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Cited by 3Epigenetics and DNA MethylationEnzyme Structure and FunctionBurkholderia infections and melioidosis

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Burkholderia cenocepacia epigenetic regulator M.BceJIV simultaneously engages two DNA recognition sequences for methylation

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Quintana-Feliciano, Richard, Kottur, Jithesh, Ni, Mi, Ghosh, Rikhia, Salas-Estrada, Leslie, Ahlsen, Goran, Rechkoblit, Olga, Shapiro, Lawrence, Filizola, Marta, Fang, Gang, Aggarwal, Aneel K.·2024·Nature Communications
DOI 10.1038/s41467-024-52130-xPMC PMC11380664

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Abstract

Abstract Burkholderia cenocepacia is an opportunistic and infective bacterium containing an orphan DNA methyltransferase (M.BceJIV) with roles in regulating gene expression and motility of the bacterium. M.BceJIV recognizes a GTWWAC motif (where W can be an adenine or a thymine) and methylates the N6 of the adenine at the fifth base position (GTWW A C). Here, we present a high-resolution crystal structure of M.BceJIV/DNA/sinefungin ternary complex and allied biochemical, computational, and thermodynamic analyses. Remarkably, the structure shows not one, but two DNA substrates bound to the M.BceJIV dimer, wherein each monomer contributes to the recognition of two recognition sequences. This unexpected mode of DNA binding and methylation has not been observed previously and sets a new precedent for a DNA methyltransferase. We also show that methylation at two recognition sequences occurs independently, and that GTWW A C motifs are enriched in intergenic regions of a strain of B. cenocepacia’s genome. We further computationally assess the interactions underlying the affinities of different ligands (SAM, SAH, and sinefungin) for M.BceJIV, as a step towards developing selective inhibitors for limiting B. cenocepacia infection.

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Research works printed but not linked: 38

