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When anaerobes encounter oxygen: mechanisms of oxygen toxicity, tolerance and defence

Abstract

The defining trait of obligate anaerobes is that oxygen blocks their growth, yet the underlying mechanisms are unclear. A popular hypothesis was that these microorganisms failed to evolve defences to protect themselves from reactive oxygen species (ROS) such as superoxide and hydrogen peroxide, and that this failure is what prevents their expansion to oxic habitats. However, studies reveal that anaerobes actually wield most of the same defences that aerobes possess, and many of them have the capacity to tolerate substantial levels of oxygen. Therefore, to understand the structures and real-world dynamics of microbial communities, investigators have examined how anaerobes such as Bacteroides, Desulfovibrio, Pyrococcus and Clostridium spp. struggle and cope with oxygen. The hypoxic environments in which these organisms dwell — including the mammalian gut, sulfur vents and deep sediments — experience episodic oxygenation. In this Review, we explore the molecular mechanisms by which oxygen impairs anaerobes and the degree to which bacteria protect their metabolic pathways from it. The emergent view of anaerobiosis is that optimal strategies of anaerobic metabolism depend upon radical chemistry and low-potential metal centres. Such catalytic sites are intrinsically vulnerable to direct poisoning by molecular oxygen and ROS. Observations suggest that anaerobes have evolved tactics that either minimize the extent to which oxygen disrupts their metabolism or restore function shortly after the stress has dissipated.

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Fig. 1: Lifestyles of anaerobes.
Fig. 2: O2-dependent respiration in anaerobes.
Fig. 3: O2 inactivates pyruvate formate-lyase.
Fig. 4: Structures of O2-sensitive metalloenzymes.
Fig. 5: Metabolism in Bacteroides spp. is blocked upon aeration and resumes in anoxia.

References

  1. 1.

    Slesak, I., Kula, M., Slesak, H., Miszalski, Z. & Strzalka, K. How to define obligatory anaerobiosis? An evolutionary view on the antioxidant response system and the early stages of the evolution of life on Earth. Free. Radic. Biol. Med. 140, 61–73 (2019).

    CAS  PubMed  Article  PubMed Central  Google Scholar 

  2. 2.

    Lyons, T. W., Reinhard, C. T. & Planavsky, N. J. The rise of oxygen in Earth’s early ocean and atmosphere. Nature 506, 307–315 (2014). This paper describes current thinking on the history of O2 on Earth.

    CAS  PubMed  Article  PubMed Central  Google Scholar 

  3. 3.

    Gould, S. B. et al. Adaptation to life on land at high O2 via transition from ferredoxin- to NADH-dependent redox balance. Proc. R. Soc. Lond. B Biol. Sci. 286, 20191491 (2019).

    CAS  Google Scholar 

  4. 4.

    Clemmey, H. & Badham, N. Oxygen in the Precambrian atmosphere: an evaluation of the geological evidence. Geology 10, 141–146 (1982).

    CAS  Article  Google Scholar 

  5. 5.

    Fischer, W. W., Hemp, J. & Johnson, J. E. Evolution of oxygenic photosynthesis. Annu. Rev. Earth Planet. Sci. 44, 647–683 (2016).

    CAS  Article  Google Scholar 

  6. 6.

    Schad, M., Konhauser, K. O., Sanchez-Baracaldo, P., Kappler, A. & Bryce, C. How did the evolution of oxygenic photosynthesis influence the temporal and spatial development of the microbial iron cycle on ancient Earth? Free. Radic. Biol. Med. 140, 154–166 (2019).

    CAS  PubMed  Article  PubMed Central  Google Scholar 

  7. 7.

    Hamilton, T. L., Bryant, D. A. & Macalady, J. L. The role of biology in planetary evolution: cyanobacterial primary production in low-oxygen Proterozoic oceans. Environ. Microbiol. 18, 325–340 (2016).

    CAS  PubMed  Article  PubMed Central  Google Scholar 

  8. 8.

    Bekker, A. et al. Dating the rise of atmospheric oxygen. Nature 427, 117–120 (2004).

    CAS  PubMed  Article  PubMed Central  Google Scholar 

  9. 9.

    Muller, M. et al. Biochemistry and evolution of anaerobic energy metabolism in eukaryotes. Microbiol. Mol. Biol. Rev. 76, 444–495 (2012).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  10. 10.

    Friedman, E. S. et al. Microbes vs. chemistry in the origin of the anaerobic gut lumen. Proc. Natl Acad. Sci. USA 115, 4170–4175 (2018).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  11. 11.

    Zheng, L., Kelly, C. J. & Colgan, S. P. Physiologic hypoxia and oxygen homeostasis in the healthy intestine. A review in the theme: cellular responses to hypoxia. Am. J. Physiol. Cell Physiol. 309, C350–C360 (2015).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  12. 12.

    Marie, B., Genard, B., Rees, J. F. & Zal, F. Effect of ambient oxygen concentration on activities of enzymatic antioxidant defences and aerobic metabolism in the hydrothermal vent worm, Paralvinella grasslei. Mar. Biol. 150, 273–284 (2006).

    CAS  Article  Google Scholar 

  13. 13.

    Lesser, M. P. Oxidative stress in marine environments: biochemistry and physiological ecology. Annu. Rev. Physiol. 68, 253–278 (2006).

