How antibiotics kill bacteria: from targets to networks

Walsh, C. Antibiotics: actions, origins, resistance (ASM Press, Washington, D.C., 2003).

Fleming, A. On antibacterial action of culture of penicillium, with special reference to their use in isolation of B. influenzae. Br. J. Exp. Pathol. 10, 226–236 (1929).

Taubes, G. The bacteria fight back. Science 321, 356–361 (2008).

Drlica, K., Malik, M., Kerns, R. J. & Zhao, X. Quinolone-mediated bacterial death. Antimicrob. Agents Chemother. 52, 385–392 (2008).

Floss, H. G. & Yu, T. W. Rifamycin-mode of action, resistance, and biosynthesis. Chem. Rev. 105, 621–632 (2005).

Tomasz, A. The mechanism of the irreversible antimicrobial effects of penicillins: how the beta-lactam antibiotics kill and lyse bacteria. Annu. Rev. Microbiol. 33, 113–137 (1979). This seminal review of β-lactam-mediated cell death discusses the intricacies of killing by various members of this antibiotic class in terms of the specific drug-inhibited protein targets and their related cell wall maintenance functions.

Vakulenko, S. B. & Mobashery, S. Versatility of aminoglycosides and prospects for their future. Clin. Microbiol. Rev. 16, 430–450 (2003).

Kohanski, M. A., Dwyer, D. J., Hayete, B., Lawrence, C. A. & Collins, J. J. A common mechanism of cellular death induced by bactericidal antibiotics. Cell 130, 797–810 (2007). Reveals that treatment of Gram-positive and Gram-negative bacteria with lethal levels of bactericidal antibiotics induces the formation of hydroxyl radicals through a common mechanism involving drug-induced changes in NADH consumption and central metabolism, notably the TCA cycle.

Dwyer, D. J., Kohanski, M. A., Hayete, B. & Collins, J. J. Gyrase inhibitors induce an oxidative damage cellular death pathway in Escherichia coli. Mol. Syst. Biol. 3, 91 (2007). Describes the physiological responses of E. coli following inhibition of topoisomerase by a fluoroquinolone and a peptide toxin, which include activation of the superoxide stress response and increased Fe–S cluster synthesis. These physiological changes result in hydroxyl radical production, which contributes to cell death.

Kohanski, M. A., Dwyer, D. J., Wierzbowski, J., Cottarel, G. & Collins, J. J. Mistranslation of membrane proteins and two-component system activation trigger antibiotic-mediated cell death. Cell 135, 679–690 (2008). Shows that systems which facilitate membrane protein trafficking are central to aminoglycoside-induced oxidative stress and cell death. This occurs by signalling through the redox- and the envelope stress-responsive two-component systems.

Espeli, O. & Marians, K. J. Untangling intracellular DNA topology. Mol. Microbiol. 52, 925–931 (2004).

Drlica, K. & Snyder, M. Superhelical Escherichia coli DNA: relaxation by coumermycin. J. Mol. Biol. 120, 145–154 (1978).

Gellert, M., Mizuuchi, K., O'Dea, M. H. & Nash, H. A. DNA gyrase: an enzyme that introduces superhelical turns into D.NA. Proc. Natl Acad. Sci. USA 73, 3872–3876 (1976).

Sugino, A., Peebles, C. L., Kreuzer, K. N. & Cozzarelli, N. R. Mechanism of action of nalidixic acid: purification of Escherichia coli nalA gene product and its relationship to DNA gyrase and a novel nicking-closing enzyme. Proc. Natl Acad. Sci. USA 74, 4767–4771 (1977).

Gellert, M., Mizuuchi, K., O'Dea, M. H., Itoh, T. & Tomizawa, J. I. Nalidixic acid resistance: a second genetic character involved in DNA gyrase activity. Proc. Natl Acad. Sci. USA 74, 4772–4776 (1977). References 14 and 15 discuss the results of complementary in vivo and in vitro studies that characterized the genetic locus ( nalA , later gyrA) and the basic mechanism of quinolone antibiotic action (prevention of DNA duplex strand rejoining yielding double-stranded DNA breaks), while postulating on the composition and energetic requirements of DNA gyrase activity.

