Current Protein and Peptide Science - Volume 13, Issue 5, 2012

The endoplasmic reticulum (ER) is the site for maturation of proteins destined for the secretory pathway. Failure in maturation leads to production of misfolded proteins that are eliminated through the ER-associated degradation (ERAD) pathway. ERAD is a complex process that includes misfolded protein recognition, retrotranslocation to the cytosol, ubiquitination and proteasomal degradation. gp78 is an E3 ubiquitin ligase that integrates these ERAD steps by nucleating a unique degradation machine, which uses the p97/VCP-Npl4 complex for retrotranslocation instead of the wellknown p97/VCP-Ufd1-Npl4 complex. A growing list of substrates have been identified for gp78, which highlights the importance of gp78-mediated ERAD in essential physiological pathways and pathological processes.

In the secretory pathway, quality control for the correct folding of proteins is largely occurring in the endoplasmic reticulum (ER), at the earliest possible stage and in an environment where early folding intermediates mix with terminally misfolded species. An elaborate cellular mechanism aims at dividing the former from the latter and promotes the selective transport of misfolded species back into the cytosol, a step called retrotranslocation. During retrotranslocation proteins will become ubiquitinated on the cytosolic side of the ER membrane by dedicated machineries and will be targeted to the proteasome for degradation. The entire process, from protein recognition to final degradation, has been named ER-associated protein degradation, or simply ERAD. Ubiquitin has well known functions in aiding late steps of substrate retrotranslocation and in targeting substrates to the proteasome. Recent results show that several cytosolic machineries allow ubiquitinated substrates to undergo extensive remodeling, or processing, on their poly-ubiquitin chains (PUCs). Although still ill-defined, PUC processing might have a unique function for ERAD in that it might provide a mechanism to generate optimal PUCs for recognition by proteasomal ubiquitin receptors. Ubiquitination might also have a previously unanticipated role in quality control of ER membrane proteins. This review recapitulates the current knowledge and recent findings about ERAD-specific roles of ubiquitin.

To maintain protein homeostasis in the ER, an ER protein quality control system retains unfolded polypeptides and misassembled membrane proteins, allowing only properly folded proteins to exit the ER. Misfolded proteins held in the ER are retrotranslocated into the cytosol, ubiquitinated, and degraded by the proteasome through the ER-associated degradation pathway (ERAD). By timely eliminating misfolded proteins, the ERAD system alleviates cytotoxic stress imposed by protein misfolding. It is well established that ER-associated ubiquitin ligases play pivotal roles in ERAD by assembling ubiquitin conjugates on retrotranslocation substrates, which serve as degradation signals for the proteasome. Surprisingly, recent studies have revealed an equally important function for deubiquitinases (DUBs), enzymes that disassemble ubiquitin chains, in ERAD. Intriguingly, many ERAD specific DUBs are physically associated with the retrotranslocation- driving ATPase p97. Here we discuss the potential functions of p97-associated DUBs including ataxin-3 and YOD1. Our goal is to integrate the emerging evidence into models that may explain how protein quality control could benefit from deubiquitination, a process previously deemed destructive for proteasomal degradation.

Myriad covalent post-translational modifications of histones have been demonstrated to play crucial roles in regulating gene transcription, gene repression, DNA damage and repair, and beyond. It has been long known that these modifications are often dynamic, such as histone ubiquitination and deubiquitination, and the processes through adding and/or removing these modified marks catalyzed by various classes of enzymes commonly influence many important physiological functions. In recent few years, studies on histone ubiquitination re-garners much attention arising from lots of new exciting findings emerged. Several important histone ubiquitination sites have been mapped in different organisms. In addition, the identification and characterization of numerous ubiquitin modifying enzymes, especially ligases and deubiquitinases, have facilitated the progress in understanding the roles of histone ubiquitination/deubiquitination events. Of particular interest, histone ubiquitination interplays with many other chromatin modifications, namely “crosstalk”, which contributes to a variety of cellular events. In this review, I summarize the enzymes and factors involved in regulating the attachment and removal of ubiquitin from histones, and focus on what essential roles this modification plays. I also present new evidence that links histone ubiquitination with other histone modifications, which comprises an intricate crosstalk network.

Posttranslational protein modification by small ubiquitin-related modifier (SUMO) has emerged as an important regulatory mechanism for chromosome segregation during mitosis. This review focuses on how SUMOylation regulates the centromere and kinetochore activities to achieve accurate chromosome segregation during mitosis. Kinetochores are assembled on the specialized chromatin domains called centromeres and serve as the sites for attaching spindle microtubule to segregate sister chromatids to daughter cells. Many proteins associated with mitotic centromeres and kinetochores have been recently found to be modified by SUMO. Although we are still at the early stage of elucidating how SUMOylation controls chromosome segregation during mitosis, a substantial progress has been achieved over the past decade. Furthermore, a major theme that has emerged from the recent studies of SUMOylation in mitosis is that both SUMO conjugation and deconjugation are critical for kinetochore assembly and disassembly. Lastly, we propose a model that SUMOylation coordinates multiple centromere and kinetochore activities to ensure accurate chromosome segregation.

Ubiquitin (Ub) is widely distributed in eukaryotic cells as its name means. There are many kinds of Ub-like proteins (for example, SUMO, NEDD8 and ISG15) and Ub-like domains (UbLs) included in multi-domain proteins. To date, a large number of Ub-binding domains (UBDs), such as UBA, CUE, UIM, ZnF, and Pru, are coming up to us with different affinities to Ub and its homologues. The binding specificities provide the basis for controlling various cellular events as well as for delivering ubiquitinated proteins to proteasome for degradation. Structural details of these UBDs and their complexes with Ub might as well show us the delicate mechanism of Ub recognition and regulation. This review summarizes recent progresses on deciphering the structure-based Ub-binding specificities, which are the importantly fundamental elements in orchestrating the ubiquitination and deubiquitination processes in eukaryotic cells.

Various aminopeptidases belong to the M1 aminopeptidase family. They are all zinc dependent enzymes playing important roles in several biological processes such as regulation of blood pressure under both physiological and pathological conditions, and the angiogenesis and metastasis of tumor, etc. They all have the highly conserved HEXXH(X)18E zinc-binding and GAMEN motifs essential for enzyme activities. In this review, the current situation regarding the biochemical characteristics, biological functions and inhibitors of three important members of these enzymes, aminopeptidase A, aminopeptidase N and aminopeptidase B are summarized.