Structure and function of the yeast amino acid-sensing SEAC-EGOC supercomplex

The Seh1-associated complex (SEAC) transduces amino acid signals to the Target of Rapamycin Complex 1 (TORC1), a master regulator of cell growth located on the vacuole membrane. The SEAC acts as a GTPase activating protein (GAP) for Gtr1, a small GTPase that forms a heterodimer with Gtr2, and as part of the EGO complex (EGOC), relays nutrient signals to TORC1. The SEAC is composed of two subcomplexes, SEACIT, an inhibitor of TORC1 that contains the GAP activity, and SEACAT, that has been proposed to regulate the activity of SEACIT. However, molecular details of its regulation are unclear. Here, we determined the cryo-electron microscopy structure of the SEAC-EGOC supercomplex and studied its function in TORC1 amino acid signalling. A single SEAC can interact with two EGOC molecules via SEACIT, binding exclusively to the “active” version of the EGOC as their interaction depends on Gtr1 being loaded with GTP. SEACAT does not modulate nor interact with the EGOC. The GAP activity of the SEAC is essential for the regulation of TORC1 by amino acids, and its loss phenocopies the lack of Gtr1-Gtr2, establishing the SEAC-EGOC complex as an amino acid-sensing hub. Despite being located far from the active site, deletion of Sea2, or its N-terminal β-propeller domain, also results in defects in amino acid signalling to TORC1. We propose that the SEAC-EGOC supercomplex integrates coatomer-like mechanisms of regulation via bidirectional feedback between GAP-GTPase (SEACIT-EGOC) and coat (SEACAT) modules that explain the functional interaction between Sea2 and the GAP activity. Given the conservation between the SEAC and its mammalian ortholog GATOR, we envision that this mechanism is similar in different organisms.