Genomic tools to profile antibiotic mode of action

References

• Akerley BJ, Rubin EJ, Novick VL, et al. (2002). A genome-scale analysis for identification of genes required for growth or survival of Haemophilus influenzae. Proc Natl Acad Sci USA 99:966–71
   PubMed Web of Science ®Google Scholar
• Baba T, Ara T, Hasegawa M, et al. (2006). Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection. Mol Syst Biol 2: 2006.0008
   Web of Science ®Google Scholar
• Baba T, Huan HC, Datsenko K, et al. (2008). The applications of systematic in-frame, single-gene knockout mutant collection of Escherichia coli K-12. Methods Mol Biol 416:183–94
   PubMedGoogle Scholar
• Babu M, Diaz-Mejia JJ, Vlasblom J, et al. (2011a). Genetic interaction maps in Escherichia coli reveal functional crosstalk among cell envelope biogenesis pathways. PLoS Genet 7:e1002377
   PubMedGoogle Scholar
• Babu M, Gagarinova A, Emili A. (2011b). Array-based synthetic genetic screens to map bacterial pathways and functional networks in Escherichia coli. Methods Mol Biol 781:99–126
   PubMedGoogle Scholar
• Babu M, Gagarinova A, Greenblatt J, Emili A. (2011c). Array-based synthetic genetic screens to map bacterial pathways and functional networks in Escherichia coli. Methods Mol Biol 765:125–53
   PubMedGoogle Scholar
• Badarinarayana V, Estep PW, 3rd Shendure J, et al. (2001). Selection analyses of insertional mutants using subgenic-resolution arrays. Nat Biotechnol 19:1060–65
   PubMed Web of Science ®Google Scholar
• Berens C, Hillen W. (2004). Gene regulation by tetracyclines. Genet Eng (NY) 26:255–77
   PubMedGoogle Scholar
• Bloodworth RA, Gislason AS, Cardona ST. (2013). Burkholderia cenocepacia conditional growth mutant library created by random promoter replacement of essential genes. MicrobiologyOpen 2:243–58
   PubMed Web of Science ®Google Scholar
• Brochado AR, Typas A. (2013). High-throughput approaches to understanding gene function and mapping network architecture in bacteria. Curr Opin Microbiol 16:199–206
   PubMed Web of Science ®Google Scholar
• Brown ED. (2013). Is the GAIN Act a turning point in new antibiotic discovery? Can J Microbiol 59:153–6
   PubMed Web of Science ®Google Scholar
• Brown ED, Thomas DY. (2008). Canadian Chemical Biology Network: biochemistry back to the future. Biochem Cell Biol 86:ix, xi–xii
   Web of Science ®Google Scholar
• Brown ED, Wright GD. (2005). New targets and screening approaches in antimicrobial drug discovery. Chem Rev 105:759–74
   PubMed Web of Science ®Google Scholar
• Bugrysheva JV, Froehlich BJ, Freiberg JA, Scott JR. (2011). The histone-like protein Hlp is essential for growth of Streptococcus pyogenes: comparison of genetic approaches to study essential genes. Appl Environ Microbiol 77:4422–8
   PubMed Web of Science ®Google Scholar
• Butland G, Peregrin-Alvarez JM, Li J, et al. (2005). Interaction network containing conserved and essential protein complexes in Escherichia coli. Nature 433:531–7
   PubMed Web of Science ®Google Scholar
• Cardona ST, Mueller C, Valvano MA. (2006). Identification of essential operons in Burkholderia cenocepacia with a rhamnose inducible promoter. Appl Environ Microbiol 72:2547–55
   PubMed Web of Science ®Google Scholar
• Cardona ST, Valvano MA. (2005). An expression vector containing a rhamnose-inducible promoter provides tightly regulated gene expression in Burkholderia cenocepacia. Plasmid 54:219–28
   PubMed Web of Science ®Google Scholar
