Convergent Cysteine Enrichment in Diverse Gut Phage Capsids Suggests Gut-Associated Structural Adaptation

Abstract

BackgroundThe gut environment is hostile to life, yet the human virome, dominated by bacteriophages, persists. Adaptations to the major capsid protein (MCP) may explain this. Phage MCPs conserve the HK97 fold, ideal for detecting convergent features across phage populations. Prior capsid stability research focused on individual phages, limiting broader pattern identification. MethodsMCPs from the Gut Phage Database (GPD) (n=8,478) and INPHARED (n=4,905) were predicted using ProtPhage + Phold and clustered using MMseqs2 (GPD=902 vs INPHARED=606). Structural predictions, conservation analysis, and capsomere modeling were used to characterize cysteine environments. ResultsBioinformatics analysis identified cysteine enrichment in GPD MCPs. Phylogenetic mapping was consistent with convergent evolution of high-cysteine MCPs. Over 50% of cysteines were [≥]90% conserved within and between clusters. Simulated capsomeres showed 83% of cysteines are buried (RSA <10%). ConclusionsThese findings suggest gut phages may have convergently evolved cysteine-based capsid stabilization, with implications for engineering therapeutic phages.