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Mol Neurobiol DOI 10.1007/s12035-012-8351-0

Misfolded Recognition Strategies of E3 and Neurodegenerative Diseases

Deepak Chhangani & Nihar Ranjan Jana & Amit Mishra

Received: 24 July 2012 /Accepted: 12 September 2012 # Springer Science+Business Media New York 2012

Abstract Impairment in the clearance of misfolded proteins by , misfolding induces high neurotoxic threat functional proteins leads to various late-onset neurodegenera- because they cannot reduce the deposition of toxic species tive diseases. applies a strict quality control mechanism through cell division [2, 3]. Consequently, sequestration of against malfunctioned proteins which may generate cellular normal proteins with misfolded proteinaceous species trig- proteoxicity. Under proteotoxic insults, cells immediately adopt gers aggregation cascade and initiates disturbance in normal two major approaches to either refold the misfolded proteina- cellular functions [4, 5]. To cope under such situation, cells ceous species or degrade the unmanageable candidates. How- possibly try to make two major decisions: (1) degradation of ever, the main cellular proteostasis quality control mechanism is misfolded proteins and (2) replacement of aberrant or dam- not clear. It is therefore important to understand the events and aged proteins with newly synthesized proteins. Both pro- cellular pathways, which are implicated in the clearance of cesses are highly selective in nature and tightly controlled recalcitrant proteins. Ubiquitin system manages by various cellular factors [6]. Cellular failures in the intracellular protein degradation. In this process, E3 ubiquitin clearance of misfolded and damaged proteins lead to provides specificity for recognition of client formation of intra- or extracellular insoluble deposits proteins. In this review, we summarize various molecular such as - and amyloid-like structures [7]. approaches governed by E3 ubiquitin ligases in the degradation Misfolded protein accumulation has been observed in of aberrant proteins. A clear understanding of E3 ubiquitin most of the neurodegenerative diseases such as - ligases can offer a well tractable therapeutic approach against son’s diseases, Alzheimer’s disease, amyotrophic lateral neurodegenerative diseases. sclerosis, and Huntington’s disease [8]. How cellular machinery challenges protein misfolding and degrada- Keywords Misfolded proteins . Protein aggregation . tion of aberrant proteins to maintain protein Neurodegenerative diseases . E3 ubiquitin ligases is a big question of debate? Eukaryotic cells have evolved quality control system for degradation of damaged proteins and simultaneously pre- Introduction vent cross talk between normal and misfolded proteins. To achieve protein homeostasis, quality control system requires Numerous evidences suggest that various neurodegenerative inclusive regular activities of molecular chaperones and diseases have a common cause of accumulation of aberrant ubiquitin proteasome system (UPS). Chaperones are the or misfolding proteins [1]. In postmitotic cells, such as highly conserved proteins that actively mediate protein fold- ing and prevent protein aggregation in cells [9]. During : D. Chhangani A. Mishra (*) stress conditions, cells enormously increase the synthesis Cellular and Molecular Neurobiology Laboratory, Indian Institute of a particular class of heat shock proteins (HSPs) [10]. of Technology Rajasthan, HSP family members act as chaperones and generate cyto- Jodhpur 342011, India e-mail: [email protected] protective response against cellular toxicity induced by mis- folded protein aggregates [11]. Induction of chaperones N. R. Jana prevents accumulation of toxic species and provides neuro- Cellular and Molecular Neuroscience Laboratory, National Brain protective response in various neurodegenerative diseases Research Centre, – Manesar, [12 14]. It is unclear how misfolded proteins are selectively Gurgaon 122050, India targeted and eliminated from the dense cellular pool, and Mol Neurobiol cells retain an efficient quality control mechanism [15]. aggregation [21]. We do not know whether recognition of Addition of a small (8⋅5 kDa) ubiquitin molecule to an aberrant protein by E3 ubiquitin ligases is a real residue of target protein is a multistep process. Three differ- beneficiary challenge or, probably, a mysterious risk. It ent enzymatic components are required for protein ubiquiti- may be possible that, after recognition, recruitment of E3 nylation process. These are ubiquitin-activating enzyme ubiquitin ligases towards the site of aggregation from the (E1), ubiquitin-conjugating enzyme (E2s), and ubiquitin- site of action unknowingly progresses to another side, i.e. ligating (E3s). Degradation of aberrant proteins ultrasensitive sequestration. via UPS progresses through various steps: (1) covalent Apart from chaperones and UPS components, several tagging of several ubiquitin molecules on the protein marks other essential proteins such as factors, e.g., for degradation. In UPS, E3 ubiquitin ligases exist in a heat shock transcription factor 1, CREB-binding protein broad range and play a key role in this complex process, (CBP), NF-Y transcriptional factor, tumor suppressor pro- i.e., specific recognition and transferring ubiquitin tein , TATA-binding protein, specificity protein (Sp1), molecule to it [6, 16], and (2) polyubiquitin chain linkage and transcription initiation