• Carroll P, Muttucumaru DG, Parish T. (2005). Use of a tetracycline-inducible system for conditional expression in Mycobacterium tuberculosis and Mycobacterium smegmatis. Appl Environ Microbiol 71:3077–84
   PubMed Web of Science ®Google Scholar
• Christen B, Abeliuk E, Collier JM, et al. (2011). The essential genome of a bacterium. Mol Syst Biol 7:528
   PubMedGoogle Scholar
• Clatworthy AE, Pierson E, Hung DT. (2007). Targeting virulence: a new paradigm for antimicrobial therapy. Nat Chem Biol 3:541–8
   PubMed Web of Science ®Google Scholar
• Davies J, Davies D. (2010). Origins and evolution of antibiotic resistance. Microbiol Mol Biol Rev 74:417–33
   PubMed Web of Science ®Google Scholar
• Deigan KE, Ferre-D'Amare AR. (2011). Riboswitches: discovery of drugs that target bacterial gene-regulatory RNAs. Acc Chem Res 44:1329–38
   PubMed Web of Science ®Google Scholar
• D'Elia MA, Pereira MP, Brown ED. (2009). Are essential genes really essential? Trends Microbiol 17:433–8
   PubMed Web of Science ®Google Scholar
• Dennis JJ, Zylstra GJ. (1998). Plasposons: modular self-cloning minitransposon derivatives for rapid genetic analysis of gram-negative bacterial genomes. Appl Environ Microbiol 64:2710–15
   PubMed Web of Science ®Google Scholar
• DeVito JA, Mills JA, Liu VG, et al. (2002). An array of target-specific screening strains for antibacterial discovery. Nat Biotechnol 20:478–83
   PubMed Web of Science ®Google Scholar
• Diller DJ. (2008). The synergy between combinatorial chemistry and high-throughput screening. Curr Opin Drug Discov Devel 11:346–55
   PubMedGoogle Scholar
• Donald RGK, Skwish S, Forsyth RA, et al. (2009). A Staphylococcus aureus fitness test platform for mechanism-based profiling of antibacterial compounds. Chem Biol 16:826–36
   PubMed Web of Science ®Google Scholar
• Ehrt S, Guo XV, Hickey CM, et al. (2005). Controlling gene expression in mycobacteria with anhydrotetracycline and Tet repressor. Nucleic Acids Res 33:e21
   PubMed Web of Science ®Google Scholar
• Eidem TM, Roux CM, Dunman PM. (2012). RNA decay: a novel therapeutic target in bacteria. Wiley Interdiscip Rev RNA 3:443–54
   PubMed Web of Science ®Google Scholar
• Forsyth RA, Haselbeck RJ, Ohlsen KL, et al. (2002). A genome-wide strategy for the identification of essential genes in Staphylococcus aureus. Mol Microbiol 43:1387–400
   PubMed Web of Science ®Google Scholar
• Fortney K, Xie W, Kotlyar M, et al. (2013). NetwoRx: connecting drugs to networks and phenotypes in Saccharomyces cerevisiae. Nucleic Acids Res 41:D720–7
   PubMed Web of Science ®Google Scholar
• Gallagher LA, Shendure J, Manoil C. (2011). Genome-scale identification of resistance functions in Pseudomonas aeruginosa using Tn-seq. MBio 2:e00315–10
   PubMed Web of Science ®Google Scholar
• Galperin MY, Koonin EV. (2004). ‘Conserved hypothetical’ proteins: prioritization of targets for experimental study. Nucleic Acids Res 32:5452–63
   PubMed Web of Science ®Google Scholar
• Gawronski JD, Wong SM, Giannoukos G, et al. (2009). Tracking insertion mutants within libraries by deep sequencing and a genome-wide screen for Haemophilus genes required in the lung. Proc Natl Acad Sci USA 106:16422–7
   PubMed Web of Science ®Google Scholar
• Gerdes SY, Scholle MD, Campbell JW, et al. (2003). Experimental determination and system level analysis of essential genes in Escherichia coli MG1655. J Bacteriol 185:5673–84
   PubMed Web of Science ®Google Scholar
• Gil R, Silva FJ, Pereto J, Moya A. (2004). Determination of the core of a minimal bacterial gene set. Microbiol Mol Biol Rev 68:518–37
   PubMed Web of Science ®Google Scholar
