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Type I Toxin-Antitoxin Systems: Regulating Toxin Expression via Shine-Dalgarno Sequence Sequestration and Small RNA Binding

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  • Authors: Sara Masachis1, Fabien Darfeuille2
  • Editors: Gisela Storz3, Kai Papenfort4
  • VIEW AFFILIATIONS HIDE AFFILIATIONS
    Affiliations: 1: ARNA Laboratory, INSERM U1212, CNRS UMR 5320, University of Bordeaux, F-33000 Bordeaux, France; 2: ARNA Laboratory, INSERM U1212, CNRS UMR 5320, University of Bordeaux, F-33000 Bordeaux, France; 3: Division of Molecular and Cellular Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, MD; 4: Department of Biology I, Microbiology, LMU Munich, Martinsried, Germany
  • Source: microbiolspec July 2018 vol. 6 no. 4 doi:10.1128/microbiolspec.RWR-0030-2018
  • Received 08 March 2018 Accepted 17 May 2018 Published 27 July 2018
  • Fabien Darfeuille, [email protected]
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  • Abstract:

    Toxin-antitoxin (TA) systems are small genetic loci composed of two adjacent genes: a toxin and an antitoxin that prevents toxin action. Despite their wide distribution in bacterial genomes, the reasons for TA systems being on chromosomes remain enigmatic. In this review, we focus on type I TA systems, composed of a small antisense RNA that plays the role of an antitoxin to control the expression of its toxin counterpart. It does so by direct base-pairing to the toxin-encoding mRNA, thereby inhibiting its translation and/or promoting its degradation. However, in many cases, antitoxin binding is not sufficient to avoid toxicity. Several -encoded mRNA elements are also required for repression, acting to uncouple transcription and translation via the sequestration of the ribosome binding site. Therefore, both antisense RNA binding and compact mRNA folding are necessary to tightly control toxin synthesis and allow the presence of these toxin-encoding systems on bacterial chromosomes.

  • Citation: Masachis S, Darfeuille F. 2018. Type I Toxin-Antitoxin Systems: Regulating Toxin Expression via Shine-Dalgarno Sequence Sequestration and Small RNA Binding. Microbiol Spectrum 6(4):RWR-0030-2018. doi:10.1128/microbiolspec.RWR-0030-2018.

