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

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 angstrom 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. The cyanophage S-2L incorporates 2-aminoadenine (Z) instead of adenine (A) in its genome. Here, the authors provide an explanation for the absence of A in S-2L genome by identifying and characterising functionally and structurally both the HD phosphohydrolase (datZ) that specifically cleaves dATP, and the sole DNA primase-polymerase of S-2L, nonspecific of dATP or dZTP.

Automated summary

The cyanophage S-2L incorporates 2-aminoadenine (Z) instead of adenine (A) in its genome. The study provides an explanation for the absence of A in S-2L genome by identifying and characterising functionally and structurally both the HD phosphohydrolase (datZ) that specifically cleaves dATP, and the sole DNA primase-polymerase of S-2L, nonspecific of dATP or dZTP.