• Goodman AL, McNulty NP, Zhao Y, et al. (2009). Identifying genetic determinants needed to establish a human gut symbiont in its habitat. Cell Host Microbe 6:279–89
   PubMed Web of Science ®Google Scholar
• Guzman LM, Belin D, Carson MJ, Beckwith J. (1995). Tight regulation, modulation, and high-level expression by vectors containing the arabinose PBAD promoter. J Bacteriol 177:4121–30
   PubMed Web of Science ®Google Scholar
• Gwynn MN, Portnoy A, Rittenhouse SF, Payne DJ. (2010). Challenges of antibacterial discovery revisited. Ann N Y Acad Sci 1213:5–19
   PubMed Web of Science ®Google Scholar
• Haldimann A, Daniels LL, Wanner BL. (1998). Use of new methods for construction of tightly regulated arabinose and rhamnose promoter fusions in studies of the Escherichia coli phosphate regulon. J Bacteriol 180:1277–86
   PubMed Web of Science ®Google Scholar
• Huber J, Donald RG, Lee SH, et al. (2009). Chemical genetic identification of peptidoglycan inhibitors potentiating carbapenem activity against methicillin-resistant Staphylococcus aureus. Chem Biol 16:837–48
   PubMed Web of Science ®Google Scholar
• Hutchison CA, Peterson SN, Gill SR, et al. (1999). Global transposon mutagenesis and a minimal Mycoplasma genome. Science 286:2165–9
   PubMed Web of Science ®Google Scholar
• Inglese J, Johnson RL, Simeonov A, et al. (2007). High-throughput screening assays for the identification of chemical probes. Nat Chem Biol 3:466–79
   PubMed Web of Science ®Google Scholar
• Jacobs MA, Alwood A, Thaipisuttikul I, et al. (2003). Comprehensive transposon mutant library of Pseudomonas aeruginosa. Proc Natl Acad Sci USA 100:14339–44
   PubMed Web of Science ®Google Scholar
• Joyce AR, Palsson BO. (2008). Predicting gene essentiality using genome-scale in silico models. Methods Mol Biol 416:433–57
   PubMedGoogle Scholar
• Judson N, Mekalanos JJ. (2000). TnAraOut, a transposon-based approach to identify and characterize essential bacterial genes. Nat Biotechnol 18:740–5
   PubMed Web of Science ®Google Scholar
• Kang Y, Durfee T, Glasner JD, et al. (2004). Systematic mutagenesis of the Escherichia coli genome. J Bacteriol 186:4921–30
   PubMed Web of Science ®Google Scholar
• Kaur P, Agarwal S, Datta S. (2009). Delineating bacteriostatic and bactericidal targets in mycobacteria using IPTG inducible antisense expression. PLoS One 4:e5923
   PubMedGoogle Scholar
• Kitagawa M, Ara T, Arifuzzaman M, et al. (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 12:291–9
   PubMed Web of Science ®Google Scholar
• Lagace-Wiens PR, Adam HJ, Low DE, et al. (2013). Trends in antibiotic resistance over time among pathogens from Canadian hospitals: results of the CANWARD study 2007–11. J Antimicrob Chemother 68:i23–9
   PubMed Web of Science ®Google Scholar
• Langridge GC, Phan MD, Turner DJ, et al. (2009). Simultaneous assay of every Salmonella typhi gene using one million transposon mutants. Genome Res 19:2308–16
   PubMed Web of Science ®Google Scholar
• Lu TK, Koeris MS. (2011). The next generation of bacteriophage therapy. Curr Opin Microbiol 14:524–31
   PubMed Web of Science ®Google Scholar
• Meng J, Kanzaki G, Meas D, et al. (2012). A genome-wide inducible phenotypic screen identifies antisense RNA constructs silencing Escherichia coli essential genes. FEMS Microbiol Lett 329:45–53
   PubMed Web of Science ®Google Scholar
• Metzker ML. (2010). Sequencing technologies – the next generation. Nat Rev Genet 11:31–46
   PubMed Web of Science ®Google Scholar
