Ribosome-associated quality control of membrane proteins at the endoplasmic reticulum

Abstract

Protein synthesis is an energetically costly, complex and risky process. Aberrant protein biogenesis can result in cellular toxicity and disease, with membrane-embedded proteins being particularly challenging for the cell. In order to protect the cell from consequences of defects in membrane proteins, quality control systems act to maintain protein homeostasis. The majority of these pathways act post-translationally; however, recent evidence reveals that membrane proteins are also subject to co-translational quality control during their synthesis in the endoplasmic reticulum (ER). This newly identified quality control pathway employs components of the cytosolic ribosome-associated quality control (RQC) machinery but differs from canonical RQC in that it responds to biogenesis state of the substrate rather than mRNA aberrations. This ER-associated RQC (ER-RQC) is sensitive to membrane protein misfolding and malfunctions in the ER insertion machinery. In this Review, we discuss the advantages of co-translational quality control of membrane proteins, as well as potential mechanisms of substrate recognition and degradation. Finally, we discuss some outstanding questions concerning future studies of ER-RQC of membrane proteins.

Keywords: Endoplasmic reticulum; Membrane protein; Protein folding; Ribosome; Translation.

Fig. 1. Potential sites of error during co-translational insertion of membrane proteins at the ER.

Membrane protein biogenesis at the ER begins with targeting of a translating nascent chain to an hour-glass shaped channel called the Sec61 translocon. The nascent chain is inserted into the Sec61 translocon and then partitions into the phospholipid bilayer through a lateral gate. During this process there are several instances where errors may arise. (A) Orientation of the first TMD as it enters the membrane, where the N-terminus must be correctly localised to the ER lumen (N_exo) or cytoplasm (N_cyt). This orientation defines the topology of the subsequent TMDs, meaning errors at this stage can result in incorrect topology of the entire protein. (B) Failed insertion of poor TMDs. Some TMDs are weakly hydrophobic or charged and, as a result, may not insert correctly in the absence of their cognate binding TMDs. (C) Misfolding of soluble domains. In some instances, MPs contain large soluble domains, which are required to fold correctly for overall protein fold. Failure to fold such domains can therefore also impact TMD packing.

Fig. 2. Membrane protein biogenesis defects result in ER-RQC.

Defects in TMD insertion through the EMC or Sec61, attempted insertion of poorly hydrophobic TMDs or poor shielding of TMD charges might all contribute to ribosome stalls. Additionally, insertion of TMDs after large soluble domains might also present a challenge due to release of the ribosome from the translocon while cytoplasmic domains are synthesised. Translational stalls at the ER that result in ribosome collisions are recognised by the ubiquitin ligase Hel2, followed by splitting of the ribosome by the RQT complex (and potentially also Dom34-Hbs1). Following splitting of the ribosome, the exposed nascent chain-tRNA complex is recognised by Rqc2 and listerin (Ltn1). This complex ubiquitylates the nascent chain, targeting it for degradation. The final step of extraction and degradation of the chain is less well understood, and evidence concerning details of this process at the ER is sparse. Extraction and degradation of substrates at the ER may involve as yet unidentified proteins, potentially including ERAD machinery.

Fig. 3. Sources of tension to overcome ribosome stalls.

Interactions between nascent TMDs and the ribosomal exit tunnel may result in a slowing down in translation. There are multiple sources of tension that may provide the force on the nascent chain required to overcome this type of stall. Tension may be generated by any of the following: interactions between the nascent chain and the Sec61 translocon, favourable partitioning of a TMD into the lipid bilayer, action of the EMC (either as an insertase or as a chaperone), inter-TMD interactions within the MP, or interactions between TMDs and a chaperone.