    CAS  PubMed  Article  PubMed Central  Google Scholar 

  14. 14.

    Rivera–Chavez, F., Lopez, C. A. & Baumler, A. J. Oxygen as a driver of gut dysbiosis. Free. Radic. Biol. Med. 105, 93–101 (2017).

    PubMed  Article  CAS  PubMed Central  Google Scholar 

  15. 15.

    Espey, M. G. Role of oxygen gradients in shaping redox relationships between the human intestine and its microbiota. Free. Radic. Biol. Med. 55, 130–140 (2013). This study details that intestinal anaerobes may encounter a range of O2 concentrations, depending upon their proximity to the epithelium.

    CAS  PubMed  Article  PubMed Central  Google Scholar 

  16. 16.

    Kelly, C. J. & Colgan, S. P. Breathless in the gut: Implications of luminal O2 for microbial pathogenicity. Cell Host Microbe 19, 427–428 (2016).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  17. 17.

    Schwerdtfeger, L. A., Nealon, N. J., Ryan, E. P. & Tobet, S. A. Human colon function ex vivo: dependence on oxygen and sensitivity to antibiotic. PLoS ONE 14, e0217170 (2019).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  18. 18.

    Sawyer, R. G., Spengler, M. D., Adams, R. B. & Pruett, T. L. The peritoneal environment during infection. The effect of monomicrobial and polymicrobial bacteria on pO2 and pH. Ann. Surg. 213, 253–260 (1991).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  19. 19.

    Renvall, S. & Niinikoski, J. Intraperitoneal oxygen and carbon dioxide tensions in experimental adhesion disease and peritonitis. Am. J. Surg. 130, 286–292 (1975).

    CAS  PubMed  Article  PubMed Central  Google Scholar 

  20. 20.

    Smalley, D., Rocha, E. R. & Smith, C. J. Aerobic-type ribonucleotide reductase in the anaerobe Bacteroides fragilis. J. Bacteriol. 184, 895–903 (2002).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  21. 21.

    Whitham, J. M., Tirado-Acevedo, O., Chinn, M. S., Pawlak, J. J. & Grunden, A. M. Metabolic response of Clostridium ljungdahlii to oxygen exposure. Appl. Environ. Microbiol. 81, 8379–8391 (2015).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  22. 22.

    Talukdar, P. K., Olguin-Araneda, V., Alnoman, M., Paredes-Sabja, D. & Sarker, M. R. Updates on the sporulation process in Clostridium species. Res. Microbiol. 166, 225–235 (2015).

    PubMed  Article  PubMed Central  Google Scholar 

  23. 23.

    Tracy, B. P., Jones, S. W., Fast, A. G., Indurthi, D. C. & Papoutsakis, E. T. Clostridia: the importance of their exceptional substrate and metabolite diversity for biofuel and biorefinery applications. Curr. Opin. Biotechnol. 23, 364–381 (2012).

    CAS  PubMed  Article  PubMed Central  Google Scholar 

  24. 24.

    Kint, N. et al. How the anaerobic enteropathogen Clostridioides difficile tolerates low O2 tensions. mBio 11, e01559-20 (2020). This study shows that Clostridioides difficile responds to O2 exposure by inducing enzymes that scavenge O2 and H2O2.

    CAS  PubMed  PubMed Central  Google Scholar 

  25. 25.

    Kawasaki, S. et al. Adaptive responses to oxygen stress in obligatory anaerobes Clostridium acetobutylicum and Clostridium aminovalericum. Appl. Environ. Microbiol. 71, 8442–8450 (2005).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  26. 26.

    Fournier, M. et al. Function of oxygen resistance proteins in the anaerobic, sulfate-reducing bacterium Desulfovibrio vulgaris Hildenborough. J. Bacteriol. 185, 71–79 (2003).

    PubMed  PubMed Central  Article  CAS  Google Scholar 

  27. 27.

    Silaghi-Dumitrescu, R., Ng, K. Y., Viswanathan, R. & Kurtz, D. M. Jr. A flavo-diiron protein from Desulfovibrio vulgaris with oxidase and nitric oxide reductase activities. Evidence for an in vivo nitric oxide scavenging function. Biochem. 44, 3572–3579 (2005).

    CAS  Article  Google Scholar 

  28. 28.

    Rowan, F. et al. Desulfovibrio bacterial species are increased in ulcerative colitis. Dis. Colon. Rectum. 53, 1530–1536 (2010).

    PubMed  Article  PubMed Central  Google Scholar 

  29. 29.

    Johnson, M. S., Zhulin, I. B., Gapuzan, M. E. & Taylor, B. L. Oxygen-dependent growth of the obligate anaerobe Desulfovibrio vulgaris Hildenborough. J. Bacteriol. 179, 5598–5601 (1997).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  30. 30.

    Le Fourn, C. et al. An oxygen reduction chain in the hyperthermophilic anaerobe Thermotoga maritima highlights horizontal gene transfer between Thermococcales and Thermotogales. Environ. Microbiol. 13, 2132–2145 (2011).

    PubMed  Article  CAS  PubMed Central  Google Scholar 

  31. 31.

