How Is the Fidelity of Proteins Ensured in Terms of Both Quality and Quantity at the Endoplasmic Reticulum? Mechanistic Insights into E3 Ubiquitin Ligases

Abstract

The endoplasmic reticulum (ER) is an interconnected organelle that plays fundamental roles in the biosynthesis, folding, stabilization, maturation, and trafficking of secretory and transmembrane proteins. It is the largest organelle and critically modulates nearly all aspects of life. Therefore, in the endoplasmic reticulum, an enormous investment of resources, including chaperones and protein folding facilitators, is dedicated to adequate protein maturation and delivery to final destinations. Unfortunately, the folding and assembly of proteins can be quite error-prone, which leads to the generation of misfolded proteins. Notably, protein homeostasis, referred to as proteostasis, is constantly exposed to danger by flows of misfolded proteins and subsequent protein aggregates. To maintain proteostasis, the ER triages and eliminates terminally misfolded proteins by delivering substrates to the ubiquitin–proteasome system (UPS) or to the lysosome, which is termed ER-associated degradation (ERAD) or ER-phagy, respectively. ERAD not only eliminates misfolded or unassembled proteins via protein quality control but also fine-tunes correctly folded proteins via protein quantity control. Intriguingly, the diversity and distinctive nature of E3 ubiquitin ligases determine efficiency, complexity, and specificity of ubiquitination during ERAD. ER-phagy utilizes the core autophagy machinery and eliminates ERAD-resistant misfolded proteins. Here, we conceptually outline not only ubiquitination machinery but also catalytic mechanisms of E3 ubiquitin ligases. Further, we discuss the mechanistic insights into E3 ubiquitin ligases involved in the two guardian pathways in the ER, ERAD and ER-phagy. Finally, we provide the molecular mechanisms by which ERAD and ER-phagy conduct not only protein quality control but also protein quantity control to ensure proteostasis and subsequent organismal homeostasis.

Ubiquitination-Proteasome System (UPS) and Autophagy Two Main Protein Degradation Machineries in Response to Cell Stress

“…However, when the unnatural proteins can no longer be refolded, it is necessary to identify these misfolded proteins and degrade them through the ubiquitin–proteasome pathway. Misfolded and unfolded proteins are firstly recognized by chaperones, such as Hsp70 and Hsp90, which are mainly chaperones in PQC, and both of them utilize co-chaperones to recognize and bind substrate [ 21 ]. Then unnatural proteins either refold in an ATP-dependent manner or are labeled by ubiquitin under the action of chaperon-bound ubiquitin E3 enzymes, such as STIP1 Homology and U-Box Containing Protein 1 (CHIP), BAG Cochaperone 1 (BAG1), and Scythe ( Figure 1 ).…”

“…Interestingly, CHIP also mediates the ubiquitination degradation of Hsp70 ( Figure 1 ). Misfolded cystic fibrosis transmembrane conductance regulator (CFTR) [ 18 , 19 , 20 ], glucocorticoid hormone receptor (GR) [ 21 ], Erb-B2 Receptor Tyrosine Kinase 2 (ErbB2) [ 22 ], and Pael receptor (Pael-R) [ 22 ] have been identified as substrates for CHIP. Misfolded Integrin, Pdr5, and HMG-CoA reductase (HMGCR) are the substrates of ERAD-related E3 Ligase Der3, gp78, and SCF Fbx2 [ 23 ].…”

Modulating the Ubiquitin–Proteasome System: A Therapeutic Strategy for Autoimmune Diseases

“…The ubiquitin ligases NEDL1 and gp78 target SOD1 and NEDL1, and SOD1 inclusions colocalize in motor neurons of the ventral horn of the spinal cord of patients with ALS and in transgenic SOD1 mutant mice. The ubiquitin ligase gp78 also plays a role in SOD1 ubiquitination [ 54 ].…”

Volleying plasma membrane proteins from birth to death: Role of J-domain proteins

“…Another mammalian channel protein, ENaC, is differentially regulated by Hsc70 and Hsp70. While overexpression of Hsc70 favors the degradation, Hsp70 stabilizes the protein, thus modulating its trafficking and surface expression ( Chanoux et al, 2013 ; Kang and Jeon, 2021 ). The Hsp70:DNAJA1 regulate the degradation of CFTR and other proteins via the CHIP E3 Ub ligase mediated ubiquitination.…”