Researchers Use Artificial Intelligence to Identify New Viral Families That Silence Bacterial Immune Communication

Weizmann Institute researchers use AI to find "sponge" proteins in phages that silence bacterial immune systems by trapping communication molecules.

By: AXL Media

Published: May 1, 2026, 6:47 AM EDT

Source: Information for this report was sourced from EurekAlert!

Weaponizing Viral Dark Matter Against Bacterial Defenses

The genomes of phages, viruses that infect bacteria, are largely comprised of genes with unknown functions often referred to as dark matter. Recent research has revealed that some of these genes encode specialized proteins known as sponges, which possess deep, porous pockets designed to trap communication molecules. These molecules serve as the primary alarm system for bacterial immunity. By absorbing these signals, the phage effectively silences the host's defenses, allowing the virus to take control of the bacterium and replicate without interference.

Structural Patterns and the Role of Artificial Intelligence

Detecting sponge proteins has historically been difficult because their genetic sequences vary significantly. However, a team led by Professor Rotem Sorek noticed a recurring architectural pattern: the proteins are small, composed of identical subunits, and feature positively charged pockets. These pockets are electrostatically attracted to the negatively charged immune alarm molecules. Using Google’s AlphaFold AI, the researchers scanned a database of 32 million phage protein genes to identify structures matching this specific physical profile, moving beyond traditional sequence based searching.

Discovery of the Lockin and Sequestin Protein Families

The AI driven scan identified over 120 candidate proteins, leading to the discovery of a new family named Lockin. Structural analysis confirmed that Lockin proteins consist of six identical subunits arranged in a circular, petal like formation that captures immune molecules. In addition to AI methods, the researchers utilized genomic observations to identify another family called Sequestin. This discovery was made by noticing that genes for sponge proteins often appear fused together in the phage genome, proving that human scientific observation remains a vital complement to computational tools.