References

1. Harms A, Brodersen DE, Mitarai N, Gerdes K. 2018. Toxins, targets, and triggers: an overview of toxin-antitoxin biology. Mol Cell 70:768–784. http://dx.doi.org/10.1016/j.molcel.2018.01.003.
2. Benz J, Meinhart A. 2014. Antibacterial effector/immunity systems: it’s just the tip of the iceberg. Curr Opin Microbiol 17:1–10. http://dx.doi.org/10.1016/j.mib.2013.11.002. [PubMed]
3. Van Melderen L. 2010. Toxin-antitoxin systems: why so many, what for? Curr Opin Microbiol 13:781–785. http://dx.doi.org/10.1016/j.mib.2010.10.006.
4. Goeders N, Van Melderen L. 2014. Toxin-antitoxin systems as multilevel interaction systems. Toxins (Basel) 6:304–324. http://dx.doi.org/10.3390/toxins6010304. [PubMed]
5. Greenfield TJ, Ehli E, Kirshenmann T, Franch T, Gerdes K, Weaver KE. 2000. The antisense RNA of the par locus of pAD1 regulates the expression of a 33-amino-acid toxic peptide by an unusual mechanism. Mol Microbiol 37:652–660. http://dx.doi.org/10.1046/j.1365-2958.2000.02035.x.
6. Weaver KE. 2012. The par toxin-antitoxin system from Enterococcus faecalis plasmid pAD1 and its chromosomal homologs. RNA Biol 9:1498–1503. http://dx.doi.org/10.4161/rna.22311.
7. Greenfield TJ, Franch T, Gerdes K, Weaver KE. 2001. Antisense RNA regulation of the par post-segregational killing system: structural analysis and mechanism of binding of the antisense RNA, RNAII and its target, RNAI. Mol Microbiol 42:527–537. http://dx.doi.org/10.1046/j.1365-2958.2001.02663.x.
8. Gerdes K, Bech FW, Jørgensen ST, Løbner-Olesen A, Rasmussen PB, Atlung T, Boe L, Karlstrom O, Molin S, von Meyenberg K. 1986. Mechanism of postsegregational killing by the hok gene product of the parB system of plasmid Rl and its homology with the relF gene product of the E. coli relB operon. EMBO J 5:2023–2029. [PubMed]
9. Gerdes K, Gultyaev AP, Franch T, Pedersen K, Mikkelsen ND. 1997. Antisense RNA-regulated programmed cell death. Annu Rev Genet 31:1–31. http://dx.doi.org/10.1146/annurev.genet.31.1.1.
10. Gerdes K, Wagner EG. 2007. RNA antitoxins. Curr Opin Microbiol 10:117–124. http://dx.doi.org/10.1016/j.mib.2007.03.003.
11. Nielsen AK, Thorsted P, Thisted T, Wagner EG, Gerdes K. 1991. The rifampicin-inducible genes srnB from F and pnd from R483 are regulated by antisense RNAs and mediate plasmid maintenance by killing of plasmid-free segregants. Mol Microbiol 5:1961–1973. http://dx.doi.org/10.1111/j.1365-2958.1991.tb00818.x.
12. Pedersen K, Gerdes K. 1999. Multiple hok genes on the chromosome of Escherichia coli. Mol Microbiol 32:1090–1102. http://dx.doi.org/10.1046/j.1365-2958.1999.01431.x.
13. Weaver KE. 2015. The type I toxin-antitoxin par locus from Enterococcus faecalis plasmid pAD1: RNA regulation by both cis- and trans-acting elements. Plasmid 78:65–70. http://dx.doi.org/10.1016/j.plasmid.2014.10.001.
14. Kwong SM, Jensen SO, Firth N. 2010. Prevalence of Fst-like toxin-antitoxin systems. Microbiology 156:975–977, discussion 977. http://dx.doi.org/10.1099/mic.0.038323-0.
15. Weaver KE, Reddy SG, Brinkman CL, Patel S, Bayles KW, Endres JL. 2009. Identification and characterization of a family of toxin-antitoxin systems related to the Enterococcus faecalis plasmid pAD1 par addiction module. Microbiology 155:2930–2940. http://dx.doi.org/10.1099/mic.0.030932-0.
16. Fozo EM, Kawano M, Fontaine F, Kaya Y, Mendieta KS, Jones KL, Ocampo A, Rudd KE, Storz G. 2008. Repression of small toxic protein synthesis by the Sib and OhsC small RNAs. Mol Microbiol 70:1076–1093. http://dx.doi.org/10.1111/j.1365-2958.2008.06394.x.
17. Kawano M, Oshima T, Kasai H, Mori H. 2002. 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. http://dx.doi.org/10.1046/j.1365-2958.2002.03042.x.
18. Vogel J, Argaman L, Wagner EG, Altuvia S. 2004. The small RNA IstR inhibits synthesis of an SOS-induced toxic peptide. Curr Biol 14:2271–2276. http://dx.doi.org/10.1016/j.cub.2004.12.003.
19. Durand S, Jahn N, Condon C, Brantl S. 2012. Type I toxin-antitoxin systems in Bacillus subtilis. RNA Biol 9:1491–1497. http://dx.doi.org/10.4161/rna.22358. [PubMed]
20. Weel-Sneve R, Kristiansen KI, Odsbu I, Dalhus B, Booth J, Rognes T, Skarstad K, Bjørås M. 2013. Single transmembrane peptide DinQ modulates membrane-dependent activities. PLoS Genet 9:e1003260. http://dx.doi.org/10.1371/journal.pgen.1003260.
21. Sharma CM, Hoffmann S, Darfeuille F, Reignier J, Findeiss S, Sittka A, Chabas S, Reiche K, Hackermüller J, Reinhardt R, Stadler PF, Vogel J. 2010. The primary transcriptome of the major human pathogen Helicobacter pylori. Nature 464:250–255. http://dx.doi.org/10.1038/nature08756.
22. Fozo EM, Makarova KS, Shabalina SA, Yutin N, Koonin EV, Storz G. 2010. Abundance of type I toxin-antitoxin systems in bacteria: searches for new candidates and discovery of novel families. Nucleic Acids Res 38:3743–3759. http://dx.doi.org/10.1093/nar/gkq054.
