Structure of the Schizosaccharomyces pombe Gtr-Lam complex reveals evolutionary divergence of mTORC1-dependent amino acid sensing

mTORC1 is a protein kinase complex that controls cellular growth in response to nutrient availability. Amino acid signals are transmitted toward mTORC1 via the Rag/Gtr GTPases and their upstream regulators. An important regulator is LAMTOR, which localizes Rag/Gtr on the lysosomal/vacuole membrane. In human cells, LAMTOR consists of five subunits, but in yeast, only three or four. Currently, it is not known how variation of the subunit stoichiometry may affect its structural organization and biochemical properties. Here, we report a 3.1 Å-resolution structural model of the Gtr-Lam complex in Schizosaccharomyces pombe. We found that SpGtr shares conserved architecture as HsRag, but the intersubunit communication that coordinates nucleotide loading on the two subunits differs. In contrast, SpLam contains distinctive structural features, but its GTP-specific GEF activity toward SpGtr is evolutionarily conserved. Our results revealed unique evolutionary paths of the protein components of the mTORC1 pathway. [Display omitted] •A cryo-EM structural model of the Gtr-Lam complex in S. pombe has been determined•SpLam represents an intermediate state during the evolution of the LAMTOR complex•SpGtr heterodimer functions through a different mechanism than human Rags•Human GATOR1 can be used as a “cryo-EM chaperone” to assist structure determinations Different organisms have developed distinct strategies to sense and adapt to the surrounding environment. Here, Tettoni et al. describe a structural model of the Gtr-Lam complex in S. pombe. This finding reveals architectural and mechanistic details of the mTORC1 pathway during evolution.