Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

How antibiotics kill bacteria: from targets to networks

Nature Reviews Microbiology volume 8, pages 423–435 (2010)Cite this article

Subjects

Key Points

  • Substantial progress has been made in our understanding of the mechanistic details of bacterial cell death induced by bactericidal antibiotics. In this Review, we discuss how bactericidal antibiotics kill bacteria by inhibiting essential cellular processes and by activating cellular response pathways that contribute to cell death.

  • Bactericidal antibiotics target a diverse set of biomolecules for inhibition to achieve cell death, including DNA topoisomerases (involved in modulating DNA topology), RNA polymerase (involved in RNA transcription), penicillin-binding proteins, transglycosylases and peptidoglycan building blocks (involved in cell wall homeostasis), as well as ribosomes (involved in protein synthesis).

  • Treatment with lethal concentrations of bactericidal antibiotics has been shown to trigger several stress responses and additional off-target effects in the face of drug-induced stress. These responses include the recently described oxidative damage cellular death pathway, which is commonly induced by all major classes of bactericidal antibiotics and involves alterations in metabolism (that is, central carbon and iron) that culminate in the production of cytotoxic superoxide and hydroxyl radicals.

  • Several approaches have been employed to provide a more complete understanding of the sequences of events underlying bactericidal antibiotic-induced cell death for each drug class, beginning with the binding of a drug molecule to its primary target. Biological network analysis provides a powerful method for predicting and characterizing the potential interplay between genes and proteins functionally interacting to coordinate bacterial stress response pathways.

  • Given the threat and continued rise of antibiotic-resistant bacteria, it is crucial that improvements be made to current antibacterial therapies and that new antibiotics are developed. Antibiotic network biology provides a means to comparatively study the response mechanisms of diverse bacterial species to various bactericidal drug classes to predict the responses of pathogenic bacteria to available treatment regimens, and to determine the mode of action of new antibacterial agents.

Abstract

Antibiotic drug–target interactions, and their respective direct effects, are generally well characterized. By contrast, the bacterial responses to antibiotic drug treatments that contribute to cell death are not as well understood and have proven to be complex as they involve many genetic and biochemical pathways. In this Review, we discuss the multilayered effects of drug–target interactions, including the essential cellular processes that are inhibited by bactericidal antibiotics and the associated cellular response mechanisms that contribute to killing. We also discuss new insights into these mechanisms that have been revealed through the study of biological networks, and describe how these insights, together with related developments in synthetic biology, could be exploited to create new antibacterial therapies.

This is a preview of subscription content, access via your institution

Relevant articles

Open Access articles citing this article.

Access options

Rent or buy this article

Get just this article for as long as you need it

$39.95

Learn more

Prices may be subject to local taxes which are calculated during checkout

Figure 1: Drug-target interactions and associated cell death mechanisms.
Figure 2: Common mechanism of cell death induced by bactericidal antibiotics.
Figure 3: Aminoglycosides trigger hydroxyl radical-mediated cell death.

References

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

    Book  Google Scholar 

  2. 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).

    CAS  PubMed Central  Google Scholar 

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

    Article  CAS  PubMed  Google Scholar 

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

    Article  CAS  PubMed  Google Scholar 

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

    Article  CAS  PubMed  Google Scholar 

  6. 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.

    Article  CAS  PubMed  Google Scholar 

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

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  8. 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.

    Article  CAS  PubMed  Google Scholar 

  9. 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.

  10. 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.

    CAS  PubMed  PubMed Central  Google Scholar 

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

    Article  CAS  PubMed  Google Scholar 

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

    Article  CAS  PubMed  Google Scholar 

  13. 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).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  14. 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).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  15. 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.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

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

    Google Scholar 

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

    Article  CAS  PubMed  Google Scholar 

  18. 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).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  19. 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.

    Article  CAS  PubMed  Google Scholar 

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

    CAS  PubMed  PubMed Central  Google Scholar 

  21. 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).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  22. 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).

    Article  CAS  PubMed  Google Scholar 

  23. 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).

    Article  CAS  PubMed  Google Scholar 

  24. 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).

    Article  CAS  PubMed  Google Scholar 

  25. 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.