factor TFIID subunit 4 recognition by multicatalytic 26S proteasome complex [17]. (TAFII130), sequester with misfolded proteinaceous species The most challenging question is to know how these and consequently affect entire cellular proteostasis [22–24]. E3 ubiquitin ligases identify abnormal or misfolded sub- Sequestration of proteins with aberrant complex aggregates strates and distinguish them for degradation. Interestingly, is a widespread mechanism and most probably influences there are few E3s known which actively participate in proteostasis network. Recently, in a quantitative proteomic cellular quality control mechanism. In this review, we analysis, it was observed that numerous metastable proteins, concise our current understanding of various cellular including preexisting and newly synthesized proteins, se- defense approaches, planned by E3 for quester with amyloidogenic aggregates. The same study misfolded protein degradation and their implication in suggests that numerous proteins responsible for various and protein conformation disorders. cellular functions interact with amyloid-like aggregates Together with the recent findings, in our current review, and thereby generate toxicity and successive failure of crit- we elucidate critical substrates recognition process gov- ical cellular functions [25]. Under stress conditions, mis- erned by E3s, specifically employed for clearance of folded protein generation load dramatically increases, and misfolded protein aggregation. As shown in Fig. 1,we due to insufficient capacity, cells became unable propose a model of cellular protein quality control mech- to cope against these disastrous effects. Consequently, mis- anism, and probably, failure of this system leads to folded and damaged proteins get actively sequestered in a various neurodegenerative diseases. pericentriolar structure known as [26, 27]. EPM2B encodes an end product malin protein which serves as really interesting new gene (RING) finger domain Is Hunting of Misfolded Protein by E3 Ubiquitin Ligases E3 ubiquitin ligase. Missense in malin were a Reward or Cost? reported with an autosomal recessive neurodegenerative epilepsy disorder. Malin loss of function impairs the degra- Cells always keep doing their regular and efficient efforts to dation of laforin [28]. Recently, it was investigated that maintain a proper proteostasis balance via quality control ubiquitinated Lafora bodies are co-localized with Hsc/ mechanism [18]. Nascent polypeptides generation and re- chaperones, 20S proteasome, and mutant malin. As- placement of old proteins are common events in living cells. sociation of mutant malin, chaperones, and proteasome In an entire life-span from nascent to mature state, polypep- components with Lafora bodies indicates failure of the qual- tide chains always stand with a persistent cytotoxic threat of ity control system and one of the possible reasons of disease misfolding and aggregation [15]. Under stress conditions, progression [29]. Mutated form of laforin protein and E3 protein misfolding vulnerability and aggregation propensity ubiquitin ligase malin makes perinuclear-like structures and exponentially rise in cells [19]. To avoid such cytotoxic is nicely co-localized with ribosomes [30]. potential, cells continuously try to fold nonnative proteins Earlier studies suggested that few E3 ubiquitin ligases’ and degrade unsolved misfolded proteins through UPS [20]. aberrant function would generate serious imbalance in Aggregated proteinaceous structures represent a defective cellular quality control events [31, 32]. On beneficiary or exhaustive cellular quality control system in the cells. side, E3 ubiquitin ligases try to solve the problem of Inefficient degradation leads to overburden of misfolded aggregation and play a major role in protein quality proteins and finally crosses the refolding or chaperone control mechanism [33], but in the same pool, absence capacity of a cell. This failure of protein quality control at the site of origin due to major recruitment with an mechanism leads to frequent probability of sequestration earlier aggregate possibly leads to accumulation of unat- of noncomplex polypeptides that are more prone towards tended client proteins. We are not sure, but most Mol Neurobiol

Fig. 1 Cellular and molecular steps of protein quality control mecha- hallmark in several neurodegenerative diseases. In living cells, ubiq- nism primarily implicated in various neurodegenerative diseases. In uitin proteasome pathway is responsible for the intracellular protein living cells, DNA transcribed into messenger RNA; this information is degradation. In this pathway, E3 ubiquitin ligases provide various translated into polypeptide chains. Ribosome is a large macromolecular cellular strategies to select specific substrates or misfolded proteins. cellular machine responsible for the synthesis of nascent polypeptide Neurons are postmitotic cells that are more prone towards the aggre- chains as per information reserved in mRNA transcripts. A newly gation of misfolded proteinaceous structures. Still, the molecular path- translated emerging nascent polypeptide chains from the ribosome face omechanism of various neurodegenerative diseases linked with a constant risk of misfolding and aggregation. To overcome this prob- malfunctioned/damaged proteins is not known. Even though it is lem, molecular chaperones govern immediate into their tempting to speculate that the E3 ubiquitin ligases