Structural signatures of salinity adaptation in Microviricetes capsids

Phages, like their bacterial hosts, have evolved to proliferate across the full range of environments on Earth, but the specific amino acid residues that underlie their environmental adaptations remain elusive. Here, we developed a computational framework that uses structure-based multiple sequence alignments, a random forest classifier, and a phylogeny-aware regression model to find amino acid residues linked to specific environments. Applying this framework to public metagenomic data, we analyzed 1,110 Microviricetes major capsid proteins (MCPs) from the lake and ocean biomes, and found that ocean virus capsids were highly enriched in negatively charged residues on internal and external surfaces. This adaptation likely helps maintain solubility at high salt concentrations and stabilizes ssDNA-capsid interactions by sequestering positively charged ions inside the capsid. At intersubunit interfaces, ocean capsids showed enrichment of cation-π and π-π interactions, which are more resistant to solvation than salt bridges and hydrogen bonds. Amino acid residues in lake capsids were more often substituted by biochemically dissimilar amino acids in ocean capsids than the reverse. Together, these results show that microvirus capsids adapt to high-salt environments through changes in surface charge and substitutions affecting intersubunit interactions. Further, we describe a general approach for studying the adaptation and stability of any protein family under complementary environmental or phenotypic conditions.