Hooper, D. C. & Rubinstein, E. Quinolone antimicrobial agents (ASM Press, Washington, D.C., 2003).

Rubinstein, E. History of quinolones and their side effects. Chemotherapy 47 (Suppl. 3), 3–8 (2001).

Lu, T. et al. Enhancement of fluoroquinolone activity by C-8 halogen and methoxy moieties: action against a gyrase resistance mutant of Mycobacterium smegmatis and a gyrase-topoisomerase IV double mutant of Staphylococcus aureus. Antimicrob. Agents Chemother. 45, 2703–2709 (2001).

Chen, C. R., Malik, M., Snyder, M. & Drlica, K. DNA gyrase and topoisomerase IV on the bacterial chromosome: quinolone-induced DNA cleavage. J. Mol. Biol. 258, 627–637 (1996). Identifies topoisomerase IV as a second target of fluoroquinolone antibiotics in Gram-negative bacteria and characterizes subtle but crucial differences in the mechanism of killing by various quinolone drugs.

Drlica, K. & Zhao, X. DNA gyrase, topoisomerase IV, and the 4-quinolones. Microbiol. Mol. Biol. Rev. 61, 377–392 (1997).

Munoz, R. & De La Campa, A. G. ParC subunit of DNA topoisomerase IV of Streptococcus pneumoniae is a primary target of fluoroquinolones and cooperates with DNA gyrase A subunit in forming resistance phenotype. Antimicrob. Agents Chemother. 40, 2252–2257 (1996).

Belland, R. J., Morrison, S. G., Ison, C. & Huang, W. M. Neisseria gonorrhoeae acquires mutations in analogous regions of gyrA and parC in fluoroquinolone-resistant isolates. Mol. Microbiol. 14, 371–380 (1994).

Critchlow, S. E. & Maxwell, A. DNA cleavage is not required for the binding of quinolone drugs to the DNA gyrase-DNA complex. Biochemistry 35, 7387–7393 (1996).

Marians, K. J. & Hiasa, H. Mechanism of quinolone action. A drug-induced structural perturbation of the DNA precedes strand cleavage by topoisomerase, IV. J. Biol. Chem. 272, 9401–9409 (1997).

Kampranis, S. C. & Maxwell, A. The DNA gyrase-quinolone complex. ATP hydrolysis and the mechanism of DNA cleavage. J. Biol. Chem. 273, 22615–22626 (1998). Reveals that quinolone antibiotic binding to the topoisomerase II–DNA complex occurs before DNA strand breakage and that DNA cleavage can occur, albeit at a slower rate, in the presence of the drug based on the results of ATP hydrolysis and DNA cleavage assays.

Yoshida, H., Bogaki, M., Nakamura, M. & Nakamura, S. Quinolone resistance-determining region in the DNA gyrase gyrA gene of Escherichia coli. Antimicrob. Agents Chemother. 34, 1271–1272 (1990).

Morais Cabral, J. H. et al. Crystal structure of the breakage-reunion domain of DNA gyrase. Nature 388, 903–906 (1997).

Heddle, J. & Maxwell, A. Quinolone-binding pocket of DNA gyrase: role of GyrB. Antimicrob. Agents Chemother. 46, 1805–1815 (2002).

Goss, W. A., Deitz, W. H. & Cook, T. M. Mechanism of action of nalidixic acid on Escherichia coli.II. Inhibition of deoxyribonucleic acid synthesis. J. Bacteriol. 89, 1068–1074 (1965).

Snyder, M. & Drlica, K. DNA gyrase on the bacterial chromosome: DNA cleavage induced by oxolinic acid. J. Mol. Biol. 131, 287–302 (1979).

Cox, M. M. et al. The importance of repairing stalled replication forks. Nature 404, 37–41 (2000).

Courcelle, J. & Hanawalt, P. C. RecA-dependent recovery of arrested DNA replication forks. Annu. Rev. Genet. 37, 611–646 (2003).

