Regulation of the ubiquitin-mediated proteolytic pathway: role of the substrate alpha-NH2 group and of transfer RNA

Degradation of intracellular proteins via the ubiquitin pathway involves several steps. In the initial event, ubiquitin becomes covalently linked to the protein substrate in an ATP-requiring reaction. Following ubiquitin conjugation, the protein moiety of the adduct is selectively degraded with the release of free and reusable ubiquitin. Ubiquitin modification of a variety of protein targets in the cell plays a role in basic cellular functions. Modification of core nucleosomal histones is probably involved in regulation of gene expression at the level of chromatin structure. Ubiquitin attachment to cell surface proteins may play roles in processes of cell-cell interaction and adhesion, and conjugation of ubiquitin to other yet to be identified protein(s) could be involved in the progression of cells through the cell cycle. Despite the considerable progress that has been made in the elucidation of the mode of action and cellular roles of the ubiquitin pathway, many major problems remain unsolved. A problem f central importance is the specificity in the ubiquitin ligation system. Why are certain proteins conjugated and committed for degradation, whereas other proteins are not? A free α-NH₂ group is an important feature of the protein structure recognized by the ubiquitin conjugation system, and tRNA is required for the conjugation of ubiquitin to selective proteo-lytic substrates and for their subsequent degradation. These findings can shed light on some of the features of a substrate that render it susceptile to ubiquitin-mediated degradation.     

Cooperation of a ubiquitin domain protein and an E3 ubiquitin ligase during chaperone/proteasome coupling.

BACKGROUND: Molecular chaperones recognize nonnative proteins and orchestrate cellular folding processes in conjunction with regulatory cofactors. However, not every attempt to fold a protein is successful, and misfolded proteins can be directed to the cellular degradation machinery for destruction. Molecular mechanisms underlying the cooperation of molecular chaperones with the degradation machinery remain largely enigmatic so far. RESULTS: By characterizing the chaperone cofactors BAG-1 and CHIP, we gained insight into the cooperation of the molecular chaperones Hsc70 and Hsp70 with the ubiquitin/proteasome system, a major system for protein degradation in eukaryotic cells. The cofactor CHIP acts as a ubiquitin ligase in the ubiquitination of chaperone substrates such as the raf-1 protein kinase and the glucocorticoid hormone receptor. During targeting of signaling molecules to the proteasome, CHIP may cooperate with BAG-1, a ubiquitin domain protein previously shown to act as a coupling factor between Hsc/Hsp70 and the proteasome. BAG-1 directly interacts with CHIP; it accepts substrates from Hsc/Hsp70 and presents associated proteins to the CHIP ubiquitin conjugation machinery. Consequently, BAG-1 promotes CHIP-induced degradation of the glucocorticoid hormone receptor in vivo. CONCLUSIONS: The ubiquitin domain protein BAG-1 and the CHIP ubiquitin ligase can cooperate to shift the activity of the Hsc/Hsp70 chaperone system from protein folding to degradation. The chaperone cofactors thus act as key regulators to influence protein quality control.     

Ubiquitin conjugation to endogenous proteins in the dormant tuber of Helianthus tuberosus and during the first cell cycle

Ubiquitin is a small protein involved in an ATP-dependent proteolytic pathway in all eukaryotes. This pathway has been demonstrated to be required for both the bulk degradation of cellular proteins and the targeted proteolysis of specific regulatory proteins. We have investigated the presence of ubiquitin (Ub) and the ubiquitin-conjugating system in dormant and activated tubers of Helianthus tuberosus L. cv. OB 1 that represent a widely used model system for studies on the cell cycle in plants. Immunoblot experiments revealed the presence of free ubiquitin and ubiquitin conjugates. Furthermore, the presence of an active ubiquitin-conjugating system, both time- and ATP-dependent, was demonstrated by incubation with ¹²⁵I-labeled ubiquitin. A few proteins able to form thiol esters with ¹²⁵I-Ub and probably corresponding to ubiquitin-conjugating enzymes, E1 and E2s, were also found. During the first cell cycle, several proteins become ubiquitinated. In particular a large amount of protein conjugates was present at 6 h when the lowest content of free ubiquitin was found. Subsequently, a dramatic decrease in ubiquitin conjugates occurred. It is well known that cell cycle progression in eukaryotes depends on cyclin levels and cyclin B degradation is ubiquitin- and ATP-dependent. By immunoblot experiments we showed that cyclin B in H. tuberosus is present as at least two protein bands of 50 and 54 kDa and that their amounts undergo profound changes during the cell cycle. The 54-kDa band was also recognized by an anti-ubiquitin antibody. These data seem to indicate that in H. tuberosus activated tuber slices, the ATP-dependent ubiquitin proteolytic pathway is involved in the dedifferentiation process occurring after the artificial break of dormancy when the cells acquire the characteristics linked to the meristematic state.     

