Inducible auto-phosphorylation regulates a widespread family of nucleotidyltransferase toxins.
Journal
Nature communications
ISSN: 2041-1723
Titre abrégé: Nat Commun
Pays: England
ID NLM: 101528555
Informations de publication
Date de publication:
04 Sep 2024
04 Sep 2024
Historique:
received:
29
02
2024
accepted:
22
08
2024
medline:
5
9
2024
pubmed:
5
9
2024
entrez:
4
9
2024
Statut:
epublish
Résumé
Nucleotidyltransferases (NTases) control diverse physiological processes, including RNA modification, DNA replication and repair, and antibiotic resistance. The Mycobacterium tuberculosis NTase toxin family, MenT, modifies tRNAs to block translation. MenT toxin activity can be stringently regulated by diverse MenA antitoxins. There has been no unifying mechanism linking antitoxicity across MenT homologues. Here we demonstrate through structural, biochemical, biophysical and computational studies that despite lacking kinase motifs, antitoxin MenA
Identifiants
pubmed: 39231966
doi: 10.1038/s41467-024-51934-1
pii: 10.1038/s41467-024-51934-1
doi:
Substances chimiques
Nucleotidyltransferases
EC 2.7.7.-
Bacterial Toxins
0
Bacterial Proteins
0
RNA, Transfer
9014-25-9
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
7719Subventions
Organisme : RCUK | Engineering and Physical Sciences Research Council (EPSRC)
ID : EP/S022791/1
Organisme : Fondation pour la Recherche Médicale (Foundation for Medical Research in France)
ID : EQU202403018015
Organisme : National Natural Science Foundation of China (National Science Foundation of China)
ID : 32000021
Organisme : Academy of Medical Sciences
ID : SBF002\1104
Pays : United Kingdom
Informations de copyright
© 2024. The Author(s).
Références
Kuchta, K., Knizewski, L., Wyrwicz, L. S., Rychlewski, L. & Ginalski, K. Comprehensive classification of nucleotidyltransferase fold proteins: identification of novel families and their representatives in human. Nucleic Acids Res. 37, 7701 (2009).
pubmed: 19833706
pmcid: 2794190
doi: 10.1093/nar/gkp854
Aravind, L. & Koonin, E. V. DNA polymerase β-like nucleotidyltransferase superfamily: identification of three new families, classification and evolutionary history. Nucleic Acids Res. 27, 1609–1618 (1999).
pubmed: 10075991
pmcid: 148363
doi: 10.1093/nar/27.7.1609
Tomita, K. & Yamashita, S. Molecular mechanisms of template-independent RNA polymerization by tRNA nucleotidyltransferases. Front. Genet. 5, 81062 (2014).
doi: 10.3389/fgene.2014.00036
Bassenden, A. V., Park, J., Rodionov, D. & Berghuis, A. M. Revisiting the catalytic cycle and kinetic mechanism of aminoglycoside O-nucleotidyltransferase(2″): a structural and kinetic study. ACS Chem. Biol. 15, 686–694 (2020).
pubmed: 32100995
doi: 10.1021/acschembio.9b00904
Zheng, M., Zheng, M. & Lupoli, T. J. Expanding the substrate scope of a bacterial nucleotidyltransferase via allosteric mutations. ACS Infect. Dis. 8, 2035 (2022).
pubmed: 36106727
pmcid: 10322145
doi: 10.1021/acsinfecdis.2c00402
Cai, Y. et al. A nucleotidyltransferase toxin inhibits growth of Mycobacterium tuberculosis through inactivation of tRNA acceptor stems. Sci. Adv 6, 6651–6680 (2020).
doi: 10.1126/sciadv.abb6651
Chung, C. Z. et al. Gld2 activity is regulated by phosphorylation in the N-terminal domain. RNA Biol. 16, 1022 (2019).
pubmed: 31057087
pmcid: 6602411
doi: 10.1080/15476286.2019.1608754
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).
pubmed: 24465005
pmcid: 3985639
doi: 10.1093/nar/gkt1419
Peltier, J. et al. Type I toxin-antitoxin systems contribute to the maintenance of mobile genetic elements in Clostridioides difficile. Commun. Biol. 3, 1–13 (2020).