Howard, B. M., Pinney, R. J. & Smith, J. T. Function of the SOS process in repair of DNA damage induced by modern 4-quinolones. J. Pharm. Pharmacol. 45, 658–662 (1993).

Cirz, R. T. et al. Inhibition of mutation and combating the evolution of antibiotic resistance. PLoS Biol. 3, e176 (2005).

Guerin, E. et al. The SOS response controls integron recombination. Science 324, 1034 (2009).

Beaber, J. W., Hochhut, B. & Waldor, M. K. SOS response promotes horizontal dissemination of antibiotic resistance genes. Nature 427, 72–74 (2004).

Lewin, C. S., Howard, B. M. & Smith, J. T. Protein- and RNA-synthesis independent bactericidal activity of ciprofloxacin that involves the A subunit of DNA gyrase. J. Med. Microbiol 34, 19–22 (1991).

Wang, X., Zhao, X., Malik, M., & Drlica, K. Contribution of reactive oxygen species to pathways of quinolone-mediated bacterial cell death. J. Antimicrob. Chemother. 65, 520–524 (2010).

Kolodkin-Gal, I., Sat, B., Keshet, A. & Engelberg-Kulka, H. The communication factor EDF and the toxin-antitoxin module mazEF determine the mode of action of antibiotics. PLoS Biol. 6, e319 (2008).

Dukan, S. et al. Protein oxidation in response to increased transcriptional or translational errors. Proc. Natl Acad. Sci. USA 97, 5746–5749 (2000).

Hartmann, G., Honikel, K. O., Knusel, F. & Nuesch, J. The specific inhibition of the DNA-directed RNA synthesis by rifamycin. Biochim. Biophys. Acta 145, 843–844 (1967).

Campbell, E. A. et al. Structural mechanism for rifampicin inhibition of bacterial RNA polymerase. Cell 104, 901–912 (2001). Describes the intricacies of binding between rifamycin, rifampicin and a DNA-engaged RNA polymerase, and provides a detailed mechanism for rifamycin action.

Naryshkina, T., Mustaev, A., Darst, S. A. & Severinov, K. The β' subunit of Escherichia coli RNA polymerase is not required for interaction with initiating nucleotide but is necessary for interaction with rifampicin. J. Biol. Chem. 276, 13308–13313 (2001).

Chamberlin, M. & Losick, R. (eds) RNA polymerase (Cold Spring Harbor, New York, 1976).

McClure, W. R. & Cech, C. L. On the mechanism of rifampicin inhibition of RNA synthesis. J. Biol. Chem. 253, 8949–8956 (1978).

Artsimovitch, I., Chu, C., Lynch, A. S. & Landick, R. A new class of bacterial RNA polymerase inhibitor affects nucleotide addition. Science 302, 650–654 (2003).

Sensi, P., Margalith, P. & Timbal, M. T. Rifomycin, a new antibiotic; preliminary report. Farmaco Sci. 14, 146–147 (1959).

Sensi, P. History of the development of rifampin. Rev. Infect. Dis. 5 (Suppl. 3), 402–406 (1983).

Wehrli, W. Rifampin: mechanisms of action and resistance. Rev. Infect. Dis. 5 (Suppl. 3), 407–411 (1983).

Burman, W. J., Gallicano, K. & Peloquin, C. Comparative pharmacokinetics and pharmacodynamics of the rifamycin antibacterials. Clin. Pharmacokinet 40, 327–341 (2001).

Hobby, G. L. & Lenert, T. F. The action of rifampin alone and in combination with other antituberculous drugs. Am. Rev. Respir. Dis. 102, 462–465 (1970).

Kono, Y. Oxygen enhancement of bactericidal activity of rifamycin SV on Escherichia coli and aerobic oxidation of rifamycin SV to rifamycin S catalyzed by manganous ions: the role of superoxide. J. Biochem. (Tokyo) 91, 381–395 (1982). Reveals that redox cycling of rifamycin results in the formation of ROS, which contributes to the bactericidal activity of the antibiotic.