The ubiquitin-mediated proteolytic pathway: enzymology and mechanisms of recognition of the proteolytic substrates

Degradation of proteins by the ubiquitin system involves two discrete steps. Initially, ubiquitin is covalently linked in an ATP-dependent mode to the protein substrate. The protein moiety of the conjugate is subsequently degraded by a specific protease into peptides and free amino acids with the release of free and reutilizable ubiquitin. The degradation process also requires energy. In this review we shall discuss the mechanisms involved in ubiquitin activation, selection of substrates for conjugation, and subsequent degradation of ubiquitin-conjugated proteins. In addition, we shall briefly summarize what is currently known of the role of the ubiquitin system in protein degradation in vitro and in vivo.     

蛋白质泛素化系统

泛素化是单个或多个泛素在泛素激活酶,泛素结合酶及泛素蛋白质连接酶的作用下共价修饰底物蛋白质的过程,近年来的研究发现,许多含环指的蛋白质本身是蛋白质泛素连接酶,或是多亚基连接酶中的重要成分。由于细胞内可表达200以上的环指蛋白,并且多亚基连接酶可利用同一环指蛋白但不同的底物识别蛋白。这些研究极大地丰富了对泛素化系统酶的认识,也使进一步调节和干预连接酶与底物的相互作用成为可能,新近的研究还发现,泛素化不仅可导致蛋白质的降解,还可直接影响蛋白质的活性和细胞内定位,是调节细胞内蛋白质功能和水平的主要机制之一。     

E3 Ubiquitin Ligases in Protein Quality Control Mechanism

In living cells, polypeptide chains emerging from ribosomes and preexisting polypeptide chains face constant threat of misfolding and aggregation. To prevent protein aggregation and to fulfill their biological activity, generally, protein must fold into its proper three-dimensional structure throughout their lifetimes. Eukaryotic cell possesses a quality control (QC) system to contend the problem of protein misfolding and aggregation. Cells achieve this functional QC system with the help of molecular chaperones and ubiquitin-proteasome system (UPS). The well-conserved UPS regulates the stability of various proteins and maintains all essential cellular function through intracellular protein degradation. E3 ubiquitin ligase enzyme determines specificity for degradation of certain substrates via UPS. New emerging evidences have provided considerable information that various E3 ubiquitin ligases play a major role in cellular QC mechanism and principally designated as QC E3 ubiquitin ligases. Nevertheless, very little is known about how E3 ubiquitin ligase maintains QC mechanism against abnormal proteins under various stress conditions. Here in this review, we highlight and discuss the functions of various E3 ubiquitin ligases implicated in protein QC mechanism. Improving our knowledge about such processes may provide opportunities to modulate protein QC mechanism in age-of-onset diseases that are caused by protein aggregation.     

Illuminating the ubiquitin/proteasome system

The ubiquitin/proteasome system (UPS) is responsible for the regulated processive degradation of proteins residing in the cytosol, nucleus, and endoplasmic reticulum. The two central players are ubiquitin, a small protein that is conjugated to substrates, and the proteasome, a large multi-subunit proteolytic complex that executes degradation of ubiquitylated proteins. Ubiquitylation and proteasomal degradation are highly dynamic processes. During the last decade, many researchers have started taking advantage of fluorescent proteins, which allow studying the dynamic nature of this system in the context of its natural environment: the living cell. In this review, we will summarize studies that have implemented this approach to examine the UPS and discuss novel insights in the dynamic organization of the UPS.     

Effect of stress on protein degradation: role of the ubiquitin system.

Many factors which induce the stress response (heat shock protein synthesis) in eukaryotes also cause the formation of aberrant proteins. Such aberrant proteins are usually rapidly and selectively degraded in cells. Temperature step-up accelerates the degradation of a subset of normally stable proteins. This effect is transient and is confined to a narrow range of heat shock temperatures above which proteolysis is inhibited. The time course and extent of proteolysis elicited by a mild heat shock is consistent with data on the thermal transitions of cellular proteins. Biochemical and genetic evidence strongly supports the view that the ubiquitin system is primarily responsible for heat- or stress-damaged protein degradation in eukaryotic cells. It still remains to be determined how stress-damaged proteins are recognized by the ubiquitin system and selected for degradation. Ubiquitin-protein ligases (E3's) which attach multi-ubiquitin chains to proteins are thought to be responsible for the selection of proteins for degradation. Several species of E3 have recently been characterized. However, none of the known E3's seems to fulfil the role of selecting aberrant proteins for breakdown. Heat shock proteins which are thought to repair unfolded or misfolded proteins probably have a complementary function to the ubiquitin system which destroys damage proteins. The relationship between the ubiquitin system and the regulation of heat shock protein synthesis, which is still not understood, is discussed.     