23. Verstraeten N, Knapen WJ, Kint CI, Liebens V, Van den Bergh B, Dewachter L, Michiels JE, Fu Q, David CC, Fierro AC, Marchal K, Beirlant J, Versées W, Hofkens J, Jansen M, Fauvart M, Michiels J. 2015. Obg and membrane depolarization are part of a microbial bet-hedging strategy that leads to antibiotic tolerance. Mol Cell 59:9–21. http://dx.doi.org/10.1016/j.molcel.2015.05.011. [PubMed]
24. Dörr T, Vulić M, Lewis K. 2010. Ciprofloxacin causes persister formation by inducing the TisB toxin in Escherichia coli. PLoS Biol 8:e1000317. http://dx.doi.org/10.1371/journal.pbio.1000317.
25. Berghoff BA, Hoekzema M, Aulbach L, Wagner EG. 2017. Two regulatory RNA elements affect TisB-dependent depolarization and persister formation. Mol Microbiol 103:1020–1033. http://dx.doi.org/10.1111/mmi.13607.
26. Tsilibaris V, Maenhaut-Michel G, Mine N, Van Melderen L. 2007. What is the benefit to Escherichia coli of having multiple toxin-antitoxin systems in its genome? J Bacteriol 189:6101–6108. http://dx.doi.org/10.1128/JB.00527-07.
27. Unoson C, Wagner EGH. 2008. A small SOS-induced toxin is targeted against the inner membrane in Escherichia coli. Mol Microbiol 70:258–270. http://dx.doi.org/10.1111/j.1365-2958.2008.06416.x.
28. Fozo EM, Hemm MR, Storz G. 2008. Small toxic proteins and the antisense RNAs that repress them. Microbiol Mol Biol Rev 72:579–589. http://dx.doi.org/10.1128/MMBR.00025-08.
29. Wen J, Fozo EM. 2014. sRNA antitoxins: more than one way to repress a toxin. Toxins (Basel) 6:2310–2335. http://dx.doi.org/10.3390/toxins6082310.
30. Brantl S, Jahn N. 2015. sRNAs in bacterial type I and type III toxin-antitoxin systems. FEMS Microbiol Rev 39:413–427. http://dx.doi.org/10.1093/femsre/fuv003. [PubMed]
31. Arnion H, Korkut DN, Masachis Gelo S, Chabas S, Reignier J, Iost I, Darfeuille F. 2017. Mechanistic insights into type I toxin antitoxin systems in Helicobacter pylori: the importance of mRNA folding in controlling toxin expression. Nucleic Acids Res 45:4782–4795. http://dx.doi.org/10.1093/nar/gkw1343.
32. Turnbull KJ, Gerdes K. 2017. HicA toxin of Escherichia coli derepresses hicAB transcription to selectively produce HicB antitoxin. Mol Microbiol 104:781–792. http://dx.doi.org/10.1111/mmi.13662.
33. Christensen-Dalsgaard M, Gerdes K. 2006. Two higBA loci in the Vibrio cholerae superintegron encode mRNA cleaving enzymes and can stabilize plasmids. Mol Microbiol 62:397–411. http://dx.doi.org/10.1111/j.1365-2958.2006.05385.x.
34. Wang X, Lord DM, Hong SH, Peti W, Benedik MJ, Page R, Wood TK. 2013. Type II toxin/antitoxin MqsR/MqsA controls type V toxin/antitoxin GhoT/GhoS. Environ Microbiol 15:1734–1744. http://dx.doi.org/10.1111/1462-2920.12063. [PubMed]
35. Guo Y, Quiroga C, Chen Q, McAnulty MJ, Benedik MJ, Wood TK, Wang X. 2014. RalR (a DNase) and RalA (a small RNA) form a type I toxin-antitoxin system in Escherichia coli. Nucleic Acids Res 42:6448–6462. http://dx.doi.org/10.1093/nar/gku279.
36. Kawano M, Aravind L, Storz G. 2007. An antisense RNA controls synthesis of an SOS-induced toxin evolved from an antitoxin. Mol Microbiol 64:738–754. http://dx.doi.org/10.1111/j.1365-2958.2007.05688.x.
37. Mok WW, Patel NH, Li Y. 2010. Decoding toxicity: deducing the sequence requirements of IbsC, a type I toxin in Escherichia coli. J Biol Chem 285:41627–41636. http://dx.doi.org/10.1074/jbc.M110.149179.
38. Wen J, Won D, Fozo EM. 2014. The ZorO-OrzO type I toxin-antitoxin locus: repression by the OrzO antitoxin. Nucleic Acids Res 42:1930–1946. http://dx.doi.org/10.1093/nar/gkt1018.
39. Jahn N, Brantl S, Strahl H. 2015. Against the mainstream: the membrane-associated type I toxin BsrG from Bacillus subtilis interferes with cell envelope biosynthesis without increasing membrane permeability. Mol Microbiol 98:651–666. http://dx.doi.org/10.1111/mmi.13146.
40. Patel S, Weaver KE. 2006. Addiction toxin Fst has unique effects on chromosome segregation and cell division in Enterococcus faecalis and Bacillus subtilis. J Bacteriol 188:5374–5384. http://dx.doi.org/10.1128/JB.00513-06.
41. Wang X, Lord DM, Cheng HY, Osbourne DO, Hong SH, Sanchez-Torres V, Quiroga C, Zheng K, Herrmann T, Peti W, Benedik MJ, Page R, Wood TK. 2012. A new type V toxin-antitoxin system where mRNA for toxin GhoT is cleaved by antitoxin GhoS. Nat Chem Biol 8:855–861. http://dx.doi.org/10.1038/nchembio.1062.
42. Proshkin S, Rahmouni AR, Mironov A, Nudler E. 2010. Cooperation between translating ribosomes and RNA polymerase in transcription elongation. Science 328:504–508. http://dx.doi.org/10.1126/science.1184939.
43. Strahl H, Turlan C, Khalid S, Bond PJ, Kebalo JM, Peyron P, Poljak L, Bouvier M, Hamoen L, Luisi BF, Carpousis AJ. 2015. Membrane recognition and dynamics of the RNA degradosome. PLoS Genet 11:e1004961. http://dx.doi.org/10.1371/journal.pgen.1004961.
44. Khemici V, Prados J, Linder P, Redder P. 2015. Decay-initiating endoribonucleolytic cleavage by RNase Y is kept under tight control via sequence preference and sub-cellular localisation. PLoS Genet 11:e1005577. http://dx.doi.org/10.1371/journal.pgen.1005577.
