Santos-Zavaleta A, Gama-Castro S, Bonavides-Martinez C, Fulcher C, Huerta AM, Kothari A, Krummenacker M, et al. (2013). EcoCyc: fusing model organism databases with systems biology. Nucleic Acids Res 41, D605-D612.
18. Kitagawa M, Ara T, Arifuzzaman M, Ioka-Nakamichi T, Inamoto E, Toyonaga H, Mori H (2005). Complete set of ORF clones of Escherichia coli ASKA library (a complete set of E. coli K-12 ORF archive): unique resources for biological research. DNA Res 12, 291-299.
19. Lee AY, St Onge RP, Proctor MJ, Wallace IM, Nile AH, Spagnuolo PA, Jitkova Y, Gronda M, Wu Y, Kim MK, et al. (2014). Mapping the cellular response to small molecules using chemogenomic fitness signatures. Science 344, 208-211.
20. Liu A, Tran L, Becket E, Lee K, Chinn L, Park E, Tran K, Miller JH (2010). Antibiotic sensitivity profiles determined with an Escherichia coli gene knockout collection: generating an antibiotic bar code. Antimicrob Agents Chemother 54, 1393-1403.
21. Lock RL, Harry EJ (2008). Cell-Division inhibitors: new insights for future antibiotics. Nat Rev Drug Discov 7, 324-338.
22. Mangat CS, Bharat A, Gehrke SS, Brown ED (2014). Rank ordering plate data facilitates data visualization and normalization in high-Throughput screening. J Biomol Screen 19, 1314-1320.
23. Meier-Dieter U, Barr K, Starman R, Hatch L, Rick PD (1992). Nucleotide sequence of the Escherichia coli rfe gene involved in the synthesis of enterobacterial common antigen. Molecular cloning of the rfe-rff gene cluster. J Biol Chem 267, 746-753.
24. Michaut M, Bader GD (2012). Multiple genetic interaction experiments provide complementary information useful for gene function prediction. PLoS Comput Biol 8, e1002559.
25. Naganathan A, Wood MP, Moore SD (2015). The large ribosomal subunit protein L9 enables the growth of EF-P deficient cells and enhances small subunit maturation. PLoS One 10, e0120060.
26. Nichols RJ, Sen S, Choo YJ, Beltrao P, Zietek M, Chaba R, Lee S, Kazmierczak KM, Lee KJ, Wong A, et al. (2011). Phenotypic landscape of a bacterial cell. Cell 144, 143-156.
27. Nikaido H (1996). Multidrug efflux pumps of gram-negative bacteria. J Bacteriol 178, 5853.
28. Nikaido H (2003). Molecular basis of bacterial outer membrane permeability revisited. Microbiol Mol Biol Rev 67, 593-656.
29. Nikaido H, Basina M, Nguyen V, Rosenberg EY (1998). Multidrug efflux pump AcrAB of Salmonella typhimurium excretes only those beta-lactam antibiotics containing lipophilic side chains. J Bacteriol 180, 4686-4692.
30. Nishino K, Yamaguchi A (2001). Analysis of a complete library of putative drug transporter genes in Escherichia coli. J Bacteriol 183, 5803-5812.
31. Ohara M, Wu HC, Sankaran K, Rick PD (1999). Identification and characterization of a new lipoprotein, NlpI, in Escherichia coli K-12. J Bacteriol 181, 4318-4325.
32. Okusu H, Ma D, Nikaido H (1996). AcrAB efflux pump plays a major role in the antibiotic resistance phenotype of Escherichia coli multiple-Antibiotic-resistance (Mar) mutants. J Bacteriol 178, 306-308.
33. Paradis-Bleau C, Markovski M, Uehara T, Lupoli TJ, Walker S, Kahne DE, Bernhardt TG (2010). Lipoprotein cofactors located in the outer membrane activate bacterial cell wall polymerases. Cell 143, 1110-1120.
34. Peters JM, Silvis MR, Zhao D, Hawkins JS, Gross CA, Qi LS (2015). Bacterial CRISPR: accomplishments and prospects. Curr Opin Microbiol 27, 121-126.
35. Piddock LJ, Walters RN (1992). Bactericidal activities of five quinolones for Escherichia coli strains with mutations in genes encoding the SOS response or cell division. Antimicrob Agents Chemother 36, 819-825.
36. Ruusala T, Andersson D, Ehrenberg M, Kurland CG (1984). Hyper-Accurate ribosomes inhibit growth. EMBO J 3, 2575-2580.
37. Schneider CA, Rasband WS, Eliceiri KW (2012). NIH Image to ImageJ: 25 years of image analysis. Nat Methods 9, 671-675.
38. Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT, Ramage D, Amin N, Schwikowski B, Ideker T (2003). Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res 13, 2498-2504.
39. Stokes JM, Davis JH, Mangat CS, Williamson JR, Brown ED (2014). Discovery of a small molecule that inhibits bacterial ribosome biogenesis. Elife 3, e03574.
40. Takeuchi R, Tamura T, Nakayashiki T, Tanaka Y, Muto A, Wanner BL, Mori H (2014). Colony-Live-A high-Throughput method for measuring microbial colony growth kinetics-reveals diverse growth effects of gene knockouts in Escherichia coli. BMC Microbiol 14, 171.
41. Tamae C, Liu A, Kim K, Daniel S, Hong J, Becket E, Bui A, Solaimani P, Tran KP, Yang H, et al. (2008). Determination of antibiotic hypersensitivity among 4,000 single-gene-knockout mutants of Escherichia coli. J Bacteriol 190, 5981-5988.
42. Theocharidis A, van Dongen S, Enright AJ, Freeman TC (2009). Network visualization and analysis of gene expression data using BioLayout Express3D. Nat Protocols 4, 1535-1550.
43. Tong A, Evangelista M, Parsons AB, Xu H (2001). Systematic genetic analysis with ordered arrays of yeast deletion mutants. Science 294, 2364-2368.
44. Typas A, Banzhaf M, van den Berg van Saparoea B, Verheul J, Biboy J, Nichols RJ, Zietek M, Beilharz K, Kannenberg K, von Rechenberg M, et al. (2010). Regulation of peptidoglycan synthesis by outer-membrane proteins. Cell 143, 1097-1109.
45. Typas A, Nichols RJ, Siegele DA, Shales M (2008). High-Throughput, quantitative analyses of genetic interactions in E. coli. Nat Methods 5, 781-787.
46. Vales LD, Rabin BA, Chase JW (1982). Subunit structure of Escherichia coli exonuclease VII. J Biol Chem 257, 8799-8805.
47. Vales LD, Rabin BA, Chase JW (1983). Isolation and preliminary characterization of Escherichia coli mutants deficient in exonuclease VII. J Bacteriol 155, 1116-1122.
48. Van Dongen S (2008). Graph clustering via a discrete uncoupling process. SIAM J Matrix Anal App 30, 121-141.
49. Wagih O, Parts L (2014). gitter: a robust and accurate method for quantification of colony sizes from plate images. G3 (Bethesda) 4, 547-552.
50. Zlitni S, Ferruccio LF, Brown ED (2013). Metabolic suppression identifies new antibacterial inhibitors under nutrient limitation. Nat Chem Biol 9, 796-804.
51. Zwietering MH, Jongenburger I, Rombouts FM, van 't Riet K (1990). Modeling of the bacterial growth curve. Appl Environ Microbiol 56, 1875-1881.