Phages reconstitute NAD⁺to counter bacterial immunity

Abstract

Bacteria defend against phage infection via a variety of antiphage defense systems. Many defense systems were recently shown to deplete cellular nicotinamide adenine dinucleotide (NAD+) in response to infection, by breaking NAD+to ADP-ribose (ADPR) and nicotinamide. It was demonstrated that NAD+depletion during infection deprives the phage from this essential molecule and impedes phage replication. Here we show that a substantial fraction of phages possess enzymatic pathways allowing reconstitution of NAD+from its degradation products in infected cells. We describe NAD+reconstitution pathway 1 (NARP1), a two-step pathway in which one enzyme phosphorylates ADPR to generate ADPR-pyrophosphate (ADPR-PP), and the second enzyme conjugates ADPR-PP and nicotinamide to generate NAD+. Phages encoding the NARP1 pathway can overcome a diverse set of defense systems, including Thoeris, DSR1, DSR2, SIR2-HerA, and SEFIR, all of which deplete NAD+as part of their defensive mechanism. Phylogenetic analyses show that NARP1 is primarily encoded on phage genomes, suggesting a phage-specific function in countering bacterial defenses. A second pathway, NARP2, allows phages to overcome bacterial defenses by building NAD+via metabolites different than ADPR-PP. Our findings report a unique immune evasion strategy where viruses rebuild molecules depleted by defense systems, thus overcoming host immunity.

AVibrio choleraeAnti-Phage System Depletes Nicotinamide Adenine Dinucleotide to Restrict Virulent Bacteriophages

“…Based on homology, we initially assumed NrsA was a phosphoribosyl pyrophosphate synthetase, converting ribose 5-phosphate to phosphoribosyl pyrophosphate, and NrsB, a nicotinate phosphoribosyl transferase that adds nicotinic acid to phosphoribosyl pyrophosphate to generate nicotinic acid mononucleotide (34). However, during the preparation of this manuscript, a biochemical characterization of proteins highly homologous to NrsAB was deposited in bioRxiv (35). The authors reported that homologs of In summary, we establish that the classical biotype V. cholerae encodes two phage defensive systems, Gabija and Nezha, absent from El Tor biotype strains.…”