• Mnaimneh S, Davierwala AP, Haynes J, et al. (2004). Exploration of essential gene functions via titratable promoter alleles. Cell 118:31–44
   PubMed Web of Science ®Google Scholar
• Morrison JM, Dunman PM. (2011). The modulation of Staphylococcus aureus mRNA turnover. Future Microbiol 6:1141–50
   PubMed Web of Science ®Google Scholar
• Opijnen T, Camilli A. (2010). Genome-wide fitness and genetic interactions determined by Tn-seq, a high-throughput massively parallel sequencing method for microorganisms. Curr Protoc Microbiol 19:1E.3.1--1E.3.16
   Google Scholar
• Pal C, Hurst LD. (2004). Evidence against the selfish operon theory. Trends Genet 20:232–34
   PubMed Web of Science ®Google Scholar
• Pathania R, Zlitni S, Barker C, et al. (2009). Chemical genomics in Escherichia coli identifies an inhibitor of bacterial lipoprotein targeting. Nat Chem Biol 5:849–56
   PubMed Web of Science ®Google Scholar
• Patil SD, Sharma R, Srivastava S, et al. (2013). Downregulation of yidC in Escherichia coli by antisense RNA expression results in sensitization to antibacterial essential oils eugenol and carvacrol. PLoS One 8:e57370
   PubMedGoogle Scholar
• Payne DJ, Gwynn MN, Holmes DJ, Pompliano DL. (2007). Drugs for bad bugs: confronting the challenges of antibacterial discovery. Nat Rev Drug Discov 6:29–40
   PubMed Web of Science ®Google Scholar
• Projan SJ, Shlaes DM. (2004). Antibacterial drug discovery: is it all downhill from here? Clin Microbiol Infect, Suppl 4:18–22
   Google Scholar
• Rabizadeh S, Sears C. (2008). New horizons for the infectious diseases specialist: how gut microflora promote health and disease. Curr Infect Dis Rep 10:92–8
   PubMedGoogle Scholar
• Raju RM, Unnikrishnan M, Rubin DHF, et al. (2012). Mycobacterium tuberculosis ClpP1 and ClpP2 function together in protein degradation and are required for viability in vitro and during infection. PLoS Pathog 8:1–8
   Google Scholar
• Reznikoff WS, Winterberg KM. (2008). Transposon-based strategies for the identification of essential bacterial genes. Methods Mol Biol 416:13–26
   PubMedGoogle Scholar
• Roemer T, Boone C. (2013). Systems-level antimicrobial drug and drug synergy discovery. Nat Chem Biol 9:222–31
   PubMed Web of Science ®Google Scholar
• Roemer T, Davies J, Giaever G, Nislow C. (2011). Bugs, drugs and chemical genomics. Nat Chem Biol 8:46–56
   PubMed Web of Science ®Google Scholar
• Rognan D. (2007). Chemogenomic approaches to rational drug design. Br J Pharmacol 152:38–52
   PubMed Web of Science ®Google Scholar
• Sassetti CM, Boyd DH, Rubin EJ. (2003). Genes required for mycobacterial growth defined by high density mutagenesis. Mol Microbiol 48:77–84
   PubMed Web of Science ®Google Scholar
• Serina S, Nozza F, Nicastro G, et al. (2004). Scanning the Escherichia coli chromosome by random transposon mutagenesis and multiple phenotypic screening. Res Microbiol 155:692–701
   PubMed Web of Science ®Google Scholar
• Shendure J, Ji H. (2008). Next-generation DNA sequencing. Nat Biotechnol 26:1135–45
   PubMed Web of Science ®Google Scholar
• Silander OK, Nikolic N, Zaslaver A, et al. (2012). A genome-wide analysis of promoter-mediated phenotypic noise in Escherichia coli. PLoS Genet 8:e1002443
   PubMed Web of Science ®Google Scholar
• Smith AM, Heisler LE, Mellor J, et al. (2009). Quantitative phenotyping via deep barcode sequencing. Genome Res 19:1836–42
   PubMed Web of Science ®Google Scholar
• Smith AM, Heisler LE, St Onge RP, et al. (2010). Highly-multiplexed barcode sequencing: an efficient method for parallel analysis of pooled samples. Nucleic Acids Res 38:e142