  1. Loutet, S. A. & Valvano, M. A. A decade of Burkholderia cenocepacia virulence determinant research. Infect. Immun. 78, 4088–4100 (2010). · DOI
  2. Roberts, R. J., Vincze, T., Posfai, J. & Macelis, D. REBASE–enzymes and genes for DNA restriction and modification. Nucleic Acids Res. 35, D269–D270 (2007). · DOI
  3. Beaulaurier, J., Schadt, E. E. & Fang, G. Deciphering bacterial epigenomes using modern sequencing technologies. Nat. Rev. Genet. 20, 157–172 (2019). · DOI
  4. Oliveira, P. H. & Fang, G. Conserved DNA methyltransferases: A window into fundamental mechanisms of epigenetic regulation in bacteria. Trends Microbiol. 29, 28–40 (2021). · DOI
  5. Zhou, J., Horton, J. R., Blumenthal, R. M., Zhang, X. & Cheng, X. Clostridioides difficile specific DNA adenine methyltransferase CamA squeezes and flips adenine out of DNA helix. Nat. Commun. 12, 3436 (2021). · DOI
  6. Zhou, J. et al. Repurposing epigenetic inhibitors to target the Clostridioides difficile-specific DNA adenine methyltransferase and sporulation regulator CamA. Epigenetics 17, 1–12 (2021). · DOI
  7. Anton, B. P. & Roberts, R. J. Beyond restriction modification: Epigenomic roles of DNA methylation in prokaryotes. Annu Rev. Microbiol. 75, 129–149 (2021). · DOI
  8. Oliveira, P. H. et al. Epigenomic characterization of Clostridioides difficile finds a conserved DNA methyltransferase that mediates sporulation and pathogenesis. Nat. Microbiol. 5, 166–180 (2020). · DOI
  9. Zhou, J. et al. Systematic design of adenosine analogs as inhibitors of a clostridioides difficile-Specific DNA adenine methyltransferase required for normal sporulation and persistence. J. Med. Chem. 66, 934–950 (2023). · DOI
  10. Vandenbussche, I. et al. DNA Methylation epigenetically regulates gene expression in burkholderia cenocepacia and controls biofilm formation, cell aggregation, and motility. mSphere 5, e00455–20 (2020). · DOI
  11. Malone, T., Blumenthal, R. M. & Cheng, X. Structure-guided analysis reveals nine sequence motifs conserved among DNA amino-methyltransferases, and suggests a catalytic mechanism for these enzymes. J. Mol. Biol. 253, 618–632 (1995). · DOI
  12. Goedecke, K., Pignot, M., Goody, R. S., Scheidig, A. J. & Weinhold, E. Structure of the N6-adenine DNA methyltransferase M.TaqI in complex with DNA and a cofactor analog. Nat. Struct. Biol. 8, 121–125 (2001). · DOI
  13. Halford, S. E. et al. Restriction endonuclease reactions requiring two recognition sites. Biochem. Soc. Trans. 27, 696–699 (1999). · DOI
  14. Vanamee, E. S., Santagata, S. & Aggarwal, A. K. FokI requires two specific DNA sites for cleavage. J. Mol. Biol. 309, 69–78 (2001). · DOI
  15. Vanamee, E. S. et al. A view of consecutive binding events from structures of tetrameric endonuclease SfiI bound to DNA. EMBO J. 24, 4198–4208 (2005). · DOI
  16. Shen, B. W. et al. Coordination of phage genome degradation versus host genome protection by a bifunctional restriction-modification enzyme visualized by CryoEM. Structure 29, 521–530.e525 (2021). · DOI
  17. Morgan, R. D., Dwinell, E. A., Bhatia, T. K., Lang, E. M. & Luyten, Y. A. The MmeI family: type II restriction-modification enzymes that employ single-strand modification for host protection. Nucleic Acids Res. 37, 5208–5221 (2009). · DOI
  18. Scavetta, R. D. et al. Structure of RsrI methyltransferase, a member of the N6-adenine beta class of DNA methyltransferases. Nucleic Acids Res. 28, 3950–3961 (2000). · DOI
  19. Osipiuk, J., Walsh, M. A. & Joachimiak, A. Crystal structure of MboIIA methyltransferase. Nucleic Acids Res. 31, 5440–5448 (2003). · DOI
  20. Horowitz, S. et al. Conservation and functional importance of carbon-oxygen hydrogen bonding in AdoMet-dependent methyltransferases. J. Am. Chem. Soc. 135, 15536–15548 (2013). · DOI
  21. Albanese, K. I. et al. Comparative analysis of sulfonium-pi, ammonium-pi, and sulfur-pi interactions and relevance to SAM-dependent methyltransferases. J. Am. Chem. Soc. 144, 2535–2545 (2022). · DOI
  22. Urig, S. et al. The Escherichia coli dam DNA methyltransferase modifies DNA in a highly processive reaction. J. Mol. Biol. 319, 1085–1096 (2002). · DOI
  23. Woodcock, C. B., Yakubov, A. B. & Reich, N. O. Caulobacter crescentus cell cycle-regulated DNA methyltransferase uses a novel mechanism for substrate recognition. Biochemistry 56, 3913–3922 (2017). · DOI
  24. Horton, J. R. et al. The cell cycle-regulated DNA adenine methyltransferase CcrM opens a bubble at its DNA recognition site. Nat. Commun. 10, 4600 (2019). · DOI
  25. Gupta, Y. K., Chan, S. H., Xu, S. Y. & Aggarwal, A. K. Structural basis of asymmetric DNA methylation and ATP-triggered long-range diffusion by EcoP15I. Nat. Commun. 6, 7363 (2015). · DOI
  26. Ferreira de Freitas, R., Ivanochko, D. & Schapira, M. Methyltransferase inhibitors: Competing with, or exploiting the bound cofactor. Molecules 24, 4492 (2019). · DOI
  27. Kaniskan, H, U., Martini, M. L. & Jin, J. Inhibitors of protein methyltransferases and demethylases. Chem. Rev. 118, 989–1068 (2018). · DOI
  28. Nencka, R. et al. Coronaviral RNA-methyltransferases: function, structure and inhibition. Nucleic Acids Res. 50, 635–650 (2022). · DOI
  29. Kottur, J. et al. Structures of SARS-CoV-2 N7-methyltransferase with DOT1L and PRMT7 inhibitors provide a platform for new antivirals. PLoS Pathog. 19, e1011546 (2023). · DOI
  30. Emsley, P. & Cowtan, K. Coot: model-building tools for molecular graphics. Acta Crystallogr. D Biol. Crystallogr. 60, 2126–2132 (2004). · DOI · Paper page
  31. Adams, P. D. et al. PHENIX: a comprehensive Python-based system for macromolecular structure solution. Acta Crystallogr. D Biol. Crystallogr. 66, 213–221 (2010). · DOI · Paper page
  32. Moriarty, N. W., Grosse-Kunstleve, R. W. & Adams, P. D. Electronic ligand builder and optimization workbench (eLBOW): a tool for ligand coordinate and restraint generation. Acta Crystallogr. D Biol. Crystallogr. 65, 1074–1080 (2009). · DOI
  33. Shen, W., Le, S., Li, Y. & Hu, F. SeqKit: A cross-platform and ultrafast toolkit for FASTA/Q file manipulation. PLoS ONE 11, e0163962 (2016). · DOI · Paper page
  34. Berendsen, H. J. C., Vanderspoel, D. & Vandrunen, R. Gromacs - a Message-Passing Parallel Molecular-Dynamics Implementation. Comput. Phys. Commun. 91, 43–56 (1995). · DOI
  35. Jo, S., Kim, T., Iyer, V. G. & Im, W. CHARMM-GUI: a web-based graphical user interface for CHARMM. J. Comput. Chem. 29, 1859–1865 (2008). · DOI · Paper page
  36. Huang, J. et al. CHARMM36m: an improved force field for folded and intrinsically disordered proteins. Nat. Methods 14, 71–73 (2017). · DOI
  37. Vanommeslaeghe, K. et al. CHARMM general force field: A force field for drug-like molecules compatible with the CHARMM all-atom additive biological force fields. J. Comput. Chem. 31, 671–690 (2010). · DOI
  38. Hsiao, K., Zegzouti, H. & Goueli, S. A. Methyltransferase-Glo: a universal, bioluminescent and homogenous assay for monitoring all classes of methyltransferases. Epigenomics 8, 321–339 (2016). · DOI

