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Type II Toxin-Antitoxins: Structural and Functional Aspects of Type II Loci in Mycobacteria

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Abstract

Several prokaryotes have genomes that are densely populated with toxin–antitoxin (TA) loci. For example, the aquatic bloom-forming cyanobacterium Microcystis aeruginosa habours more than 110 TA loci, and the nematode symbiont Photorhabdus luminescens has at least 58 TAs encoded in its genome. Amongst this group of unrelated bacteria lies Mycobacterium tuberculosis whose genome encodes more than 68 TAs. M. tuberculosis causes the devastating human disease tuberculosis (TB) and is, therefore, the subject of intense research. The presence of so many TAs begs the question as to their evolutionary origin, contemporary biological functions and their potential as therapeutic targets in this important human pathogen. This chapter reviews the distribution of TAs in the mycobacterial genus and the experimental results that provide clues to TA function in M. tuberculosis.

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References

  • Ahidjo, B. A., Kuhnert, D., Mckenzie, J. L., et al. (2011). VapC toxins from Mycobacterium tuberculosis are ribonucleases that differentially inhibit growth and are neutralized by cognate VapB antitoxins. PLoS ONE, 6, e21738. doi:10.1371/journal.pone.0021738.

    Article  PubMed  CAS  Google Scholar 

  • Anantharaman, V., & Aravind, L. (2003). New connections in the prokaryotic toxin–antitoxin network: Relationship with the eukaryotic nonsense-mediated RNA decay system. Genome Biology, 4, R81. doi:10.1186/gb-2003-4-12-r81.

    Article  PubMed  Google Scholar 

  • Anantharaman, V., & Aravind, L. (2006). The NYN domains: Novel predicted RNAses with a PIN domain-like fold. RNA Biology, 3, 18–27.

    Article  PubMed  CAS  Google Scholar 

  • Andersson, J. O., & Andersson, S. G. (1999). Insights into the evolutionary process of genome degradation. Current Opinion in Genetics & Development, 9, 664–671.

    Article  CAS  Google Scholar 

  • Andreeva, A., Howorth, D., Chandonia, J.-M., et al. (2008). Data growth and its impact on the SCOP database: New developments. Nucleic Acids Research, 36, D419–D425. doi:10.1093/nar/gkm993.

    Article  PubMed  CAS  Google Scholar 

  • Arcus, V. L., Bäckbro, K., Roos, A., et al. (2004). Distant structural homology leads to the functional characterization of an archaeal PIN domain as an exonuclease. Journal of Biological Chemistry, 279, 16471–16478. doi:10.1074/jbc.M313833200.

    Article  PubMed  CAS  Google Scholar 

  • Arcus, V. L., Rainey, P. B., & Turner, S. J. (2005). The PIN-domain toxin–antitoxin array in mycobacteria. Trends in Microbiology, 13, 360–365. doi:10.1016/j.tim.2005.06.008.

    Article  PubMed  CAS  Google Scholar 

  • Arcus, V. L., Mckenzie, J. L., Robson, J., & Cook, G. M. (2011). The PIN-domain ribonucleases and the prokaryotic VapBC toxin–antitoxin array. Protein Engineering Design Select, 24, 33–40. doi:10.1093/protein/gzq081.

    Article  CAS  Google Scholar 

  • Beste, D., Espasa, M., Bonde, B., & Kierzek, A. (2009). The genetic requirements for fast and slow growth in Mycobacteria. PLoS ONE, 4, e5349. doi:10.1371/journal.pone.0005349.

    Article  PubMed  Google Scholar 

  • Bordes, P., Cirinesi, A.-M., Ummels, R., et al. (2011). SecB-like chaperone controls a toxin–antitoxin stress-responsive system in Mycobacterium tuberculosis. Proceedings of the National academy of Sciences of the United States of America, 108, 8438–8443. doi:10.1073/pnas.1101189108.

    Article  PubMed  CAS  Google Scholar 

  • Bunker, R. D., Mckenzie, J. L., Baker, E. N., & Arcus, V. L. (2008). Crystal structure of PAE0151 from Pyrobaculum aerophilum, a PIN-domain (VapC) protein from a toxin–antitoxin operon. Proteins, 72, 510–518. doi:10.1002/prot.22048.