provide various native structure for proper cellular functions. This is a challenging task, cellular approaches for specific substrate selection to regulate protein and lack of chaperone capacity and various cellular insults generate a aggregation, still, it is not clear how these E3 ubiquitin ligases sense cumulative imbalance in protein homeostasis, which leads to misfolded misfolded protein aggregation phenomenon protein aggregation in cells. Misfolded protein aggregation is a pivotal probably, those unattended accumulated substrates are response lipid mediator neuroprotectin D1 (NPD1) attenuates more prone to sequestration with preformed aggregates ataxin-1 poly(Q)-induced proteotoxic stress, and aspirin- which are already targeted by respective E3 ubiquitin triggered NPD1 treatment suppresses cerebral ischemic injury ligase. This situation is likely to be aggravated because of the [42, 43]. It may be possible that stress response-mediated loss of function of E3 ubiquitin ligase due to sequestration with chaperones and other proteins also participate in sequestration preformed aggregates as we depict in a proposed model in process. Still, it is not clear that what typical molecular features Fig. 2. In support of our proposed model, there is another or signatures are responsible for discrimination between mis- interesting study which states that, like expanded polyglutamine folded protein and native protein.However,themostprominent aggregates, chimera GFP170* protein also forms cytoplasmic assumption is that these E3 ubiquitin ligases may be recruited and nuclear aggregates. GFP170* protein recruits promyelo- for the clearance of aberrant proteins. cytic leukemia protein (bodies), chaperones, proteasomal com- ponents, SUMO-1, and transcription factors, e.g., CBP and p53 [34]. In our previous studies, we observed that E3 ubiquitin Misfolded Proteins Recognition Tactics of E3 Ubiquitin ligase E6–AP regulates the turnover of expanded polyglut- Ligases amine, p53 and p27 proteins act as a quality control E3 ubiquitin ligase [35–37]. However, earlier reports suggest that various Possibly, without much disturbing normal cellular homeo- essential cellular proteins get attracted towards misfolded protein stasis, cells apply different strategies for identification and inclusions such as vimentin [38], [39], elongation factor degradation of a damaged protein in crowded milieu of 1 alpha [40], and ubiquitin protein [41]. In support of cellular cells. In this section, we focus on the emerging roles of E3 defense line mechanism, recently, it was shown that a stress ubiquitin ligases associated with specific selection of their Mol Neurobiol

Fig. 2 A schematic diagram proposed to represent sequestration of transcription factors, chaperone family members, UPS components, numerous cellular components and aggravate the aggregation process and microtubules to increased amounts of aberrant proteins in cells as with a preformed misfolded protein structure. Nascent polypeptide earlier discussed in the same review. To overcome uncontrolled and chains fold through different intermediates to achieve their three- disastrous aggregation process, how E3 ubiquitin ligases govern mis- dimensional structure for their proper cellular functions. Partially folded protein degradation and promote protein disaggregation is not folded or misfolded polypeptide chain may provide an attractive tem- completely known. Why these essential cellular proteins are recruited plate for deposition of other essential cellular proteins and probably towards metastable amorphous aggregates is an open question for develop a metastable inclusion structure enriched with several needful debate. Maybe interaction of E3 ubiquitin ligases with preformed cellular components. Transational errors or proteotoxic insults may aggregates generates lack of function at the previous site of action cause protein misfolding and leads to huge aggregates in various and consequently promotes global disturbance linked with their client cellular compartments. The detailed structure and nature of these proteins and leads to impairment in normal cellular functions. Action aggregated inclusions is not well understood. Previous reports suggest of chaperons and UPS components tries to stimulate disaggregation that, during failure of cellular quality control mechanism, more intrigu- and degradation process to make various cellular defense lines against ing is the possibility that misfolded intermediates can attract various proteotoxic species critical substrates and misfolded proteins. Here, we discuss 30 % of the nascent polypeptide chains are misfolded due to and summarize various basic E3 ubiquitin ligases based on posttranslational slips related with folding process [44, 45]. cellular strategies for the clearance of misfolded proteins to Because disordered proteins tend to form cytotoxic aggre- avoid interference with normal cellular functions. In this gates, cellular quality control system immediately recruits section, we summarize most possible tactics govern by E3 E3 ubiquitin ligases for clearances of misfolded protein via ubiquitin ligases in the clearance of misfolded proteins or UPS [46], but how these E3 ubiquitin ligases discriminate critical substrates as shown in Fig. 3. between normal and misfolded proteins is not clear. Recently, it was shown that Sir Antagonist 1 (San1) E3 ubiquitin ligase Conformational Plasticity of Disorder contributes in both nuclear and cytoplasmic protein quality control mechanisms [47, 48]. Mostly, functional proteins are Eukaryotic cells achieve intracellular degradation through natively organized into three-dimensional structure with well- ubiquitin proteasome system [6]. E3s enzymes provide spec- ordered structural motifs, thus easily accessible for recogni- ificity for protein degradation in ubiquitination-based quality tion by other interacting proteins, but misfolded proteins lose control (QC) system. In crowded cellular environment, nearly their native structures and adopt irregular shapes, so how is it Mol Neurobiol