   PubMedGoogle Scholar
• Spellberg B, Guidos R, Gilbert D, et al. (2008). The epidemic of antibiotic-resistant infections: a call to action for the medical community from the Infectious Diseases Society of America. Clin Infect Dis 46:155–64
   PubMed Web of Science ®Google Scholar
• Thanassi JA, Hartman-Neumann SL, Dougherty TJ, et al. (2002). Identification of 113 conserved essential genes using a high-throughput gene disruption system in Streptococcus pneumoniae. Nucleic Acids Res 30:3152–62
   PubMed Web of Science ®Google Scholar
• Thanbichler M, Iniesta AA, Shapiro L. (2007). A comprehensive set of plasmids for vanillate- and xylose-inducible gene expression in Caulobacter crescentus. Nucleic Acids Res 35:e137
   PubMedGoogle Scholar
• Therien AG, Huber JL, Wilson KE, et al. (2012). Broadening the spectrum of beta-lactam antibiotics through inhibition of signal peptidase type I. Antimicrob Agents Chemother 56:4662–70
   PubMed Web of Science ®Google Scholar
• Topp S, Reynoso CM, Seeliger JC, et al. (2010). Synthetic riboswitches that induce gene expression in diverse bacterial species. Appl Environ Microbiol 76:7881–4
   PubMed Web of Science ®Google Scholar
• van Opijnen T, Bodi KL, Camilli A. (2009). Tn-seq: high-throughput parallel sequencing for fitness and genetic interaction studies in microorganisms. Nat Methods 6:767–72
   PubMed Web of Science ®Google Scholar
• van Opijnen T, Camilli A. (2012). A fine scale phenotype-genotype virulence map of a bacterial pathogen. Genome Res 22:2541–51
   PubMed Web of Science ®Google Scholar
• Wang H, Claveau D, Vaillancourt JP, et al. (2011). High-frequency transposition for determining antibacterial mode of action. Nat Chem Biol 7:720–29
   PubMed Web of Science ®Google Scholar
• Wang J, Soisson SM, Young K, et al. (2006). Platensimycin is a selective FabF inhibitor with potent antibiotic properties. Nature 441:358–61
   PubMed Web of Science ®Google Scholar
• Wei JR, Krishnamoorthy V, Murphy K, et al. (2011). Depletion of antibiotic targets has widely varying effects on growth. Proc Natl Acad Sci USA 108:4176–81
   PubMed Web of Science ®Google Scholar
• Wong SM, Akerley BJ. (2003). Inducible expression system and marker-linked mutagenesis approach for functional genomics of Haemophilus influenzae. Gene 316:177–86
   PubMed Web of Science ®Google Scholar
• Wright GD. (2007). The antibiotic resistome: the nexus of chemical and genetic diversity. Nat Rev Microbiol 5:175–86
   PubMed Web of Science ®Google Scholar
• Xiao Y, Gerth K, Muller R, Wall D. (2012). Myxobacterium-produced antibiotic TA (myxovirescin) inhibits type II signal peptidase. Antimicrob Agents Chemother 56:2014–21
   PubMed Web of Science ®Google Scholar
• Xu HH, Trawick JD, Haselbeck RJ, et al. (2010). Staphylococcus aureus TargetArray: comprehensive differential essential gene expression as a mechanistic tool to profile antibacterials. Antimicrob Agents Chemother 54:3659–70
   PubMed Web of Science ®Google Scholar
• Yin D, Ji Y. (2007). Identification of essential genes in Staphylococcus aureus by construction and screening of conditional mutant library. Methods Mol Biol 416:297–306
   Google Scholar
• Zhanel GG, Adam HJ, Baxter MR, et al. (2013). Antimicrobial susceptibility of 22746 pathogens from Canadian hospitals: results of the CANWARD 2007–11 study. J Antimicrob Chemother 68:i7–22
   PubMed Web of Science ®Google Scholar
• Zhang CT, Zhang R. (2007). Gene essentiality analysis based on DEG, a database of essential genes. Methods Mol Biol 416:391–400
   Google Scholar