    Article  PubMed  CAS  Google Scholar 

  • Caminero, J. A., Sotgiu, G., Zumla, A., & Migliori, G. B. (2010). Best drug treatment for multidrug-resistant and extensively drug-resistant tuberculosis. The Lancet Infectious Diseases, 10, 621–629. doi:10.1016/S1473-3099(10)70139-0.

    Article  PubMed  CAS  Google Scholar 

  • Clissold, P., & Ponting, C. (2000). PIN domains in nonsense-mediated mRNA decay and RNAi. Current Biology, 10, R888–R890.

    Article  PubMed  CAS  Google Scholar 

  • Cole, S. T., Eiglmeier, K., Parkhill, J., et al. (2001). Massive gene decay in the leprosy bacillus. Nature, 409, 1007–1011. doi:10.1038/35059006.

    Article  PubMed  CAS  Google Scholar 

  • Cooper, T. F., & Heinemann, J. A. (2000). Postsegregational killing does not increase plasmid stability but acts to mediate the exclusion of competing plasmids. Proceedings of the National Academy of Sciences USA, 97, 12643–12648. doi:10.1073/pnas.220077897.

    Article  CAS  Google Scholar 

  • de Carvalho, L. P. S., Fischer, S. M., Marrero, J., et al. (2010). Metabolomics of Mycobacterium tuberculosis reveals compartmentalized co-catabolism of carbon substrates. Chemistry & Biology, 17, 1122–1131. doi:10.1016/j.chembiol.2010.08.009.

    Article  Google Scholar 

  • Finn, R. D., Mistry, J., Tate, J., et al. (2010). The Pfam protein families database. Nucleic Acids Research, 38, D211–D222. doi:10.1093/nar/gkp985.

    Article  PubMed  CAS  Google Scholar 

  • Fivian-Hughes, A. S., & Davis, E. O. (2010). Analyzing the regulatory role of the HigA antitoxin within Mycobacterium tuberculosis. Journal of Bacteriology, 192, 4348–4356. doi:10.1128/JB.00454-10.

    Article  PubMed  CAS  Google Scholar 

  • Frampton, R. A., Aggio, R. B. M., Villas-BĂ´as, S. G., et al. (2011). Toxin–antitoxin systems of Mycobacterium smegmatis are essential for cell survival. Journal of Biological Chemistry, 287, 5340–5356. doi:10.1074/jbc.M111.286856.

    Article  PubMed  Google Scholar 

  • Gerdes, K., Rasmussen, P. B., & Molin, S. (1986). Unique type of plasmid maintenance function: Postsegregational killing of plasmid-free cells. Proceedings of the National academy of Sciences of the United States of America, 83, 3116–3120.

    Article  PubMed  CAS  Google Scholar 

  • Gerdes, K., Christensen, S. K., & Løbner-Olesen, A. (2005). Prokaryotic toxin–antitoxin stress response loci. Nature Reviews Microbiology, 3, 371–382. doi:10.1038/nrmicro1147.

    Article  PubMed  CAS  Google Scholar 

  • Gupta, A. (2009). Killing activity and rescue function of genome-wide toxin–antitoxin loci of Mycobacterium tuberculosis. FEMS Microbiology Letters, 290, 45–53. doi:10.1111/j.1574-6968.2008.01400.x.

    Article  PubMed  CAS  Google Scholar 

  • Han, J.-S., Lee, J. J., Anandan, T., et al. (2010). Characterization of a chromosomal toxin–antitoxin, Rv1102c-Rv1103c system in Mycobacterium tuberculosis. Biochemical & Biophysical Research Communications, 400, 293–298. doi:10.1016/j.bbrc.2010.08.023.

    Article  CAS  Google Scholar 

  • Hayes, F. (2003). Toxins-antitoxins: Plasmid maintenance, programmed cell death, and cell cycle arrest. Science, 301, 1496–1499.

    Article  Google Scholar 

  • Huang, F., & He, Z.-G. (2010). Characterization of an interplay between a Mycobacterium tuberculosis MazF homolog, Rv1495 and its sole DNA topoisomerase I. Nucleic Acids Research, 38, 8219–8230. doi:10.1093/nar/gkq737.

