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PreprintCited by 34Bacterial Genetics and BiotechnologyAntibiotic Resistance in BacteriaEnzyme Structure and Function

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Metamorphism of catalytic domain controls transposition in Tn3 family transposases

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Shkumatov, Alexander V., Aryanpour, Nicolas, Oger, Cédric A., Goossens, Gérôme, Hallet, Bernard F., Efremov, Rouslan G.·2022·Nature Communications
DOI 10.1101/2022.02.23.481423PMC PMC9579193

Preprint — published as 10.1038/s41467-022-33871-z · Paper page

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Abstract

Transposons account for a remarkable diversity of mobile genetic elements that play the role of genome architects in all domains of life. Tn3 is a family of widespread and among first identified bacterial transposons notorious for their contribution to dissemination of antibiotic resistance. Transposition within this family is mediated by a large TnpA transposase facilitating both transposition and target immunity. The structural framework for understanding the mechanism of the TnpA transposition is however absent. Here, we describe the cryo-EM structures of TnpA from Tn4430 in apo form and paired with transposon ends. We show that TnpA has a unique architecture and exhibits a family-specific regulation mechanism involving metamorphic refolding of the RNase H-like catalytic domain. The TnpA structure, constrained by a double dimerization interface, creates a unique topology that suggests a specific role for target DNA in transpososome assembly, activation, and target immunity.

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Research works printed but not linked: 63

  1. 10.1126/science.1089670 · DOI · Paper page
  2. 10.1128/9781555819217.ch1 · DOI
  3. 10.1038/nrmicro1235 · DOI
  4. 2020, A Field Guide to Eukaryotic Transposable Elements, Annu Rev Genet, 54, 539, 10.1146/annurev-genet-040620-022145 · DOI · Paper page
  5. 10.1016/S0923-2508(01)01265-7 · DOI
  6. 10.1111/j.1574-6976.2011.00277.x · DOI
  7. 10.1111/j.1574-6976.2011.00273.x · DOI
  8. 10.1128/CMR.00088-17 · DOI · Paper page
  9. 10.1007/BF00268228 · DOI
  10. Nicolas, E. et al. The Tn3-family of Replicative Transposons. Microbiol Spectr 3, (2015). · DOI
  11. 10.1128/AAC.05202-11 · DOI
  12. 10.1016/j.molmed.2012.03.003 · DOI
  13. 2017, Identification of a novel transposon-associated phosphoethanolamine transferase gene, mcr-5, conferring colistin resistance in d-tartrate fermenting Salmonella enterica subsp. enterica serovar Paratyphi B, J Antimicrob Chemother, 72, 3317, 10.1093/jac/dkx327 · DOI
  14. 2019, A Genomic, Evolutionary, and Mechanistic Study of MCR-5 Action Suggests Functional Unification across the MCR Family of Colistin Resistance, Adv Sci (Weinh), 6, 1900034, 10.1002/advs.201900034 · DOI
  15. 2020, Emerging Transcriptional and Genomic Mechanisms Mediating Carbapenem and Polymyxin Resistance in Enterobacteriaceae: a Systematic Review of Current Reports, mSystems, 5, e00783
  16. 10.1021/acs.chemrev.6b00003 · DOI
  17. 10.1016/j.sbi.2011.03.004 · DOI
  18. 10.1016/j.molcel.2006.03.013 · DOI · Paper page
  19. 10.1093/nar/gkt1414 · DOI
  20. 10.1038/sj.emboj.7600395 · DOI
  21. 2021, Structures of ISCth4 transpososomes reveal the role of asymmetry in copy-out/paste-in DNA transposition, EMBO J, 40, e105666, 10.15252/embj.2020105666 · DOI
  22. 1977, Inhibition of TnA translocation by TnA, Journal of Bacteriology, 129, 407, 10.1128/jb.129.1.407-414.1977 · DOI
  23. 10.1146/annurev.biochem.66.1.437 · DOI
  24. 10.1016/S0968-0004(98)01325-5 · DOI
  25. 10.1016/0092-8674(89)90170-0 · DOI
  26. 2010, Immunity of replicating Mu to self-integration: a novel mechanism employing MuB protein, Mob DNA, 1, 8, 10.1186/1759-8753-1-8 · DOI
  27. 10.1128/JB.00477-10 · DOI
  28. 10.1111/j.1365-2958.2012.07967.x · DOI
  29. 10.1073/pnas.1611701114 · DOI
  30. 10.7554/eLife.36861 · DOI
  31. 10.1126/science.289.5476.77 · DOI
  32. 10.1038/s41586-019-1753-7 · DOI
  33. 2016, Sleeping Beauty transposase structure allows rational design of hyperactive variants for genetic engineering, Nature Communications, 7, 11126, 10.1038/ncomms11126 · DOI
  34. 2020, Structural basis of seamless excision and specific targeting by piggyBac transposase, Nature Communications, 11, 3446, 10.1038/s41467-020-17128-1 · DOI
  35. 10.1038/nature11602 · DOI · Paper page
  36. 2016, A bend, flip and trap mechanism for transposon integration, eLife, 5, e15537, 10.7554/eLife.15537 · DOI · Paper page
  37. 10.1101/gad.252122.114 · DOI
  38. 10.1006/jmbi.1994.1115 · DOI
  39. 10.1093/nar/gkt1414 · DOI
  40. 10.1021/acschembio.8b00276 · DOI
  41. 10.1074/jbc.274.17.11904 · DOI
  42. 10.1073/pnas.76.4.1933 · DOI
  43. Harshey, R. M. Transposable Phage Mu. Microbiol Spectr 2,(2014). · DOI
  44. 10.1128/mBio.00762-15 · DOI
  45. He, S. et al. Mechanisms of Evolution in High-Consequence Drug Resistance Plasmids. mBio 7, (2016). · DOI
  46. 10.1107/S2059798319006880 · DOI
  47. 2021, Coma-corrected rapid single-particle cryo-EM data collection on the CRYO ARM 300, Acta Crystallogr D Struct Biol, 77, 555, 10.1107/S2059798321002151 · DOI
  48. 10.1016/j.jsb.2005.07.007 · DOI
  49. 10.7554/eLife.42166 · DOI
  50. 2017, MotionCor2: Anisotropic correction of beam-induced motion for improved cryo-electron microscopy, Nat Meth, 14, 331, 10.1038/nmeth.4193 · DOI
  51. 10.1016/j.jsb.2015.08.008 · DOI
  52. 2017, cryoSPARC: algorithms for rapid unsupervised cryo-EM structure determination, Nat Meth, 14, 290, 10.1038/nmeth.4169 · DOI · Paper page
  53. 10.1107/S2052252520000081 · DOI
  54. 2017, Addressing preferred specimen orientation in single-particle cryo-EMthrough tilting, Nat Meth, 14, 793, 10.1038/nmeth.4347 · DOI
  55. 2018, A fully automatic method yielding initial models from high-resolution cryo-electron microscopy maps, Nat Meth, 15, 905, 10.1038/s41592-018-0173-1 · DOI
  56. 2020, Current developments in Coot for macromolecular model building of Electron Cryo-microscopy and Crystallographic Data, Protein Sci, 29, 1069
  57. 2013, New tool: phenix. real_space_refine, Computational Crystallography Newsletter, 4, 43
  58. 10.1002/pro.3330 · DOI · Paper page
  59. 10.1002/PRO.3943 · DOI
  60. 10.1093/nar/gkq313 · DOI · Paper page
  61. 10.1093/nar/gku316 · DOI · Paper page
  62. 2021, TnCentral: a Prokaryotic Transposable Element Database and Web Portal for Transposon Analysis, mBio, 12, e0206021, 10.1128/mBio.02060-21 · DOI
  63. 10.1093/nar/gkw408 · DOI · Paper page

