Detection of preQ0 deazaguanine modifications in bacteriophage CAjan DNA using Nanopore sequencing reveals same hypermodification at two distinct DNA motifs

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DOI

  • Witold Kot, University of Copenhagen
  • ,
  • Nikoline S. Olsen
  • ,
  • Tue K. Nielsen, University of Copenhagen
  • ,
  • Geoffrey Hutinet, University of Florida
  • ,
  • Valérie de Crécy-Lagard, University of Florida
  • ,
  • Liang Cui, Singapore-MIT Alliance for Research and Technology
  • ,
  • Peter C. Dedon, Singapore-MIT Alliance for Research and Technology, Massachusetts Institute of Technology
  • ,
  • Alexander B. Carstens, University of Copenhagen
  • ,
  • Sylvain Moineau, Universite Laval
  • ,
  • Manal A. Swairjo, San Diego State University
  • ,
  • Lars H. Hansen, University of Copenhagen

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.

Original languageEnglish
JournalNucleic Acids Research
Volume48
Issue18
Pages (from-to)10383-10396
Number of pages14
ISSN0305-1048
DOIs
Publication statusPublished - Oct 2020

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