    Article  PubMed  CAS  Google Scholar 

  • JaffĂ©, A., Ogura, T., & Hiraga, S. (1985). Effects of the ccd function of the F plasmid on bacterial growth. Journal of Bacteriology, 163, 841–849.

    PubMed  Google Scholar 

  • Kaneko, T., Nakajima, N., Okamoto, S., et al. (2007). Complete genomic structure of the bloom-forming toxic cyanobacterium Microcystis aeruginosa NIES-843. DNA Research, 14, 247–256. doi:10.1093/dnares/dsm026.

    Article  PubMed  CAS  Google Scholar 

  • Kolodkin-Gal, I., Hazan, R., & Gaathon, A., et al. (2007). A linear pentapeptide is a quorum-sensing factor required for mazEF-mediated cell death in Escherichia coli. Science, 318, 652–655. doi:10.1126/science.1147248.

    Article  PubMed  CAS  Google Scholar 

  • Korch, S. B., Contreras, H., & Clark-Curtiss, J. E. (2009). Three Mycobacterium tuberculosis Rel toxin–antitoxin modules inhibit mycobacterial growth and are expressed in infected human macrophages. Journal of Bacteriology, 191, 1618–1630. doi:10.1128/JB.01318-08.

    Article  PubMed  CAS  Google Scholar 

  • Lee, B., Holkenbrink, C., Treuner-Lange, A., & Higgs, P. I. (2012). Myxococcus xanthus developmental cell fate production: Heterogeneous accumulation of developmental regulatory proteins and reexamination of the role of MazF in developmental lysis. Journal of Bacteriology, 194, 3058–3068. doi:10.1128/JB.06756-11.

    Article  PubMed  CAS  Google Scholar 

  • Levin, I., Schwarzenbacher, R., Page, R., et al. (2004). Crystal structure of a PIN (PilT N-terminus) domain (AF0591) from Archaeoglobus fulgidus at 1.90 Å resolution. Proteins, 56, 404–408. doi:10.1002/prot.20090.

    Article  PubMed  CAS  Google Scholar 

  • Lewis, K. (2007). Persister cells, dormancy and infectious disease. Nature Reviews Microbiology, 5, 48–56. doi:10.1038/nrmicro1557.

    Article  PubMed  CAS  Google Scholar 

  • Lewis, K. (2010). Persister cells. Annual Review of Microbiology, 64, 357–372. doi:10.1146/annurev.micro.112408.134306.

    Article  PubMed  CAS  Google Scholar 

  • Magnuson, R. D. (2007). Hypothetical functions of toxin-antitoxin systems. Journal of Bacteriology, 189, 6089–6092. doi:10.1128/JB.00958-07.

    Article  PubMed  CAS  Google Scholar 

  • Maisonneuve, E., Shakespeare, L. J., Jørgensen, M. G., & Gerdes, K. (2011). Bacterial persistence by RNA endonucleases. Proceedings of the National academy of Sciences of the United States of America, 108, 13206–13211. doi:10.1073/pnas.1100186108.

    Article  PubMed  CAS  Google Scholar 

  • Makarova, K. S., Wolf, Y. I., & Koonin, E. V. (2009). Comprehensive comparative-genomic analysis of Type 2 toxin–antitoxin systems and related mobile stress response systems in prokaryotes. Biology Direct, 4, 19. doi:10.1186/1745-6150-4-19.

    Article  PubMed  Google Scholar 

  • Mattison, K., Wilbur, J. S., So, M., & Brennan, R. G. (2006). Structure of FitAB from Neisseria gonorrhoeae bound to DNA reveals a tetramer of toxin–antitoxin heterodimers containing PIN-domains and ribbon-helix-helix motifs. Journal of Biological Chemistry, 281, 37942–37951. doi:10.1074/jbc.M605198200.

    Article  PubMed  CAS  Google Scholar 

  • Mckenzie, J. L., Duyvestyn, J. M., Smith, T., et al. (2012a). Determination of ribonuclease sequence-specificity using pentaprobes and mass spectrometry. RNA, 18, 1267–1278. doi:10.1261/rna.031229.111.

