Evolutionary and Comparative Genome Analysis of Phage NAD Metabolic Genes

Bacteriophages typically carry an essential core of genes that enables their infection and replication. In addition to this “core” genome, they may carry auxiliary metabolic genes (AMG) which presumably provide a selective benefit to the phages’ biology, ultimately affecting their evolutionary success. The actual roles of these accessory phage genes, which are mostly acquired from host genomes, are not always well understood. A thorough comparative genomic analysis of completely sequenced viral genomes revealed that a statistically significant subset of T4‐like phages carry two genes, i.e. nadV and nadM that implement a two‐step synthesis of nicotinamide adenine dinucleotide (NAD) from Vitamin B 3 . NAD is an essential coenzyme that plays important roles in metabolic reactions and cell regulation in all organisms. Interestingly, the genomic reconstruction of NAD metabolic subsystem of the corresponding bacterial hosts highlighted that the infected bacteria use alternative routes, i.e., a different set of genes, for synthesizing NAD. This evidence suggests that NadV‐NadM metabolic shunt has been retained by phages in order to provide some sort of fitness to their biology. What could it be? This enhanced NAD synthesis in phage‐infected cells could be rationalized by the occurrence of phage‐encoded NAD‐consuming activities, such as those catalyzed by RNA polymerase‐ADP‐ribosyltransferase (gene alt ), NAD‐dependent DNA ligases (gene ligA ), and NAD‐dependent deacetylase (gene cobB ) which often co‐occurr with nadM and nadV in T4‐like phage genomes. Sequence analysis and construction of 3D models of viral NadM and NadV indicated that all the key residues responsible for their enzymatic activities are present, and are properly oriented in the active sites. To conclude, we performed a phylogenetic study on the NadM and NadV family of enzymes from Bacteria, Archaea, Viruses, including the eukaryotic counterparts. The results offer a complex evolutionary scenario whereby some bacteriophages acquired the genetic capability to synthesize NAD, and also played a role in the spread of these functional roles across different organisms through horizontal gene transfer events.