The role of ubiquitin linkages on α-synuclein induced-toxicity in a Drosophila model of Parkinson's disease

Parkinson's disease (PD) is a common movement disorder marked by the loss of dopaminergic (DA) neurons in the brain stem and the presence of intraneuronal inclusions designated as Lewy bodies (LB). The cause of neurodegeneration in PD is not clear, but it has been suggested that protein misfolding and aggregation contribute significantly to the development of the disease. Misfolded and aggregated proteins are cleared by ubiquitin proteasomal system (UPS) and autophagy lysosomal pathway (ALP). Recent studies suggested that different types of ubiquitin linkages can modulate these two pathways in the process of protein degradation. In this study, we found that co-expression of ubiquitin can rescue neurons from α-syn-induced neurotoxicity in a Drosophila model of PD. This neuroprotection is dependent on the formation of lysine 48 polyubiquitin linkage which is known to target protein degradation via the proteasome. Consistent with our results that we observed in vivo , we found that ubiquitin co-expression in the cell can facilitate cellular protein degradation by the proteasome in a lysine 48 polyubiquitin-dependent manner. Taken together, these results suggest that facilitation of proteasomal protein degradation can be a potential therapeutic approach for PD.     

Ubiquitin‐like domains can target to the proteasome but proteolysis requires a disordered region

Ubiquitin and some of its homologues target proteins to the proteasome for degradation. Other ubiquitin‐like domains are involved in cellular processes unrelated to the proteasome, and proteins containing these domains remain stable in the cell. We find that the 10 yeast ubiquitin‐like domains tested bind to the proteasome, and that all 11 identified domains can target proteins for degradation. Their apparent proteasome affinities are not directly related to their stabilities or functions. That is, ubiquitin‐like domains in proteins not part of the ubiquitin proteasome system may bind the proteasome more tightly than domains in proteins that are bona fide components. We propose that proteins with ubiquitin‐like domains have properties other than proteasome binding that confer stability. We show that one of these properties is the absence of accessible disordered regions that allow the proteasome to initiate degradation. In support of this model, we find that Mdy2 is degraded in yeast when a disordered region in the protein becomes exposed and that the attachment of a disordered region to Ubp6 leads to its degradation.     

The Ever Expanding Role of Ubiquitin and SUMO in Plant Biology

When it was discovered in the 1970s as a ubiquitous protein,ubiquitin, a 76-aminoacid peptide, had no assigned function. It was not until later that ubiquitin was found to be a necessary cofactor in a vital cellular process: the degradation of proteins.Work by Avram Hershko, Aaron Ciechanover, and Irwin Rose     

System-wide Analysis Reveals Intrinsically Disordered Proteins Are Prone to Ubiquitylation after Misfolding Stress