    Article  PubMed  CAS  Google Scholar 

  • Mckenzie, J. L., Robson, J., Berney, M., et al. (2012b). A VapBC toxin–antitoxin module is a post-transcriptional regulator of metabolic flux in mycobacteria. Journal of Bacteriology, 194, 2189–2204. doi:10.1128/JB.06790-11.

    Article  PubMed  CAS  Google Scholar 

  • Miallau, L., Faller, M., & Chiang, J., et al. (2009). Structure and proposed activity of a member of the VapBC family of toxin-antitoxin systems. VapBC-5 from Mycobacterium tuberculosis. Journal of Biological Chemistry, 284, 276–283. doi:10.1074/jbc.M805061200.

    CAS  Google Scholar 

  • Nariya, H., & Inouye, M. (2008). MazF, an mRNA interferase, mediates programmed cell death during multicellular Myxococcus development. Cell, 132, 55–66. doi:10.1016/j.cell.2007.11.044.

    Article  PubMed  CAS  Google Scholar 

  • Niederweis, M. (2008). Nutrient acquisition by mycobacteria. Microbiology, 154, 679–692. doi:10.1099/mic.0.2007/012872-0.

    Article  PubMed  CAS  Google Scholar 

  • Pandey, D. P., & Gerdes, K. (2005). Toxin–antitoxin loci are highly abundant in free-living but lost from host-associated prokaryotes. Nucleic Acids Research, 33, 966–976. doi:10.1093/nar/gki201.

    Article  PubMed  CAS  Google Scholar 

  • Provvedi, R., Boldrin, F., Falciani, F., et al. (2009). Global transcriptional response to vancomycin in Mycobacterium tuberculosis. Microbiology, 155, 1093–1102. doi:10.1099/mic.0.024802-0.

    Article  PubMed  CAS  Google Scholar 

  • Ramage, H. R., Connolly, L. E., & Cox, J. S. (2009). Comprehensive functional analysis of Mycobacterium tuberculosis toxin–antitoxin systems: Implications for pathogenesis, stress responses, and evolution. PLoS Genetics, 5, e1000767. doi:10.1371/journal.pgen.1000767.

    Article  PubMed  Google Scholar 

  • Robson, J., Mckenzie, J. L., Cursons, R. T., et al. (2009). The vapBC operon from Mycobacterium smegmatis is an autoregulated toxin–antitoxin module that controls growth via inhibition of translation. Journal of Molecular Biology, 390, 353–367. doi:10.1016/j.jmb.2009.05.006.

    Article  PubMed  CAS  Google Scholar 

  • Schumacher, M. A., Piro, K. M., Xu, W., et al. (2009). Molecular mechanisms of HipA-mediated multidrug tolerance and its neutralization by HipB. Science, 323, 396–401. doi:10.1126/science.1163806.

    Article  PubMed  CAS  Google Scholar 

  • Schuster-Böckler, B., Schultz, J., & Rahmann, S. (2004). HMM logos for visualization of protein families. BMC Bioinformatics, 5, 7. doi:10.1186/1471-2105-5-7.

    Article  PubMed  Google Scholar 

  • Sevin, E. W., & Barloy-Hubler, F. (2007). RASTA-Bacteria: A web-based tool for identifying toxin–antitoxin loci in prokaryotes. Genome Biology, 8, R155. doi:10.1186/gb-2007-8-8-r155.

    Article  PubMed  Google Scholar 

  • Shao, Y., Harrison, E. M., Bi, D., et al. (2011). TADB: A web-based resource for type 2 toxin–antitoxin loci in bacteria and archaea. Nucleic Acids Research, 39, D606–D611. doi:10.1093/nar/gkq908.

    Article  PubMed  Google Scholar 

  • Sharp, J. D., Cruz, J. W., Raman, S., et al. (2012). Growth and translation inhibition through sequence specific RNA binding by a Mycobacterium tuberculosis VapC toxin. Journal of Biological Chemistry, 287, 12835–12847. doi:10.1074/jbc.M112.340109.