Metadata

Authors
Shkumatov, A. V., Aryanpour, N., Oger, C. A., Goossens, G., Hallet, B. F., & Efremov, R. G.
Affiliations
  • Vrije Universiteit Brussel (BE)
  • UCLouvain (BE)
Corresponding author
  • Hallet, Bernard F.
  • Efremov, Rouslan G.
ORCID
Venue
Nature Communications
Publisher
openRxiv
Published
2022-02-24
Volume
13
Issue
1
Pages
6155-6155
ISSN
2041-1723 (ISSN-L)
DOI
10.1101/2022.02.23.481423
PMC
PMC9579193
OpenAlex
W4306721683
Cited by
34
References
1
Citations by year
2026: 13 · 2025: 11 · 2024: 3 · 2023: 6 · 2022: 1
FWCI
3.32
Type
journal article
Language
en
Open access
Licence
cc-by
Locations
  • Nature Communications (publishedVersion, cc-by)
  • bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
  • RePEc: Research Papers in Economics (submittedVersion)
  • Digital Access to Libraries (submittedVersion, other-oa)
  • DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
Funders
  • Université Catholique de Louvain
  • Netherlands Centre for Electron Nanoscopy
  • European Synchrotron Radiation Facility
  • Universiteit Leiden
  • Fonds Wetenschappelijk Onderzoek (G054617N, G0H5916N)
  • Vlaams Instituut voor Biotechnologie
  • Fonds Spéciaux de Recherche
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Bacterial Genetics and Biotechnology
  • Health Sciences › Medicine › Microbiology (medical) › Antibiotic Resistance in Bacteria
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Structural Biology › Enzyme Structure and Function
Keywords
Tn3 transposon, DNA strand transfer, DNA cleavage, transposon ends, dimer interface, antibiotic resistance dissemination, cryo-EM structure
MeSH terms
DNA Transposable Elements, Escherichia coli, Ribonuclease H, Transposases

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