Scrutton, M. C. Divalent metal ion catalysis of the oxidation of rifamycin SV to rifamycin S. FEBS Lett. 78, 216–220 (1977).

Bugg, T. D. & Walsh, C. T. Intracellular steps of bacterial cell wall peptidoglycan biosynthesis: enzymology, antibiotics, and antibiotic resistance. Nat. Prod. Rep. 9, 199–215 (1992).

Holtje, J. V. Growth of the stress-bearing and shape-maintaining murein sacculus of Escherichia coli. Microbiol. Mol. Biol. Rev. 62, 181–203 (1998).

Park, J. T. & Uehara, T. How bacteria consume their own exoskeletons (turnover and recycling of cell wall peptidoglycan). Microbiol. Mol. Biol. Rev. 72, 211–227 (2008).

Wise, E. M. Jr & Park, J. T. Penicillin: its basic site of action as an inhibitor of a peptide cross-linking reaction in cell wall mucopeptide synthesis. Proc. Natl Acad. Sci. USA 54, 75–81 (1965).

Tipper, D. J. & Strominger, J. L. Mechanism of action of penicillins: a proposal based on their structural similarity to acyl-D-alanyl-D-alanine. Proc. Natl Acad. Sci. USA 54, 1133–1141 (1965). References 57 and 58 describe the results of complementary studies first revealing that inhibition of cell wall biosynthesis by β-lactams is due to catalytic site modification of transpeptidase and carboxypeptidase enzymes (later PBPs), which misrecognize the drug as a peptidoglycan substrate mimic.

Waxman, D. J., Yocum, R. R. & Strominger, J. L. Penicillins and cephalosporins are active site-directed acylating agents: evidence in support of the substrate analogue hypothesis. Philos. Trans. R. Soc. Lond. B Biol. Sci. 289, 257–271 (1980).

Josephine, H. R., Kumar, I. & Pratt, R. F. The perfect penicillin? Inhibition of a bacterial DD-peptidase by peptidoglycan-mimetic β-lactams. J. Am. Chem. Soc. 126, 8122–8123 (2004).

Kahne, D., Leimkuhler, C., Lu, W. & Walsh, C. Glycopeptide and lipoglycopeptide antibiotics. Chem. Rev. 105, 425–448 (2005).

Cooper, M. A. & Williams, D. H. Binding of glycopeptide antibiotics to a model of a vancomycin-resistant bacterium. Chem. Biol. 6, 891–899 (1999).

Ge, M. et al. Vancomycin derivatives that inhibit peptidoglycan biosynthesis without binding D-Ala-D-Ala. Science 284, 507–511 (1999).

Tomasz, A., Albino, A. & Zanati, E. Multiple antibiotic resistance in a bacterium with suppressed autolytic system. Nature 227, 138–140 (1970). Shows for the first time that β-lactam-induced cell lysis is regulated by the activity of peptidoglycan hydrolases. Also reveals that wild-type pneumococci and lysis-defective, peptidoglycan hydrolase activity-deficient pneumococci are equally sensitive to β-lactam treatment despite starkly different phenotypic effects.

Heidrich, C., Ursinus, A., Berger, J., Schwarz, H. & Holtje, J. V. Effects of multiple deletions of murein hydrolases on viability, septum cleavage, and sensitivity to large toxic molecules in Escherichia coli. J. Bacteriol. 184, 6093–6099 (2002). Reveals that peptidoglycan hydrolases in E. coli are important for cell separation following cell division and shows that the deletion of multiple peptidoglycan hydrolase enzymes delays β-lactam-induced lysis.

Uehara, T., Dinh, T. & Bernhardt, T. G. LytM-domain factors are required for daughter cell separation and rapid ampicillin-induced lysis in Escherichia coli. J. Bacteriol. 191, 5094–5107 (2009).

Moreillon, P., Markiewicz, Z., Nachman, S. & Tomasz, A. Two bactericidal targets for penicillin in pneumococci: autolysis-dependent and autolysis-independent killing mechanisms. Antimicrob. Agents Chemother. 34, 33–39 (1990). Describes the characterization of the cid system in pneumococci, which contributes to killing by β-lactams independently of peptidoglycan hydrolase (autolysin) activity.

