Structural and mechanistic basis of the EMC-dependent biogenesis of distinct transmembrane clients

Abstract

Membrane protein biogenesis in the endoplasmic reticulum (ER) is complex and failure-prone. The ER membrane protein complex (EMC), comprising eight conserved subunits, has emerged as a central player in this process. Yet, we have limited understanding of how EMC enables insertion and integrity of diverse clients, from tail-anchored to polytopic transmembrane proteins. Here, yeast and human EMC cryo-EM structures reveal conserved intricate assemblies and human-specific features associated with pathologies. Structure-based functional studies distinguish between two separable EMC activities, as an insertase regulating tail-anchored protein levels and a broader role in polytopic membrane protein biogenesis. These depend on mechanistically coupled yet spatially distinct regions including two lipid-accessible membrane cavities which confer client-specific regulation, and a non-insertase EMC function mediated by the EMC lumenal domain. Our studies illuminate the structural and mechanistic basis of EMC's multifunctionality and point to its role in differentially regulating the biogenesis of distinct client protein classes.

Membrane protein biogenesis at the ER: the highways and byways

“…understanding of how the evolutionarily conserved EMC acts in concert with the Sec61 complex to perform two important, yet apparently discrete, roles during co-translational TMP biogenesis [92]. Firstly, the EMC acts as a membrane insertase that enables the stable integration of certain types of TMD into the lipid bilayer [92][93][94][95]. Hence, following SRP-dependent delivery to the ER (cf.…”

A unified evolutionary origin for the ubiquitous protein transporters SecY and YidC

“…Although not detected by less sensitive methods, comparisons of profile hidden Markov models for archaeal YidC and eukaryotic proteins identified three YidC paralogs in the ER: TMCO1, EMC3, and GET1. Recent single-particle electron cryomicroscopy (cryo-EM) studies yielded structural models for all three paralogs (Bai et al, 2020; McDowell et al, 2020; McGilvray et al, 2020; Miller-Vedam et al, 2020; O’Donnell et al, 2020; Pleiner et al, 2020), which together with the prokaryotic crystal structures reveal a conserved core consisting of a three-TMH bundle interrupted after the first TMH by a cytosolic helical hairpin. In the prokaryotic forms, a sixth, N-terminal peripheral helix is also present.…”

EMC is required for biogenesis and membrane insertion of Xport-A, an essential chaperone of rhodopsin-1 and the TRP channel

“…An outstanding question is whether such non-canonical membrane protein clients are in fact engaged by the EMC for their biogenesis and if so, how? Several studies have reported the loss of multi-pass membrane proteins with loss of EMC functionality 15,23,24 . Often, these studies correlate EMC-dependence with abundance changes at steady-state, rather than monitoring EMC-dependent biogenesis directly.…”

“…Recently, studies from the Weissman lab identified features within the EMC structure that differentially impact TA protein clients when compared to multi-pass membrane proteins including TMEM97, a 4-TMD protein with a similar cytoplasmic N-terminal topology to TRP 23 . One interpretation is that EMC may be able to handle distinct classes of clients through different features.…”

“…The structure of both the human and yeast EMC have recently been determined using cryoelectron microscopy (cryo-EM) [20][21][22][23] and a model has been proposed for EMC-mediated co-and posttranslational insertion of client proteins 20 . According to this model, a captured client protein is directed towards the membrane by the flexible cytosolic loop of EMC3, the insertase subunit of EMC; the EMC then presumably reduces the energetic cost of insertion by inducing a local thinning of the membrane and by arranging polar and positively charged residues within the bilayer.…”