Damaged and misfolded proteins that are no longer functional in the cell need to be eliminated. Failure to do so might lead to their accumulation and aggregation, a hallmark of many neurodegenerative diseases. Protein quality control pathways play a major role in the degradation of these proteins, which is mediated mainly by the ubiquitin proteasome system. Despite significant focus on identifying ubiquitin ligases involved in these pathways, along with their substrates, a systems-level understanding of these pathways has been lacking. For instance, as misfolded proteins are rapidly ubiquitylated, unconjugated ubiquitin is rapidly depleted from the cell upon misfolding stress; yet it is unknown whether certain targets compete more efficiently to be ubiquitylated. Using a system-wide approach, we applied statistical and computational methods to identify characteristics enriched among proteins that are further ubiquitylated after heat shock. We discovered that distinct populations of structured and, surprisingly, intrinsically disordered proteins are prone to ubiquitylation. Proteomic analysis revealed that abundant and highly structured proteins constitute the bulk of proteins in the low-solubility fraction after heat shock, but only a portion is ubiquitylated. In contrast, ubiquitylated, intrinsically disordered proteins are enriched in the low-solubility fraction after heat shock. These proteins have a very low abundance in the cell, are rarely encoded by essential genes, and are enriched in binding motifs. In additional experiments, we confirmed that several of the identified intrinsically disordered proteins were ubiquitylated after heat shock and demonstrated for two of them that their disordered regions are important for ubiquitylation after heat shock. We propose that intrinsically disordered regions may be recognized by the protein quality control machinery and thereby facilitate the ubiquitylation of proteins after heat shock.Cells face the constant threat of protein misfolding and aggregation, and thus protein quality control pathways are important in selectively targeting damaged and misfolded proteins for degradation (1, 2). The ubiquitin proteasome system serves as a major mediator of this pathway by conjugating the small protein ubiquitin onto substrates through the E1-E2-E3 (ubiquitin-activating enzyme, ubiquitin-conjugating enzyme, and ubiquitin ligase, respectively) cascade for their recognition and degradation by the proteasome (3, 4). It is known that the activity of the ubiquitin-proteasome system is associated with many neurodegenerative diseases. For instance, ubiquitin is found enriched in protein inclusions associated with these diseases (5). Furthermore, proteasome activity has been shown to decrease with age in a large variety of organisms (6), leading to increased proteotoxicity in the cell.Because of the importance of maintaining protein homeostasis, numerous ubiquitin ligases in different cellular compartments function in protein quality control pathways to target misfolded or damaged proteins for degradation via the proteasome. For instance, the conserved Hrd1 ubiquitin ligase is involved in the endoplasmic-reticulum-associated degradation pathway that targets endoplasmic reticulum proteins for retro-translocation to the cytoplasm and proteasome degradation (7). A major question is what features are recognized by ubiquitin ligases that allow them to selectively target terminally misfolded proteins for degradation, given that the folding rates and physicochemical properties vary largely from protein to protein. Several E3 ubiquitin ligases involved in cytosolic protein quality control target their substrates via their interactions with chaperone proteins. For instance, the CHIP ubiquitin ligase can directly bind to Hsp70 and Hsp90 proteins (8), which may hand over client proteins that are not successfully folded. Understanding which features are recognized by these degradation quality-control pathways might help us understand how certain misfolded proteins evade this system, leading to their accumulation and aggregation in the cell.Many studies investigating degradation protein quality control have employed model substrates (e.g. mutated proteins that misfold) to reveal which components are involved in a given quality control machinery. However, these approaches do not typically reveal the whole spectrum of substrates for these pathways. Thus, alternative system-wide approaches are also needed to provide a bigger picture. Heat shock (HS)¹ induces general misfolding at the proteome level by increasing thermal energy and was shown to cause an increase in ubiquitylation levels in the cell over 25 years ago (9, 10). However, the exact mechanism and pathways that target misfolded proteins have remained uncharacterized for a long time. We recently showed that the Hul5 ubiquitin ligase plays a major role in this heat stress response that mainly affects cytosolic proteins (11). Absence of Hul5 averts the ubiquitylation in the cytoplasm of several misfolded targets after HS, as well as low-solubility proteins in unstressed cells. Other E3 ubiquitin ligases are likely involved in this pathway (12). Interestingly, as ubiquitin constitutes about only 1% of the proteome, free unconjugated ubiquitin is rapidly depleted under stress conditions (13, 14). Given the limited amount of this protein, how does the cell triage ubiquitin among an excess of misfolded proteins? In order to gain systems-level insight, we sought to identify characteristics enriched among proteins ubiquitylated after HS using a combination of statistical and computational analysis, and we conducted additional proteomics and biochemical experiments to support our hypotheses. We discovered an unexpected susceptibility of intrinsically disordered proteins for ubiquitylation after misfolding stress.     

Ubiquitination-mediated protein degradation and modification： an emerging theme in plant-microbe interactions

Post-translational modification is central to protein stability and to the naodulation of protein activity.Various types ofprotein modification,such as phosphorylation,methylation,acetylation,myristoylation,glycosylation,and ubiquitina-tion,have been reported.Among them,ubiquitination distinguishes itself from others in that most of the ubiquitinatedproteins are targeted to the 26S proteasome for degradation.The ubiquitin/26S proteasome system constitutes the majorprotein degradation pathway in the cell.In recent years,the importance of the ubiquitination machinery in the controlof numerous eukaryotic cellular functions has been increasingly appreciated.Increasing number of E3 ubiquitin ligasesand their substrates,including a variety of essential cellular regulators have been identified.Studies in the past severalyears have revealed that the ubiquitination system is important for a broad range of plant developmental processes andresponses to abiotic and biotic stresses.This review discusses recent advances in the functional analysis of ubiquitina-tion-associated proteins from plants and pathogens that play important roles in plant-microbe interactions.     

Adenovirus degradation of cellular proteins

Eukaryotic cells orchestrate constant synthesis and degradation of intracellular components, including soluble proteins and organelles. The two major intracellular degradation pathways are the ubiquitin/proteasome system and autophagy. Whereas ubiquitin/proteasome system is involved in rapid degradation of proteins, autophagy selectively removes protein aggregates and damaged organelles. Failure of these highly adjusted proteolytic systems to maintain basal turnover leads to altered cellular homeostasis. During evolution, certain viruses have developed mechanisms to exploit their functions to facilitate their own replication, prevent viral clearance and promote the outcome of infection. In this article, we summarize the current opinion on adenoviruses (Ad) and molecular host cell targets, extending on recent evidences for protein degradation pathways in infected cells. We describe recently identified connections between Ad-mediated proteolysis and viral replication with main emphasis on the function of certain Ad proteins.