Hoch, J. A. Two-component and phosphorelay signal transduction. Curr. Opin. Microbiol. 3, 165–170 (2000).

Novak, R., Henriques, B., Charpentier, E., Normark, S. & Tuomanen, E. Emergence of vancomycin tolerance in Streptococcus pneumoniae. Nature 399, 590–593 (1999).

Novak, R., Charpentier, E., Braun, J. S. & Tuomanen, E. Signal transduction by a death signal peptide: uncovering the mechanism of bacterial killing by penicillin. Mol. Cell 5, 49–57 (2000).

Brunskill, E. W. & Bayles, K. W. Identification and molecular characterization of a putative regulatory locus that affects autolysis in Staphylococcus aureus. J. Bacteriol. 178, 611–618 (1996).

Brunskill, E. W. & Bayles, K. W. Identification of LytSR-regulated genes from Staphylococcus aureus. J. Bacteriol. 178, 5810–5812 (1996).

Groicher, K. H., Firek, B. A., Fujimoto, D. F. & Bayles, K. W. The Staphylococcus aureus lrgAB operon modulates murein hydrolase activity and penicillin tolerance. J. Bacteriol. 182, 1794–1801 (2000).

Rice, K. C. et al. The Staphylococcus aureus cidAB operon: evaluation of its role in regulation of murein hydrolase activity and penicillin tolerance. J. Bacteriol. 185, 2635–2643 (2003). Suggests that CidAB and LrgAB function as holin–anti-holin-like systems that regulates that activity of peptidoglycan hydrolases, and subsequently, tolerance to β-lactam treatment.

Bayles, K. W. The biological role of death and lysis in biofilm development. Nature Rev. Microbiol. 5, 721–726 (2007).

Spratt, B. G. Distinct penicillin binding proteins involved in the division, elongation, and shape of Escherichia coli K12. Proc. Natl Acad. Sci. USA 72, 2999–3003 (1975).

Kitano, K. & Tomasz, A. Triggering of autolytic cell wall degradation in Escherichia coli by beta-lactam antibiotics. Antimicrob. Agents Chemother. 16, 838–848 (1979).

Lewin, C. S., Howard, B. M., Ratcliffe, N. T. & Smith, J. T. 4-quinolones and the SOS response. J. Med. Microbiol. 29, 139–144 (1989).

Bi, E. & Lutkenhaus, J. Cell division inhibitors SulA and MinCD prevent formation of the FtsZ ring. J. Bacteriol. 175, 1118–1125 (1993).

Goehring, N. W. & Beckwith, J. Diverse paths to midcell: assembly of the bacterial cell division machinery. Curr. Biol. 15, R514–R526 (2005).

Miller, C. et al. SOS response induction by β-lactams and bacterial defense against antibiotic lethality. Science 305, 1629–1631 (2004). Describes observations made in E. coli that β-lactam antibiotics can uniquely stimulate the expression of the SOS stress response through activation of the DpiBA two-component signal transduction system, and suggests that SOS-mediated arrest of cell division may be a protective reaction to transpeptidase inactivation by these drugs.

Varma, A. & Young, K. D. FtsZ collaborates with penicillin binding proteins to generate bacterial cell shape in Escherichia coli. J. Bacteriol. 186, 6768–6774 (2004).

Vincent, S., Glauner, B. & Gutmann, L. Lytic effect of two fluoroquinolones, ofloxacin and pefloxacin, on Escherichia coli W7 and its consequences on peptidoglycan composition. Antimicrob. Agents Chemother. 35, 1381–1385 (1991).

Garrett, R. A. The Ribosome: Structure, Function, Antibiotics, and Cellular Interactions (ASM Press, Washington, D.C., 2000).

Nissen, P., Hansen, J., Ban, N., Moore, P. B. & Steitz, T. A. The structural basis of ribosome activity in peptide bond synthesis. Science 289, 920–930 (2000).