    Article  PubMed  CAS  Google Scholar 

  • Shleeva, M., Mukamolova, G. V., Young, M., et al. (2004). Formation of “non-culturable” cells of Mycobacterium smegmatis in stationary phase in response to growth under suboptimal conditions and their Rpf-mediated resuscitation. Microbiology, 150, 1687–1697. doi:10.1099/mic.0.26893-0.

    Article  PubMed  CAS  Google Scholar 

  • Singh, R., Barry, C. E., & Boshoff, H. I. M. (2010). The three RelE homologs of Mycobacterium tuberculosis have individual, drug-specific effects on bacterial antibiotic tolerance. Journal of Bacteriology, 192, 1279–1291. doi:10.1128/JB.01285-09.

    Article  PubMed  CAS  Google Scholar 

  • Szekeres, S., Dauti, M., & Wilde, C., et al. (2007). Chromosomal toxin-antitoxin loci can diminish large-scale genome reductions in the absence of selection. Molecular Microbiology, 63, 1588–1605. doi:10.1111/j.1365-2958.2007.05613.x.

    Article  PubMed  CAS  Google Scholar 

  • Titgemeyer, F., Amon, J., Parche, S., et al. (2007). A genomic view of sugar transport in Mycobacterium smegmatis and Mycobacterium tuberculosis. Journal of Bacteriology, 189, 5903–5915. doi:10.1128/JB.00257-07.

    Article  PubMed  CAS  Google Scholar 

  • 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? Journal of Bacteriology, 189, 6101–6108. doi:10.1128/JB.00527-07.

    Article  PubMed  CAS  Google Scholar 

  • van Melderen, L., & Saavedra De Bast, M. (2009). Bacterial toxin-antitoxin systems: More than selfish entities? PLoS Genetics, 5, e1000437. doi:10.1371/journal.pgen.1000437.

    Article  PubMed  Google Scholar 

  • Winther, K. S., & Gerdes, K. (2011). Enteric virulence associated protein VapC inhibits translation by cleavage of initiator tRNA. Proceedings of the National academy of Sciences of the United States of America, 108, 7403–7407. doi:10.1073/pnas.1019587108.

    Article  PubMed  CAS  Google Scholar 

  • Yang, M., Gao, C., Wang, Y., et al. (2010). Characterization of the interaction and cross-regulation of three Mycobacterium tuberculosis RelBE modules. PLoS ONE, 5, e10672. doi:10.1371/journal.pone.0010672.

    Article  PubMed  Google Scholar 

  • Zhao, L., & Zhang, J. (2008). Biochemical characterization of a chromosomal toxin–antitoxin system in Mycobacterium tuberculosis. FEBS Letters, 582, 710–714. doi:10.1016/j.febslet.2008.01.045.

    Article  PubMed  CAS  Google Scholar 

  • Zhu, L., Zhang, Y., Teh, J., et al. (2006). Characterization of mRNA interferases from Mycobacterium tuberculosis. Journal of Biological Chemistry, 281, 18638–18643. doi:10.1074/jbc.M512693200.

    Article  PubMed  CAS  Google Scholar 

  • Zhu, L., Phadtare, S., Nariya, H., et al. (2008). The mRNA interferases, MazF-mt3 and MazF-mt7 from Mycobacterium tuberculosis target unique pentad sequences in single-stranded RNA. Molecular Microbiology, 69, 559–569. doi:10.1111/j.1365-2958.2008.06284.x.

    Article  PubMed  CAS  Google Scholar 

  • Zhu, L., Sharp, J. D., Kobayashi, H., et al. (2010). Noncognate Mycobacterium tuberculosis toxin–antitoxins can physically and functionally interact. Journal of Biological Chemistry, 285, 39732–39738. doi:10.1074/jbc.M110.163105.

    Article  PubMed  CAS  Google Scholar 

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Acknowledgments

We thank Valerie Mizrahi for helpful discussions. We gratefully acknowledge funding from the Health Research Council of New Zealand and the Marsden Fund that has supported research in the Arcus and Cook laboratories.

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Correspondence to Vickery L. Arcus .

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Arcus, V.L., Cook, G.M. (2013). Type II Toxin-Antitoxins: Structural and Functional Aspects of Type II Loci in Mycobacteria. In: Gerdes, K. (eds) Prokaryotic Toxin-Antitoxins. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-33253-1_8

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