Four additional natural 7-deazaguanine derivatives in phages and how to make them.

Bacteria / genetics Bacteriophages / genetics DNA / genetics Guanine / analogs & derivatives

Journal

Nucleic acids research
ISSN: 1362-4962
Titre abrégé: Nucleic Acids Res
Pays: England
ID NLM: 0411011

Informations de publication

Date de publication:
22 09 2023
Historique:
accepted: 06 08 2023
revised: 20 07 2023
received: 14 04 2023
medline: 25 9 2023
pubmed: 13 8 2023
entrez: 12 8 2023
Statut: ppublish

Résumé

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 (mdPreQ1), 2'-deoxy-7-(formylamino)methyl-7-deazaguanine (fdPreQ1), 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), dPreQ1 formyltransferase (DpdN) and dPreQ1 methyltransferase (DpdM), which was experimentally validated and harbors a unique fold not previously observed for nucleic acid methylases.

Identifiants

DOI: 10.1093/nar/gkad657 PMID: 37572349 PMC: PMC10516641
pubmed: 37572349
pii: 7241753
doi: 10.1093/nar/gkad657
pmc: PMC10516641
doi:

Substances chimiques

7-deazaguanine GPL8T5ZO3M
DNA 9007-49-2
Guanine 5Z93L87A1R
N,N-di-n-propyldopamine 66185-61-3

Types de publication

Journal Article Research Support, N.I.H., Extramural Research Support, Non-U.S. Gov't

Langues

eng

Sous-ensembles de citation

IM

Pagination

9214-9226

Subventions

Organisme : NIEHS NIH HHS
ID : R01 ES031576
Pays : United States
Organisme : NIH HHS
ID : GM70641
Pays : United States

Commentaires et corrections

Type : ErratumIn

Informations de copyright

© The Author(s) 2023. Published by Oxford University Press on behalf of Nucleic Acids Research.

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Auteurs

Liang Cui (L)

Singapore-MIT Alliance for Research and Technology, Antimicrobial Resistance Interdisciplinary Research Group, Campus for Research Excellence and Technological Enterprise, Singapore 138602, Singapore.

Seetharamsing Balamkundu (S)

Singapore-MIT Alliance for Research and Technology, Antimicrobial Resistance Interdisciplinary Research Group, Campus for Research Excellence and Technological Enterprise, Singapore 138602, Singapore.
School of Biological Sciences, Nanyang Technological University, Singapore.

Chuan-Fa Liu (CF)

School of Biological Sciences, Nanyang Technological University, Singapore.

Hong Ye (H)

School of Biological Sciences, Nanyang Technological University, Singapore.

Jacob Hourihan (J)

Department of Microbiology and Cell Science, University of Florida, Gainesville, FL 32611, USA.

Astrid Rausch (A)

Department of Microbiology and Cell Science, University of Florida, Gainesville, FL 32611, USA.

Christopher Hauß (C)

Department of Microbiology and Cell Science, University of Florida, Gainesville, FL 32611, USA.

Emelie Nilsson (E)

Centre for Ecology and Evolution in Microbial Model Systems (EEMiS), Linnaeus University, 391 82 Kalmar, Sweden.

Matthias Hoetzinger (M)

Centre for Ecology and Evolution in Microbial Model Systems (EEMiS), Linnaeus University, 391 82 Kalmar, Sweden.

Karin Holmfeldt (K)

Centre for Ecology and Evolution in Microbial Model Systems (EEMiS), Linnaeus University, 391 82 Kalmar, Sweden.

Weijia Zhang (W)

Department of Biology, University of Copenhagen, Copenhagen N, Denmark.

Laura Martinez-Alvarez (L)

Department of Biology, University of Copenhagen, Copenhagen N, Denmark.
ORCID: 0000-0001-8404-3478

Xu Peng (X)

Department of Biology, University of Copenhagen, Copenhagen N, Denmark.
ORCID: 0000-0003-3926-7514

Denise Tremblay (D)

Département de biochimie, de microbiologie et de bio-informatique, Faculté des sciences et de génie, Université Laval, Québec City, Québec, Canada.
Groupe de recherche en écologie buccale, Faculté de médecine dentaire, Université Laval, Québec City, Québec, Canada.
Félix d'Hérelle Reference Center for Bacterial Viruses, Université Laval, Québec City, Québec, Canada.

Sylvain Moinau (S)

Département de biochimie, de microbiologie et de bio-informatique, Faculté des sciences et de génie, Université Laval, Québec City, Québec, Canada.
Groupe de recherche en écologie buccale, Faculté de médecine dentaire, Université Laval, Québec City, Québec, Canada.
Félix d'Hérelle Reference Center for Bacterial Viruses, Université Laval, Québec City, Québec, Canada.
ORCID: 0000-0002-2832-5101

Natalie Solonenko (N)

Department of Microbiology, Ohio State University, Columbus, OH, USA.

Matthew B Sullivan (MB)

Department of Microbiology, Ohio State University, Columbus, OH, USA.
Department of Civil, Environmental, and Geodetic Engineering, and Center of Microbiome Science, Ohio State University, Columbus, OH, USA.

Yan-Jiun Lee (YJ)

Research Department, New England Biolabs, Ipswich, MA 01938, USA.

Andrew Mulholland (A)

Research Department, New England Biolabs, Ipswich, MA 01938, USA.

Peter R Weigele (PR)

Research Department, New England Biolabs, Ipswich, MA 01938, USA.
ORCID: 0000-0003-3696-4541

Valérie de Crécy-Lagard (V)

Department of Microbiology and Cell Science, University of Florida, Gainesville, FL 32611, USA.
University of Florida, Genetics Institute, Gainesville, FL 32610, USA.
ORCID: 0000-0002-9955-3785

Peter C Dedon (PC)

Singapore-MIT Alliance for Research and Technology, Antimicrobial Resistance Interdisciplinary Research Group, Campus for Research Excellence and Technological Enterprise, Singapore 138602, Singapore.
Department of Biological Engineering and Center for Environmental Health Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.

Geoffrey Hutinet (G)

Department of Microbiology and Cell Science, University of Florida, Gainesville, FL 32611, USA.
ORCID: 0000-0002-1269-6127

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Classifications MeSH

questionsmedicales.fr › Bactéries › Four additional natural 7-deazaguanine...
questionsmedicales.fr › Virus › Bactériophages › Four additional natural 7-deazaguanine...
questionsmedicales.fr › Acides nucléiques, nucléotides et nucléosides › Acides nucléiques › ADN › Four additional natural 7-deazaguanine...
questionsmedicales.fr › Composés hétérocycliques › Composés hétérocycliques à cycles fusionnés › Composés hétérobicycliques › Purines › Purinones › Hypoxanthines › Guanine › Four additional natural 7-deazaguanine...