45. McGary K, Nudler E. 2013. RNA polymerase and the ribosome: the close relationship. Curr Opin Microbiol 16:112–117. http://dx.doi.org/10.1016/j.mib.2013.01.010. [PubMed]
46. Sanamrad A, Persson F, Lundius EG, Fange D, Gynnå AH, Elf J. 2014. Single-particle tracking reveals that free ribosomal subunits are not excluded from the Escherichia coli nucleoid. Proc Natl Acad Sci U S A 111:11413–11418. http://dx.doi.org/10.1073/pnas.1411558111.
47. Richardson JP. 1991. Preventing the synthesis of unused transcripts by Rho factor. Cell 64:1047–1049. http://dx.doi.org/10.1016/0092-8674(91)90257-Y.
48. Simonetti A, Marzi S, Jenner L, Myasnikov A, Romby P, Yusupova G, Klaholz BP, Yusupov M. 2009. A structural view of translation initiation in bacteria. Cell Mol Life Sci 66:423–436. http://dx.doi.org/10.1007/s00018-008-8416-4.
49. Shine J, Dalgarno L. 1974. The 3′-terminal sequence of Escherichia coli 16S ribosomal RNA: complementarity to nonsense triplets and ribosome binding sites. Proc Natl Acad Sci U S A 71:1342–1346. http://dx.doi.org/10.1073/pnas.71.4.1342. [PubMed]
50. Steitz JA, Jakes K. 1975. How ribosomes select initiator regions in mRNA: base pair formation between the 3′ terminus of 16S rRNA and the mRNA during initiation of protein synthesis in Escherichia coli. Proc Natl Acad Sci U S A 72:4734–4738. http://dx.doi.org/10.1073/pnas.72.12.4734.
51. Chen H, Bjerknes M, Kumar R, Jay E. 1994. Determination of the optimal aligned spacing between the Shine-Dalgarno sequence and the translation initiation codon of Escherichia coli mRNAs. Nucleic Acids Res 22:4953–4957. http://dx.doi.org/10.1093/nar/22.23.4953.
52. Komarova AV, Tchufistova LS, Dreyfus M, Boni IV. 2005. AU-rich sequences within 5′ untranslated leaders enhance translation and stabilize mRNA in Escherichia coli. J Bacteriol 187:1344–1349. http://dx.doi.org/10.1128/JB.187.4.1344-1349.2005.
53. Duval M, Korepanov A, Fuchsbauer O, Fechter P, Haller A, Fabbretti A, Choulier L, Micura R, Klaholz BP, Romby P, Springer M, Marzi S. 2013. Escherichia coli ribosomal protein S1 unfolds structured mRNAs onto the ribosome for active translation initiation. PLoS Biol 11:e1001731. http://dx.doi.org/10.1371/journal.pbio.1001731.
54. Duval M, Simonetti A, Caldelari I, Marzi S. 2015. Multiple ways to regulate translation initiation in bacteria: mechanisms, regulatory circuits, dynamics. Biochimie 114:18–29. http://dx.doi.org/10.1016/j.biochi.2015.03.007.
55. Yamamoto H, Wittek D, Gupta R, Qin B, Ueda T, Krause R, Yamamoto K, Albrecht R, Pech M, Nierhaus KH. 2016. 70S-scanning initiation is a novel and frequent initiation mode of ribosomal translation in bacteria. Proc Natl Acad Sci U S A 113:E1180–E1189. http://dx.doi.org/10.1073/pnas.1524554113.
56. Franch T, Gerdes K. 1996. Programmed cell death in bacteria: translational repression by mRNA end-pairing. Mol Microbiol 21:1049–1060. http://dx.doi.org/10.1046/j.1365-2958.1996.771431.x.
57. Gultyaev AP, Franch T, Gerdes K. 1997. Programmed cell death by hok/sok of plasmid R1: coupled nucleotide covariations reveal a phylogenetically conserved folding pathway in the hok family of mRNAs. J Mol Biol 273:26–37. http://dx.doi.org/10.1006/jmbi.1997.1295.
58. Darfeuille F, Unoson C, Vogel J, Wagner EG. 2007. An antisense RNA inhibits translation by competing with standby ribosomes. Mol Cell 26:381–392. http://dx.doi.org/10.1016/j.molcel.2007.04.003.
59. Wen J, Harp JR, Fozo EM. 2017. The 5′ UTR of the type I toxin ZorO can both inhibit and enhance translation. Nucleic Acids Res 45:4006–4020. http://dx.doi.org/10.1093/nar/gkw1172.
60. Kristiansen KI, Weel-Sneve R, Booth JA, Bjørås M. 2016. Mutually exclusive RNA secondary structures regulate translation initiation of DinQ in Escherichia coli. RNA 22:1739–1749. http://dx.doi.org/10.1261/rna.058461.116.
61. Shokeen S, Patel S, Greenfield TJ, Brinkman C, Weaver KE. 2008. Translational regulation by an intramolecular stem-loop is required for intermolecular RNA regulation of the par addiction module. J Bacteriol 190:6076–6083. http://dx.doi.org/10.1128/JB.00660-08.
62. Sayed N, Jousselin A, Felden B. 2011. A cis-antisense RNA acts in trans in Staphylococcus aureus to control translation of a human cytolytic peptide. Nat Struct Mol Biol 19:105–112. http://dx.doi.org/10.1038/nsmb.2193. [PubMed]
63. Durand S, Gilet L, Condon C. 2012. The essential function of B. subtilis RNase III is to silence foreign toxin genes. PLoS Genet 8:e1003181. http://dx.doi.org/10.1371/journal.pgen.1003181.
64. Jahn N, Brantl S. 2013. One antitoxin—two functions: SR4 controls toxin mRNA decay and translation. Nucleic Acids Res 41:9870–9880. http://dx.doi.org/10.1093/nar/gkt735.
65. Müller P, Jahn N, Ring C, Maiwald C, Neubert R, Meißner C, Brantl S. 2016. A multistress responsive type I toxin-antitoxin system: bsrE/SR5 from the B. subtilis chromosome. RNA Biol 13:511–523. http://dx.doi.org/10.1080/15476286.2016.1156288. [PubMed]
