Evolved resistance against the type 6 secretion system is toxin specific

Across ecosystems, microbes face attacks by competitors armed with lethal weapons, including toxin-injecting Type 6 Secretion Systems (T6SSs). This in turn selects for T6SS resistance, reducing the future effectiveness of T6SS weaponry in competition. However, we have only a limited understanding of how resistance to T6SS attacks evolves de novo. A key challenge is that T6SS-armed bacteria are highly diverse in the number and type of toxins they inject, spanning multiple distinct modes of action. Do functionally distinct T6SS toxins select for different mechanisms of resistance? To address this, we combine genomics, resistance assays and fluorescence microscopy, to characterise evolved resistances against common T6SS toxin classes across spatial scales. We discovered that amidase and lipase toxins select for mutations in distinct sets of genes, resulting in toxin-specific resistance phenotypes and fitness costs. We also discovered resistance trade-offs: lipase-evolved E. coli became less vulnerable to lipase membrane damage, at the cost of increased susceptibility to lysis by amidase toxins. Finally, using single-gene knockout mutants from the Keio collection we confirmed that specific genes not previously linked to T6SS resistance, including inner membrane transporters, osmo-sensing systems and stress response pathways, conferred resistance to specific toxins while generating sensitivity to others. The specificity of resistance, and associated trade-offs observed, are likely to constrain de novo evolution of resistance against T6SS attackers armed with multiple functionally distinct toxins, helping to explain why T6SS systems are so widespread in nature.