    Thorgersen, M. P., Stirrett, K., Scott, R. A. & Adams, M. W. W. Mechanism of oxygen detoxification by the surprisingly oxygen-tolerant hyperthermophilic archaeon, Pyrococcus furiosus. Proc. Natl Acad. Sci. USA 109, 18547–18552 (2012).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  32. 32.

    Strand, K. R. et al. Oxidative stress protection and the repair response to hydrogen peroxide in the hyperthermophilic archaeon Pyrococcus furiosus and in related species. Arch. Microbiol. 192, 447–459 (2010).

    CAS  PubMed  Article  PubMed Central  Google Scholar 

  33. 33.

    McCord, J. M., Keele, B. B. Jr. & Fridovich, I. An enzyme-based theory of obligate anaerobiosis: the physiological function of superoxide dismutase. Proc. Natl Acad. Sci. USA 68, 1024–1027 (1971).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  34. 34.

    Chance, B., Sies, H. & Boveris, A. Hydroperoxide metabolism in mammalian organs. Physiol. Rev. 59, 527–605 (1979).

    CAS  PubMed  Article  PubMed Central  Google Scholar 

  35. 35.

    Jenney, F. E. Jr., Verhagen, M. F., Cui, X. & Adams, M. W. Anaerobic microbes: oxygen detoxification without superoxide dismutase. Science 286, 306–309 (1999).

    CAS  PubMed  Article  PubMed Central  Google Scholar 

  36. 36.

    Niviere, V. & Fontecave, M. Discovery of superoxide reductase: an historical perspective. J. Biol. Inorg. Chem. 9, 119–123 (2004).

    CAS  PubMed  Article  PubMed Central  Google Scholar 

  37. 37.

    Degli Esposti, M., Mentel, M., Martin, W. & Sousa, F. L. Oxygen reductases in alphaproteobacterial genomes: physiological evolution from low to high oxygen environments. Front. Microbiol. 10, 499 (2019).

    PubMed  PubMed Central  Article  Google Scholar 

  38. 38.

    Weiss, M. C. et al. The physiology and habitat of the last universal common ancestor. Nat. Microbiol. 1, 16116 (2016).

    CAS  PubMed  Article  PubMed Central  Google Scholar 

  39. 39.

    Morris, R. L. & Schmidt, T. M. Shallow breathing: bacterial life at low O2. Nat. Rev. Microbiol. 11, 205–212 (2013).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  40. 40.

    Wildschut, J. D., Lang, R. M., Voordouw, J. K. & Voordouw, G. Rubredoxin:oxygen oxidoreductase enhances survival of Desulfovibrio vulgaris Hildenborough under microaerophilic conditions. J. Bacteriol. 188, 6253–6260 (2006).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  41. 41.

    Victor, B. L., Baptista, A. M. & Soares, C. M. Dioxygen and nitric oxide pathways and affinity to the catalytic site of rubredoxin:oxygen oxidoreductase from Desulfovibrio gigas. J. Biol. Inorg. Chem. 14, 853–862 (2009).

    CAS  PubMed  Article  PubMed Central  Google Scholar 

  42. 42.

    Sund, C. J. et al. The Bacteroides fragilis transcriptome response to oxygen and H2O2: the role of OxyR and its effect on survival and virulence. Mol. Microbiol. 67, 129–142 (2008).

    CAS  PubMed  Article  PubMed Central  Google Scholar 

  43. 43.

    Meehan, B. M., Baughn, A. D., Gallegos, R. & Malamy, M. H. Inactivation of a single gene enables microaerobic growth of the obligate anaerobe Bacteroides fragilis. Proc. Natl Acad. Sci. USA 109, 12153–12158 (2012).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  44. 44.

    Lu, Z. & Imlay, J. A. The fumarate reductase of Bacteroides thetaiotaomicron, unlike that of Escherichia coli, is configured so that it does not generate reactive oxygen species. mBio 8, e01873-16 (2017).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  45. 45.

    Borisov, V. B., Gennis, R. B., Hemp, J. & Verkhovsky, M. I. The cytochrome bd respiratory oxygen reductases. Biochim. Biophys. Acta 1807, 1398–1413 (2011).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  46. 46.

    Das, A., Silaghi-Dumitrescu, R., Ljungdahl, L. G. & Kurtz, D. M. Jr. Cytochrome bd oxidase, oxidative stress, and dioxygen tolerance of the strictly anaerobic bacterium Moorella thermoacetica. J. Bacteriol. 187, 2020–2029 (2005).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  47. 47.

    Ligeza, A., Tikhonov, A. N., Hyde, J. S. & Subczynski, W. K. Oxygen permeability of thylakoid membranes: electron paramagnetic resonance spin labeling study. Biochim. Biophys. Acta 1365, 453–463 (1998).

    CAS  PubMed  Article  PubMed Central  Google Scholar 

  48. 48.

    Wexler, H. M. Bacteroides: the good, the bad, and the nitty-gritty. Clin. Microbiol. Rev. 20, 593–621 (2007).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  49. 49.

    Poole, R. K. & Hill, S. Respiratory protection of nitrogenase activity in Azotobacter vinelandii — roles of the terminal oxidases. Biosci. Rep. 17, 303–317 (1997).

    CAS  PubMed  Article  PubMed Central  Google Scholar 

  50. 50.

    Rakoff-Nahoum, S., Foster, K. R. & Comstock, L. E. The evolution of cooperation within the gut microbiota. Nature 533, 255–259 (2016).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  51. 51.

    Chen, L. et al. Rubredoxin oxidase, a new flavo-hemo-protein, is the site of oxygen reduction to water by the “strict anaerobe” Desulfovibrio gigas. Biochem. Biophys. Res. Commun. 193, 100–105 (1993).

    CAS  PubMed  Article  PubMed Central  Google Scholar 

  52. 52.

    Silaghi-Dumitrescu, R. et al. A flavodiiron protein and high molecular weight rubredoxin from Moorella thermoacetica with nitric oxide reductase activity. Biochemistry 42, 2806–2815 (2003).

    CAS  PubMed  Article  PubMed Central  Google Scholar 

  53. 53.

    Silva, G., Oliveira, S., LeGall, J., Xavier, A. V. & Rodrigues-Pousada, C. Analysis of the Desulfovibrio gigas transcriptional unit containing rubredoxin (rd) and rubredoxin–oxygen oxidoreductase (roo) genes and upstream ORFs. Biochem. Biophys. Res. Commun. 280, 491–502 (2001).

    CAS  PubMed  Article  PubMed Central  Google Scholar 

  54. 54.

    Spellerberg, B. et al. Pyruvate oxidase, as a determinant of virulence in Streptococcus pneumoniae. Mol. Microbiol. 19, 803–813 (1996).

    CAS  PubMed  Article  PubMed Central  Google Scholar 

  55. 55.

    Seki, M., Iida, K., Saito, M., Nakayama, H. & Yoshida, S. Hydrogen peroxide production in Streptococcus pyogenes: involvement of lactate oxidase and coupling with aerobic utilization of lactate. J. Bacteriol. 186, 2046–2051 (2004).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  56. 56.

    Baughn, A. D. & Malamy, M. H. The strict anaerobe Bacteroides fragilis grows in and benefits from nanomolar concentrations of oxygen. Nature 427, 441–444 (2004). This paper demonstrates that the cytochrome bd oxidase of B. fragilis enhances its growth in the presence of nanomolar concentrations of O2.

    CAS  PubMed  Article  PubMed Central  Google Scholar 

  57. 57.

    Kim, J., Hetzel, M., Boiangiu, C. D. & Buckel, W. Dehydration of (R)-2-hydroxyacyl-CoA to enoyl-CoA in the fermentation of α-amino acids by anaerobic bacteria. FEMS Microbiol. Rev. 28, 455–468 (2004). This paper explains how ‘archerases’ manage the dehydration of non-activated substrates, yet are O2-sensitive because of the mechanism that is involved.

    CAS  PubMed  Article  PubMed Central  Google Scholar 

  58. 58.

    Thauer, R. K. Methyl (alkyl)-coenzyme M reductases: nickel F-430-containing enzymes involved in anaerobic methane formation and in anaerobic oxidation of methane or of short chain alkanes. Biochemistry 58, 5198–5220 (2019).

    CAS  PubMed  Article  PubMed Central  Google Scholar 

  59. 59.

    Wagner, A. F., Frey, M., Neugebauer, F. A., Schäfer, W. & Knappe, J. The free radical in pyruvate formate-lyase is located on glycine-734. Proc. Natl Acad. Sci. USA 89, 996–1000 (1992).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  60. 60.

    Shibata, N. & Toraya, T. Molecular architectures and functions of radical enzymes and their (re)activating proteins. J. Biochem. 158, 271–292 (2015).

    CAS  PubMed  Article  PubMed Central  Google Scholar 

  61. 61.

    Sawers, G. & Watson, G. A glycyl radical solution: oxygen-dependent interconversion of pyruvate formate-lyase. Mol. Microbiol. 29, 945–954 (1998).

    CAS  PubMed  Article  PubMed Central  Google Scholar 

  62. 62.

    Naqui, A., Chance, B. & Cadenas, E. Reactive oxygen intermediates in biochemistry. Annu. Rev. Biochem. 55, 137–166 (1986).

    CAS  PubMed  Article  PubMed Central  Google Scholar 

  63. 63.

    Knappe, J., Elbert, S., Frey, M. & Wagner, A. F. Pyruvate formate-lyase mechanism involving the protein-based glycyl radical. Biochem. Soc. Trans. 21, 731–734 (1993).

    CAS  PubMed  Article  PubMed Central  Google Scholar 

  64. 64.

    Zhang, W., Wong, K. K., Magliozzo, R. S. & Kozarich, J. W. Inactivation of pyruvate formate-lyase by dioxygen: defining the mechanistic interplay of glycine 734 and cysteine 419 by rapid freeze-quench EPR. Biochemistry 40, 4123–4130 (2001). This paper details how O2 cleaves the PFL polypeptide.

    CAS  PubMed  Article  PubMed Central  Google Scholar 

  65. 65.

    Imlay, J. A. The molecular mechanisms and physiological consequences of oxidative stress: lessons from a model bacterium. Nat. Rev. Microbiol. 11, 443–454 (2013).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  66. 66.

    Gardner, P. R. & Fridovich, I. Superoxide sensitivity of the Escherichia coli aconitase. J. Biol. Chem. 266, 19328–19333 (1991).

    CAS  PubMed  Article  PubMed Central  Google Scholar 

  67. 67.

    Hausladen, A. & Fridovich, I. Superoxide and peroxynitrite inactivate aconitases, but nitric oxide does not. J. Biol. Chem. 269, 29405–29408 (1994).

    CAS  PubMed  Article  PubMed Central  Google Scholar 

  68. 68.

    Lu, Z., Sethu, R. & Imlay, J. A. Endogenous superoxide is a key effector of the oxygen sensitivity of a model obligate anaerobe. Proc. Natl Acad. Sci. USA 115, E3266–E3275 (2018).

    PubMed  PubMed Central  Article  CAS  Google Scholar 

  69. 69.

    Frey, M. Hydrogenases: hydrogen-activating enzymes. Chembiochem 3, 153–160 (2002).

    CAS  PubMed  Article  PubMed Central  Google Scholar 

  70. 70.

    Ragsdale, S. W. Pyruvate ferredoxin oxidoreductase and its radical intermediate. Chem. Rev. 103, 2333–2346 (2003).

    CAS  PubMed  Article  PubMed Central  Google Scholar 

  71. 71.

    Pandelia, M. E., Lubitz, W. & Nitschke, W. Evolution and diversification of Group 1 [NiFe] hydrogenases. Is there a phylogenetic marker for O2-tolerance? Biochim. Biophys. Acta 1817, 1565–1575 (2012).

    CAS  PubMed  Article  PubMed Central  Google Scholar 

  72. 72.

    Kubas, A. et al. Mechanism of O2 diffusion and reduction in FeFe hydrogenases. Nat. Chem. 9, 88–95 (2017). This paper explores how molecular O2 attacks iron-only hydrogenases.

    CAS  PubMed  Article  PubMed Central  Google Scholar 

  73. 73.

    Swanson, K. D. et al. [FeFe]-hydrogenase oxygen inactivation is initiated at the H cluster 2Fe subcluster. J. Am. Chem. Soc. 137, 1809–1816 (2015).

    CAS  PubMed  Article  PubMed Central  Google Scholar 

  74. 74.

    Stripp, S. T. et al. How oxygen attacks [FeFe] hydrogenases from photosynthetic organisms. Proc. Natl Acad. Sci. USA 106, 17331–17336 (2009).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  75. 75.

    Hilton, M. G. The metabolism of pyrimidines by proteolytic Clostridia. Arch. Microbiol. 102, 145–149 (1975).

    CAS  PubMed  Article  PubMed Central  Google Scholar 

  76. 76.

    Buckel, W. et al. Enzyme catalyzed radical dehydrations of hydroxy acids. Biochim. Biophys. Acta 1824, 1278–1290 (2012).

    CAS  PubMed  Article  PubMed Central  Google Scholar 

  77. 77.

    Gardner, P. R. & Fridovich, I. Inactivation-reactivation of aconitase in Escherichia coli. A sensitive measure of superoxide radical. J. Biol. Chem. 267, 8757–8763 (1992).

    CAS  PubMed  Article  PubMed Central  Google Scholar 

  78. 78.

    Pan, N. & Imlay, J. A. How does oxygen inhibit central metabolism in the obligate anaerobe Bacteroides thetaiotaomicron. Mol. Microbiol. 39, 1562–1571 (2001).

    CAS  PubMed  Article  PubMed Central  Google Scholar 

  79. 79.

    Khademian, M. & Imlay, J. A. Do reactive oxygen species or does oxygen itself confer obligate anaerobiosis? The case of Bacteroides thetaiotaomicron. Mol. Microbiol. 114, 333–347 (2020).

    CAS  PubMed  Article  PubMed Central  Google Scholar 

  80. 80.

    Reddy, S. G. et al. Dioxygen inactivation of pyruvate formate-lyase: EPR evidence for the formation of protein-based sulfinyl and peroxyl radicals. Biochemistry 37, 558–563 (1998).

    CAS  PubMed  Article  PubMed Central  Google Scholar 

  81. 81.

    Vita, N., Hatchikian, E. C., Nouailler, M., Dolla, A. & Pieulle, L. Disulfide bond-dependent mechanism of protection against oxidative stress in pyruvate-ferredoxin oxidoreductase of anaerobic Desulfovibrio bacteria. Biochemistry 47, 957–964 (2008).

    CAS  PubMed  Article  PubMed Central  Google Scholar 

  82. 82.

    Pieulle, L. et al. Study of the thiol/disulfide redox systems of the anaerobe Desulfovibrio vulgaris points out pyruvate:ferredoxin oxidoreductase as a new target for thioredoxin 1. J. Biol. Chem. 286, 7812–7821 (2011).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  83. 83.

    Flint, D. H., Tuminello, J. F. & Emptage, M. H. The inactivation of Fe-S cluster containing hydro-lyases by superoxide. J. Biol. Chem. 268, 22369–22376 (1993). This article presents the first analysis of the mechanism by which oxidants degrade enzymic ironsulfur clusters.

    CAS  PubMed  Article  PubMed Central  Google Scholar 

  84. 84.

    Flint, D. H. & Allen, R. M. Iron–sulfur proteins with nonredox functions. Chem. Rev. 96, 2315–2334 (1996).

    CAS  PubMed  Article  PubMed Central  Google Scholar 

  85. 85.

    Jang, S. & Imlay, J. A. Micromolar intracellular hydrogen peroxide disrupts metabolism by damaging iron–sulfur enzymes. J. Biol. Chem. 282, 929–937 (2007).

    CAS  PubMed  Article  PubMed Central  Google Scholar 

  86. 86.

    Liochev, S. I. & Fridovich, I. Modulation of the fumarases of Escherichia coli in response to oxidative stress. Arch. Biochem. Biophys. 301, 379–384 (1993).

    CAS  PubMed  Article  PubMed Central  Google Scholar 

  87. 87.

    Lu, Z. & Imlay, J. A. A conserved motif liganding the [4Fe–4S] cluster in [4Fe–4S] fumarases prevents irreversible inactivation of the enzyme during hydrogen peroxide stress. Redox Biol. 26, 101296 (2019).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  88. 88.

    Kuo, C. F., Mashino, T. & Fridovich, I. α,β-Dihydroxyisovalerate dehydratase. A superoxide-sensitive enzyme. J. Biol. Chem. 262, 4724–4727 (1987).

    CAS  PubMed  Article  PubMed Central  Google Scholar 

  89. 89.

    Gardner, P. R. & Fridovich, I. Superoxide sensitivity of the Escherichia coli 6-phosphogluconate dehydratase. J. Biol. Chem. 266, 1478–1483 (1991).

    CAS  PubMed  Article  PubMed Central  Google Scholar 

  90. 90.

    Shimoyama, T., Rajashekhara, E., Ohmori, D., Kosaka, T. & Watanabe, K. MmcBC in Pelotomaculum thermopropionicum represents a novel group of prokaryotic fumarases. FEMS Microbiol. Lett. 270, 207–213 (2007).

    CAS  PubMed  Article  PubMed Central  Google Scholar 

  91. 91.

    Flint, D. H. Initial kinetic and mechanistic characterization of Escherichia coli fumarase A. Arch. Biochem. Biophys. 311, 509–516 (1994).

    CAS  PubMed  Article  PubMed Central  Google Scholar 

  92. 92.

    Woods, S. A., Schwartzbach, S. D. & Guest, J. R. Two biochemically distinct classes of fumarase in Escherichia coli. Biochim. Biophys. Acta 954, 14–26 (1988).

    CAS  PubMed  Article  PubMed Central  Google Scholar 

  93. 93.

    Sobota, J. M., Gu, M. & Imlay, J. A. Intracellular hydrogen peroxide and superoxide poison 3-deoxy-D-arabinoheptulosonate 7-phosphate synthase, the first committed enzyme in the aromatic biosynthetic pathway of Escherichia coli. J. Bacteriol. 196, 1980–1991 (2014).

    PubMed  PubMed Central  Article  CAS  Google Scholar 

  94. 94.

    Gu, M. Z. & Imlay, J. A. Superoxide poisons mononuclear iron enzymes by causing mismetallation. Mol. Microbiol. 89, 123–134 (2013).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  95. 95.

    Li, X. & Imlay, J. A. Improved measurements of scant hydrogen peroxide enable experiments that define its threshold of toxicity for Escherichia coli. Free. Radic. Biol. Med. 120, 217–227 (2018).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  96. 96.

    Mishra, S. & Imlay, J. A. An anaerobic bacterium, Bacteroides thetaiotaomicron, uses a consortium of enzymes to scavenge hydrogen peroxide. Mol. Microbiol. 90, 1356–1371 (2013).

    CAS  PubMed  Article  PubMed Central  Google Scholar 

  97. 97.

    Korshunov, S. & Imlay, J. A. Two sources of endogenous hydrogen peroxide in Escherichia coli. Mol. Microbiol. 75, 1389–1401 (2010).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  98. 98.

    Imlay, J. A. & Fridovich, I. Assay of metabolic superoxide production in Escherichia coli. J. Biol. Chem. 266, 6957–6965 (1991).

    CAS  PubMed  Article  PubMed Central  Google Scholar 

  99. 99.

    Dan Dunn, J., Alvarez, L. A., Zhang, X. & Soldati, T. Reactive oxygen species and mitochondria: a nexus of cellular homeostasis. Redox Biol. 6, 472–485 (2015).

    Article  CAS  Google Scholar 

  100. 100.

    Meyer, J. Ferredoxins of the third kind. FEBS Lett. 509, 1–5 (2001).

    CAS  PubMed  Article  PubMed Central  Google Scholar 

  101. 101.

    Valentine, R. C. Bacterial ferredoxin. Bacteriol. Rev. 28, 497–517 (1964).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  102. 102.

    Misra, H. P. & Fridovich, I. The generation of superoxide radical during the autoxidation of ferredoxins. J. Biol. Chem. 246, 6886–6890 (1971).

    CAS  PubMed  Article  PubMed Central  Google Scholar 

  103. 103.

    Rocha, E. R., Herren, C. D., Smalley, D. J. & Smith, C. J. The complex oxidative stress response of Bacteroides fragilis: the role of OxyR in control of gene expression. Anaerobe 9, 165–173 (2003).

    CAS  PubMed  Article  PubMed Central  Google Scholar 

  104. 104.

    Hillmann, F. et al. The role of PerR in O2-affected gene expression of Clostridium acetobutylicum. J. Bacteriol. 191, 6082–6093 (2009).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  105. 105.

    Partridge, J. D., Poole, R. K. & Green, J. The Escherichia coli yhjA gene, encoding a predicted cytochrome c peroxidase, is regulated by FNR and OxyR. Microbiology 153, 1499–1509 (2007).

    CAS  PubMed  Article  PubMed Central  Google Scholar 

  106. 106.

    Khademian, M. & Imlay, J. A. Escherichia coli cytochrome c peroxidase is a respiratory oxidase that enables the use of hydrogen peroxide as a terminal electron acceptor. Proc. Natl Acad. Sci. USA 114, E6922–E6931 (2017).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  107. 107.

    Pericone, C. D., Park, S., Imlay, J. A. & Weiser, J. N. Factors contributing to hydrogen peroxide resistance in Streptococcus pneumoniae include pyruvate oxidase (SpxB) and avoidance of the toxic effects of the Fenton reaction. J. Bacteriol. 185, 6815–6825 (2003).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  108. 108.

    Figueiredo, M. C., Lobo, S. A., Carita, J. N., Nobre, L. S. & Saraiva, L. M. Bacterioferritin protects the anaerobe Desulfovibrio vulgaris Hildenborough against oxygen. Anaerobe 18, 454–458 (2012).

    CAS  PubMed  Article  PubMed Central  Google Scholar 

  109. 109.

    Rocha, E. R., Owens, G. Jr. & Smith, C. J. The redox-sensitive transcriptional activator OxyR regulates the peroxide response regulon in the obligate anaerobe Bacteroides fragilis. J. Bacteriol. 182, 5059–5069 (2000).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  110. 110.

    Raskin, L., Rittmann, B. E. & Stahl, D. A. Competition and coexistence of sulfate-reducing and methanogenic populations in anaerobic biofilms. Appl. Environ. Microbiol. 62, 3847–3857 (1996).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  111. 111.

    Rocha, E. R. & Smith, C. J. Ferritin-like family proteins in the anaerobe Bacteroides fragilis: when an oxygen storm is coming, take your iron to the shelter. Biometals 26, 577–591 (2013). This paper shows that when O2 is sensed, the anaerobe B. fragilis sequesters its iron to avoid lethal Fenton chemistry.

    CAS  PubMed  Article  PubMed Central  Google Scholar 

  112. 112.

    Li, X. et al. Transcriptomic analysis reveals hub genes and subnetworks related to ROS metabolism in Hylocereus undatus through novel superoxide scavenger trypsin treatment during storage. BMC Genomics 21, 437 (2020).

    PubMed  PubMed Central  Article  CAS  Google Scholar 

  113. 113.

    Andrews, S. C., Robinson, A. K. & Rodriguez-Quinones, F. Bacterial iron homeostasis. FEMS Microbiol. Rev. 27, 215–237 (2003).

    CAS  PubMed  Article  PubMed Central  Google Scholar 

  114. 114.

    Zeth, K. Dps biomineralizing proteins: multifunctional architects of nature. Biochem. J. 445, 297–311 (2012).

    CAS  PubMed  Article  PubMed Central  Google Scholar 

  115. 115.

    Lee, J. W. & Helmann, J. D. The PerR transcription factor senses H2O2 by metal-catalysed histidine oxidation. Nature 440, 363–367 (2006). This study reports how the PerR transcription factor uses Fenton chemistry to sense the presence of H2O2.

    CAS  PubMed  Article  PubMed Central  Google Scholar 

  116. 116.

    Marinho, H. S., Real, C., Cyrne, L., Soares, H. & Antunes, F. Hydrogen peroxide sensing, signaling and regulation of transcription factors. Redox Biol. 2, 535–562 (2014).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  117. 117.

    Mukhopadhyay, A. et al. Cell-wide responses to low–oxygen exposure in Desulfovibrio vulgaris Hildenborough. J. Bacteriol. 189, 5996–6010 (2007).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  118. 118.

    Hillmann, F., Fischer, R. J., Saint-Prix, F., Girbal, L. & Bahl, H. PerR acts as a switch for oxygen tolerance in the strict anaerobe Clostridium acetobutylicum. Mol. Microbiol. 68, 848–860 (2008). This study demonstrates that the activation of a peroxide defence system enables some growth of an obligate anaerobe in the presence of O2.

    CAS  PubMed  Article  PubMed Central  Google Scholar 

  119. 119.

    Liochev, S. I. & Fridovich, I. The role of O2.– in the production of HO•: in vitro and in vivo. Free. Radic. Biol. Med. 16, 29–33 (1994).

    CAS  PubMed  Article  PubMed Central  Google Scholar 

  120. 120.

    Tulstrup, M. V. et al. Antibiotic treatment affects intestinal permeability and gut microbial composition in wistar rats dependent on antibiotic class. PLoS ONE 10, e0144854 (2015).

    PubMed  PubMed Central  Article  CAS  Google Scholar 

  121. 121.

    Rigottier-Gois, L. Dysbiosis in inflammatory bowel diseases: the oxygen hypothesis. ISME J. 7, 1256–1261 (2013).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  122. 122.

    Winter, S. E. et al. Gut inflammation provides a respiratory electron acceptor for Salmonella. Nature 467, 426–429 (2010).

    CAS  PubMed  Article  PubMed Central  Google Scholar 

  123. 123.

    Keyer, K. & Imlay, J. A. Inactivation of dehydratase [4Fe–4S] clusters and disruption of iron homeostasis upon cell exposure to peroxynitrite. J. Biol. Chem. 272, 27652–27659 (1997).

    CAS  PubMed  Article  PubMed Central  Google Scholar 

  124. 124.

    Jang, S. & Imlay, J. A. Hydrogen peroxide inactivates the Escherichia coli Isc iron–sulphur assembly system, and OxyR induces the Suf system to compensate. Mol. Microbiol. 78, 1448–1467 (2010).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  125. 125.

    Imlay, J. A., Sethu, R. & Rohaun, S. K. Evolutionary adaptations that enable enzymes to tolerate oxidative stress. Free. Radic. Biol. Med. 140, 4–13 (2019).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  126. 126.

    Bowman, S. E. J. et al. Solution structure and biochemical characterization of a spare part protein that restores activity to an oxygen-damaged glycyl radical enzyme. J. Biol. Inorg. Chem. 24, 817–829 (2019). This structural analysis shows how a complementary protein can reactivate O2-damaged PFL.

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  127. 127.

    Savageau, M. A. Escherichia coli habitats, cell types, and molecular mechanisms of gene control. Am. Nat. 122, 732–744 (1983).

    CAS  Article  Google Scholar 

  128. 128.

    Lin, W. C., Coppi, M. V. & Lovley, D. R. Geobacter sulfurreducens can grow with oxygen as a terminal electron acceptor. Appl. Environ. Microbiol. 70, 2525–2528 (2004).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  129. 129.

    Tally, F. P., Stewart, P. R., Sutter, V. L. & Rosenblatt, J. E. Oxygen tolerance of fresh clinical anaerobic bacteria. J. Clin. Microbiol. 1, 161–164 (1975).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  130. 130.

    Khan, M. T. et al. The gut anaerobe Faecalibacterium prausnitzii uses an extracellular electron shuttle to grow at oxic–anoxic interphases. ISME J. 6, 1578–1585 (2012).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  131. 131.

    Rolfe, R. D., Hentges, D. J., Barrett, J. T. & Campbell, B. J. Oxygen tolerance of human intestinal anaerobes. Am. J. Clin. Nutr. 30, 1762–1769 (1977).

    CAS  PubMed  Article  PubMed Central  Google Scholar 

  132. 132.

    Jernberg, C., Lofmark, S., Edlund, C. & Jansson, J. K. Long-term ecological impacts of antibiotic administration on the human intestinal microbiota. ISME J. 1, 56–66 (2007).

    CAS  PubMed  Article  PubMed Central  Google Scholar 

  133. 133.

    Kelly, C. J. et al. Crosstalk between microbiota-derived short-chain fatty acids and intestinal epithelial HIF augments tissue barrier function. Cell Host Microbe 17, 662–671 (2015).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  134. 134.

    Imlay, J. A. Where in the world do bacteria experience oxidative stress? Environ. Microbiol. 21, 521–530 (2019).

    CAS  PubMed  Article  PubMed Central  Google Scholar 

  135. 135.

    Macfarlane, G. T., Gibson, G. R. & Cummings, J. H. Comparison of fermentation reactions in different regions of the human colon. J. Appl. Bacteriol. 72, 57–64 (1992).

    CAS  PubMed  PubMed Central  Google Scholar 

  136. 136.

    Pitcher, M. C., Beatty, E. R. & Cummings, J. H. The contribution of sulphate reducing bacteria and 5-aminosalicylic acid to faecal sulphide in patients with ulcerative colitis. Gut 46, 64–72 (2000).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  137. 137.

    Zhu, H. & Li, Y. R. Oxidative stress and redox signaling mechanisms of inflammatory bowel disease: updated experimental and clinical evidence. Exp. Biol. Med. 237, 474–480 (2012).

    CAS  Article  Google Scholar 

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Acknowledgements

This work was supported by the National Natural Science Foundation of China (No. 31970101), the National Institutes of Health (NIH) (GM049640), the Natural Science Foundation of Guangdong Province (No. 2019A1515011685) and the Research Start-up Project of Shantou University (NTF18018).

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Correspondence to Zheng Lu or James A. Imlay.

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Glossary

Reducing equivalents

Chemical species that are capable of transferring the equivalent of one electron in redox reactions.

Proton motive force

The transmembrane electrochemical gradient, established by metabolic proton translocation, that powers the membrane proteins that synthesize ATP and import substrates.

Antibonding orbitals

High-energy molecular orbitals; they are typically incompletely filled and are the orbitals involved in electron-transfer reactions.

Anoxic glove boxes

Boxes (chambers) that provide a strict anaerobic atmosphere of 0–5 ppm molecular oxygen (O2). A palladium catalyst eliminates O2 by using hydrogen gas as a co-reactant; a vacuum airlock reduces O2 levels prior to transfer of items into the glove box.

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Lu, Z., Imlay, J.A. When anaerobes encounter oxygen: mechanisms of oxygen toxicity, tolerance and defence. Nat Rev Microbiol (2021). https://doi.org/10.1038/s41579-021-00583-y

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