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

Dariusz Czernecki, Pierre Legrand, Mustafa Tekpinar, Sandrine Rosario, Pierre-Alexandre Kaminski and Marc Delarue ()
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Dariusz Czernecki: Unit of Structural Dynamics of Biological Macromolecules, CNRS UMR 3528, 25-28 rue du Docteur Roux, Institut Pasteur
Pierre Legrand: Unit of Structural Dynamics of Biological Macromolecules, CNRS UMR 3528, 25-28 rue du Docteur Roux, Institut Pasteur
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

Nature Communications, 2021, vol. 12, issue 1, 1-11

Abstract: 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.

Date: 2021
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DOI: 10.1038/s41467-021-22626-x

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