Fig. 3 Proposed diagrammatic representation of comprehend cellular comprehensive tactics of different E3 ubiquitin ligases from various tactics adopted by various E3 ubiquitin ligases implicated in the family members that induce the clearance or degradation of misfolded clearance of misfolded and other client proteins. Newly synthesized proteins as serially discussed in the above review section. Most likely, protein folds into their correct three-dimensional structure and trans- E3 ubiquitin ligases can assist various protein quality control- ported into various cellular compartments or extracellular environment disapproved candidates/client proteins in different manners according for normal cellular functions. Improperly or poorly folded proteins to their specificity and subcellular localization. Caption of various E3 need immediate assistance from chaperones to further fold into their ubiquitin ligases tactics as shown in the figure include the following: 1 native form. Absence of sufficient chaperone capacity leads to protein conformational plasticity of disorder, 2 ribosomal association of qual- misfolding and aggregation. In neuronal cells, it is a well-established ity control mechanism, 3 harmonious interaction of E3 ubiquitin fact that, generally, protein misfolding leads to , and the ligases with chaperones, 4 disposal of endoplasmic reticulum- aggravation of such situation can cause neurodegenerative disorder anchored misfolded proteins, 5 hand to hand coordination, 6 modulated linked with protein aggregation. Here, we have proposed seven recruitment with misfolded proteins, 7 sugar chains recognition possible to recognize and separate them from crowded envi- bacterial and mammalian cells, respectively [51]. Polysomes ronment? Interestingly, a recent report suggests that E3 ubiq- arrange in such a fashion that polypeptide exit faces outward uitin ligase San1 applies a novel conformational plasticity and thereby probably inhibits unwanted interactions among strategy in the recognition of toxic abnormal proteins. San1 them [52]. In addition to this arrangement to minimize targets misfolded substrates through highly disordered N- and unfavorable early misfolding and aggregation, cells have C-terminal regions that retain substrates identification mod- evolved ribosomal-associated chaperones, which promote ules [49, 50]. It is reasonable to believe that, probably, other protein folding [53]. In bacteria, trigger factor, the archaeal E3 ubiquitin ligases exhibit such capability and may contrib- and eukaryotic nascent polypeptide-associated complex, ute in protein quality control mechanism. and particular heat shock proteins serve as ribosomal- associated chaperones [9, 54, 55]. Because of high local Ribosomal Association of Quality Control Mechanism concentration of nonnative proteins, most probably, aggre- gation propensity of nascent polypeptides chains sharply Protein synthesis cellular machinery, i.e., ribosomes, trans- increased at polyribosomal site. forms messenger RNA (mRNA) transcript into nascent Still, it is an unsolved puzzle that, under such macromo- polypeptide chains. Ribosomes hold about 30 % of entire lecular crowded environment, how it is possible to maintain cell bulk, and approximately 105 and 106 ribosomes exist in proper quality control mechanism? Recently, it was Mol Neurobiol demonstrated that ribosomal-associated Ltn1, a really inter- design an accurate scheme for the clearance of misfolded esting new gene domain containing E3 ubiquitin ligase, pro- proteins. vides quality control mechanism against newly synthesized nonstop proteins [56]. Recently, it was shown that mutations Disposal of Endoplasmic Reticulum-Anchored Misfolded in LISTERIN, which is a homolog of Ltn1, cause neurode- Proteins generation in mice and critically involved in embryonic de- velopment [57]. It was reported that proteasomal subunit 19S Endoplasmic reticulum (ER) is an important cell organelle coimmunoprecipitates with ubiquitin ligases [58]. Saccharo- for the posttranslational modifications of nascent polypep- myces cerevisiae Not4 RING finger domain E3 ubiquitin tide chains synthesized by ribosomes. ER membrane- ligase, involved in transcriptional regulation and transcription- anchored gp78 RING finger domain E3 ubiquitin ligase is al elongation, has been detectable in polysome fractions encoded by tumor autocrine motility factor receptor gene. [59, 60]. These studies provide a clue that protein quality Gp78 targets ataxin-3 and superoxide dismutase-1 for pro- control mechanism and degradation of nascent polypeptides teasomal degradation involved in Machado–Joseph disease/ chains are possible during protein synthesis. However, we are spinocerebellar ataxia type 3 and familial amyotrophic lat- far from understanding the exact molecular mechanism of eral sclerosis neurodegenerative disease, respectively [71]. ribosomal-associated