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Four additional natural 7-deazaguanine derivatives in phages and how to make them
Open accessPreprint — published as 10.1093/nar/gkad657
Abstract
Bacteriophages and bacteria are engaged in a constant arms race, continually evolving new molecular tools to survive one another. To protect their genomic DNA from restriction enzymes, the most common bacterial defence systems, double-stranded DNA phages have evolved complex modifications that affect all four bases. This study focuses on modifications at position 7 of guanines. Eight derivatives of 7-deazaguanines were identified, including four previously unknown ones: 2’-deoxy-7-(methylamino)methyl-7-deazaguanine (mdPreQ 1 ), 2’-deoxy-7-(formylamino)methyl-7-deazaguanine (fdPreQ 1 ), 2’-deoxy-7-deazaguanine (dDG), and 2’-deoxy-7-carboxy-7-deazaguanine (dCDG). These modifications are inserted in DNA by a guanine transglycosylase named DpdA. Three subfamilies of DpdA had been previously characterized: bDpdA, DpdA1, and DpdA2. Two additional subfamilies were identified in this work: DpdA3, which allows for complete replacement of the guanines, and DpdA4, which is specific to archaeal viruses. Transglycosylases have now been identified in all phages and viruses carrying 7-deazaguanine modifications, indicating that the insertion of these modifications is a post-replication event. Three enzymes were predicted to be involved in the biosynthesis of these newly identified DNA modifications: 7-carboxy-7-deazaguanine decarboxylase (DpdL), dPreQ 1 formyltransferase (DpdN), and dPreQ 1 methyltransferase (DpdM), which was experimentally validated and harbors a unique fold not previously observed for nucleic acid methylases.
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Metadata
- Authors
- Cui, L., Balalkundu, S., Liu, C., Ye, H., Hourihan, J., Rausch, A., Hauß, C., Nilsson, E., Hoetzinger, M., Holmfeldt, K., Zhang, W., Martinez-Alvarez, L., Peng, X., Tremblay, D., Moinau, S., Solonenko, N., Sullivan, M. B., Lee, Y.-J., Mulholland, A., Weigele, P., de Crécy-Lagard, V., Dedon, P. C., & Hutinet, G.
- Affiliations
- Nanyang Technological University (SG)
- University of Florida (US)
- Linnaeus University (SE)
- University of Copenhagen (DK)
- Université Laval (CA)
- The Ohio State University (US)
- New England Biolabs (United States) (US)
- Singapore-MIT Alliance for Research and Technology (SG)
- Corresponding author
- Hutinet, Geoffrey
- ORCID
- Venue
- Nucleic Acids Research
- Publisher
- openRxiv
- Published
- 2023-04-16
- Volume
- 51
- Issue
- 17
- Pages
- 9214-9226
- ISSN
- 0305-1048 (ISSN-L)
- PMC
- PMC10516641
- OpenAlex
- W4385775360
- Cited by
- 12
- References
- 1
- Citations by year
- 2026: 3 · 2025: 6 · 2024: 3
- FWCI
- 1.94
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- cc-by-nc
- Locations
- Nucleic Acids Research (publishedVersion, cc-by-nc)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by-nc)
- PubMed (publishedVersion)
- Research at the University of Copenhagen (University of Copenhagen) (publishedVersion, cc-by-nc)
- Diva portal (Dalarna University Library) (submittedVersion, other-oa)
- DR-NTU (Nanyang Technological University) (submittedVersion, cc-by-nc)
- Funders
- Human Frontier Science Program (HFSP-RGP0024/2018)
- National Research Foundation Singapore
- Novo Nordisk Fonden (NNF18OC0031154)
- National Institutes of Health (ES031576)
- National Institute of General Medical Sciences (R01GM070641)
- National Institute of Environmental Health Sciences (R01ES031576)
- Topics
- Life Sciences › Immunology and Microbiology › Virology › Bacteriophages and microbial interactions
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › DNA and Nucleic Acid Chemistry
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Bacterial Genetics and Biotechnology
- Keywords
- 7-deazaguanine, preQ1, restriction-modification systems, archaeal viruses, phage-bacteria arms race
- MeSH terms
- Bacteria, Bacteriophages, DNA, Dopamine, Guanine
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