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How cyanophage S-2L rejects adenine and incorporates 2-aminoadenine to saturate hydrogen bonding in its DNA

Author

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  • Dariusz Czernecki

    (Unit of Structural Dynamics of Biological Macromolecules, CNRS UMR 3528, 25-28 rue du Docteur Roux, Institut Pasteur
    Sorbonne Université, Collège Doctoral, ED 515)

  • Pierre Legrand

    (Unit of Structural Dynamics of Biological Macromolecules, CNRS UMR 3528, 25-28 rue du Docteur Roux, Institut Pasteur
    Synchrotron SOLEIL, L’Orme des Merisiers)

  • Mustafa Tekpinar

    (Unit of Structural Dynamics of Biological Macromolecules, CNRS UMR 3528, 25-28 rue du Docteur Roux, Institut Pasteur)

  • Sandrine Rosario

    (Unit of Structural Dynamics of Biological Macromolecules, CNRS UMR 3528, 25-28 rue du Docteur Roux, Institut Pasteur)

  • Pierre-Alexandre Kaminski

    (Unit of Biology of Pathogenic Gram-Positive Bacteria, 25-28 rue du Docteur Roux, Institut Pasteur)

  • Marc Delarue

    (Unit of Structural Dynamics of Biological Macromolecules, CNRS UMR 3528, 25-28 rue du Docteur Roux, Institut Pasteur)

Abstract

Bacteriophages have long been known to use modified bases in their DNA to prevent cleavage by the host’s restriction endonucleases. Among them, cyanophage S-2L is unique because its genome has all its adenines (A) systematically replaced by 2-aminoadenines (Z). Here, we identify a member of the PrimPol family as the sole possible polymerase of S-2L and we find it can incorporate both A and Z in front of a T. Its crystal structure at 1.5 Å resolution confirms that there is no structural element in the active site that could lead to the rejection of A in front of T. To resolve this contradiction, we show that a nearby gene is a triphosphohydolase specific of dATP (DatZ), that leaves intact all other dNTPs, including dZTP. This explains the absence of A in S-2L genome. Crystal structures of DatZ with various ligands, including one at sub-angstrom resolution, allow to describe its mechanism as a typical two-metal-ion mechanism and to set the stage for its engineering.

Suggested Citation

  • Dariusz Czernecki & Pierre Legrand & Mustafa Tekpinar & Sandrine Rosario & Pierre-Alexandre Kaminski & Marc Delarue, 2021. "How cyanophage S-2L rejects adenine and incorporates 2-aminoadenine to saturate hydrogen bonding in its DNA," Nature Communications, Nature, vol. 12(1), pages 1-11, December.
    • Handle: RePEc:nat:natcom:v:12:y:2021:i:1:d:10.1038_s41467-021-22626-x
    DOI: 10.1038/s41467-021-22626-x
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