doi: 10.1038/s42003-020-01448-5
Ogura, T. & Hiraga, S. Mini-F plasmid genes that couple host cell division to plasmid proliferation. Proc. Natl Acad. Sci. 80, 4784–4788 (1983).
pubmed: 6308648
pmcid: 384129
doi: 10.1073/pnas.80.15.4784
Kolodkin-Gal, I., Gutierrez, C., Wood, T. K. & Song, S. A primary physiological role of toxin/antitoxin systems is phage inhibition. Front. Microbiol. 11, 1895 (2020).
doi: 10.3389/fmicb.2020.01895
Lobato-Márquez, D., Díaz-Orejas, R. & García-del Portillo, F. Toxin-antitoxins and bacterial virulence. FEMS Microbiol. Rev. 40, 592–609 (2016).
pubmed: 27476076
doi: 10.1093/femsre/fuw022
De Bast, M. S., Mine, N. & Van Melderen, L. Chromosomal toxin-antitoxin systems may act as antiaddiction modules. J. Bacteriol. 190, 4603–4609 (2008).
doi: 10.1128/JB.00357-08
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 (2021).
pubmed: 33838104
pmcid: 8284924
doi: 10.1016/j.molcel.2021.03.027
Xu, X. et al. Nucleotidyltransferase toxin MenT targets and extends the aminoacyl acceptor ends of serine tRNAs in vivo to control Mycobacterium tuberculosis growth. Preprint at bioRxiv https://www.biorxiv.org/content/10.1101/2024.03.07.583660v1 (2024).
Singh, G., Yadav, M., Ghosh, C. & Rathore, J. S. Bacterial toxin-antitoxin modules: classification, functions, and association with persistence. Curr. Res. Microb. Sci. 2, 100047 (2021).
pubmed: 34841338
pmcid: 8610362
Sala, A., Bordes, P. & Genevaux, P. Multiple toxin-antitoxin systems in Mycobacterium tuberculosis. Toxins 6, 1002–1020 (2014).
pubmed: 24662523
pmcid: 3968373
doi: 10.3390/toxins6031002
Kamruzzaman, M. & Iredell, J. A parDe-family toxin antitoxin system in major resistance plasmids of enterobacteriaceae confers antibiotic and heat tolerance. Sci. Rep. 9, 9872 (2019).
pubmed: 31285520
pmcid: 6614396
doi: 10.1038/s41598-019-46318-1
Agarwal, S. et al. VapBC22 toxin-antitoxin system from Mycobacterium tuberculosis is required for pathogenesis and modulation of host immune response. Sci. Adv. 6, eaba6944 (2020).
pubmed: 32537511
pmcid: 7269643
doi: 10.1126/sciadv.aba6944
Xu, X. et al. MenT nucleotidyltransferase toxins extend tRNA acceptor stems and can be inhibited by asymmetrical antitoxin binding. Nat. Commun. 14, 4644 (2023).
pubmed: 37591829
pmcid: 10435456
doi: 10.1038/s41467-023-40264-3
Yu, X. et al. Characterization of a toxin-antitoxin system in Mycobacterium tuberculosis suggests neutralization by phosphorylation as the antitoxicity mechanism. Commun. Biol. 3, 1–5 (2020).
doi: 10.1038/s42003-020-0941-1
Sassetti, C. M., Boyd, D. H. & Rubin, E. J. Genes required for mycobacterial growth defined by high density mutagenesis. Mol. Microbiol. 48, 77–84 (2003).
pubmed: 12657046
doi: 10.1046/j.1365-2958.2003.03425.x
Gosain, T. P., Singh, M., Singh, C., Thakur, K. G. & Singh, R. Disruption of MenT2 toxin impairs the growth of Mycobacterium tuberculosis in guinea pigs. Microbiology 168, 001246 (2022).
doi: 10.1099/mic.0.001246
Tesson, F. et al. Systematic and quantitative view of the antiviral arsenal of prokaryotes. Nat. Commun. 13, 2561 (2022).