66. Maikova A, Peltier J, Boudry P, Hajnsdorf E, Kint N, Monot M, Poquet I, Martin-Verstraete I, Dupuy B, Soutourina O. 2018. Discovery of new type I toxin-antitoxin systems adjacent to CRISPR arrays in Clostridium difficile. Nucleic Acids Res 46:4733–4751. http://dx.doi.org/10.1093/nar/gky124. [PubMed]
67. Pinel-Marie ML, Brielle R, Felden B. 2014. Dual toxic-peptide-coding Staphylococcus aureus RNA under antisense regulation targets host cells and bacterial rivals unequally. Cell Rep 7:424–435. http://dx.doi.org/10.1016/j.celrep.2014.03.012. [PubMed]
68. Reif C, Löser C, Brantl S. 2018. Bacillus subtilis type I antitoxin SR6 promotes degradation of toxin yonT mRNA and is required to prevent toxic yoyJ overexpression. Toxins (Basel) 10:74. http://dx.doi.org/10.3390/toxins10020074.
69. Thisted T, Sørensen NS, Gerdes K. 1995. Mechanism of post-segregational killing: secondary structure analysis of the entire Hok mRNA from plasmid R1 suggests a fold-back structure that prevents translation and antisense RNA binding. J Mol Biol 247:859–873. http://dx.doi.org/10.1006/jmbi.1995.0186. [PubMed]
70. Han K, Kim KS, Bak G, Park H, Lee Y. 2010. Recognition and discrimination of target mRNAs by Sib RNAs, a cis-encoded sRNA family. Nucleic Acids Res 38:5851–5866. http://dx.doi.org/10.1093/nar/gkq292.
71. van Meerten D, Girard G, van Duin J. 2001. Translational control by delayed RNA folding: identification of the kinetic trap. RNA 7:483–494. http://dx.doi.org/10.1017/S1355838201001984.
72. Møller-Jensen J, Franch T, Gerdes K. 2001. Temporal translational control by a metastable RNA structure. J Biol Chem 276:35707–35713. http://dx.doi.org/10.1074/jbc.M105347200.
73. Xayaphoummine A, Bucher T, Isambert H. 2005. Kinefold web server for RNA/DNA folding path and structure prediction including pseudoknots and knots. Nucleic Acids Res 33(Web Server issue):W605–W610. http://dx.doi.org/10.1093/nar/gki447.
74. Gan W, Guan Z, Liu J, Gui T, Shen K, Manley JL, Li X. 2011. R-loop-mediated genomic instability is caused by impairment of replication fork progression. Genes Dev 25:2041–2056. http://dx.doi.org/10.1101/gad.17010011.
75. Iost I, Dreyfus M. 1995. The stability of Escherichia coli lacZ mRNA depends upon the simultaneity of its synthesis and translation. EMBO J 14:3252–3261. [PubMed]
76. Franch T, Gultyaev AP, Gerdes K. 1997. Programmed cell death by hok/sok of plasmid R1: processing at the hok mRNA 3′-end triggers structural rearrangements that allow translation and antisense RNA binding. J Mol Biol 273:38–51. http://dx.doi.org/10.1006/jmbi.1997.1294.
77. Smirnov A, Förstner KU, Holmqvist E, Otto A, Günster R, Becher D, Reinhardt R, Vogel J. 2016. Grad-seq guides the discovery of ProQ as a major small RNA-binding protein. Proc Natl Acad Sci U S A 113:11591–11596. http://dx.doi.org/10.1073/pnas.1609981113.
78. Thisted T, Gerdes K. 1992. Mechanism of post-segregational killing by the hok/sok system of plasmid R1. Sok antisense RNA regulates hok gene expression indirectly through the overlapping mok gene. J Mol Biol 223:41–54. http://dx.doi.org/10.1016/0022-2836(92)90714-U.
79. Kawano M, Reynolds AA, Miranda-Rios J, Storz G. 2005. Detection of 5′- and 3′-UTR-derived small RNAs and cis-encoded antisense RNAs in Escherichia coli. Nucleic Acids Res 33:1040–1050. http://dx.doi.org/10.1093/nar/gki256. [PubMed]
80. Jahn N, Preis H, Wiedemann C, Brantl S. 2012. BsrG/SR4 from Bacillus subtilis—the first temperature-dependent type I toxin-antitoxin system. Mol Microbiol 83:579–598. http://dx.doi.org/10.1111/j.1365-2958.2011.07952.x.
81. Shokeen S, Greenfield TJ, Ehli EA, Rasmussen J, Perrault BE, Weaver KE. 2009. An intramolecular upstream helix ensures the stability of a toxin-encoding RNA in Enterococcus faecalis. J Bacteriol 191:1528–1536. http://dx.doi.org/10.1128/JB.01316-08.
82. Greenfield TJ, Weaver KE. 2000. Antisense RNA regulation of the pAD1 par post-segregational killing system requires interaction at the 5′ and 3′ ends of the RNAs. Mol Microbiol 37:661–670. http://dx.doi.org/10.1046/j.1365-2958.2000.02034.x.
83. Koyanagi S, Lévesque CM. 2013. Characterization of a Streptococcus mutans intergenic region containing a small toxic peptide and its cis-encoded antisense small RNA antitoxin. PLoS One 8:e54291. http://dx.doi.org/10.1371/journal.pone.0054291.
84. Folli C, Levante A, Percudani R, Amidani D, Bottazzi S, Ferrari A, Rivetti C, Neviani E, Lazzi C. 2017. Toward the identification of a type I toxin-antitoxin system in the plasmid DNA of dairy Lactobacillus rhamnosus. Sci Rep 7:12051. http://dx.doi.org/10.1038/s41598-017-12218-5.
85. de Smit MH, van Duin J. 1990. Secondary structure of the ribosome binding site determines translational efficiency: a quantitative analysis. Proc Natl Acad Sci U S A 87:7668–7672. http://dx.doi.org/10.1073/pnas.87.19.7668.
86. de Smit MH, van Duin J. 2003. Translational standby sites: how ribosomes may deal with the rapid folding kinetics of mRNA. J Mol Biol 331:737–743. http://dx.doi.org/10.1016/S0022-2836(03)00809-X.
