Detection of preQ0 deazaguanine modifications in bacteriophage CAjan DNA using Nanopore sequencing reveals same hypermodification at two distinct DNA motifs.
Bacteriophages
/ drug effects
Base Sequence
/ drug effects
CRISPR-Cas Systems
/ genetics
DNA
/ drug effects
DNA Restriction-Modification Enzymes
/ drug effects
Escherichia coli
/ virology
Gene Editing
Guanine
/ analogs & derivatives
Humans
Nanopore Sequencing
Nucleotide Motifs
/ drug effects
Pyrimidinones
/ pharmacology
Pyrroles
/ pharmacology
Siphoviridae
/ genetics
Journal
Nucleic acids research
ISSN: 1362-4962
Titre abrégé: Nucleic Acids Res
Pays: England
ID NLM: 0411011
Informations de publication
Date de publication:
09 10 2020
09 10 2020
Historique:
accepted:
26
08
2020
revised:
19
08
2020
received:
18
03
2020
pubmed:
18
9
2020
medline:
5
11
2020
entrez:
17
9
2020
Statut:
ppublish
Résumé
In the constant evolutionary battle against mobile genetic elements (MGEs), bacteria have developed several defense mechanisms, some of which target the incoming, foreign nucleic acids e.g. restriction-modification (R-M) or CRISPR-Cas systems. Some of these MGEs, including bacteriophages, have in turn evolved different strategies to evade these hurdles. It was recently shown that the siphophage CAjan and 180 other viruses use 7-deazaguanine modifications in their DNA to evade bacterial R-M systems. Among others, phage CAjan genome contains a gene coding for a DNA-modifying homolog of a tRNA-deazapurine modification enzyme, together with four 7-cyano-7-deazaguanine synthesis genes. Using the CRISPR-Cas9 genome editing tool combined with the Nanopore Sequencing (ONT) we showed that the 7-deazaguanine modification in the CAjan genome is dependent on phage-encoded genes. The modification is also site-specific and is found mainly in two separate DNA sequence contexts: GA and GGC. Homology modeling of the modifying enzyme DpdA provides insight into its probable DNA binding surface and general mode of DNA recognition.
Identifiants
pubmed: 32941607
pii: 5907968
doi: 10.1093/nar/gkaa735
pmc: PMC7544227
doi:
Substances chimiques
7-(aminomethyl)-7-deazaguanine
0
DNA Restriction-Modification Enzymes
0
Pyrimidinones
0
Pyrroles
0
Guanine
5Z93L87A1R
DNA
9007-49-2
7-deazaguanine
GPL8T5ZO3M
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
10383-10396Subventions
Organisme : NIGMS NIH HHS
ID : R01 GM110588
Pays : United States
Informations de copyright
© The Author(s) 2020. Published by Oxford University Press on behalf of Nucleic Acids Research.
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