Metadata

Authors
Quintana-Feliciano, R., Kottur, J., Ni, M., Ghosh, R., Salas-Estrada, L., Ahlsen, G., Rechkoblit, O., Shapiro, L., Filizola, M., Fang, G., & Aggarwal, A. K.
Affiliations
  • Icahn School of Medicine at Mount Sinai (US)
  • Columbia University (US)
Corresponding author
  • Kottur, Jithesh
  • Aggarwal, Aneel K.
ORCID
Venue
Nature Communications
Publisher
Springer Science and Business Media LLC
Published
2024-09-07
Volume
15
Issue
1
Pages
7839-7839
ISSN
2041-1723 (ISSN-L)
DOI
10.1038/s41467-024-52130-x
PMC
PMC11380664
OpenAlex
W4402329621
Cited by
3
References
1
Citations by year
2026: 1 · 2025: 2
FWCI
0.41
Type
journal article
Language
en
Open access
Licence
Locations
  • Nature Communications (publishedVersion, cc-by-nc-nd)
  • bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by-nc)
  • PubMed Central (publishedVersion, cc-by-nc-nd)
  • PubMed (publishedVersion)
  • PubMed Central (submittedVersion, cc-by-nc)
  • RePEc: Research Papers in Economics (submittedVersion)
  • DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion)
Funders
U.S. Department of Health & Human Services | National Institutes of Health (R35-GM131780, R35GM13965)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Epigenetics and DNA Methylation
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Structural Biology › Enzyme Structure and Function
  • Health Sciences › Medicine › Epidemiology › Burkholderia infections and melioidosis
Keywords
Burkholderia cenocepacia, DNA methyltransferases, epigenetic regulation, DNA methylation, DNA recognition sequence, ternary complex crystal structure, sinefungin, intergenic regions, gene expression regulation, bacterial motility, inhibitor development

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