Bioinformatics and comparative genomics unveil an evolutionary conserved phage NAD metabolism

Bacteriophages, in addition to genes essential for their own propagation, can harbor a second class of genes which are not directly implicated in the viral infection and replication. Although there is a general consensus that these genes confer selective advantage to viruses, there is a paucity of information on their possible function. Thus, more evidence is needed to support this paradigm. Enormous advances have been made in phage genomics in the last few years, offering novel opportunities to tackle this problem with bioinformatics approaches. Using comparative genome analysis performed on nearly two thousand complete phage genomes currently available, we identified a group of nearly fifty phages encoding their own biosynthesis pathways to the essential NAD cofactor from the vitamin precursors nicotinamide (Nm) and nicotinamide riboside (NmR). This viral NAD synthesis is distinct from the bacterial host NAD biosynthesis which is supported by a different set of genes. A comprehensive genomic reconstruction of phage-encoded NAD metabolism, which included NAD-consuming activities, identified three distinct metabolic variants capable of i) synthesizing and consuming NAD, ii) consuming NAD, or iii) synthesizing nicotinamide mononucleotide, a rare NAD metabolic intermediate in bacteria. We propose that these variants reflect different strategies contributing to subvert the machinery of the host cell. Finally, a phylogenetic analysis of the phage NAD biosynthetic shunt revealed a complex evolutionary scenario dominated by cross-kingdom gene transfer events. Notably, these phages assembled their own NAD pathway by acquiring and possibly modifying functionally related genes from host cells, but also contributed to spread these functional roles across a diverse group of bacteria. This case may be a relevant, and yet undisclosed example of how viruses contributed to fine-tune metabolic processes in the early evolutionary history of life.