87. Sterk M, Romilly C, Wagner EG. 2018. Unstructured 5′-tails act through ribosome standby to override inhibitory structure at ribosome binding sites. Nucleic Acids Res 46:4188–4199. http://dx.doi.org/10.1093/nar/gky073.
88. Franch T, Petersen M, Wagner EG, Jacobsen JP, Gerdes K. 1999. Antisense RNA regulation in prokaryotes: rapid RNA/RNA interaction facilitated by a general U-turn loop structure. J Mol Biol 294:1115–1125. http://dx.doi.org/10.1006/jmbi.1999.3306.
89. Thisted T, Sørensen NS, Wagner EG, Gerdes K. 1994. Mechanism of post-segregational killing: Sok antisense RNA interacts with Hok mRNA via its 5′-end single-stranded leader and competes with the 3′-end of Hok mRNA for binding to the mok translational initiation region. EMBO J 13:1960–1968. [PubMed]
90. Knoop V. 2011. When you can’t trust the DNA: RNA editing changes transcript sequences. Cell Mol Life Sci 68:567–586. http://dx.doi.org/10.1007/s00018-010-0538-9. [PubMed]
91. Wolf J, Gerber AP, Keller W. 2002. tadA, an essential tRNA-specific adenosine deaminase from Escherichia coli. EMBO J 21:3841–3851. http://dx.doi.org/10.1093/emboj/cdf362.
92. Keller W, Wolf J, Gerber A. 1999. Editing of messenger RNA precursors and of tRNAs by adenosine to inosine conversion. FEBS Lett 452:71–76. http://dx.doi.org/10.1016/S0014-5793(99)00590-6.
93. Bar-Yaacov D, Mordret E, Towers R, Biniashvili T, Soyris C, Schwartz S, Dahan O, Pilpel Y. 2017. RNA editing in bacteria recodes multiple proteins and regulates an evolutionarily conserved toxin-antitoxin system. Genome Res 27:1696–1703. http://dx.doi.org/10.1101/gr.222760.117.
94. Poulsen LK, Larsen NW, Molin S, Andersson P. 1992. Analysis of an Escherichia coli mutant strain resistant to the cell-killing function encoded by the gef gene family. Mol Microbiol 6:895–905. http://dx.doi.org/10.1111/j.1365-2958.1992.tb01540.x.
95. Gerdes K, Rasmussen PB, Molin S. 1986. Unique type of plasmid maintenance function: postsegregational killing of plasmid-free cells. Proc Natl Acad Sci U S A 83:3116–3120. http://dx.doi.org/10.1073/pnas.83.10.3116.
96. Coray DS, Wheeler NE, Heinemann JA, Gardner PP. 2017. Why so narrow: distribution of anti-sense regulated, type I toxin-antitoxin systems compared with type II and type III systems. RNA Biol 14:275–280. http://dx.doi.org/10.1080/15476286.2016.1272747.
97. Silvaggi JM, Perkins JB, Losick R. 2005. Small untranslated RNA antitoxin in Bacillus subtilis. J Bacteriol 187:6641–6650. http://dx.doi.org/10.1128/JB.187.19.6641-6650.2005.
98. Michaux C, Hartke A, Martini C, Reiss S, Albrecht D, Budin-Verneuil A, Sanguinetti M, Engelmann S, Hain T, Verneuil N, Giard J-C. 2014. Involvement of Enterococcus faecalis small RNAs in stress response and virulence. Infect Immun 82:3599–3611. http://dx.doi.org/10.1128/IAI.01900-14.
99. Sayed N, Nonin-Lecomte S, Réty S, Felden B. 2012. Functional and structural insights of a Staphylococcus aureus apoptotic-like membrane peptide from a toxin-antitoxin module. J Biol Chem 287:43454–43463. http://dx.doi.org/10.1074/jbc.M112.402693.
100. Meißner C, Jahn N, Brantl S. 2016. In vitro characterization of the type I toxin-antitoxin system bsrE/SR5 from Bacillus subtilis. J Biol Chem 291:560–571. http://dx.doi.org/10.1074/jbc.M115.697524.
101. Pelliciari S, Pinatel E, Vannini A, Peano C, Puccio S, De Bellis G, Danielli A, Scarlato V, Roncarati D. 2017. Insight into the essential role of the Helicobacter pylori HP1043 orphan response regulator: genome-wide identification and characterization of the DNA-binding sites. Sci Rep 7:41063. http://dx.doi.org/10.1038/srep41063.
102. Gerdes K. 2016. Hypothesis: type I toxin-antitoxin genes enter the persistence field—a feedback mechanism explaining membrane homoeostasis. Philos Trans R Soc Lond B Biol Sci 371:20160189. http://dx.doi.org/10.1098/rstb.2016.0189.
103. Redko Y, Galtier E, Arnion H, Darfeuille F, Sismeiro O, Coppée JY, Médigue C, Weiman M, Cruveiller S, De Reuse H. 2016. RNase J depletion leads to massive changes in mRNA abundance in Helicobacter pylori. RNA Biol 13:243–253. http://dx.doi.org/10.1080/15476286.2015.1132141.
104. Dar D, Shamir M, Mellin JR, Koutero M, Stern-Ginossar N, Cossart P, Sorek R. 2016. Term-seq reveals abundant ribo-regulation of antibiotics resistance in bacteria. Science 352:aad9822. http://dx.doi.org/10.1126/science.aad9822.
105. Fozo EM. 2012. New type I toxin-antitoxin families from “wild” and laboratory strains of E. coli: Ibs-Sib, ShoB-OhsC and Zor-Orz. RNA Biol 9:1504–1512. http://dx.doi.org/10.4161/rna.22568.
106. Nagel JH, Gultyaev AP, Gerdes K, Pleij CW. 1999. Metastable structures and refolding kinetics in hok mRNA of plasmid R1. RNA 5:1408–1418. http://dx.doi.org/10.1017/S1355838299990805.
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/content/journal/microbiolspec/10.1128/microbiolspec.RWR-0030-2018
2018-07-27
2018-08-16