pubmed: 35538097
pmcid: 9090908
doi: 10.1038/s41467-022-30269-9
Beck, I. N., Usher, B., Hampton, H. G., Fineran, P. C. & Blower, T. R. Antitoxin autoregulation of M. tuberculosis toxin-antitoxin expression through negative cooperativity arising from multiple inverted repeat sequences. Biochem. J. 477, 2401–2419 (2020).
pubmed: 32519742
doi: 10.1042/BCJ20200368
Hampton, H. G. et al. AbiEi binds cooperatively to the type IV abiE toxin-antitoxin operator via a positively-charged surface and causes DNA bending and negative autoregulation. J. Mol. Biol. 430, 1141–1156 (2018).
pubmed: 29518409
doi: 10.1016/j.jmb.2018.02.022
Frando, A. et al. The Mycobacterium tuberculosis protein O-phosphorylation landscape. Nat. Microbiol. 8, 548–561 (2023).
pubmed: 36690861
doi: 10.1038/s41564-022-01313-7
Timm, J., Lim, E. M. & Gicquel, B. Escherichia coli-mycobacteria shuttle vectors for operon and gene fusions to lacZ: the pJEM series. J. Bacteriol. 176, 6749–6753 (1994).
pubmed: 7961429
pmcid: 197033
doi: 10.1128/jb.176.21.6749-6753.1994
Beck, I. N. et al. Toxin release by conditional remodelling of ParDE1 from Mycobacterium tuberculosis leads to gyrase inhibition. Nucleic Acids Res. 52, 1909–1929 (2024).
pubmed: 38113275
doi: 10.1093/nar/gkad1220
Lunde, B. M., Magler, I. & Meinhart, A. Crystal structures of the Cid1 poly (U) polymerase reveal the mechanism for UTP selectivity. Nucleic Acids Res. 40, 9815 (2012).
pubmed: 22885303
pmcid: 3479196
doi: 10.1093/nar/gks740
Pedersen, L. C., Benning, M. M. & Holden, H. M. Structural investigation of the antibiotic and ATP-binding sites in kanamycin nucleotidyltransferase. Biochemistry 34, 13305–13311 (1995).
pubmed: 7577914
doi: 10.1021/bi00041a005
Taylor, S. S. & Radzio-Andzelm, E. Three protein kinase structures define a common motif. Structure 2, 345–355 (1994).
pubmed: 8081750
doi: 10.1016/S0969-2126(00)00036-8
Liu, J. & Yashiro, Y. Substrate specificity of Mycobacterium tuberculosis tRNA terminal nucleotidyltransferase toxin MenT3. Nucleic Acids Res. 2024, 1–15 (2024).
Arter, C., Trask, L., Ward, S., Yeoh, S. & Bayliss, R. Structural features of the protein kinase domain and targeted binding by small-molecule inhibitors. J. Biol. Chem. 298, 102247 (2022).
pubmed: 35830914
pmcid: 9382423
doi: 10.1016/j.jbc.2022.102247
Damle, N. P. & Mohanty, D. Mechanism of autophosphorylation of mycobacterial PknB explored by molecular dynamics simulations. Biochemistry 53, 4715–4726 (2014).
pubmed: 24988180
doi: 10.1021/bi500245v
Makarova, K. S., Wolf, Y. I. & Koonin, E. V. Comparative genomics of defense systems in archaea and bacteria. Nucleic Acids Res. 41, 4360 (2013).
pubmed: 23470997
pmcid: 3632139
doi: 10.1093/nar/gkt157
Kim, B. H., Sadreyev, R. & Grishin, N. V. COG4849 is a novel family of nucleotidyltransferases. J. Mol. Recognit. 18, 422–425 (2005).
pubmed: 15983981
doi: 10.1002/jmr.746
Lu, S. et al. CDD/SPARCLE: the conserved domain database in 2020. Nucleic Acids Res. 48, D265–D268 (2020).
pubmed: 31777944
doi: 10.1093/nar/gkz991
Li, Z., Song, Q., Wang, Y., Xiao, X. & Xu, J. Identification of a functional toxin-antitoxin system located in the genomic island PYG1 of piezophilic hyperthermophilic archaeon Pyrococcus yayanosii. Extremophiles 22, 347–357 (2018).