E3 ubiquitin ligases that are implicated ER-associated gp78 E3 ubiquitin ligase also recognizes in early quality control events. CFTRΔF508 and promotes their polyubiquitylation [72]. Apart from correct folding of nascent polypeptide chains, Harmonious Interaction of E3 Ubiquitin Ligases to ensure proper function of a protein, ER cellular network with Chaperones helps in the placement of polypeptide chains into their correct subcellular localization. Gene SMAD ubiquitination Capacity of refolding of misfolded proteins via chaperones regulatory factor 1 (Smurf1) encodes Smurf1 E3 ubiquitin or degradation through E3 ubiquitin ligases determines the ligase [73]. Smurf1 targets Wolfram syndrome (WFS1) pro- overall efficiency of cellular quality control system in cells tein for proteasomal degradation at ER, and its endogenous [61]. During stress conditions, cells need extensive protein- levels are elevated against ER stress condition [74]. folding capacity through chaperones to overcome the expo- Misfolded protein aggregation interrupts the normal nential load of misfolded proteins [62]. Because all folding structure and function of ER and generates ER stress, which attempts are not successful in one go and to avoid unsolic- consequently leads to cell death governed by proteasome ited aggregation of this failure, UPS immediately governs [75, 76]. BAX-induced inhibitor, bifunctional ap- QC E3 ubiquitin ligases for intracellular degradation of optosis regulator, is an ER-linked RING finger type E3 misfolded proteins. Under such improper protein-folding ubiquitin ligase, which is mainly expressed in neurons and capacity, it is not well known that how chaperones help E3 protects cell death against various cell death stimuli, e.g., ubiquitin ligases in aberrant protein recognition process and ER stress [77]. In the same context, ER-linked E3 ubiquitin make their job easier. Earlier studies and models suggest ligase Der3/Hrd1p contains six transmembrane domains, that the best instantaneously available help is possible and membrane topology of Hrd1p is implicated in endoplas- through chaperones in this triage process [63–66]. CHIP mic reticulum-associated degradation (ERAD) pathway (C-terminus of Hsc70-interacting protein) is a tetratricopep- [78]. Under ER stress conditions, to avoid aggravation of tide repeat containing co-chaperone protein, which controls proteoxicity, cells actively governs ER-associated E3s for chaperone activities of Hsc70 [67]. This U-box domain the clearance of damaged proteins through endoplasmic containing E3 ubiquitin ligase CHIP cooperates with HSP reticulum-associated degradation pathway. ERAD-E3 ubiq- family chaperones and facilitates the ubiquitinylation of uitin ligase ret finger protein 2 is a family member of RBCC unfolded proteins [68]. (RING finger, B-box, and coiled-coil) proteins that associate Cullin5 RING E3 ubiquitin ligase interacts with with valosin-containing protein (VCP), T cell receptor sub- chaperone complex and promotes the degradation of its unit CD3-δ, and Ubc6 [79]. Several E3 ubiquitin ligases client proteins, i.e., ErbB2 and HIF1-α [69]. Similarly, have been found to be involved in mammalian endoplasmic another homologous to E6-AP C-terminus (HECT) domain reticulum-associated degradation pathway. RING finger E3 ubiquitin ligase E6-AP also promotes the ubiquitinyla- protein 103 Kf-1 is an ER-localized E3 ubiquitin ligase, tion of misfolded proteins captured by Hsp70 molecular and its expression level has been found increased in Alz- chaperone [70]. Undoubtedly, these observations clearly heimer’s disease patient; Kf-1 interacts with Derlin–VCP indicate that E3 ubiquitin ligases take help from various complex and acts as component of ERAD pathway [80, chaperones. Most possibly, interaction of various E3 ubiq- 81]. Human ER membrane E3 ubiquitin ligase TEB4 uitin ligases with chaperones facilitate their misfolded pro- (MARCH-VI) is an ortholog of Doa10 and induces the teins recognition mechanism, and these cumulative efforts degradation of type 2 iodothyronine deiodinase [82, 83]. Mol Neurobiol

Hand to Hand Coordination are not completely known? Earlier studies indicate that the most suspicious interacting proteins are chaperones, com- Deregulation of ubiquitin proteasome system can lead to ponent of UPS, and transcriptional factors [99]. As we know intracellular accumulation of damaged or abnormal proteins that few QC E3 ubiquitin ligases are dedicated for misfolded and consequently leads to neurodegeneration [84]. To chal- protein clearance process, but the reason of recruitment with lenge this condition, cells possess highly evolved protein misfolded protein is not known yet. Still, it is a big question quality control system which is well organized with various of debate whether QC E3 ubiquitin ligase recruitment with quality control E3 ubiquitin ligases. Interestingly, few stud- damaged proteins facilitates their degradation or may un- ies suggest that cooperation of various E3 ligases among knowingly generate a mysterious problem. themselves may play a critical role in substrate recognition UBE3A gene encodes a conserved HECT domain family and, most probably, promotes an efficient degradation via E3 ubiquitin ligase, i.e., E6-AP, mutated in Angelman men- ubiquitin system. Ubr1 gene encodes UBR box-containing tal retardation syndrome [100]. Recently, we have observed Ubr1 (ubiquitin-protein ligase E3 component n-recognin 1), that E6-AP retains QC