Kingdom-wide Discovery of Type VI Secretion Effectors via AI Uncovers Three New Bacterial Toxins

The type VI secretion system (T6SS) is a molecular harpoon used by 19% of bacteria to inject toxic proteins into microbial or host cells. Despite its widespread distribution, many T6SS effector (T6E) genes remain unidentified.

To address this gap, the authors developed an XGBoost classifier integrating 42 genetic and biochemical features to identify novel T6Es. Applying the model to 2,559 T6SS-encoding bacterial genomes revealed 19,958 T6E candidates.

The team validated its computational predictions and confirmed three effector candidates that have new 3D structures and demonstrated cytotoxicity to bacteria and yeast, mostly in the bacterial periplasm. For two of these effectors, cognate immunity proteins that neutralize toxicity were validated. T6EC11 is a new peptidoglycan-degrading effector that quickly leads to spherical E. coli, with inner membrane separation and gradual peptidoglycan degradation in a unipolar manner, producing an intriguing moon-like structural phenotype. T6EC12 is toxic to bacteria and yeast and carries a conserved zinc-binding motif; mutations in the motif markedly reduced toxicity, suggesting that T6EC12 represents a novel metalloprotease.

Overall, the study expands the known T6E repertoire and provides thousands of T6E predictions across all T6SS-encoding bacteria.