Katz, L. & Ashley, G. W. Translation and protein synthesis: macrolides. Chem. Rev. 105, 499–528 (2005).

Mukhtar, T. A. & Wright, G. D. Streptogramins, oxazolidinones, and other inhibitors of bacterial protein synthesis. Chem. Rev. 105, 529–542 (2005).

Patel, U. et al. Oxazolidinones mechanism of action: inhibition of the first peptide bond formation. J. Biol. Chem. 276, 37199–37205 (2001).

Vannuffel, P. & Cocito, C. Mechanism of action of streptogramins and macrolides. Drugs 51 (Suppl. 1), 20–30 (1996).

Menninger, J. R. & Otto, D. P. Erythromycin, carbomycin, and spiramycin inhibit protein synthesis by stimulating the dissociation of peptidyl-tRNA from ribosomes. Antimicrob. Agents Chemother. 21, 811–818 (1982).

Tenson, T., Lovmar, M. & Ehrenberg, M. The mechanism of action of macrolides, lincosamides and streptogramin B reveals the nascent peptide exit path in the ribosome. J. Mol. Biol. 330, 1005–1014 (2003). Reveals that 50S ribosomal subunit binding to macrolides, lincosamides and streptogramin B allow elongation of distinct amino acid chain lengths during translation, which are determined by the fit between drug molecule and the peptidyltransferase centre of the ribosome before forcing dissociation of the nacent peptidyl tRNA.

Chopra, I. & Roberts, M. Tetracycline antibiotics: mode of action, applications, molecular biology, and epidemiology of bacterial resistance. Microbiol Mol. Biol. Rev. 65, 232–260 (2001).

Davis, B. D. Mechanism of bactericidal action of aminoglycosides. Microbiol. Rev. 51, 341–350 (1987).

Weisblum, B. & Davies, J. Antibiotic inhibitors of the bacterial ribosome. Bacteriol. Rev. 32, 493–528 (1968).

Hancock, R. E. Aminoglycoside uptake and mode of action—with special reference to streptomycin and gentamicin. I. Antagonists and mutants. J. Antimicrob. Chemother. 8, 249–276 (1981).

Davies, J., Gorini, L. & Davis, B. D. Misreading of RNA codewords induced by aminoglycoside antibiotics. Mol. Pharmacol. 1, 93–106 (1965). Describes the results of detailed studies that determine the degree of mistranslation and types of mutagenesis induced by various aminoglycosides while the genetic code was first being deciphered.

Karimi, R. & Ehrenberg, M. Dissociation rate of cognate peptidyl-tRNA from the A-site of hyper-accurate and error-prone ribosomes. Eur. J. Biochem. 226, 355–360 (1994).

Fourmy, D., Recht, M. I., Blanchard, S. C. & Puglisi, J. D. Structure of the A site of Escherichia coli 16S ribosomal RNA complexed with an aminoglycoside antibiotic. Science 274, 1367–1371 (1996).

Pape, T., Wintermeyer, W. & Rodnina, M. V. Conformational switch in the decoding region of 16S rRNA during aminoacyl-tRNA selection on the ribosome. Nature Struct. Biol. 7, 104–107 (2000).

Rahal, J. J. Jr & Simberkoff, M. S. Bactericidal and bacteriostatic action of chloramphenicol against memingeal pathogens. Antimicrob. Agents Chemother. 16, 13–18 (1979).

Goldstein, F. W., Emirian, M. F., Coutrot, A. & Acar, J. F. Bacteriostatic and bactericidal activity of azithromycin against Haemophilus influenzae. J. Antimicrob. Chemother. 25 (Suppl. A), 25–28 (1990).

Roberts, E., Sethi, A., Montoya, J., Woese, C. R. & Luthey-Schulten, Z. Molecular signatures of ribosomal evolution. Proc. Natl Acad. Sci. USA 105, 13953–13958 (2008).

Davis, B. D., Chen, L. L. & Tai, P. C. Misread protein creates membrane channels: an essential step in the bactericidal action of aminoglycosides. Proc. Natl Acad. Sci. USA 83, 6164–6168 (1986).