    Article  CAS  PubMed  Google Scholar 

  26. 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).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

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

    Article  CAS  PubMed  Google Scholar 

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

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  29. 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).

    CAS  PubMed  PubMed Central  Google Scholar 

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

    Article  CAS  PubMed  Google Scholar 

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

    Article  CAS  PubMed  Google Scholar 

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

    Article  CAS  PubMed  Google Scholar 

  33. 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).

    Article  CAS  PubMed  Google Scholar 

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

    Article  CAS  PubMed  PubMed Central  Google Scholar 

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

    Article  CAS  PubMed  Google Scholar 

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

    Article  CAS  PubMed  Google Scholar 

  37. 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).

    Article  CAS  PubMed  Google Scholar 

  38. 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).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  39. 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).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

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

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  41. 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).

    Article  CAS  PubMed  Google Scholar 

  42. 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.

    Article  CAS  PubMed  Google Scholar 

  43. 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).

    Article  CAS  PubMed  Google Scholar 

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

    Google Scholar 

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

    CAS  PubMed  Google Scholar 

  46. 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).

    Article  CAS  PubMed  Google Scholar 

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

    CAS  PubMed  Google Scholar 

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

    Article  Google Scholar 

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

    Article  Google Scholar 

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

    Article  CAS  PubMed  Google Scholar 

  51. 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).

    CAS  PubMed  Google Scholar 

  52. 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.

    Article  CAS  Google Scholar 

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

    Article  CAS  PubMed  Google Scholar 

  54. 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).

    Article  CAS  PubMed  Google Scholar 

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

    CAS  PubMed  PubMed Central  Google Scholar 

  56. 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).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  57. 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).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  58. 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.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  59. 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).

    Article  CAS  PubMed  Google Scholar 

  60. 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).

    Article  CAS  PubMed  Google Scholar 

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

    Article  CAS  PubMed  Google Scholar 

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

    Article  CAS  PubMed  Google Scholar 

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

    Article  CAS  PubMed  Google Scholar 

  64. 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.

    Article  CAS  PubMed  Google Scholar 

  65. 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.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  66. 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).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  67. 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.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

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

    Article  CAS  PubMed  Google Scholar 

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

    Article  CAS  PubMed  Google Scholar 

  70. 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).

    Article  CAS  PubMed  Google Scholar 

  71. 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).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

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

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  73. 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).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  74. 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.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

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

    Article  CAS  Google Scholar 

  76. 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).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

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

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  78. 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).

    Article  CAS  PubMed  Google Scholar 

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

    Article  CAS  PubMed  PubMed Central  Google Scholar 

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

    Article  CAS  PubMed  Google Scholar 

  81. 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.

    Article  CAS  PubMed  Google Scholar 

  82. 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).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  83. 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).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

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

    Google Scholar 

  85. 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).

    Article  CAS  PubMed  Google Scholar 

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

    Article  CAS  PubMed  Google Scholar 

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

    Article  CAS  PubMed  Google Scholar 

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

    Article  CAS  PubMed  Google Scholar 

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

    Article  CAS  PubMed  Google Scholar 

  90. 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).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  91. 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.

    Article  CAS  PubMed  Google Scholar 

  92. 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).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

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

    CAS  PubMed  PubMed Central  Google Scholar 

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

    CAS  PubMed  PubMed Central  Google Scholar 

  95. 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).

    Article  CAS  PubMed  Google Scholar 

  96. 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.

    CAS  PubMed  Google Scholar 

  97. 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).

    Article  CAS  PubMed  Google Scholar 

  98. 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).

    Article  CAS  PubMed  Google Scholar 

  99. 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).

    Article  CAS  PubMed  Google Scholar 

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

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  101. 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).

    Article  CAS  PubMed  Google Scholar 

  102. 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).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  103. 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).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  104. 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).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  105. 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.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

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

    Article  CAS  PubMed  Google Scholar 

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

    Article  CAS  PubMed  Google Scholar 

  108. 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).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

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

    Article  CAS  PubMed  Google Scholar 

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

    Article  CAS  PubMed  Google Scholar 

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

    Article  CAS  PubMed  Google Scholar 

  112. 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).

    Article  CAS  PubMed  Google Scholar 

  113. 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).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  114. 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.