pubmed: 29335804
doi: 10.1007/s00792-018-1002-2
Eun, H. J., Lee, J., Kang, S. J. & Lee, B. J. The structural and functional investigation of the VapBC43 complex from Mycobacterium tuberculosis. Biochem. Biophys. Res. Commun. 616, 19–25 (2022).
pubmed: 35636251
doi: 10.1016/j.bbrc.2022.05.061
Hazan, R., Sat, B. & Engelberg-Kulka, H. Escherichia coli mazEF-mediated cell death is triggered by various stressful conditions. J. Bacteriol. 186, 3663–3669 (2004).
pubmed: 15150257
pmcid: 415763
doi: 10.1128/JB.186.11.3663-3669.2004
Parry, B. R. et al. The bacterial cytoplasm has glass-like properties and is fluidized by metabolic activity. Cell 156, 183–194 (2014).
pubmed: 24361104
doi: 10.1016/j.cell.2013.11.028
Rao, S. P. S., Alonso, S., Rand, L., Dick, T. & Pethe, K. The protonmotive force is required for maintaining ATP homeostasis and viability of hypoxic, nonreplicating Mycobacterium tuberculosis. Proc. Natl Acad. Sci. USA 105, 11945–11950 (2008).
pubmed: 18697942
pmcid: 2575262
doi: 10.1073/pnas.0711697105
Gaora, P. O. Expression of genes in mycobacteria. Methods Mol. Biol. 101, 261–273 (1998).
pubmed: 9921485
Coppens, L. & Lavigne, R. SAPPHIRE: a neural network based classifier for σ70 promoter prediction in Pseudomonas. BMC Bioinform. 21, 1–7 (2020).
doi: 10.1186/s12859-020-03730-z
Miller, J. Experiments in molecular genetics. (Cold Spring Harbor Laboratory, 1972).
Evans, P. R. & Murshudov, G. N. How good are my data and what is the resolution? Acta Crystallogr. D Biol. Crystallogr. 69, 1204–1214 (2013).
pubmed: 23793146
pmcid: 3689523
doi: 10.1107/S0907444913000061
Winn, M. D. et al. Overview of the CCP4 suite and current developments. Acta Cryst. 67, 235–242 (2011).
McCoy, A. J. et al. Phaser crystallographic software. J. Appl. Crystallogr. 40, 658–674 (2007).
pubmed: 19461840
pmcid: 2483472
doi: 10.1107/S0021889807021206
Murshudov, G. N., Vagin, A. A. & Dodson, E. J. Refinement of macromolecular structures by the maximum-likelihood method. Acta Crystallogr. D Biol. Crystallogr. 53, 240–255 (1997).
pubmed: 15299926
doi: 10.1107/S0907444996012255
Emsley, P., Lohkamp, B., Scott, W. G. & Cowtan, K. Features and development of Coot. Acta Crystallogr. Sect. D 66, 486–501 (2010).
doi: 10.1107/S0907444910007493
Berman, H., Henrick, K., Nakamura, H. & Markley, J. L. The worldwide Protein Data Bank (wwPDB): ensuring a single, uniform archive of PDB data. Nucleic Acids Res. 35, D301–D303 (2007).
pubmed: 17142228
doi: 10.1093/nar/gkl971
The PyMOL Molecular graphics system, Version 2.0 Schrödinger, LLC.
Semisotnov, G. V. et al. Study of the “molten globule” intermediate state in protein folding by a hydrophobic fluorescent probe. Biopolymers 31, 119–128 (1991).
pubmed: 2025683
doi: 10.1002/bip.360310111
Grøftehauge, M. K., Hajizadeh, N. R., Swann, M. J. & Pohl, E. Protein-ligand interactions investigated by thermal shift assays (TSA) and dual polarization interferometry (DPI). Acta Crystallogr. Sect. D 71, 36–44 (2015).
doi: 10.1107/S1399004714016617
Rueden, C. T. et al. ImageJ2: ImageJ for the next generation of scientific image data. BMC Bioinform. 18, 529 (2017).
doi: 10.1186/s12859-017-1934-z
Jumper, J. et al. Highly accurate protein structure prediction with AlphaFold. Nature 596, 583 (2021).
pubmed: 34265844
pmcid: 8371605
doi: 10.1038/s41586-021-03819-2
Fleming, P. J., Fleming, K. G. & Jenkins, T. C. HullRad: fast calculations of folded and disordered protein and nucleic acid hydrodynamic properties. Biophys. J. 114, 856–869 (2018).
pubmed: 29490246
pmcid: 5984988
doi: 10.1016/j.bpj.2018.01.002
BioSolveIT GmbH. SeeSAR version 13.0.4. www.biosolveit.de/SeeSAR .
