Phylogenetic support of pebS as a phage-exclusive auxiliary metabolic gene

Marine picocyanobacteria, including the genera Prochlorococcus and Synechococcus, are major contributors to oceanic photosynthesis and global primary production. Their populations are influenced by T4-like cyanophages, which frequently encode auxiliary metabolic genes (AMGs) capable of altering host metabolism during infection. One such AMG, pebS, encodes a ferredoxin-dependent bilin reductase (FDBR) phycoerythrobilin (PEB) synthase, which converts biliverdin IXα to PEB. In contrast, cyanobacteria perform a two-step reaction using the FDBR enzymes PebA (15,16-dihydrobiliverdin: ferredoxin oxidoreductase) and PebB (PEB:ferredoxin oxidoreductase), whereas pebS has not been reported in cyanobacterial genomes. Here, we re-evaluated whether pebS is truly restricted to cyanophages by searching the Ocean Gene Atlas (OGA) and all available cyanobacterial genomes at National Center for Biotechnology Information (NCBI) using a cyanophage-derived PebS sequence as query. Using protein phylogenies, we found that most search hits group with PebA or PebB, while few sequences from cyanobacterial genome assemblies were confirmed to belong to PebS based on phylogenetic placement. However, genomic context analysis of these pebS sequences revealed their phage origin, consistent with cyanophage infection at the time of sampling. In conclusion, our results support that pebS is absent in cyanobacterial genomes, raising questions about the evolutionary and biochemical causes for the two-step reduction of biliverdin IXα to PEB in these organisms.