Arrow, A. S. & Taber, H. W. Streptomycin accumulation by Bacillus subtilis requires both a membrane potential and cytochrome aa3. Antimicrob. Agents Chemother. 29, 141–146 (1986).

Bryan, L. E. & Kwan, S. Roles of ribosomal binding, membrane potential, and electron transport in bacterial uptake of streptomycin and gentamicin. Antimicrob. Agents Chemother. 23, 835–845 (1983). Discusses the role of respiration in the uptake of aminoglycosides and the effects of feedback on respiratory activity on initial drug molecule–target binding.

Hancock, R. Uptake of 14C-streptomycin by some microorganisms and its relation to their streptomycin sensitivity. J. Gen. Microbiol. 28, 493–501 (1962).

Kogut, M., Lightbrown, J. W. & Isaacson, P. Streptomycin action and anaerobiosis. J. Gen. Microbiol. 39, 155–164 (1965).

Bryan, L. E., Kowand, S. K. & Van Den Elzen, H. M. Mechanism of aminoglycoside antibiotic resistance in anaerobic bacteria: Clostridium perfringens and Bacteroides fragilis. Antimicrob. Agents Chemother. 15, 7–13 (1979).

Anand, N. & Davis, B. D. Damage by streptomycin to the cell membrane of Escherichia coli. Nature 185, 22–23 (1960).

Anand, N., Davis, B. D. & Armitage, A. K. Uptake of streptomycin by Escherichia coli. Nature 185, 23–24 (1960).

Ruiz, N. & Silhavy, T. J. Sensing external stress: watchdogs of the Escherichia coli cell envelope. Curr. Opin. Microbiol. 8, 122–126 (2005).

Liu, X. & De Wulf, P. Probing the ArcA-P modulon of Escherichia coli by whole genome transcriptional analysis and sequence recognition profiling. J. Biol. Chem. 279, 12588–12597 (2004).

Malpica, R., Franco, B., Rodriguez, C., Kwon, O. & Georgellis, D. Identification of a quinone-sensitive redox switch in the ArcB sensor kinase. Proc. Natl Acad. Sci. USA 101, 13318–13323 (2004).

Brazas, M. D. & Hancock, R. E. Using microarray gene signatures to elucidate mechanisms of antibiotic action and resistance. Drug Discov. Today 10, 1245–1252 (2005). Discusses the utility of studying gene expression signatures (or patterns in gene expression), derived from microarray-based studies of antibiotic-treated bacteria, in efforts to uncover new drug targets and off-target effects that contribute to drug-induced cell death.

Tamae, C. et al. Determination of antibiotic hypersensitivity among 4,000 single-gene-knockout mutants of Escherichia coli. J. Bacteriol. 190, 5981–5988 (2008).

Breidenstein, E. B., Khaira, B. K., Wiegand, I., Overhage, J. & Hancock, R. E. Complex ciprofloxacin resistome revealed by screening a Pseudomonas aeruginosa mutant library for altered susceptibility. Antimicrob. Agents Chemother. 52, 4486–4491 (2008).

Dwyer, D. J., Kohanski, M. A. & Collins, J. J. Networking opportunities for bacteria. Cell 135, 1153–1156 (2008).

Faith, J. J. et al. Large-scale mapping and validation of Escherichia coli transcriptional regulation from a compendium of expression profiles. PLoS Biol. 5, e8 (2007).

Gardner, T. S., di Bernardo, D., Lorenz, D. & Collins, J. J. Inferring genetic networks and identifying compound mode of action via expression profiling. Science 301, 102–105 (2003).

Bonneau, R. et al. A predictive model for transcriptional control of physiology in a free living cell. Cell 131, 1354–1365 (2007).

Ronen, M., Rosenberg, R., Shraiman, B. I. & Alon, U. Assigning numbers to the arrows: parameterizing a gene regulation network by using accurate expression kinetics. Proc. Natl Acad. Sci. USA 99, 10555–10560 (2002).

Feist, A. M., Herrgard, M. J., Thiele, I., Reed, J. L. & Palsson, B. O. Reconstruction of biochemical networks in microorganisms. Nature Rev. Microbiol. 7, 129–143 (2009).

