Bacterial defense via RES-mediated NAD⁺ depletion is countered by phage phosphatases

Many bacterial defense systems restrict phage infection by breaking down the molecule nicotinamide (Nam) adenine dinucleotide (NAD⁺) into adenosine diphosphate ribose (ADPR) and Nam. To counter NAD⁺ depletion-mediated defense, phages evolved NAD⁺ reconstitution pathway 1 (NARP1), which uses ADPR and Nam to rebuild NAD⁺. Here, we report a bacterial defense system called aRES, involving RES-domain proteins that are triggered by a phage DNA polymerase to degrade NAD⁺ into Nam and ADPR-1″-phosphate (ADPR-1P). This molecule cannot serve as a substrate for NARP1; therefore, NAD⁺ depletion by aRES defends against phages even if they encode NARP1. Some phages evolved an extended NARP1 pathway capable of overcoming aRES defense. In these phages, the NARP1 operon also includes a specialized phosphatase that dephosphorylates ADPR-1P to form ADPR. Our study describes new layers in the NAD⁺-centric arms race between bacteria and phages and highlights the centrality of the NAD⁺ pool in cellular battles between viruses and their hosts.