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PreprintCited by 53Bacterial Genetics and BiotechnologyDNA Repair MechanismsGenomics and Chromatin Dynamics

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DNA-measuring Wadjet SMC ATPases restrict smaller circular plasmids by DNA cleavage

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Liu, Hon Wing, Roisné-Hamelin, Florian, Beckert, Bertrand, Myasnikov, Alexander, Li, Yan, Gruber, Stephan·2022·Molecular Cell
DOI 10.1101/2022.10.04.510915

Preprint — published as 10.1016/j.molcel.2022.11.015 · Paper page

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Abstract

Summary: Structural maintenance of chromosomes (SMC) complexes fold DNA by loop extrusion to support chromosome segregation, genome maintenance, and gene expression. Wadjet systems (JetABCD/MksBEFG/EptABCD) are derivative SMC complexes with proposed roles in bacterial immunity against selfish DNA elements. Here, we show that JetABCD systems restrict extrachromosomal circular DNA with an upper size limit of about 100 kb, while a linear plasmid evades restriction. Recombinant preparations of a JetABCD complex cleave circular DNA regardless of its helical topology but not linear DNA; cleavage occurs at random positions and depends on ATP as well as the SMC ATPase. We solve a structure of the JetABCD core by cryo-EM revealing an alternative dimer-of-dimers configuration. The two SMC DNA motor units face in opposite orientations—rather than the same as observed with MukBEF—possibly representing a restriction-specific state of JetABCD. We hypothesize that JetABCD is a DNA-shape-specific endonuclease and present a model for the activation of DNA cleavage exclusively when extrusion of an entire plasmid has been completed by a single JetABCD complex. The self-stalling of two opposing DNA motor units may serve as signal to trigger DNA cleavage. Complete extrusion by a single complex cannot be achieved on the much larger chromosome, explaining how self-DNA may evade cleavage.

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Research works printed but not linked: 53

  1. 10.1107/S2059798318006551 · DOI
  2. 10.1016/0378-1119(91)90604-A · DOI
  3. 10.1038/s41467-020-15238-4 · DOI
  4. 10.1016/j.molcel.2021.10.011 · DOI
  5. 10.1038/s41594-019-0196-z · DOI
  6. 10.1038/nsmb.2488 · DOI
  7. 10.1038/nsmb1264 · DOI
  8. 10.1126/science.aaz3418 · DOI · Paper page
  9. 10.1093/nar/gkm216 · DOI
  10. 10.1038/nature17170 · DOI
  11. 10.1016/j.molcel.2017.06.010 · DOI
  12. 10.1186/s12860-019-0211-6 · DOI
  13. 10.1126/science.aar4120 · DOI
  14. 10.1016/j.chom.2021.03.001 · DOI
  15. 10.1107/S0907444910007493 · DOI · Paper page
  16. Evans, R. , O’Neill, M. , Pritzel, A. , Antropova, N. , Senior, A. , Green, T. , Žídek, A. , Bates, R. , Blackwell, S. , Yim, J. , et al. (2022). Protein complex prediction with AlphaFold-Multimer. bioRxiv. · DOI · Paper page
  17. 10.1038/sj.emboj.7600680 · DOI
  18. 10.1128/AEM.01392-16 · DOI
  19. 10.1099/mgen.0.000484 · DOI
  20. 10.1126/science.aar7831 · DOI · Paper page
  21. 10.1111/j.1365-2958.2011.07764.x · DOI
  22. 10.1016/j.mib.2017.10.004 · DOI
  23. 10.1371/journal.ppat.1010744 · DOI
  24. 10.1271/bbb.70.740 · DOI
  25. 10.1038/s41586-022-04546-y · DOI
  26. 10.1016/j.molcel.2019.07.035 · DOI
  27. 10.1126/science.aaz4475 · DOI · Paper page
  28. 10.1126/sciadv.aba2489 · DOI
  29. 10.1038/s41594-020-0457-x · DOI
  30. 10.1107/S2059798319011471 · DOI · Paper page
  31. 10.1016/j.celrep.2020.108344 · DOI
  32. 10.1016/j.molcel.2020.02.003 · DOI
  33. 10.1038/s41592-022-01488-1 · DOI · Paper page
  34. 10.1016/j.celrep.2016.08.026 · DOI
  35. 10.1093/emboj/18.21.6177 · DOI
  36. 10.1093/nar/gkac268 · DOI
  37. 10.1016/j.str.2015.10.004 · DOI
  38. 10.1073/pnas.1414207111 · DOI · Paper page
  39. 10.1111/j.1365-2958.2011.07763.x · DOI
  40. 10.1002/jcc.20084 · DOI
  41. 10.1002/pro.3943 · DOI
  42. 10.1016/j.jsb.2021.107702 · DOI
  43. 10.1038/nmeth.4169 · DOI · Paper page
  44. 10.1016/j.plasmid.2010.12.004 · DOI
  45. 10.1016/j.jsb.2012.09.006 · DOI · Paper page
  46. 10.1016/j.jmb.2016.07.002 · DOI
  47. 10.1016/j.molcel.2014.11.023 · DOI
  48. 10.15252/embj.2021107807 · DOI
  49. 10.3389/fmicb.2020.00761 · DOI
  50. 10.1093/emboj/cdf393 · DOI
  51. 10.1146/annurev-genet-112618-043633 · DOI
  52. 10.1016/j.celrep.2022.110411 · DOI
  53. 10.1093/gbe/evab256 · DOI

Metadata

Authors
Liu, H. W., Roisné-Hamelin, F., Beckert, B., Myasnikov, A., Li, Y., & Gruber, S.
Affiliations
  • University of Lausanne (CH)
  • École Polytechnique Fédérale de Lausanne (CH)
Corresponding author
Gruber, Stephan
ORCID
Venue
Molecular Cell
Publisher
openRxiv
Published
2022-10-05
Volume
82
Issue
24
Pages
4727-4740.e6
ISSN
1097-2765 (ISSN-L)
DOI
10.1101/2022.10.04.510915
OpenAlex
W4311746912
Cited by
53
References
1
Citations by year
2026: 2 · 2025: 19 · 2024: 17 · 2023: 15
FWCI
7.72
Type
journal article
Language
en
Open access
Locations
  • Molecular Cell (publishedVersion)
  • bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by)
  • PubMed (publishedVersion)
  • IRIS (submittedVersion)
  • SERVAL (Université de Lausanne) (submittedVersion)
Funders
H2020 European Research Council (724482)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Bacterial Genetics and Biotechnology
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › DNA Repair Mechanisms
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
Keywords
SMC complex, circular plasmids, DNA cleavage, loop extrusion, DNA topology, selfish DNA, bacterial immunity, cryo-EM structure, MukBEF
MeSH terms
Adenosine Triphosphatases, Chromosomes, Chromosomes, Bacterial, DNA, Plasmids, Cell Cycle Proteins, DNA Cleavage

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