Structural basis for malate-driven, pore lipid-regulated activation of the Arabidopsis vacuolar anion channel ALMT9.

In plant cells, the ALMTs are key plasma and vacuolar membranes anion channels regulating plant responses to the environment. Vacuolar ALMTs control stomata aperture and anion accumulation in guard cells. The activation of vacuolar ALMTs is voltage and malate dependent, but the underlying mechanisms remain elusive. Here we report the cryo-EM structure of ALMT9 from Arabidopsis thaliana (AtALMT9), a malate-activated vacuolar anion channel in various lipid-bound states. In all the states, lipids interact with the ion conduction pore of AtALMT9. We found lipid-bound states in plugged and unplugged conformations. Two unplugged states represent with distinct pore width profiles. Structural and functional analysis identified conserved residues involved in ion conduction and pore lipid plugging. Molecular dynamic simulations revealed a peculiar anion conduction mechanism in AtALMT9. We propose a voltage dependent activation mechanism based on the competition between pore-lipids and malate at the cytosolic entrance of the channel