Volkamer, A., Kuhn, D., Rippmann, F. & Rarey, M. DoGSiteScorer: a web server for automatic binding site prediction, analysis and druggability assessment. Bioinformatics 28, 2074–2075 (2012).
pubmed: 22628523
doi: 10.1093/bioinformatics/bts310
Schneider, N., Lange, G., Hindle, S., Klein, R. & Rarey, M. A consistent description of HYdrogen bond and DEhydration energies in protein-ligand complexes: methods behind the HYDE scoring function. J. Comput. Aided Mol. Des. 27, 15–29 (2013).
pubmed: 23269578
doi: 10.1007/s10822-012-9626-2
Berendsen, H. J. C., van der Spoel, D. & van Drunen, R. GROMACS: A message-passing parallel molecular dynamics implementation. Comput. Phys. Commun. 91, 43–56 (1995).
doi: 10.1016/0010-4655(95)00042-E
Wang, J., Wolf, R. M., Caldwell, J. W., Kollman, P. A. & Case, D. A. Development and testing of a general amber force field. J. Comput. Chem. 25, 1157–1174 (2004).
pubmed: 15116359
doi: 10.1002/jcc.20035
Lindorff-Larsen, K. et al. Improved side-chain torsion potentials for the Amber ff99SB protein force field. Proteins Struct. Funct. Bioinform. 78, 1950–1958 (2010).
doi: 10.1002/prot.22711
Jakalian, A., Jack, D. B. & Bayly, C. I. Fast, efficient generation of high-quality atomic charges. AM1-BCC model: II. Parameterization and validation. J. Comput. Chem. 23, 1623–1641 (2002).
pubmed: 12395429
doi: 10.1002/jcc.10128
Jorgensen, W. L., Chandrasekhar, J., Madura, J. D., Impey, R. W. & Klein, M. L. Comparison of simple potential functions for simulating liquid water. J. Chem. Phys. 79, 926–935 (1983).
doi: 10.1063/1.445869
Darden, T., York, D. & Pedersen, L. Particle mesh Ewald: an Nṡlog(N) method for Ewald sums in large systems. J. Chem. Phys. 98, 10089–10092 (1993).
doi: 10.1063/1.464397
Bussi, G., Donadio, D. & Parrinello, M. Canonical sampling through velocity-rescaling. J. Chem. Phys. 126, 014101 (2007).
pubmed: 17212484
doi: 10.1063/1.2408420
Hess, B., Bekker, H., Berendsen, H. J. C. & Fraaije, J. G. E. M. LINCS: a linear constraint solver for molecular simulations. J. Comput. Chem. 18, 14631472 (1997).
doi: 10.1002/(SICI)1096-987X(199709)18:12<1463::AID-JCC4>3.0.CO;2-H
Parrinello, M. & Rahman, A. Polymorphic transitions in single crystals: a new molecular dynamics method. J. Appl. Phys. 52, 7182–7190 (1981).
doi: 10.1063/1.328693
Humphrey, W., Dalke, A. & Schulten, K. VMD: visual molecular dynamics. J. Mol. Graph. 14, 33–38 (1996).
pubmed: 8744570
doi: 10.1016/0263-7855(96)00018-5
Galgonek, J. et al. Amino Acid Interaction (INTAA) web server. Nucleic Acids Res. 45, W388–W392 (2017).
pubmed: 28472475
pmcid: 5570164
doi: 10.1093/nar/gkx352
Bonomi, M. et al. PLUMED: a portable plugin for free-energy calculations with molecular dynamics. Comput. Phys. Commun. 180, 1961–1972 (2009).
doi: 10.1016/j.cpc.2009.05.011