properties and actively recruits with a 225-kDa RING finger domain protein [85]. Lack of func- cystic fibrosis transmembrane conductance regulator aggre- tion of UBR1 ubiquitin ligase causes mental retardation somes. E6-AP recruitment/co-localization facilitates the Johanson–Blizzard syndrome [86]. Ufd4 is a HECT domain ubiquitination of misfolded proteins anchored by Hsp70 168-kDa E3 ubiquitin ligase, joins ubiquitin carrier 4 (Ubc4) chaperone [70]. In another study, we have demonstrated that or ubiquitin carrier 5 (Ubc5) E2 enzymes for functional E6-AP recruits to neuronal intranuclear inclusions in Hun- activity in ubiquitin-fusion degradation pathway [87, 88]. tington’s disease transgenic mice model. E6-AP alleviates Dual proteolytic pathways co-target Mgt1 O6meG-DNA proteoxicity mediated by expanded polyglutamine proteins alkyltransferase protein for polyubiquitylation, mediated via degradation through ubiquitination [35]. Lafora disease by both Ubr1 and Ufd4 E3 ubiquitin ligases, and this coop- is a progressive neurodegenerative disease caused by muta- eration enhances the yield of polyubiquitylated Mgt1 [89]. tion in NHLRC1 gene, which encodes RING finger malin Physical and functional interaction complexes of HECT- E3 ubiquitin ligase [28, 101]. Proteasomal inhibition treat- type Ufd4 and RING-type Ubr1 are more effective to pro- ment leads to generation of aggresomes which are positive duce longer polyubiquitin chain linked with substrates with with malin and other UPS components [102]. In the same their E2 ubiquitin carrier enzymes Ubc4/Ubc5 and Rad6, context, several other studies report that parkin is another E3 respectively [90]. ubiquitin ligase, which co-localizes with aggresome after To reduce proteoxicity, misfolded protein degradation proteasomal inhibition [103–105]. emerges as a cellular adaptability for clearance of unwanted aggregates in cells. Ubr1 and Ubr2 ubiquitin ligases promote Sugar Chains Recognition the ubiquitinylation of unfolded polypeptides and stimulate the degradation of damaged proteins. Ubr1 specifically pro- In protein quality control process, newly synthesized pro- motes the ubiquitinylation of damaged/aberrant proteins [91, teins enter into ER through a channel termed as “translocon” 92]. To ensure correct cellular functioning, three-dimensional for N-glycosylation [106–108]. Earlier, it has been reported natively folded protein structures are essential in crowded that many E3s are implicated in the ER-associated degrada- milieu. E3 ubiquitin ligase San1 degrades misfolded nuclear tion pathway. E3 ubiquitin ligases also help in the selective proteins, and Ubr1 is involved in “N-end rule” pathway elimination of glycoproteins. However, the molecular mech- [93–96]. Recently, it was shown that both Ubr1 and San1 anism underlying the ability of E3 ubiquitin ligases to regulate proteotoxic stress via different approaches for cyto- recognize target glycoproteins remains to be understood. plasmic QC process. San1 needs chaperones function for Recently, a novel approach adopted by few ubiquitin ligases nuclear delivery of substrates, instead of this Ubr1 that gov- in the recognition and ubiquitylation of N-linked glycopro- erns chaperones for direct substrates ubiquitination [47]. teins that act as major players in ERAD pathway has been highlighted. Skp1-Cullin1-Fbx2-Roc1 (SCFFbx2) ubiquitin Modulated Recruitment with Misfolded Proteins ligase complex utilizes N-glycan signal for degradation. In this complex ubiquitin ligase, Fbs2 protein interacts with Protein misfolding, amyloid fibrils accumulation, and ag- endogenous N-linked high-mannose oligosaccharides con- gregation are well-known conformation changes in protein- taining glycoproteins and promotes their proteasomal deg- associated neurodegenerative diseases [97]. Recent evi- radation [109]. Fbx2 expression levels are very high in the dence suggests that aggravation of these aberrant proteina- organ of Corti [110]. Fbx2 lack of function leads to degen- ceous species cause neuronal apoptosis [98]. But how eration in epithelial support cells of the organ of Corti, and protein misfolding initiates neurodegeneration and what hearing loss in Fbxo2-/- mice began, which may be due to other factors are recruited with those preformed aggregates aberrant quality control mechanism of glycoprotein [111]. Mol Neurobiol

Another F-box protein Fbs2 acts as E3 ubiquitin ligase, identification and selective degradation will help in the which is bound with N-glycan of T cell receptor α subunit, development of new proteotoxicity-associated therapies. and promotes its degradation through ERAD pathway [112]. In SCFFbs1.2 ubiquitin ligase complex, Fbs1 and Fbs2 Acknowledgments This work was supported by the Department of proteins preferentially associate with denatured glycopro- Biotechnology, Government of India. AM was supported by Ramalin- ganswami Fellowship from the Department of Biotechnology, Govern- teins as compared to properly folded proteins. This study ment of India. The authors would like to thank Mr. Bharat Pareek for suggests that, due to exposed chitobiose structure, Fbs can his support and management during manuscript preparation. recognize and discriminate folded glycoproteins over un- folded glycoproteins [113]. Interaction of HRD1 E3 ubiq- Conflict of interest None. uitin ligase and SCFFbs2 ubiquitin ligase complex with uncleaved precursor of asialoglycoprotein receptor H2a pro- References motes its degradation [114].

