Nucleotide Sponges and Evasion of Antiviral Immunity

Abstract

The ability of a cell to sense and eliminate viral infection is an essential process conserved across domains of life. Nucleotide-based signaling is a central mechanism of antiviral immunity and, surprisingly, core components of animal immunity, including the cGAS-STING pathway, evolved billions of years ago in bacteria as systems that restrict phage infection. Recently, studies have shown that phages can antagonize host signaling by encoding specialized binding proteins called “sponges” that tightly sequester nucleotide-based immune signals, thus preventing them from activating downstream effectors and inhibiting antiviral immunity. To expand our understanding of sponge protein biology, we developed complementary biochemical, structural, and computational approaches to discover new families of sponge proteins. Through biochemical screening, we discover Acb4 as the founding member of a widespread family of over 1,300 sponges, allowing us to define key molecular principles that govern sponge ligand specificity and signal discrimination. Leveraging unifying biophysical principles and structural features that are conserved across sponge families, we then applied structure-guided prediction to systematically identify additional immune evasion proteins directly from ~32 million phage proteome sequences. We further demonstrate that sponge proteins exhibit remarkable functional diversity as a result of their phylogenetic divergence, enabling robust targeting of diverse nucleotide signals across multiple anti-phage defense systems. Finally, we harness this functional diversity and use sponges as molecular probes for immune signal discovery, leading to the identification of Histidine-ADPR as the first instance of an immune signal comprised of both amino acid and nucleotide subunits. Together, our findings establish phage-encoded sponge proteins as a remarkably rich class of immune evasion proteins and highlight their potential as an untapped reservoir for discovering new immune signals across the tree of life.