Abstract
Toxin–antitoxin (TA) systems widely exist in bacterial plasmids, phages, and chromosomes and play important roles in growth persistence and host-pathogen interaction. Virulence associated protein BC (VapBC) family TAs are the most abundant TAs in bacteria and many pathogens contain a large number of vapBC loci in the genome which have been extensively studied. Clostridium thermocellum, a cellulolytic anaerobic gram-positive bacterium with promising applications in biofuel production, also contains a VapBC TA in the genome. Despite the structures of several VapBC family TAs have been determined, the toxin and anti-toxin components of C. thermocellum VapBC have very low sequence identity to the proteins in PDB. Therefore, the structure and functional mechanism of this TA is largely unknown. Here we reported the NMR resonance assignments of the VapC toxin from C. thermocellum as a basis for further structural and functional studies.
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09 July 2020
In the original publication of the article, the authors found a misquote in the Reference section.
References
Akinosho H, Yee K, Close D, Ragauskas A (2014) The emergence of Clostridium thermocellum as a high utility candidate for consolidated bioprocessing applications. Front Chem 2:66. doi:10.3389/fchem.2014.00066
Arcus VL, McKenzie JL, Robson J, Cook GM (2011) The PIN-domain ribonucleases and the prokaryotic VapBC toxin–antitoxin array. Protein Eng Des Sel 24(1–2):33–40. doi:10.1093/protein/gzq081
Das U, Pogenberg V, Subhramanyam UKT, Wilmanns M, Gourinath S, Srinivasan A (2014) Crystal structure of the VapBC-15 complex from Mycobacterium tuberculosis reveals a two-metal ion dependent PIN-domain ribonuclease and a variable mode of toxin–antitoxin assembly. J Struct Biol 188(3):249–258. doi:10.1016/j.jsb.2014.10.002
Delaglio F, Grzesiek S, Vuister GW, Zhu G, Pfeifer J, Bax A (1995) NMRPipe: a multidimensional spectral processing system based on UNIX pipes. J Biomol NMR 6(3):277–293. doi:10.1007/bf00197809
Dienemann C, Boggild A, Winther KS, Gerdes K, Brodersen DE (2011) Crystal structure of the VapBC toxin–antitoxin complex from Shigella flexneri reveals a hetero-octameric DNA-binding assembly. J Mol Biol 414(5):713–722. doi:10.1016/j.jmb.2011.10.024
Geerds C, Wohlmann J, Haas A, Niemann HH (2014) Structure of Rhodococcus equi virulence-associated protein B (VapB) reveals an eight-stranded antiparallel β-barrel consisting of two Greek-key motifs. Acta Crystallogr F 70:866–871. doi:10.1107/S2053230x14009911
Gerdes K, Christensen SK, Lobner-Olesen A (2005) Prokaryotic toxin–antitoxin stress response loci. Nat Rev Microbiol 3(5):371–382. doi:10.1038/nrmicro1147
Hamilton B, Manzella A, Schmidt K, DiMarco V, Butler JS (2014) Analysis of non-typeable Haemophilous influenzae VapC1 mutations reveals structural features required for toxicity and flexibility in the active site. PLoS ONE 9(11):e112921. doi:10.1371/journal.pone.0112921
Johnson BA, Blevins RA (1994) NMRView: a computer program for the visualization and analysis of NMR data. J Biomol NMR 4(5):603–614. doi:10.1007/Bf00404272
Lee IG, Lee SJ, Chae S, Lee KY, Kim JH, Lee BJ (2015) Structural and functional studies of the Mycobacterium tuberculosis VapBC30 toxin–antitoxin system: implications for the design of novel antimicrobial peptides. Nucleic Acids Res 43(15):7624–7637. doi:10.1093/nar/gkv689
Markley JL, Bax A, Arata Y, Hilbers CW, Kaptein R, Sykes BD, Wright PE, Wuthrich K (1998) Recommendations for the presentation of NMR structures of proteins and nucleic acids (IUPAC Recommendations 1998). Pure Appl Chem 70(1):117–142. doi:10.1351/pac199870010117
Martinez-Garcia E, Benedetti I, Hueso A, De Lorenzo V (2015) Mining environmental plasmids for synthetic biology parts and devices. Microbiol Spectr 3(1):PLAS-0033-2014. doi:10.1128/microbiolspec.PLAS-0033-2014