1. Bucciantini M, Giannoni E, Chiti F, Baroni F, Formigli L, Zurdo Key Questions and Perspectives J, Taddei N, Ramponi G, Dobson CM, Stefani M (2002) Inherent toxicity of aggregates implies a common mechanism for protein misfolding diseases. Nature 416(6880):507–511. doi:10.1038/ Exposure to various cellular insults generates proteotoxic 416507a416507a stress and leads to overburden on cellular protein quality 2. Lorenzo A, Yankner B (1994) Beta-amyloid neurotoxicity requires control system; however, the molecular mechanism of protein fibril formation and is inhibited by congo red. Proc Natl Acad Sci U S A 91(25):12243–12250 quality control is unclear. Earlier studies suggest that molec- 3. Thomas T, Thomas G, McLendon C, Sutton T, Mullan M (1996) ular chaperones and quality control E3 ubiquitin ligases play a beta-Amyloid-mediated vasoactivity and vascular endothelial pivotal role in protein quality control mechanism. Individual damage. Nature 380(6570):168–239. doi:10.1038/380168a0 quality control E3 ubiquitin ligase retains their own particular 4. Lindner AB, Demarez A (2009) Protein aggregation as a para- digm of aging. Biochim Biophys Acta 1790(10):980–996. function, but the interaction with different quality control doi:10.1016/j.bbagen.2009.06.005 members, such as Hsp/chaperones, transcriptional factors, 5. Douglas P, Cyr D (2010) Interplay between protein homeostasis and UPS members, seems to be a critical role in cellular networks in protein aggregation and proteotoxicity. Biopolymers – proteome. Many questions remain unanswered, for example, 93(3):229 265. doi:10.1002/bip.21304 6. Glickman M, Ciechanover A (2002) The ubiquitin-proteasome pro- how E3 ubiquitin ligases determine the specificity for a critical teolytic pathway: destruction for the sake of construction. Physio- substrate in a crowded cellular milieu? How quality control E3 logical Reviews 82(2):373–801. doi:10.1152/physrev.00027.2001 ubiquitin ligases specifically recognize and differentiate be- 7. Glabe C (2006) Common mechanisms of amyloid oligomer path- tween nonnative/damaged proteins as compared to native ogenesis in degenerative disease. Neurobiology of Aging 27 (4):570–575. doi:10.1016/j.neurobiolaging.2005.04.017 proteins? To understand why aberrant function of E3 ubiquitin 8. Taylor JP, Hardy J, Fischbeck KH (2002) Toxic proteins in ligases is implicated in the progression of misfolded protein neurodegenerative disease. Science 296(5575):1991–1995. conformation disorders, it is mandatory to identify the molec- doi:10.1126/science.1067122296/5575/1991 ular pathways that involve E3 ubiquitin ligases. It is very 9. Hartl F, Hayer-Hartl M (2002) Molecular chaperones in the : from nascent chain to folded protein. Science (New important to understand how E3 ubiquitin ligases sense stress York, NY) 295(5561):1852–1860. doi:10.1126/science.1068408 conditions and recognize misfolded proteins for further clear- 10. Morimoto R (1993) Cells in stress: transcriptional activation of heat ance by various approaches? shock . Science (New York, NY) 259(5100):1409–1419 It is noteworthy that several neurodegenerative diseases 11. Parsell DA, Lindquist S (1993) The function of heat-shock proteins in stress tolerance: degradation and reactivation are associated with the failure in proteolytic machinery, of damaged proteins. Annu Rev Genet 27:437–496. possibly due to failure in their recognition and selective doi:10.1146/annurev.ge.27.120193.002253 degradation through E3 ubiquitin ligases. Future studies 12. Auluck PK, Chan HY, Trojanowski JQ, Lee VM, Bonini NM should be devoted to understand the problem of aberrant (2002) Chaperone suppression of alpha-synuclein toxicity in a Drosophila model for Parkinson’s disease. Science 295 protein interactions, their involvement in neuronal dysfunc- (5556):865–868. doi:10.1126/science.1067389 tion, and investigating how E3 ubiquitin ligases rescue their 13. Kieran D, Kalmar B, Dick JR, Riddoch-Contreras J, Burnstock effect? Principally, detailed study of aberrant protein inte- G, Greensmith L (2004) Treatment with arimoclomol, a coin- grators and analysis of their interaction with other cellular ducer of heat shock proteins, delays disease progression in ALS mice. Nat Med 10(4):402–405. doi:10.1038/nm1021 pathways would enable us to answer these questions. We 14. Wacker JL, Zareie MH, Fong H, Sarikaya M, Muchowski PJ expect that various experimental studies of the cross talk (2004) Hsp70 and Hsp40 attenuate formation of spherical and between E3 ubiquitin ligases and other proteotoxic response annular polyglutamine oligomers by partitioning monomer. Nat – mechanisms in cells will suggest a further understanding of Struct Mol Biol 11(12):1215 1222. doi:10.1038/nsmb860 15. Goldberg A (2003) Protein degradation and protection against cytoprotective responses. A better understanding of involve- misfolded or damaged proteins. Nature 426(6968):895–904. ment of E3 ubiquitin ligases in the misfolded protein doi:10.1038/nature02263 Mol Neurobiol