Abstract:

Toxin-antitoxin (TA) systems are small genetic loci composed of two adjacent genes: a toxin and an antitoxin that prevents toxin action. Despite their wide distribution in bacterial genomes, the reasons for TA systems being on chromosomes remain enigmatic. In this review, we focus on type I TA systems, composed of a small antisense RNA that plays the role of an antitoxin to control the expression of its toxin counterpart. It does so by direct base-pairing to the toxin-encoding mRNA, thereby inhibiting its translation and/or promoting its degradation. However, in many cases, antitoxin binding is not sufficient to avoid toxicity. Several -encoded mRNA elements are also required for repression, acting to uncouple transcription and translation via the sequestration of the ribosome binding site. Therefore, both antisense RNA binding and compact mRNA folding are necessary to tightly control toxin synthesis and allow the presence of these toxin-encoding systems on bacterial chromosomes.

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Figures

Image of FIGURE 1
FIGURE 1

Various modes of antitoxin-mediated regulation. The three main types of toxicity regulation by antitoxins. (A) Direct sequestration. In types II and VI TA systems, toxin inactivation involves a direct interaction between the toxin (T) and the antitoxin (A). The formation of an inactive TA heterocomplex (T-A) can, in its turn (for type II), lead to the transcriptional repression of the operon (red star). In type VI, the formation of the inactive TA complex favors toxin degradation by cellular proteases (yellow circle). In type III, the antitoxin is an RNA that directly binds to the toxin to prevent its toxic activity. (B) Antagonism. Both toxin and antitoxin compete for binding to the same target. The interaction can additionally have opposite functional (antagonistic) effects. (C) Control of expression. In types I and V, regulation occurs at the posttranscriptional level. In type I, antitoxins are antisense RNA molecules that base-pair to the toxin-encoded mRNA to alter its expression by either inhibiting translation initiation or promoting its degradation. In type V, the antitoxin is an RNase that cleaves the toxin-encoded mRNA.

Source: microbiolspec July 2018 vol. 6 no. 4 doi:10.1128/microbiolspec.RWR-0030-2018
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Image of FIGURE 2
FIGURE 2

Illustration of the consequences of transcription/translation uncoupling for regulation of type I TA expression. (A) The lack of nuclear compartmentalization in bacteria leads to the coupling in time and space of transcription and translation processes. (B) Transcription/translation coupling of type I toxin-encoding mRNAs would be lethal. TA systems can be conserved in bacterial genomes thanks to the decoupling of such processes through the sequestration of the SD sequence (red) during transcription . This SD sequestration is conserved in primary transcripts, making them unable to interact with both ribosomes and antitoxin sRNAs . In the cases where SD sequence sequestration involves a 5′-3′ LDI, the formation of successive metastable structures ensuring SD inaccessibility to both ribosomes and antitoxin during transcription is essential to prevent premature toxin expression and mRNA degradation, respectively. Translational activation is achieved by the enzymatic processing (of the 5′ or 3′ mRNA end, depending on the TA system) of the primary transcript followed by a structural rearrangement that renders the mRNA able to interact with both ribosomes and the antitoxin . Ribosome binding to the accessible SD sequence (green) leads to toxin production, inducing either growth arrest or cell death . On the opposite, antitoxin binding efficiently inhibits toxin translation and promoter mRNA degradation, allowing cell survival .

