Functional convergence in Z-containing DNA biosynthesis highlighted by the characterization of nucleotide metabolism enzymes in bacteriophages

Certain DNA bacteriophages exhibit a complete substitution of their genomic adenine (A) by 2-aminoadenine (Z), forming three hydrogen bonds with thymine. dZTP biosynthesis is performed by a phage-encoded 2-amino adenylosuccinate synthetase (PurZ) whereas a Z-specific DNA polymerase I (DpoZ) has been shown to incorporate the dZTP. Our investigations into the nucleotide metabolism of Z-bacteriophages, integrating modeling, biochemical, and phylogenetic approaches, reveal novel enzymatic activities. We characterized two distinct enzymes that both hydrolyze dATP and dGTP, and a DmtZ enzyme with dual activity. DmtZ acts as a dAMP-specific hydrolase, converting dAMP to adenine, and uniquely transfers deoxyribose 5-phosphate from dAMP to the Z base to produce dZMP, which is subsequently converted to dZTP. This dual functionality marks DmtZ as the first enzyme in the nucleoside deoxyribosyltransferase (NDT) family with such a mechanism and uncovers a novel biosynthetic route for dZTP. Phylogenetic analyses indicate multiple independent acquisitions of enzymes involved in nucleotide metabolism, occurring after PurZ acquisition, yet converging on equivalent metabolic functions. Deciphering these propagation mechanisms in DNA-modified bacteriophages illuminates functional diversity in viral metabolism and a striking example of functional convergence.