Analysis of Phycodnaviridae Tetrapyrrole Enzymes: Subcellular Localization and Functional Divergence from Host Homologs

Abstract

Rationale Recent viral metagenomic studies have revealed a broad repertoire of enzyme encoding genes in Phycodnaviridae, whose contributions to viral replication and host infection remain poorly understood. These genes may expand the metabolic repertoire of viruses during infection of green algal hosts. Because neither the roles of these proteins during infection nor their subcellular localization have been experimentally characterized, comparative sequence, structural, and biochemical analyses done in silico can generate testable hypotheses on structure, function and localization. Methods In a recent viral metagenomic dataset, we identified viral homologues of two eukaryotic enzymes involved in bilin biosynthesis: heme oxygenase-1 (vHMOX1) and Phycocyanobilin:Ferredoxin oxidoreductase (vPcyA). Viral and algal homologues were compared through sequence analyses and AlphaFold3 structural predictions. Predicted biochemical properties were analyzed for their compatibility with subcellular compartments. Active site architecture and putative substrate binding were compared between viral and algal proteins using homologous structures deposited in the Protein Data Bank (PDB). Results Viral HMOX1 and PcyA sequences are truncated compared to algal homologues, lacking the N-terminal extension associated with chloroplastic targeting. However biochemical properties, including isoelectric point and surface charge distribution, are compatible with localization in chloroplast. Structural comparisons reveal modifications in the viral HMOX1 active sites, including altered substrate binding and substitutions of key residues, likely indicating modified heme-binding properties. In addition to these modifications, chloroplastic ferredoxin interaction predictions show compatibility for use of this electron donor. In contrast, vPcyA models show no significant differences with their algal counterparts. Conclusions Predicted active site remodeling in vHMOX1 suggests that these viral homologues may have evolved distinct heme-binding properties. Unlike vPcyA, vHMOX1 homologs appear to have diverged more substantially from their algal counterparts, potentially reflecting functional specialization in the viral infection context.