Imlay, J. A. Pathways of oxidative damage. Annu. Rev. Microbiol. 57, 395–418 (2003).

Schurek, K. N. et al. Novel genetic determinants of low-level aminoglycoside resistance in Pseudomonas aeruginosa. Antimicrob. Agents Chemother. 52, 4213–4219 (2008).

Wigle, T. J. et al. Inhibitors of RecA activity discovered by high-throughput screening: cell-permeable small molecules attenuate the SOS response in Escherichia coli. J. Biomol. Screen 14, 1092–1101 (2009).

Imlay, J. A. How oxygen damages microbes: oxygen tolerance and obligate anaerobiosis. Adv. Microb. Physiol. 46, 111–153 (2002).

Davies, B. W. et al. Hydroxyurea induces hydroxyl radical-mediated cell death in Escherichia coli. Mol. Cell 36, 845–860 (2009).

Dwyer, D. J., Kohanski, M. A. & Collins, J. J. Role of reactive oxygen species in antibiotic action and resistance. Curr. Opin. Microbiol 12, 482–489 (2009).

Kohanski, M. A., DePristo, M. A. & Collins, J. J. Sub-lethal antibiotic treatment leads to multidrug resistance via radical-induced mutagenesis. Mol. Cell 37, 311–320 (2010).

Gusarov, I., Shatalin, K., Starodubtseva, M., & Nudler, E. Endogenous nitric oxide protects bacteria against a wide spectrum of antibiotics. Science 325, 1380–1384 (2009).

Vazquez-Torres, A. et al. Salmonella pathogenicity island 2-dependent evasion of the phagocyte NADPH oxidase. Science 287, 1655–1658 (2000).

Eggert, U. S. et al. Genetic basis for activity differences between vancomycin and glycolipid derivatives of vancomycin. Science 294, 361–364 (2001).

Muthaiyan, A., Silverman, J. A., Jayaswal, R. K. & Wilkinson, B. J. Transcriptional profiling reveals that daptomycin induces the Staphylococcus aureus cell wall stress stimulon and genes responsive to membrane depolarization. Antimicrob. Agents Chemother. 52, 980–990 (2008).

Hancock, R. E. & Rozek, A. Role of membranes in the activities of antimicrobial cationic peptides. FEMS Microbiol. Lett. 206, 143–149 (2002).

Hancock, R. E. & Sahl, H. G. Antimicrobial and host-defense peptides as new anti-infective therapeutic strategies. Nature Biotechnol. 24, 1551–1557 (2006).

Keith, C. T., Borisy, A. A. & Stockwell, B. R. Multicomponent therapeutics for networked systems. Nature Rev. Drug Discov. 4, 71–78 (2005).

Yeh, P. J., Hegreness, M. J., Aiden, A. P. & Kishony, R. Drug interactions and the evolution of antibiotic resistance. Nature Rev. Microbiol. 7, 460–466 (2009).

Yeh, P., Tschumi, A. I. & Kishony, R. Functional classification of drugs by properties of their pairwise interactions. Nature Genet. 38, 489–494 (2006). Shows a quantitative, network-based approach for studying drug–drug interactions that also allows the elucidation of the functional mechanisms underlying drug mode of action and affected cellular targets.

Bollenbach, T., Quan, S., Chait, R. & Kishony, R. Nonoptimal microbial response to antibiotics underlies suppressive drug interactions. Cell 139, 707–718 (2009).

Plotz, P. H. & Davis, B. D. Synergism between streptomycin and penicillin: a proposed mechanism. Science 135, 1067–1068 (1962).

Lu, T. K. & Collins, J. J. Dispersing biofilms with engineered enzymatic bacteriophage. Proc. Natl Acad. Sci. USA 104, 11197–11202 (2007).

Lu, T. K. & Collins, J. J. Engineered bacteriophage targeting gene networks as adjuvants for antibiotic therapy. Proc. Natl Acad. Sci. USA 106, 4629–4634 (2009).