Source: microbiolspec July 2018 vol. 6 no. 4 doi:10.1128/microbiolspec.RWR-0030-2018
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Image of FIGURE 3
FIGURE 3

Examples of secondary structures sequestering the SD sequence of toxin-encoding mRNAs. (A) Stem-loop sequences in which the SD sequence is totally or partially sequestered by an upstream aSD sequence. These secondary structures have been experimentally validated ( 58 , 61 64 ) or predicted (indicated by *) ( 105 ). For BsrG, the stem-loop sequestering the SD is shown in absence of SR4 antitoxin (**). Indeed, when the antitoxin binds to the mRNA, the stem-loop sequestering the SD is extended by 4 additional base pairs ( 64 ). (B) Stem-loop structures sequestering the SD sequence of the Mok leader peptide and the Hok toxin. In this case, the formation of the Mok SD-sequestering stem-loop is dependent on a 5′-3′ LDI ( 69 , 106 ). (C) Examples of SD sequestration achieved by a stable LDI between both mRNA ends, creating a cloverleaf structure ( 31 , 70 ). The start codon (AUG, shown in green) can additionally be partially or totally sequestered in one of the cloverleaf structures. Dotted gray lines indicate the presence of unrepresented structures/lengths. Full gray lines schematically represent structures and base pairs. SD sequences are shown in red; aSD sequences are shown in black. Positions are relative to the transcription start site of the mRNAs (+1). 5′ and 3′ indicate orientation of the mRNA. Toxin mRNA names are indicated under each structure. The small index next to each name indicates the host organisms: Ec, ; Bs, ; Ef, ; Sa, ; and Hp, .

Source: microbiolspec July 2018 vol. 6 no. 4 doi:10.1128/microbiolspec.RWR-0030-2018
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Image of FIGURE 4
FIGURE 4

Type I operon organization in Gram-negative bacteria and mechanistic consequences of its regulation. Type I antitoxin sRNAs in Gram-negative bacteria can be encoded in two main fashions: (i) overlapping the 5′ end of the toxin mRNA, the ORF, or a leader ORF (left panel) or (ii) not overlapping (right panel). In both cases, transcription/translation coupling forces the sequestration of the SD sequence by partially or totally complementary sequences called anti-SD (aSD). This sequestration starts during transcription but is maintained upon transcription termination, leading to the generation of a translationally inert and sRNA-inaccessible primary transcript (full-length mRNA). Location of the aSD sequence will determine whether the sequestration occurs via 5′-3′ LDI (5′-overlapping TA loci) or in a stem-loop (nonoverlapping TA loci). In both cases, an enzymatic activation step is required for the generation of the truncated (active) mRNA. When the SD sequestration involves 5′-3′ interaction, this activation step often occurs via 3′ trimming by 3′-5′ exonucleases (RNaseII, PNPase). In contrast, when SD is sequestered in a stem-loop, activation occurs via 5′-end processing by endonucleases. In either case, a light or strong structural rearrangement (refolding) is needed upon processing to render the SD accessible to both ribosomes and sRNA binding. Next, in noninduced conditions, antitoxin sRNAs outcompete the ribosomes for binding to the 5′ end of the toxin mRNA and render it translationally inert. This inactivation step can occur via direct sequestration of the SD sequence or the leader ORF SD sequence (5′-overlapping TA loci), or indirectly via the sequestration of the ribosome standby site (stand-by) or the stabilization of an SD-trapped structure (nonoverlapping TA loci). In most cases, sRNA binding to the toxin mRNA leads to RNase III-mediated toxin mRNA decay and cell survival.

Source: microbiolspec July 2018 vol. 6 no. 4 doi:10.1128/microbiolspec.RWR-0030-2018
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Image of FIGURE 5
FIGURE 5

Mechanistic regulatory consequences of the 3′-overlapping antitoxin sRNAs in Gram-positive bacteria. In all type I TAs described so far in Gram-positive bacteria, antitoxin sRNAs are encoded in 3′-overlapping fashion to the toxin mRNAs. As in Gram-negative bacteria, transcription/translation coupling forces the sequestration of the SD sequence during transcription, the nascent transcript being accessible neither for the ribosome nor the antitoxin. Upon transcription termination, the full-length mRNA becomes targeted by the antitoxin RNA that binds to the 3′ end of the toxin mRNA. The question marks represent how mRNA activation could occur in Gram-positive bacteria (little is known about the mRNA activation, processing, or refolding steps compared to Gram-negative bacteria). In some cases (TxpA and YonT), sRNA binding is not sufficient to impede toxin translation, and thus, mRNA degradation by RNase III is essential to avoid toxicity. In some cases, sRNA binding leads to a structural rearrangement that enhances the sequestration of the SD sequence. This interaction can in its turn lead to mRNA degradation by RNase III or on the contrary to the stabilization of the translationally inert complex. In all cases, antitoxin binding to the toxin mRNA hampers its expression and allows cell survival.

Source: microbiolspec July 2018 vol. 6 no. 4 doi:10.1128/microbiolspec.RWR-0030-2018
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Tables

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TABLE 1

Type I TA systems identified in bacteria

Source: microbiolspec July 2018 vol. 6 no. 4 doi:10.1128/microbiolspec.RWR-0030-2018

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