Large-genome phages encode diverse proteins associated with host cell envelope functions

Abstract

Huge phages (or jumbo phages, >200 kilobases) encode extensive protein repertoires, yet their functional diversity and potential roles in host physiology remain poorly understood. Using protein structure-based analyses of dominant protein families across 7,187 non-redundant genomes of huge phages, we uncovered pronounced phylogenetic and habitat-associated diversification. Notably, we identified diverse proteins associated with bacterial cell envelope functions, particularly in human gut-associated huge phages. These included previously unreported phage-encoded sortase B, whose putative substrates contain signal peptides and cell-wall sorting signals, suggesting a potential route for displaying phage proteins on bacterial surfaces. Phage-encoded phage shock protein A (PspA) was distributed across diverse lineages and frequently neighbored genes associated with membrane organization and transport, implicating potential roles in membrane physiology. We also identified 1,603 {beta}-barrel outer membrane proteins (OMPs) across 1,303 huge phages from diverse ecosystems. These OMPs exhibited structural diversity and associations with predicted host taxonomy, habitat, and neighboring envelope-related genes. Metatranscriptomic analysis supported expression of representative phage-encoded PspA and OMP genes in natural communities including the human gut. Together, these findings reveal bacterial cell envelope processes as a previously underappreciated potential interface for huge phage-host interactions.