    Article  CAS  PubMed  Google Scholar 

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

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  116. 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).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

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

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  118. 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).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  119. 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).

    Article  CAS  PubMed  Google Scholar 

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

    Article  CAS  PubMed  Google Scholar 

  121. 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).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  122. 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).

    Article  CAS  Google Scholar 

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

    Article  CAS  PubMed  Google Scholar 

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

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  125. 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).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

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

    Article  CAS  PubMed  Google Scholar 

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

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  128. 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).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  129. 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).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

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

    Article  CAS  PubMed  PubMed Central  Google Scholar 

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

    Article  CAS  PubMed  Google Scholar 

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

    Article  CAS  PubMed  Google Scholar 

  133. 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).

    Article  CAS  PubMed  Google Scholar 

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

    Article  CAS  PubMed  Google Scholar 

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

    Article  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

  137. 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).

    Article  CAS  Google Scholar 

  138. 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.

    Article  CAS  PubMed  Google Scholar 

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

    Article  CAS  PubMed  PubMed Central  Google Scholar 

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

    Article  CAS  PubMed  Google Scholar 

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

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  142. 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).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

Download references

Acknowledgements

We thank the anonymous reviewers for their helpful comments and suggestions. This work was supported by the National Institutes of Health (NIH) through the NIH Director's Pioneer Award Program, grant number DP1 OD003644, and the Howard Hughes Medical Institute.

Author information

Authors and Affiliations

  1. Howard Hughes Medical Institute and the Department of Biomedical Engineering, Center for BioDynamics, and Center for Advanced Biotechnology, Boston University, 44 Cummington Street, Boston, 02215, Massachusetts, USA

    Michael A. Kohanski, Daniel J. Dwyer & James J. Collins

  2. Boston University School of Medicine, 715 Albany Street, Boston, 02118, Massachusetts, USA

    Michael A. Kohanski & James J. Collins

  3. Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, 02115, Massachusetts, USA

    James J. Collins

Authors
  1. Michael A. Kohanski
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Daniel J. Dwyer
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. James J. Collins
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to James J. Collins.

Ethics declarations

Competing interests

The authors declare no competing financial interests.

Related links

Related links

DATABASES

Entrez Genome Project

Escherichia coli

Neisseria meningitidis

Pseudomonas aeruginosa

Staphylococcus aureus

FURTHER INFORMATION

James J. Collins' homepage

Glossary

Bactericidal

Antimicrobial exposure that leads to bacterial cell death.

Bacteriostatic

Antimicrobial exposure that inhibits growth with no loss of viability.

Cell envelope

Layers of the cell surrounding the cytoplasm that include lipid membranes and peptidoglycans.

SOS response

The DNA stress response pathway in E. coli, the prototypical network of genes of which is regulated by the transcriptional repressor LexA, and is commonly activated by the co-regulatory protein RecA, which promotes LexA self-cleavage when activated.

Lysis

Rupture of the cell envelope leading to the expulsion of intracellular contents into the surrounding environment with eventual disintegration of the cell envelope.

Peptidoglycan hydrolase

An enzyme that introduces cuts between carbon–nitrogen non-peptide bonds while pruning the peptidoglycan layer. It is important for homeostatic peptidoglycan turnover.

Autolysin

An enzyme that hydrolyses the β-linkage between the monosaccharide monomers in peptidoglycan units and can induce lysis when in excess.

Two-component system

A two-protein signal relay system composed of a sensor histidine kinase and a cognate receiver protein, which is typically a transcription factor.

Quinone pool

Membrane-associated cyclic aromatic-based compounds that shuttle electrons along the electron transport chain.

Fenton reaction

Reaction of ferrous iron (Fe2+) with hydrogen peroxide to produce ferric iron (Fe3+) and a hydroxyl radical.

Antimicrobial peptide

A short, naturally occurring cationic peptide that has antibacterial properties through its ability to interfere with bacterial membranes.

Rights and permissions

Reprints and Permissions

About this article

Cite this article

Kohanski, M., Dwyer, D. & Collins, J. How antibiotics kill bacteria: from targets to networks. Nat Rev Microbiol 8, 423–435 (2010). https://doi.org/10.1038/nrmicro2333

Download citation

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1038/nrmicro2333

This article is cited by

Search

Advanced search

Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing