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Biology and evolution of bacterial toxin–antitoxin systems

Nature Reviews Microbiology volume 20, pages 335–350 (2022)Cite this article

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Abstract

Toxin–antitoxin systems are widespread in bacterial genomes. They are usually composed of two elements: a toxin that inhibits an essential cellular process and an antitoxin that counteracts its cognate toxin. In the past decade, a number of new toxin–antitoxin systems have been described, bringing new growth inhibition mechanisms to light as well as novel modes of antitoxicity. However, recent advances in the field profoundly questioned the role of these systems in bacterial physiology, stress response and antimicrobial persistence. This shifted the paradigm of the functions of toxin–antitoxin systems to roles related to interactions between hosts and their mobile genetic elements, such as viral defence or plasmid stability. In this Review, we summarize the recent progress in understanding the biology and evolution of these small genetic elements, and discuss how genomic conflicts could shape the diversification of toxin–antitoxin systems.

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Fig. 1: Currently proposed types of toxin–antitoxin system.
Fig. 2: Major types of regulation of toxin–antitoxin systems.
Fig. 3: Cellular activities of toxins of toxin–antitoxin systems.
Fig. 4: Roles of toxin–antitoxin systems in genomic conflicts.
Fig. 5: Comparison of chromosomes and toxin–antitoxin locus between Escherichia coli strains.

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References

  1. Ogura, T. & Hiraga, S. Mini-F plasmid genes that couple host cell division to plasmid proliferation. Proc. Natl Acad. Sci. USA 80, 4784–4788 (1983).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  2. Gerdes, K., Rasmussen, P. B. & Molin, S. Unique type of plasmid maintenance function: postsegregational killing of plasmid-free cells. Proc. Natl Acad. Sci. USA 83, 3116–3120 (1986).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  3. Yarmolinsky, M. B. Programmed cell death in bacterial populations. Science 267, 836–837 (1995).

    Article  CAS  PubMed  Google Scholar 

  4. Karoui, H., Bex, F., Drèze, P. & Couturier, M. Ham22, a mini-F mutation which is lethal to host cell and promotes recA-dependent induction of lambdoid prophage. EMBO J. 2, 1863–1868 (1983).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  5. Jaffé, A., Ogura, T. & Hiraga, S. Effects of the ccd function of the F plasmid on bacterial growth. J. Bacteriol. 163, 841–849 (1985).

    Article  PubMed  PubMed Central  Google Scholar 

  6. Hiraga, S., Jaffé, A., Ogura, T., Mori, H. & Takahashi, H. F plasmid ccd mechanism in Escherichia coli. J. Bacteriol. 166, 100–104 (1986).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  7. Tam, J. E. & Kline, B. C. The F plasmid ccd autorepressor is a complex of CcdA and CcdB proteins. Mol. Gen. Genet. 219, 26–32 (1989).

    Article  CAS  PubMed  Google Scholar 

  8. Gerdes, K. et al. Mechanism of postsegregational killing by the hok gene product of the parB system of plasmid R1 and its homology with the relF gene product of the E. coli relB operon. EMBO J. 5, 2023–2029 (1986).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  9. Gerdes, K., Helin, K., Christensen, O. W. & Løbner-Olesen, A. Translational control and differential RNA decay are key elements regulating postsegregational expression of the killer protein encoded by the parB locus of plasmid R1. J. Mol. Biol. 203, 119–129 (1988).

    Article  CAS  PubMed  Google Scholar 

  10. Van Melderen, L., Bernard, P. & Couturier, M. Lon-dependent proteolysis of CcdA is the key control for activation of CcdB in plasmid-free segregant bacteria. Mol. Microbiol. 11, 1151–1157 (1994).

    Article  PubMed  Google Scholar 

  11. Tsuchimoto, S., Nishimura, Y. & Ohtsubo, E. The stable maintenance system pem of plasmid R100: degradation of PemI protein may allow PemK protein to inhibit cell growth. J. Bacteriol. 174, 4205–4211 (1992).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  12. Masuda, Y., Miyakawa, K., Nishimura, Y. & Ohtsubo, E. chpA and chpB, Escherichia coli chromosomal homologs of the pem locus responsible for stable maintenance of plasmid R100. J. Bacteriol. 175, 6850–6856 (1993).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  13. Christensen, S. K., Pedersen, K., Hansen, F. G. & Gerdes, K. Toxin-antitoxin loci as stress-response-elements: ChpAK/MazF and ChpBK cleave translated RNAs and are counteracted by tmRNA. J. Mol. Biol. 332, 809–819 (2003).

    Article  CAS  PubMed  Google Scholar 

  14. Wilbaux, M., Mine, N., Guérout, A.-M., Mazel, D. & Van Melderen, L. Functional interactions between coexisting toxin-antitoxin systems of the ccd family in Escherichia coli O157:H7. J. Bacteriol. 189, 2712–2719 (2007).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  15. Pandey, D. P. & Gerdes, K. Toxin-antitoxin loci are highly abundant in free-living but lost from host-associated prokaryotes. Nucleic Acids Res. 33, 966–976 (2005).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  16. Leplae, R. et al. Diversity of bacterial type II toxin-antitoxin systems: a comprehensive search and functional analysis of novel families. Nucleic Acids Res. 39, 5513–5525 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  17. Ramisetty, B. C. M. & Santhosh, R. S. Horizontal gene transfer of chromosomal Type II toxin-antitoxin systems of Escherichia coli. FEMS Microbiol. Lett. 363, fnv238 (2016).

    Article  PubMed  CAS  Google Scholar 

  18. Makarova, K. S., Wolf, Y. I. & Koonin, E. V. Comprehensive comparative-genomic analysis of type 2 toxin-antitoxin systems and related mobile stress response systems in prokaryotes. Biol. Direct 4, 19 (2009).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  19. Hayes, F. & Van Melderen, L. Toxins-antitoxins: diversity, evolution and function. Crit. Rev. Biochem. Mol. Biol. 46, 386–408 (2011).

    Article  CAS  PubMed  Google Scholar 

  20. Fiedoruk, K., Daniluk, T., Swiecicka, I., Sciepuk, M. & Leszczynska, K. Type II toxin-antitoxin systems are unevenly distributed among Escherichia coli phylogroups. Microbiology (Reading) 161, 158–167 (2015).

    Article  CAS  PubMed  Google Scholar 

  21. Fineran, P. C. et al. The phage abortive infection system, ToxIN, functions as a protein-RNA toxin-antitoxin pair. Proc. Natl Acad. Sci. USA 106, 894–899 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  22. Wang, X. et al. A new type V toxin-antitoxin system where mRNA for toxin GhoT is cleaved by antitoxin GhoS. Nat. Chem. Biol. 8, 855–861 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  23. Aakre, C. D., Phung, T. N., Huang, D. & Laub, M. T. A bacterial toxin inhibits DNA replication elongation through a direct interaction with the β sliding clamp. Mol. Cell 52, 617–628 (2013).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  24. Freire, D. M. et al. An NAD+ phosphorylase toxin triggers Mycobacterium tuberculosis cell death. Mol. Cell 73, 1282–1291.e8 (2019).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  25. Cai, Y. et al. A nucleotidyltransferase toxin inhibits growth of Mycobacterium tuberculosis through inactivation of tRNA acceptor stems. Sci. Adv. 6, eabb6651 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  26. Jimmy, S. et al. A widespread toxin-antitoxin system exploiting growth control via alarmone signaling. Proc. Natl Acad. Sci. USA 117, 10500–10510 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  27. Songailiene, I. et al. HEPN-MNT toxin-antitoxin system: the HEPN ribonuclease is neutralized by oligoAMPylation. Mol. Cell 80, 955–970.e7 (2020).

    Article  CAS  PubMed  Google Scholar 

  28. Kurata, T. et al. RelA-SpoT homolog toxins pyrophosphorylate the CCA end of tRNA to inhibit protein synthesis. Mol. Cell 81, 3160–3170.e9 (2021).

    Article  CAS  PubMed  Google Scholar 

  29. Li, M. et al. Toxin-antitoxin RNA pairs safeguard CRISPR-Cas systems. Science 372, eabe5601 (2021).

    Article  CAS  PubMed  Google Scholar 

  30. Hargreaves, D. et al. Structural and functional analysis of the Kid toxin protein from E. coli plasmid R1. Structure 10, 1425–1433 (2002).

    Article  CAS  PubMed  Google Scholar 

  31. Sterckx, Y. G.-J. et al. A unique hetero-hexadecameric architecture displayed by the Escherichia coli O157 PaaA2-ParE2 antitoxin-toxin complex. J. Mol. Biol. 428, 1589–1603 (2016).

    Article  CAS  PubMed  Google Scholar 

  32. Castro-Roa, D. et al. The Fic protein Doc uses an inverted substrate to phosphorylate and inactivate EF-Tu. Nat. Chem. Biol. 9, 811–817 (2013).

    Article  CAS  PubMed  Google Scholar 

  33. Harms, A. et al. Adenylylation of gyrase and Topo IV by FicT toxins disrupts bacterial DNA topology. Cell Rep. 12, 1497–1507 (2015).

    Article  CAS  PubMed  Google Scholar 

  34. Dalton, K. M. & Crosson, S. A conserved mode of protein recognition and binding in a ParD-ParE toxin-antitoxin complex. Biochemistry 49, 2205–2215 (2010).

    Article  CAS  PubMed  Google Scholar 

  35. Kumar, P., Issac, B., Dodson, E. J., Turkenburg, J. P. & Mande, S. C. Crystal structure of Mycobacterium tuberculosis YefM antitoxin reveals that it is not an intrinsically unstructured protein. J. Mol. Biol. 383, 482–493 (2008).

    Article  CAS  PubMed  Google Scholar 

  36. Brown, B. L., Lord, D. M., Grigoriu, S., Peti, W. & Page, R. The Escherichia coli toxin MqsR destabilizes the transcriptional repression complex formed between the antitoxin MqsA and the mqsRA operon promoter. J. Biol. Chem. 288, 1286–1294 (2013).

    Article  CAS  PubMed  Google Scholar 

  37. Zhang, D., de Souza, R. F., Anantharaman, V., Iyer, L. M. & Aravind, L. Polymorphic toxin systems: comprehensive characterization of trafficking modes, processing, mechanisms of action, immunity and ecology using comparative genomics. Biol. Direct 7, 18 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  38. Harms, A. et al. A bacterial toxin-antitoxin module is the origin of inter-bacterial and inter-kingdom effectors of Bartonella. PLoS Genet. 13, e1007077 (2017).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  39. Kawano, M., Oshima, T., Kasai, H. & Mori, H. Molecular characterization of long direct repeat (LDR) sequences expressing a stable mRNA encoding for a 35-amino-acid cell-killing peptide and a cis-encoded small antisense RNA in Escherichia coli. Mol. Microbiol. 45, 333–349 (2002).

    Article  CAS  PubMed  Google Scholar 

  40. Darfeuille, F., Unoson, C., Vogel, J. & Wagner, E. G. H. An antisense RNA inhibits translation by competing with standby ribosomes. Mol. Cell 26, 381–392 (2007).

    Article  CAS  PubMed  Google Scholar 

  41. Kawano, M., Aravind, L. & Storz, G. An antisense RNA controls synthesis of an SOS-induced toxin evolved from an antitoxin. Mol. Microbiol. 64, 738–754 (2007).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  42. Fozo, E. M. et al. Repression of small toxic protein synthesis by the Sib and OhsC small RNAs. Mol. Microbiol. 70, 1076–1093 (2008).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  43. Lehnherr, H., Maguin, E., Jafri, S. & Yarmolinsky, M. B. Plasmid addiction genes of bacteriophage P1: doc, which causes cell death on curing of prophage, and phd, which prevents host death when prophage is retained. J. Mol. Biol. 233, 414–428 (1993).

    Article  CAS  PubMed  Google Scholar 

  44. Li, G.-Y., Zhang, Y., Inouye, M. & Ikura, M. Inhibitory mechanism of Escherichia coli RelE-RelB toxin-antitoxin module involves a helix displacement near an mRNA interferase active site. J. Biol. Chem. 284, 14628–14636 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  45. Jurėnas, D., Van Melderen, L. & Garcia-Pino, A. Mechanism of regulation and neutralization of the AtaR-AtaT toxin-antitoxin system. Nat. Chem. Biol. 15, 285–294 (2019).

    Article  PubMed  CAS  Google Scholar 

  46. Samson, J. E., Spinelli, S., Cambillau, C. & Moineau, S. Structure and activity of AbiQ, a lactococcal endoribonuclease belonging to the type III toxin-antitoxin system. Mol. Microbiol. 87, 756–768 (2013).

    Article  CAS  PubMed  Google Scholar 

  47. Short, F. L. et al. Selectivity and self-assembly in the control of a bacterial toxin by an antitoxic noncoding RNA pseudoknot. Proc. Natl Acad. Sci. USA 110, E241–E249 (2013).

    Article  CAS  PubMed  Google Scholar 

  48. Masuda, H., Tan, Q., Awano, N., Wu, K.-P. & Inouye, M. YeeU enhances the bundling of cytoskeletal polymers of MreB and FtsZ, antagonizing the CbtA (YeeV) toxicity in Escherichia coli. Mol. Microbiol. 84, 979–989 (2012).

    Article  CAS  PubMed  Google Scholar 

  49. Jankevicius, G., Ariza, A., Ahel, M. & Ahel, I. The toxin-antitoxin system DarTG catalyzes reversible ADP-ribosylation of DNA. Mol. Cell 64, 1109–1116 (2016).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  50. Marimon, O. et al. An oxygen-sensitive toxin-antitoxin system. Nat. Commun. 7, 13634 (2016).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  51. Yu, X. et al. Characterization of a toxin-antitoxin system in Mycobacterium tuberculosis suggests neutralization by phosphorylation as the antitoxicity mechanism. Commun. Biol. 3, 216 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  52. Choi, J. S. et al. The small RNA, SdsR, acts as a novel type of toxin in Escherichia coli. RNA Biol. 15, 1319–1335 (2018).

    Article  PubMed  PubMed Central  Google Scholar 

  53. Shao, Y. et al. TADB: a web-based resource for type 2 toxin-antitoxin loci in bacteria and archaea. Nucleic Acids Res. 39, D606–D611 (2011).

    Article  CAS  PubMed  Google Scholar 

  54. Wen, J. & Fozo, E. M. sRNA antitoxins: more than one way to repress a toxin. Toxins 6, 2310–2335 (2014).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  55. Blower, T. R. et al. Identification and classification of bacterial type III toxin-antitoxin systems encoded in chromosomal and plasmid genomes. Nucleic Acids Res. 40, 6158–6173 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  56. Anantharaman, V., Makarova, K. S., Burroughs, A. M., Koonin, E. V. & Aravind, L. Comprehensive analysis of the HEPN superfamily: identification of novel roles in intra-genomic conflicts, defense, pathogenesis and RNA processing. Biol. Direct 8, 15 (2013).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  57. Otsuka, Y. et al. IscR regulates RNase LS activity by repressing rnlA transcription. Genetics 185, 823–830 (2010).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  58. Turnbull, K. J. & Gerdes, K. HicA toxin of Escherichia coli derepresses hicAB transcription to selectively produce HicB antitoxin. Mol. Microbiol. 104, 781–792 (2017).

    Article  CAS  PubMed  Google Scholar 

  59. Fraikin, N., Rousseau, C. J., Goeders, N. & Van Melderen, L. Reassessing the role of the type II MqsRA toxin-antitoxin system in stress response and biofilm formation: mqsA is transcriptionally uncoupled from mqsR. mBio 10, e02678-19 (2019).

    Article  PubMed  PubMed Central  Google Scholar 

  60. Kamada, K., Hanaoka, F. & Burley, S. K. Crystal structure of the MazE/MazF complex: molecular bases of antidote-toxin recognition. Mol. Cell 11, 875–884 (2003).

    Article  CAS  PubMed  Google Scholar 

  61. Madl, T. et al. Structural basis for nucleic acid and toxin recognition of the bacterial antitoxin CcdA. J. Mol. Biol. 364, 170–185 (2006).

    Article  CAS  PubMed  Google Scholar 

  62. Garcia-Pino, A. et al. Doc of prophage P1 is inhibited by its antitoxin partner Phd through fold complementation. J. Biol. Chem. 283, 30821–30827 (2008).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  63. Afif, H., Allali, N., Couturier, M. & Van Melderen, L. The ratio between CcdA and CcdB modulates the transcriptional repression of the ccd poison-antidote system. Mol. Microbiol. 41, 73–82 (2001).

    Article  CAS  PubMed  Google Scholar 

  64. Overgaard, M., Borch, J., Jørgensen, M. G. & Gerdes, K. Messenger RNA interferase RelE controls relBE transcription by conditional cooperativity. Mol. Microbiol. 69, 841–857 (2008).

    Article  CAS  PubMed  Google Scholar 

  65. Garcia-Pino, A. et al. Allostery and intrinsic disorder mediate transcription regulation by conditional cooperativity. Cell 142, 101–111 (2010).

    Article  CAS  PubMed  Google Scholar 

  66. Talavera, A. et al. A dual role in regulation and toxicity for the disordered N-terminus of the toxin GraT. Nat. Commun. 10, 972 (2019).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  67. Hallez, R. et al. New toxins homologous to ParE belonging to three-component toxin-antitoxin systems in Escherichia coli O157:H7. Mol. Microbiol. 76, 719–732 (2010).

    Article  CAS  PubMed  Google Scholar 

  68. Zielenkiewicz, U. & Ceglowski, P. The toxin-antitoxin system of the streptococcal plasmid pSM19035. J. Bacteriol. 187, 6094–6105 (2005).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  69. Fozo, E. M. et al. Abundance of type I toxin-antitoxin systems in bacteria: searches for new candidates and discovery of novel families. Nucleic Acids Res. 38, 3743–3759 (2010).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  70. Masachis, S. & Darfeuille, F. Type I toxin-antitoxin systems: regulating toxin expression via Shine-Dalgarno sequence sequestration and small RNA binding. Microbiol. Spectr. https://doi.org/10.1128/microbiolspec.RWR-0030-2018 (2018).

    Article  PubMed  Google Scholar 

  71. Gerdes, K., Thisted, T. & Martinussen, J. Mechanism of post-segregational killing by the hok/sok system of plasmid R1: sok antisense RNA regulates formation of a hok mRNA species correlated with killing of plasmid-free cells. Mol. Microbiol. 4, 1807–1818 (1990).

    Article  CAS  PubMed  Google Scholar 

  72. Romilly, C., Deindl, S. & Wagner, E. G. H. The ribosomal protein S1-dependent standby site in tisB mRNA consists of a single-stranded region and a 5′ structure element. Proc. Natl Acad. Sci. USA 116, 15901–15906 (2019).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  73. Romilly, C., Lippegaus, A. & Wagner, E. G. H. An RNA pseudoknot is essential for standby-mediated translation of the tisB toxin mRNA in Escherichia coli. Nucleic Acids Res. 48, 12336–12347 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  74. Vogel, J., Argaman, L., Wagner, E. G. H. & Altuvia, S. The small RNA IstR inhibits synthesis of an SOS-induced toxic peptide. Curr. Biol. 14, 2271–2276 (2004).

    Article  CAS  PubMed  Google Scholar 

  75. Durand, S., Gilet, L. & Condon, C. The essential function of B. subtilis RNase III is to silence foreign toxin genes. PLoS Genet. 8, e1003181 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  76. Li, G.-W., Burkhardt, D., Gross, C. & Weissman, J. S. Quantifying absolute protein synthesis rates reveals principles underlying allocation of cellular resources. Cell 157, 624–635 (2014).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  77. Ruiz-Echevarría, M. J., de la Cueva, G. & Díaz-Orejas, R. Translational coupling and limited degradation of a polycistronic messenger modulate differential gene expression in the parD stability system of plasmid R1. Mol. Gen. Genet. 248, 599–609 (1995).

    Article  PubMed  Google Scholar 

  78. Blower, T. R. et al. A processed noncoding RNA regulates an altruistic bacterial antiviral system. Nat. Struct. Mol. Biol. 18, 185–190 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  79. De Jonge, N. et al. Rejuvenation of CcdB-poisoned gyrase by an intrinsically disordered protein domain. Mol. Cell 35, 154–163 (2009).

    Article  PubMed  CAS  Google Scholar 

  80. Lehnherr, H. & Yarmolinsky, M. B. Addiction protein Phd of plasmid prophage P1 is a substrate of the ClpXP serine protease of Escherichia coli. Proc. Natl Acad. Sci. USA 92, 3274–3277 (1995).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  81. Diago-Navarro, E., Hernández-Arriaga, A. M., Kubik, S., Konieczny, I. & Díaz-Orejas, R. Cleavage of the antitoxin of the parD toxin-antitoxin system is determined by the ClpAP protease and is modulated by the relative ratio of the toxin and the antitoxin. Plasmid 70, 78–85 (2013).

    Article  CAS  PubMed  Google Scholar 

  82. Van Melderen, L. et al. ATP-dependent degradation of CcdA by Lon protease. Effects of secondary structure and heterologous subunit interactions. J. Biol. Chem. 271, 27730–27738 (1996).

    Article  PubMed  Google Scholar 

  83. Dubiel, A., Wegrzyn, K., Kupinski, A. P. & Konieczny, I. ClpAP protease is a universal factor that activates the parDE toxin-antitoxin system from a broad host range RK2 plasmid. Sci. Rep. 8, 15287 (2018).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  84. Ziemski, M., Leodolter, J., Taylor, G., Kerschenmeyer, A. & Weber-Ban, E. Genome-wide interaction screen for Mycobacterium tuberculosis ClpCP protease reveals toxin-antitoxin systems as a major substrate class. FEBS J. 288, 111–126 (2021).

    Article  CAS  PubMed  Google Scholar 

  85. LeRoux, M., Culviner, P. H., Liu, Y. J., Littlehale, M. L. & Laub, M. T. Stress can induce transcription of toxin-antitoxin systems without activating toxin. Mol. Cell 79, 280–292.e8 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  86. Bordes, P. et al. SecB-like chaperone controls a toxin-antitoxin stress-responsive system in Mycobacterium tuberculosis. Proc. Natl Acad. Sci. USA 108, 8438–8443 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  87. Bordes, P. et al. Chaperone addiction of toxin-antitoxin systems. Nat. Commun. 7, 13339 (2016).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  88. Texier, P. et al. ClpXP-mediated degradation of the TAC antitoxin is neutralized by the SecB-like chaperone in Mycobacterium tuberculosis. J. Mol. Biol. 433, 166815 (2021).

    Article  CAS  PubMed  Google Scholar 

  89. Schumacher, M. A. et al. Role of unusual P loop ejection and autophosphorylation in HipA-mediated persistence and multidrug tolerance. Cell Rep. 2, 518–525 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  90. Piscotta, F. J., Jeffrey, P. D. & Link, A. J. ParST is a widespread toxin-antitoxin module that targets nucleotide metabolism. Proc. Natl Acad. Sci. USA 116, 826–834 (2019).

    Article  CAS  PubMed  Google Scholar 

  91. Critchlow, S. E. et al. The interaction of the F plasmid killer protein, CcdB, with DNA gyrase: induction of DNA cleavage and blocking of transcription. J. Mol. Biol. 273, 826–839 (1997).

    Article  CAS  PubMed  Google Scholar 

  92. Bernard, P. & Couturier, M. Cell killing by the F plasmid CcdB protein involves poisoning of DNA-topoisomerase II complexes. J. Mol. Biol. 226, 735–745 (1992).

    Article  CAS  PubMed  Google Scholar 

  93. Dao-Thi, M.-H. et al. Molecular basis of gyrase poisoning by the addiction toxin CcdB. J. Mol. Biol. 348, 1091–1102 (2005).

    Article  CAS  PubMed  Google Scholar 

  94. Jiang, Y., Pogliano, J., Helinski, D. R. & Konieczny, I. ParE toxin encoded by the broad-host-range plasmid RK2 is an inhibitor of Escherichia coli gyrase. Mol. Microbiol. 44, 971–979 (2002).

    Article  CAS  PubMed  Google Scholar 

  95. Ames, J. R., Muthuramalingam, M., Murphy, T., Najar, F. Z. & Bourne, C. R. Expression of different ParE toxins results in conserved phenotypes with distinguishable classes of toxicity. Microbiologyopen 8, e902 (2019).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  96. Roberts, R. C., Ström, A. R. & Helinski, D. R. The parDE operon of the broad-host-range plasmid RK2 specifies growth inhibition associated with plasmid loss. J. Mol. Biol. 237, 35–51 (1994).

    Article  CAS  PubMed  Google Scholar 

  97. Guo, Y. et al. RalR (a DNase) and RalA (a small RNA) form a type I toxin-antitoxin system in Escherichia coli. Nucleic Acids Res. 42, 6448–6462 (2014).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  98. Jurėnas, D. & Van Melderen, L. The variety in the common theme of translation inhibition by type II toxin-antitoxin systems. Front. Genet. 11, 262 (2020).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  99. Culviner, P. H. & Laub, M. T. Global analysis of the E. coli toxin MazF reveals widespread cleavage of mRNA and the inhibition of rRNA maturation and ribosome biogenesis. Mol. Cell 70, 868–880.e10 (2018).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  100. Mets, T. et al. Toxins MazF and MqsR cleave Escherichia coli rRNA precursors at multiple sites. RNA Biol. 14, 124–135 (2017).

    Article  PubMed  Google Scholar 

  101. Mets, T. et al. Fragmentation of Escherichia coli mRNA by MazF and MqsR. Biochimie 156, 79–91 (2019).

    Article  CAS  PubMed  Google Scholar 

  102. Barth, V. C. & Woychik, N. A. The sole Mycobacterium smegmatis MazF toxin targets tRNALys to impart highly selective, codon-dependent proteome reprogramming. Front. Genet. 10, 1356 (2019).

    Article  CAS  PubMed  Google Scholar 

  103. Winther, K. S. & Gerdes, K. Enteric virulence associated protein VapC inhibits translation by cleavage of initiator tRNA. Proc. Natl Acad. Sci. USA 108, 7403–7407 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  104. Cruz, J. W. et al. Growth-regulating Mycobacterium tuberculosis VapC-mt4 toxin is an isoacceptor-specific tRNase. Nat. Commun. 6, 7480 (2015).

    Article  PubMed  Google Scholar 

  105. Winther, K., Tree, J. J., Tollervey, D. & Gerdes, K. VapCs of Mycobacterium tuberculosis cleave RNAs essential for translation. Nucleic Acids Res. 44, 9860–9871 (2016).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  106. Cintrón, M. et al. Accurate target identification for Mycobacterium tuberculosis endoribonuclease toxins requires expression in their native host. Sci. Rep. 9, 5949 (2019).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  107. Winther, K. S., Brodersen, D. E., Brown, A. K. & Gerdes, K. VapC20 of Mycobacterium tuberculosis cleaves the sarcin-ricin loop of 23S rRNA. Nat. Commun. 4, 2796 (2013).

    Article  PubMed  CAS  Google Scholar 

  108. Pedersen, K. et al. The bacterial toxin RelE displays codon-specific cleavage of mRNAs in the ribosomal A site. Cell 112, 131–140 (2003).

    Article  CAS  PubMed  Google Scholar 

  109. Goeders, N., Drèze, P.-L. & Van Melderen, L. Relaxed cleavage specificity within the RelE toxin family. J. Bacteriol. 195, 2541–2549 (2013).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  110. Schureck, M. A., Repack, A., Miles, S. J., Marquez, J. & Dunham, C. M. Mechanism of endonuclease cleavage by the HigB toxin. Nucleic Acids Res. 44, 7944–7953 (2016).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  111. Jørgensen, M. G., Pandey, D. P., Jaskolska, M. & Gerdes, K. HicA of Escherichia coli defines a novel family of translation-independent mRNA interferases in bacteria and archaea. J. Bacteriol. 191, 1191–1199 (2009).

    Article  PubMed  CAS  Google Scholar 

  112. Kaspy, I. et al. HipA-mediated antibiotic persistence via phosphorylation of the glutamyl-tRNA-synthetase. Nat. Commun. 4, 3001 (2013).

    Article  PubMed  CAS  Google Scholar 

  113. Vang Nielsen, S. et al. Serine-threonine kinases encoded by split hipA homologs inhibit tryptophanyl-tRNA synthetase. mBio 10, e01138-19 (2019).

    Article  PubMed  PubMed Central  Google Scholar 

  114. Jurėnas, D. et al. AtaT blocks translation initiation by N-acetylation of the initiator tRNAfMet. Nat. Chem. Biol. 13, 640–646 (2017).

    Article  PubMed  CAS  Google Scholar 

  115. Rycroft, J. A. et al. Activity of acetyltransferase toxins involved in Salmonella persister formation during macrophage infection. Nat. Commun. 9, 1993 (2018).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  116. Wilcox, B. et al. Escherichia coli ItaT is a type II toxin that inhibits translation by acetylating isoleucyl-tRNAIle. Nucleic Acids Res. 46, 7873–7885 (2018).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  117. Unoson, C. & Wagner, E. G. H. A small SOS-induced toxin is targeted against the inner membrane in Escherichia coli. Mol. Microbiol. 70, 258–270 (2008).

    Article  CAS  PubMed  Google Scholar 

  118. Weel-Sneve, R. et al. Single transmembrane peptide DinQ modulates membrane-dependent activities. PLoS Genet. 9, e1003260 (2013).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  119. Patel, S. & Weaver, K. E. Addiction toxin Fst has unique effects on chromosome segregation and cell division in Enterococcus faecalis and Bacillus subtilis. J. Bacteriol. 188, 5374–5384 (2006).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  120. Mutschler, H., Gebhardt, M., Shoeman, R. L. & Meinhart, A. A novel mechanism of programmed cell death in bacteria by toxin-antitoxin systems corrupts peptidoglycan synthesis. PLoS Biol. 9, e1001033 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  121. Rocker, A. et al. The ng_ζ1 toxin of the gonococcal epsilon/zeta toxin/antitoxin system drains precursors for cell wall synthesis. Nat. Commun. 9, 1686 (2018).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  122. Tan, Q., Awano, N. & Inouye, M. YeeV is an Escherichia coli toxin that inhibits cell division by targeting the cytoskeleton proteins, FtsZ and MreB. Mol. Microbiol. 79, 109–118 (2011).

    Article  CAS  PubMed  Google Scholar 

  123. Engelberg-Kulka, H., Amitai, S., Kolodkin-Gal, I. & Hazan, R. Bacterial programmed cell death and multicellular behavior in bacteria. PLoS Genet. 2, e135 (2006).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  124. Engelberg-Kulka, H., Hazan, R. & Amitai, S. mazEF: a chromosomal toxin-antitoxin module that triggers programmed cell death in bacteria. J. Cell Sci. 118, 4327–4332 (2005).

    Article  CAS  PubMed  Google Scholar 

  125. Helaine, S. et al. Internalization of Salmonella by macrophages induces formation of nonreplicating persisters. Science 343, 204–208 (2014).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  126. Maisonneuve, E. & Gerdes, K. Molecular mechanisms underlying bacterial persisters. Cell 157, 539–548 (2014).

    Article  CAS  PubMed  Google Scholar 

  127. Wang, X. et al. Antitoxin MqsA helps mediate the bacterial general stress response. Nat. Chem. Biol. 7, 359–366 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  128. Kolodkin-Gal, I., Hazan, R., Gaathon, A., Carmeli, S. & Engelberg-Kulka, H. A linear pentapeptide is a quorum-sensing factor required for mazEF-mediated cell death in Escherichia coli. Science 318, 652–655 (2007).

    Article  CAS  PubMed  Google Scholar 

  129. Belitsky, M. et al. The Escherichia coli extracellular death factor EDF induces the endoribonucleolytic activities of the toxins MazF and ChpBK. Mol. Cell 41, 625–635 (2011).

    Article  CAS  PubMed  Google Scholar 

  130. Aizenman, E., Engelberg-Kulka, H. & Glaser, G. An Escherichia coli chromosomal ‘addiction module’ regulated by guanosine [corrected] 3′,5′-bispyrophosphate: a model for programmed bacterial cell death. Proc. Natl Acad. Sci. USA 93, 6059–6063 (1996).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  131. Vesper, O. et al. Selective translation of leaderless mRNAs by specialized ribosomes generated by MazF in Escherichia coli. Cell 147, 147–157 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  132. Pedersen, K., Christensen, S. K. & Gerdes, K. Rapid induction and reversal of a bacteriostatic condition by controlled expression of toxins and antitoxins. Mol. Microbiol. 45, 501–510 (2002).

    Article  CAS  PubMed  Google Scholar 

  133. Tsilibaris, V., Maenhaut-Michel, G., Mine, N. & Van Melderen, L. What is the benefit to Escherichia coli of having multiple toxin-antitoxin systems in its genome? J. Bacteriol. 189, 6101–6108 (2007).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  134. Ramisetty, B. C. M., Raj, S. & Ghosh, D. Escherichia coli MazEF toxin-antitoxin system does not mediate programmed cell death. J. Basic. Microbiol. 56, 1398–1402 (2016).

    Article  CAS  PubMed  Google Scholar 

  135. Kaldalu, N., Maiväli, Ü., Hauryliuk, V. & Tenson, T. Reanalysis of proteomics results fails to detect MazF-mediated stress proteins. mBio 10, e00949-19 (2019).

    Article  PubMed  PubMed Central  Google Scholar 

  136. Christensen, S. K. & Gerdes, K. RelE toxins from bacteria and archaea cleave mRNAs on translating ribosomes, which are rescued by tmRNA. Mol. Microbiol. 48, 1389–1400 (2003).

    Article  CAS  PubMed  Google Scholar 

  137. Christensen, S. K., Mikkelsen, M., Pedersen, K. & Gerdes, K. RelE, a global inhibitor of translation, is activated during nutritional stress. Proc. Natl Acad. Sci. USA 98, 14328–14333 (2001).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  138. González Barrios, A. F. et al. Autoinducer 2 controls biofilm formation in Escherichia coli through a novel motility quorum-sensing regulator (MqsR, B3022). J. Bacteriol. 188, 305–316 (2006).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  139. Kwan, B. W. et al. The MqsR/MqsA toxin/antitoxin system protects Escherichia coli during bile acid stress. Environ. Microbiol. 17, 3168–3181 (2015).

    Article  CAS  PubMed  Google Scholar 

  140. Soo, V. W. C. & Wood, T. K. Antitoxin MqsA represses curli formation through the master biofilm regulator CsgD. Sci. Rep. 3, 3186 (2013).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  141. Dörr, T., Vulić, M. & Lewis, K. Ciprofloxacin causes persister formation by inducing the TisB toxin in Escherichia coli. PLoS Biol. 8, e1000317 (2010).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  142. Verstraeten, N. et al. Obg and membrane depolarization are part of a microbial Bet-Hedging strategy that leads to antibiotic tolerance. Mol. Cell 59, 9–21 (2015).

    Article  CAS  PubMed  Google Scholar 

  143. Berghoff, B. A., Hoekzema, M., Aulbach, L. & Wagner, E. G. H. Two regulatory RNA elements affect TisB-dependent depolarization and persister formation. Mol. Microbiol. 103, 1020–1033 (2017).

    Article  CAS  PubMed  Google Scholar 

  144. Ramisetty, B. C. M., Ghosh, D., Roy Chowdhury, M. & Santhosh, R. S. What is the link between stringent response, endoribonuclease encoding type II toxin-antitoxin systems and persistence? Front. Microbiol. 7, 1882 (2016).

    Article  PubMed  PubMed Central  Google Scholar 

  145. Maisonneuve, E., Castro-Camargo, M. & Gerdes, K. Retraction notice to: (p)ppGpp controls bacterial persistence by stochastic induction of toxin-antitoxin activity. Cell 172, 1135 (2018).

    Article  CAS  PubMed  Google Scholar 

  146. Retraction for Maisonneuve. et al. Bacterial persistence by RNA endonucleases. Proc. Natl Acad. Sci. USA 115, E2901 (2018).

    Google Scholar 

  147. Harms, A., Fino, C., Sørensen, M. A., Semsey, S. & Gerdes, K. Prophages and growth dynamics confound experimental results with antibiotic-tolerant persister cells. mBio 8, e01964–17 (2017).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  148. Goormaghtigh, F. et al. Reassessing the role of type II Toxin-antitoxin systems in formation of Escherichia coli type II persister cells. mBio 9, e00640-18 (2018).

    Article  PubMed  PubMed Central  Google Scholar 

  149. Pontes, M. H. & Groisman, E. A. Slow growth determines nonheritable antibiotic resistance in Salmonella enterica. Sci. Signal. 12, eaax3938 (2019).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  150. Rosendahl, S., Tamman, H., Brauer, A., Remm, M. & Hõrak, R. Chromosomal toxin-antitoxin systems in Pseudomonas putida are rather selfish than beneficial. Sci. Rep. 10, 9230 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  151. Christensen, S. K. et al. Overproduction of the Lon protease triggers inhibition of translation in Escherichia coli: involvement of the yefM-yoeB toxin-antitoxin system. Mol. Microbiol. 51, 1705–1717 (2004).

    Article  CAS  PubMed  Google Scholar 

  152. Völzing, K. G. & Brynildsen, M. P. Stationary-phase persisters to ofloxacin sustain DNA damage and require repair systems only during recovery. mBio 6, e00731-15 (2015).

    Article  PubMed  PubMed Central  Google Scholar 

  153. Goormaghtigh, F. & Van Melderen, L. Single-cell imaging and characterization of Escherichia coli persister cells to ofloxacin in exponential cultures. Sci. Adv. 5, eaav9462 (2019).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  154. Korch, S. B., Henderson, T. A. & Hill, T. M. Characterization of the hipA7 allele of Escherichia coli and evidence that high persistence is governed by (p)ppGpp synthesis. Mol. Microbiol. 50, 1199–1213 (2003).

    Article  CAS  PubMed  Google Scholar 

  155. Levin-Reisman, I. et al. Antibiotic tolerance facilitates the evolution of resistance. Science 355, 826–830 (2017).

    Article  CAS  PubMed  Google Scholar 

  156. Santi, I., Manfredi, P., Maffei, E., Egli, A. & Jenal, U. Evolution of antibiotic tolerance shapes resistance development in chronic Pseudomonas aeruginosa infections. mBio 12, e03482-20 (2021).

    Article  PubMed  PubMed Central  Google Scholar 

  157. Rotem, E. et al. Regulation of phenotypic variability by a threshold-based mechanism underlies bacterial persistence. Proc. Natl Acad. Sci. USA 107, 12541–12546 (2010).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  158. Guegler, C. K. & Laub, M. T. Shutoff of host transcription triggers a toxin-antitoxin system to cleave phage RNA and abort infection. Mol. Cell 81, 2361–2373.e9 (2021).

    Article  CAS  PubMed  Google Scholar 

  159. Cooper, T. F. & Heinemann, J. A. Postsegregational killing does not increase plasmid stability but acts to mediate the exclusion of competing plasmids. Proc. Natl Acad. Sci. USA 97, 12643–12648 (2000).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  160. Saavedra De Bast, M., Mine, N. & Van Melderen, L. Chromosomal toxin-antitoxin systems may act as antiaddiction modules. J. Bacteriol. 190, 4603–4609 (2008).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  161. Cegłowski, P., Boitsov, A., Chai, S. & Alonso, J. C. Analysis of the stabilization system of pSM19035-derived plasmid pBT233 in Bacillus subtilis. Gene 136, 1–12 (1993).

    Article  PubMed  Google Scholar 

  162. Bravo, A., Ortega, S., de Torrontegui, G. & Díaz, R. Killing of Escherichia coli cells modulated by components of the stability system ParD of plasmid R1. Mol. Gen. Genet. 215, 146–151 (1988).

    Article  CAS  PubMed  Google Scholar 

  163. Dy, R. L., Przybilski, R., Semeijn, K., Salmond, G. P. C. & Fineran, P. C. A widespread bacteriophage abortive infection system functions through a Type IV toxin-antitoxin mechanism. Nucleic Acids Res. 42, 4590–4605 (2014).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  164. de la Hoz, A. B. et al. Plasmid copy-number control and better-than-random segregation genes of pSM19035 share a common regulator. Proc. Natl Acad. Sci. USA 97, 728–733 (2000).

    Article  PubMed  PubMed Central  Google Scholar 

  165. Ni, S. et al. Conjugative plasmid-encoded toxin-antitoxin system PrpT/PrpA directly controls plasmid copy number. Proc. Natl Acad. Sci. USA 118, e2011577118 (2021).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  166. Wozniak, R. A. F. & Waldor, M. K. A toxin-antitoxin system promotes the maintenance of an integrative conjugative element. PLoS Genet. 5, e1000439 (2009).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  167. Escudero, J. A., Loot, C., Nivina, A. & Mazel, D. The integron: adaptation on demand. Microbiol. Spectr. 3, 3.2.10 (2015).

    Article  CAS  Google Scholar 

  168. Iqbal, N., Guérout, A.-M., Krin, E., Le Roux, F. & Mazel, D. Comprehensive functional analysis of the 18 Vibrio cholerae N16961 toxin-antitoxin systems substantiates their role in stabilizing the superintegron. J. Bacteriol. 197, 2150–2159 (2015).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  169. Szekeres, S., Dauti, M., Wilde, C., Mazel, D. & Rowe-Magnus, D. A. Chromosomal toxin-antitoxin loci can diminish large-scale genome reductions in the absence of selection. Mol. Microbiol. 63, 1588–1605 (2007).

    Article  CAS  PubMed  Google Scholar 

  170. Yuan, J., Yamaichi, Y. & Waldor, M. K. The three vibrio cholerae chromosome II-encoded ParE toxins degrade chromosome I following loss of chromosome II. J. Bacteriol. 193, 611–619 (2011).

    Article  CAS  PubMed  Google Scholar 

  171. Cooper, T. F. & Heinemann, J. A. Selection for plasmid post-segregational killing depends on multiple infection: evidence for the selection of more virulent parasites through parasite-level competition. Proc. Biol. Sci. 272, 403–410 (2005).

    CAS  PubMed  Google Scholar 

  172. Cooper, T. F., Paixão, T. & Heinemann, J. A. Within-host competition selects for plasmid-encoded toxin-antitoxin systems. Proc. Biol. Sci. 277, 3149–3155 (2010).

    PubMed  PubMed Central  Google Scholar 

  173. Santos-Sierra, S., Giraldo, R. & Díaz-Orejas, R. Functional interactions between homologous conditional killer systems of plasmid and chromosomal origin. FEMS Microbiol. Lett. 152, 51–56 (1997).

    Article  CAS  PubMed  Google Scholar 

  174. Santos Sierra, S., Giraldo, R. & Díaz Orejas, R. Functional interactions between chpB and parD, two homologous conditional killer systems found in the Escherichia coli chromosome and in plasmid R1. FEMS Microbiol. Lett. 168, 51–58 (1998).

    Article  CAS  PubMed  Google Scholar 

  175. Garvey, P., Fitzgerald, G. F. & Hill, C. Cloning and DNA sequence analysis of two abortive infection phage resistance determinants from the lactococcal plasmid pNP40. Appl. Environ. Microbiol. 61, 4321–4328 (1995).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  176. Pecota, D. C. & Wood, T. K. Exclusion of T4 phage by the hok/sok killer locus from plasmid R1. J. Bacteriol. 178, 2044–2050 (1996).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  177. Otsuka, Y. & Yonesaki, T. A novel endoribonuclease, RNase LS, in Escherichia coli. Genetics 169, 13–20 (2005).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  178. Otsuka, Y. & Yonesaki, T. Dmd of bacteriophage T4 functions as an antitoxin against Escherichia coli LsoA and RnlA toxins. Mol. Microbiol. 83, 669–681 (2012).

    Article  CAS  PubMed  Google Scholar 

  179. Blower, T. R., Evans, T. J., Przybilski, R., Fineran, P. C. & Salmond, G. P. C. Viral evasion of a bacterial suicide system by RNA-based molecular mimicry enables infectious altruism. PLoS Genet. 8, e1003023 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  180. Blower, T. R. et al. Evolution of Pectobacterium bacteriophage ΦM1 to escape two bifunctional type III toxin-antitoxin and abortive infection systems through mutations in a single viral gene. Appl. Environ. Microbiol. 83, e03229-16 (2017).

    Article  PubMed  PubMed Central  Google Scholar 

  181. Chen, B., Akusobi, C., Fang, X. & Salmond, G. P. C. Environmental T4-family bacteriophages evolve to escape abortive infection via multiple routes in a bacterial host employing ‘altruistic suicide’ through type III toxin-antitoxin systems. Front. Microbiol. 8, 1006 (2017).

    Article  PubMed  PubMed Central  Google Scholar 

  182. Hilliard, J. J., Maurizi, M. R. & Simon, L. D. Isolation and characterization of the phage T4 PinA protein, an inhibitor of the ATP-dependent Lon protease of Escherichia coli. J. Biol. Chem. 273, 518–523 (1998).

    Article  CAS  PubMed  Google Scholar 

  183. Sberro, H. et al. Discovery of functional toxin/antitoxin systems in bacteria by shotgun cloning. Mol. Cell 50, 136–148 (2013).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  184. Lima-Mendez, G. et al. Toxin-antitoxin gene pairs found in Tn3 family transposons appear to be an integral part of the transposition module. mBio 11, e00452-20 (2020).

    Article  PubMed  PubMed Central  Google Scholar 

  185. Loftie-Eaton, W. et al. Evolutionary paths that expand plasmid host-range: implications for spread of antibiotic resistance. Mol. Biol. Evol. 33, 885–897 (2016).

    Article  CAS  PubMed  Google Scholar 

  186. Lite, T.-L. V. et al. Uncovering the basis of protein-protein interaction specificity with a combinatorially complete library. eLife 9, e60924 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  187. Aakre, C. D. et al. Evolving new protein-protein interaction specificity through promiscuous intermediates. Cell 163, 594–606 (2015).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  188. Fiebig, A., Castro Rojas, C. M., Siegal-Gaskins, D. & Crosson, S. Interaction specificity, toxicity and regulation of a paralogous set of ParE/RelE-family toxin-antitoxin systems. Mol. Microbiol. 77, 236–251 (2010).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  189. Mine, N., Guglielmini, J., Wilbaux, M. & Van Melderen, L. The decay of the chromosomally encoded ccdO157 toxin-antitoxin system in the Escherichia coli species. Genetics 181, 1557–1566 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  190. Pedersen, K. & Gerdes, K. Multiple hok genes on the chromosome of Escherichia coli. Mol. Microbiol. 32, 1090–1102 (1999).

    Article  CAS  PubMed  Google Scholar 

  191. Goeders, N. & Van Melderen, L. Toxin-antitoxin systems as multilevel interaction systems. Toxins 6, 304–324 (2014).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  192. Moran, N. A. & Bennett, G. M. The tiniest tiny genomes. Annu. Rev. Microbiol. 68, 195–215 (2014).

    Article  CAS  PubMed  Google Scholar 

  193. Anantharaman, V. & Aravind, L. New connections in the prokaryotic toxin-antitoxin network: relationship with the eukaryotic nonsense-mediated RNA decay system. Genome Biol. 4, R81 (2003).

    Article  PubMed  PubMed Central  Google Scholar 

  194. Loris, R. et al. Crystal structure of CcdB, a topoisomerase poison from E. coli. J. Mol. Biol. 285, 1667–1677 (1999).

    Article  CAS  PubMed  Google Scholar 

  195. Arbing, M. A. et al. Crystal structures of Phd-Doc, HigA, and YeeU establish multiple evolutionary links between microbial growth-regulating toxin-antitoxin systems. Structure 18, 996–1010 (2010).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  196. Coles, M. et al. AbrB-like transcription factors assume a swapped hairpin fold that is evolutionarily related to double-psi beta barrels. Structure 13, 919–928 (2005).

    Article  CAS  PubMed  Google Scholar 

  197. Gucinski, G. C. et al. Convergent evolution of the barnase/EndoU/Ccolicin/RelE (BECR) fold in antibacterial tRNase toxins. Structure 27, 1660–1674.e5 (2019).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  198. Whitney, J. C. et al. An interbacterial NAD(P)+ glycohydrolase toxin requires elongation factor Tu for delivery to target cells. Cell 163, 607–619 (2015).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  199. Ahmad, S. et al. An interbacterial toxin inhibits target cell growth by synthesizing (p)ppApp. Nature 575, 674–678 (2019).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  200. Schirmer, T. et al. Evolutionary diversification of host-targeted bartonella effectors proteins derived from a conserved FicTA toxin-antitoxin module. Microorganisms 9, 1645 (2021).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  201. Han, Q. et al. Crystal structure of Xanthomonas AvrRxo1-ORF1, a type III effector with a polynucleotide kinase domain, and its interactor AvrRxo1-ORF2. Structure 23, 1900–1909 (2015).

    Article  CAS  PubMed  Google Scholar 

  202. Triplett, L. R. et al. AvrRxo1 is a bifunctional type III secreted effector and toxin-antitoxin system component with homologs in diverse environmental contexts. PLoS ONE 11, e0158856 (2016).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  203. Yadav, S. K. et al. Immunity proteins of dual nuclease T6SS effectors function as transcriptional repressors. EMBO Rep. 22, e53112 (2021).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  204. Bertelsen, M. B. et al. Structural basis for toxin inhibition in the VapXD toxin-antitoxin system. Structure 29, 139–150.e3 (2021).

    Article  CAS  PubMed  Google Scholar 

  205. Matelska, D., Steczkiewicz, K. & Ginalski, K. Comprehensive classification of the PIN domain-like superfamily. Nucleic Acids Res. 45, 6995–7020 (2017).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  206. Dziewit, L., Jazurek, M., Drewniak, L., Baj, J. & Bartosik, D. The SXT conjugative element and linear prophage N15 encode toxin-antitoxin-stabilizing systems homologous to the tad-ata module of the Paracoccus aminophilus plasmid pAMI2. J. Bacteriol. 189, 1983–1997 (2007).

    Article  CAS  PubMed  Google Scholar 

  207. Kang, S.-M. et al. Functional details of the Mycobacterium tuberculosis VapBC26 toxin-antitoxin system based on a structural study: insights into unique binding and antibiotic peptides. Nucleic Acids Res. 45, 8564–8580 (2017).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  208. Sayed, N., Nonin-Lecomte, S., Réty, S. & Felden, B. Functional and structural insights of a Staphylococcus aureus apoptotic-like membrane peptide from a toxin-antitoxin module. J. Biol. Chem. 287, 43454–43463 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  209. Równicki, M. et al. Artificial activation of Escherichia coli mazEF and hipBA toxin-antitoxin systems by antisense peptide nucleic acids as an antibacterial strategy. Front. Microbiol. 9, 2870 (2018).

    Article  PubMed  PubMed Central  Google Scholar 

  210. Kang, S.-M. et al. Structure-based de novo design of Mycobacterium tuberculosis VapC-activating stapled peptides. ACS Chem. Biol. 15, 2493–2498 (2020).

    Article  CAS  PubMed  Google Scholar 

  211. Kang, S.-M. et al. Structure-based design of peptides that trigger Streptococcus pneumoniae cell death. FEBS J. 288, 1546–1564 (2021).

    Article  CAS  PubMed  Google Scholar 

  212. Maleki, A., Ghafourian, S., Pakzad, I., Badakhsh, B. & Sadeghifard, N. mazE Antitoxin of toxin antitoxin system and fbpA as reliable targets to eradication of Neisseria meningitidis. Curr. Pharm. Des. 24, 1204–1210 (2018).

    Article  CAS  PubMed  Google Scholar 

  213. Trovatti, E., Cotrim, C. A., Garrido, S. S., Barros, R. S. & Marchetto, R. Peptides based on CcdB protein as novel inhibitors of bacterial topoisomerases. Bioorg. Med. Chem. Lett. 18, 6161–6164 (2008).

    Article  CAS  PubMed  Google Scholar 

  214. López-Igual, R., Bernal-Bayard, J., Rodríguez-Patón, A., Ghigo, J.-M. & Mazel, D. Engineered toxin-intein antimicrobials can selectively target and kill antibiotic-resistant bacteria in mixed populations. Nat. Biotechnol. 37, 755–760 (2019).

    Article  PubMed  CAS  Google Scholar 

  215. Park, J.-H., Yamaguchi, Y. & Inouye, M. Intramolecular regulation of the sequence-specific mRNA interferase activity of MazF fused to a MazE fragment with a linker cleavable by specific proteases. Appl. Environ. Microbiol. 78, 3794–3799 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  216. Chono, H. et al. Acquisition of HIV-1 resistance in T lymphocytes using an ACA-specific E. coli mRNA interferase. Hum. Gene Ther. 22, 35–43 (2011).

    Article  CAS  PubMed  Google Scholar 

  217. de la Cueva-Méndez, G., Mills, A. D., Clay-Farrace, L., Díaz-Orejas, R. & Laskey, R. A. Regulatable killing of eukaryotic cells by the prokaryotic proteins Kid and Kis. EMBO J. 22, 246–251 (2003).

    Article  PubMed  PubMed Central  Google Scholar 

  218. Shimazu, T., Mirochnitchenko, O., Phadtare, S. & Inouye, M. Regression of solid tumors by induction of MazF, a bacterial mRNA endoribonuclease. J. Mol. Microbiol. Biotechnol. 24, 228–233 (2014).

    CAS  PubMed  Google Scholar 

  219. Stieber, D., Gabant, P. & Szpirer, C. The art of selective killing: plasmid toxin/antitoxin systems and their technological applications. Biotechniques 45, 344–346 (2008).

    Article  CAS  PubMed  Google Scholar 

  220. Bernard, P., Gabant, P., Bahassi, E. M. & Couturier, M. Positive-selection vectors using the F plasmid ccdB killer gene. Gene 148, 71–74 (1994).

    Article  CAS  PubMed  Google Scholar 

  221. Mok, W. W. K. & Li, Y. A highly efficient molecular cloning platform that utilises a small bacterial toxin gene. Chembiochem 14, 733–738 (2013).

    Article  CAS  PubMed  Google Scholar 

  222. Szpirer, C. Y. & Milinkovitch, M. C. Separate-component-stabilization system for protein and DNA production without the use of antibiotics. Biotechniques 38, 775–781 (2005).

    Article  CAS  PubMed  Google Scholar 

  223. Nehlsen, K., Herrmann, S., Zauers, J., Hauser, H. & Wirth, D. Toxin-antitoxin based transgene expression in mammalian cells. Nucleic Acids Res. 38, e32 (2010).

    Article  CAS  PubMed  Google Scholar 

  224. Suzuki, M., Zhang, J., Liu, M., Woychik, N. A. & Inouye, M. Single protein production in living cells facilitated by an mRNA interferase. Mol. Cell 18, 253–261 (2005).

    Article  CAS  PubMed  Google Scholar 

  225. Suzuki, M., Mao, L. & Inouye, M. Single protein production (SPP) system in Escherichia coli. Nat. Protoc. 2, 1802–1810 (2007).

    Article  CAS  PubMed  Google Scholar 

  226. Kristoffersen, P., Jensen, G. B., Gerdes, K. & Piskur, J. Bacterial toxin-antitoxin gene system as containment control in yeast cells. Appl. Environ. Microbiol. 66, 5524–5526 (2000).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  227. Denkovskienė, E., Paškevičius, Š., Stankevičiūtė, J., Gleba, Y. & Ražanskienė, A. Control of T-DNA transfer from Agrobacterium tumefaciens to plants based on an inducible bacterial toxin-antitoxin system. Mol. Plant Microbe Interact. 33, 1142–1149 (2020).

    Article  PubMed  Google Scholar 

  228. Wright, O., Delmans, M., Stan, G.-B. & Ellis, T. GeneGuard: a modular plasmid system designed for biosafety. ACS Synth. Biol. 4, 307–316 (2015).

    Article  CAS  PubMed  Google Scholar 

  229. Baldacci-Cresp, F. et al. Escherichia colimazEF toxin-antitoxin system as a tool to target cell ablation in plants. J. Mol. Microbiol. Biotechnol. 26, 277–283 (2016).

    CAS  PubMed  Google Scholar 

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Acknowledgements

Work in the L.V.M. laboratory is funded by the Wallonia Region (Algotech, grant 1510598), the ARC actions 2018–2023 and the FNRS-FRS (CDR ‘PERSIST’, grant J010818F). D.J. is supported by an FRM postdoctoral fellowship (SPF201809007142).

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Author notes

  1. These authors jointly supervised this work: Dukas Jurėnas, Nathan Fraikin.

Authors and Affiliations

  1. Laboratoire d’Ingénierie des Systèmes Macromoléculaires, Institut de Microbiologie de la Méditerranée, Aix-Marseille Université, CNRS, Marseille, France

    Dukas Jurėnas

  2. Cellular and Molecular Microbiology, Faculté des Sciences, Université Libre de Bruxelles, Gosselies, Belgium

    Nathan Fraikin & Laurence Van Melderen

  3. Research Area Infection Biology, Biozentrum, University of Basel, Basel, Switzerland

    Frédéric Goormaghtigh

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  1. Dukas Jurėnas
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  2. Nathan Fraikin
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  3. Frédéric Goormaghtigh
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  4. Laurence Van Melderen
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The authors contributed equally to all aspects of the article.

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Correspondence to Laurence Van Melderen.

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Glossary

Inteins

Internal segments of proteins that self-excise and ligate the remaining segments (exteins) during protein splicing.

Chaperone-addiction motifs

Specific sequences that promote antitoxin destabilization unless recognized by the chaperone.

DNA gyrase

Type II topoisomerase enzyme that relieves positive supercoiling in front of the replication forks.

Aminoacylation

Ligation of an amino acid to its cognate tRNA, also known as tRNA charging.

AMPylase

Enzyme that ligates AMP to an amino acid side chain of a target protein.

Thymineless death

Rapid loss of viability occurring as a result of thymine deprivation.

Anti-Shine–Dalgarno sequence

Sequence in the prokaryotic ribosome that helps to align the ribosome for translation initiation at the ATG start codon.

Iteron sequences

DNA sequences recognized by replication initiation proteins that are involved in the control of the copy number of plasmids.

Genetic drift

Stochastic fluctuations in the frequency of alleles that occur randomly and can eventually lead to the loss or fixation of these alleles.

Phylogroups

Taxonomic groups of organisms related through their evolutionary history.

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Jurėnas, D., Fraikin, N., Goormaghtigh, F. et al. Biology and evolution of bacterial toxin–antitoxin systems. Nat Rev Microbiol 20, 335–350 (2022). https://doi.org/10.1038/s41579-021-00661-1

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