Structural characterization of a soil viral auxiliary metabolic gene product - a functional chitosanase

Metagenomics is revealing auxiliary metabolic genes (AMGs) in soil viral genomes. Here, authors solve the crystal structure for a soil viral AMG product, free and ligand bound, and show the protein can decompose chitin, a common carbon polymer. Metagenomics is unearthing the previously hidden world of soil viruses. Many soil viral sequences in metagenomes contain putative auxiliary metabolic genes (AMGs) that are not associated with viral replication. Here, we establish that AMGs on soil viruses actually produce functional, active proteins. We focus on AMGs that potentially encode chitosanase enzymes that metabolize chitin - a common carbon polymer. We express and functionally screen several chitosanase genes identified from environmental metagenomes. One expressed protein showing endo-chitosanase activity (V-Csn) is crystalized and structurally characterized at ultra-high resolution, thus representing the structure of a soil viral AMG product. This structure provides details about the active site, and together with structure models determined using AlphaFold, facilitates understanding of substrate specificity and enzyme mechanism. Our findings support the hypothesis that soil viruses contribute auxiliary functions to their hosts.

Automated summary

Metagenomics has revealed the presence of auxiliary metabolic genes (AMGs) in soil viral genomes, and this study provides evidence that these AMGs actually produce functional proteins that can metabolize chitin. The crystal structure of a soil viral AMG product, which exhibits chitosanase activity, has been determined, providing insights into substrate specificity and enzyme mechanism. These findings support the idea that soil viruses contribute auxiliary functions to their hosts.