Mate MJ, Vincentelli R, Foos N, Raoult D, Cambillau C, Ortiz-Lombardia M (2012) Crystal structure of the DNA-bound VapBC2 antitoxin/toxin pair from Rickettsia felis. Nucleic Acids Res 40(7):3245–3258. doi:10.1093/nar/gkr1167
Miallau L, Faller M, Chiang J, Arbing M, Guo F, Cascio D, Eisenberg D (2009) Structure and proposed activity of a member of the VapBC family of toxin–antitoxin systems VapBC-5 from Mycobacterium tuberculosis. J Biol Chem 284(1):276–283. doi:10.1074/jbc.M805061200
Min AB, Miallau L, Sawaya MR, Habel J, Cascio D, Eisenberg D (2012) The crystal structure of the Rv0301-Rv0300 VapBC-3 toxin–antitoxin complex from M. tuberculosis reveals a Mg2+ ion in the active site and a putative RNA-binding site. Protein Sci 21(11):1754–1767. doi:10.1002/pro.2161
Page R, Peti W (2016) Toxin–antitoxin systems in bacterial growth arrest and persistence. Nat Chem Biol 12(4):208–214. doi:10.1038/Nchembio.2044
Park SJ, Son WS, Lee BJ (2013) Structural overview of toxin–antitoxin systems in infectious bacteria: a target for developing antimicrobial agents. Biochim Biophys Acta 1834(6):1155–1167. doi:10.1016/j.bbapap.2013.02.027
Sevillano L, Diaz M, Santamaria RI (2013) Stable expression plasmids for Streptomyces based on a toxin–antitoxin system. Microb Cell Fact. doi:10.1186/1475-2859-12-39
Shao YC, Harrison EM, Bi DX, Tai C, He XY, Ou HY, Rajakumar K, Deng ZX (2011) TADB: a web-based resource for Type 2 toxin–antitoxin loci in bacteria and archaea. Nucleic Acids Res 39:D606–D611. doi:10.1093/nar/gkq908
Shen Y, Bax A (2013) Protein backbone and sidechain torsion angles predicted from NMR chemical shifts using artificial neural networks. J Biomol NMR 56(3):227–241. doi:10.1007/s10858-013-9741-y
Syed MA, Levesque CM (2012) Chromosomal bacterial type II toxin–antitoxin systems. Can J Microbiol 58(5):553–562. doi:10.1139/w2012-025
Wen YR, Behiels E, Devreese B (2014) Toxin–antitoxin systems: their role in persistence, biofilm formation, and pathogenicity. Pathog Dis 70(3):240–249. doi:10.1111/2049-632x.12145
Williams JJ, Hergenrother PJ (2012) Artificial activation of toxin–antitoxin systems as an antibacterial strategy. Trends Microbiol 20(6):291–298
Xu K, Dedic E, Brodersen DE (2016) Structural analysis on the active site architecture of the VapC toxin from Shigella flexneri. Proteins. doi:10.1002/prot.25002
Xuan JS, Song XX, Wang JF, Feng YA (2011) Resonance assignments of a putative PilT N-terminus domain protein SSO1118 from hyperthermophilic archaeon Sulfolobus solfataricus P2. Biomol NMR Assign 5(2):161–164. doi:10.1007/s12104-010-9291-0
Xuan JS, Song XX, Chen C, Wang JF, Feng YG (2013) A PilT N-terminus domain protein SSO1118 from hyperthemophilic archaeon Sulfolobus solfataricus P2. J Biomol NMR 57(4):363–368. doi:10.1007/s10858-013-9794-y
Yeo CC, Abu Bakar F, Chan WT, Espinosa M, Harikrishna JA (2016) Heterologous expression of toxins from bacterial toxin–antitoxin systems in eukaryotic cells: strategies and applications. Toxins. doi:10.3390/toxins8020049
Acknowledgments
We thank Dr. Jinfa Ying (in the Ad Bax group of NIDDK, NIH) for providing SMILE software and helpful comments for the NUS data processing. This work was supported by National Natural Science Foundation of China (Grant Nos. 31270784 to Y.F. and 31300635 to J.X.) and Chinese Government Scholarship (No. 201506465020 to J.X.).
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Wang, C., Xuan, J., Cui, Q. et al. Resonance assignments of a VapC family toxin from Clostridium thermocellum . Biomol NMR Assign 10, 367–371 (2016). https://doi.org/10.1007/s12104-016-9702-y
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DOI: https://doi.org/10.1007/s12104-016-9702-y