16. Pickart C (2004) Back to the future with ubiquitin. Cell 116 for proteasomal degradation and suppresses polyglutamine pro- (2):181–271 tein aggregation and toxicity. J Biol Chem 283(12):7648–7656. 17. Baumeister W, Walz J, Zühl F, Seemüller E (1998) The protea- doi:10.1074/jbc.M706620200 some: paradigm of a self-compartmentalizing protease. Cell 92 36. Mishra A, Godavarthi SK, Jana NR (2009) UBE3A/E6-AP reg- (3):367–447 ulates cell proliferation by promoting proteasomal degradation of 18. Powers E, Morimoto R, Dillin A, Kelly J, Balch W (2009) p27. Neurobiol Dis 36(1):26–34. doi:10.1016/j.nbd.2009.06.010 Biological and chemical approaches to diseases of proteostasis 37. Mishra A, Jana NR (2008) Regulation of turnover of tumor deficiency. Annu Rev Biochem 78:959–1050. doi:10.1146/ suppressor p53 and cell growth by E6-AP, a ubiquitin protein annurev.biochem.052308.114844 ligase mutated in Angelman mental retardation syndrome. Cell 19. Grune T, Jung T, Merker K, Davies K (2004) Decreased proteol- Mol Life Sci 65(4):656–666. doi:10.1007/s00018-007-7476-1 ysis caused by protein aggregates, inclusion bodies, plaques, lip- 38. Johnston J, Ward C, Kopito R (1998) Aggresomes: a cellular ofuscin, ceroid, and ‘aggresomes’ during , aging, response to misfolded proteins. J Cell Biol 143(7):1883–1981 and disease. Int J Biochem Cell Biol 36(12):2519–2549. 39. Wigley W, Fabunmi R, Lee M, Marino C, Muallem S, DeMartino doi:10.1016/j.biocel.2004.04.020 G, Thomas P (1999) Dynamic association of proteasomal ma- 20. Paul S (2008) Dysfunction of the ubiquitin-proteasome system in chinery with the centrosome. J Cell Biol 145(3):481–571 multiple disease conditions: therapeutic approaches. Bioessays 30 40. Mitsui K, Nakayama H, Akagi T, Nekooki M, Ohtawa K, Takio (11–12):1172–1256. doi:10.1002/bies.20852 K, Hashikawa T, Nukina N (2002) Purification of polyglutamine 21. Dobson CM (2003) Protein folding and misfolding. Nature 426 aggregates and identification of elongation factor-1alpha and heat (6968):884–890. doi:10.1038/nature02261 shock protein 84 as aggregate-interacting proteins. J Neurosci 22 22. Harjes P, Wanker E (2003) The hunt for huntingtin function: (21):9267–9344 interaction partners tell many different stories. Trends Biochem 41. Li JY, Englund E, Widner H, Rehncrona S, Björklund A, Lindvall Sci 28(8):425–458 O, Brundin P (2010) Characterization of pathology in 23. Sullivan E, Weirich C, Guyon J, Sif S, Kingston R (2001) 12- and 16-year-old intrastriatal mesencephalic grafts surviving in Transcriptional activation domains of human heat shock factor a patient with Parkinson’s disease. Mov Disord 25(8):1091–1097. 1 recruit human SWI/SNF. Mol Cell Biol 21(17):5826–5863 doi:10.1002/mds.23012 24. Yamanaka T, Miyazaki H, Oyama F, Kurosawa M, Washizu C, 42. Bazan NG, Eady TN, Khoutorova L, Atkins KD, Hong S, Lu Y, Doi H, Nukina N (2008) Mutant Huntingtin reduces HSP70 Zhang C, Jun B, Obenaus A, Fredman G, Zhu M, Winkler JW, expression through the sequestration of NF-Y transcription factor. Petasis NA, Serhan CN, Belayev L (2012) Novel aspirin-triggered EMBO J 27(6):827–866. doi:10.1038/emboj.2008.23 neuroprotectin D1 attenuates cerebral ischemic injury after experi- 25. Olzscha H, Schermann SM, Woerner AC, Pinkert S, Hecht MH, mental stroke. Exp Neurol 236(1):122–130. doi:10.1016/ Tartaglia GG, Vendruscolo M, Hayer-Hartl M, Hartl FU, Vabulas j.expneurol.2012.04.007 RM (2011) Amyloid-like aggregates sequester numerous meta- 43. Calandria JM, Mukherjee PK, de Rivero Vaccari JC, Zhu M, stable proteins with essential cellular functions. Cell 144(1):67– Petasis NA, Bazan NG (2012) Ataxin-1 poly(Q)-induced proteo- 78. doi:10.1016/j.cell.2010.11.050 toxic stress and apoptosis are attenuated in neural cells by doco- 26. Kopito R (2000) Aggresomes, inclusion bodies and protein ag- sahexaenoic acid-derived neuroprotectin D1. J Biol Chem 287 gregation. Trends Cell Biol 10(12):524–554 (28):23726–23739. doi:10.1074/jbc.M111.287078 27. Olzmann J, Li L, Chin L (2008) Aggresome formation and 44. Schubert U, Antón L, Gibbs J, Norbury C, Yewdell J, Bennink J (2000) neurodegenerative diseases: therapeutic implications. Curr Med Rapid degradation of a large fraction of newly synthesized proteins by Chem 15(1):47–107 . Nature 404(6679):770–774. doi:10.1038/35008096 28. Gentry M, Worby C, Dixon J (2005) Insights into Lafora disease: 45. Yewdell J, Antón L, Bennink J (1996) Defective ribosomal prod- malin is an E3 ubiquitin ligase that ubiquitinates and promotes the ucts (DRiPs): a major source of antigenic peptides for MHC class degradation of laforin. Proc Natl Acad Sci U S A 102(24):8501– I molecules? J Immunol 157(5):1823–1829 8507. doi:10.1073/pnas.0503285102 46. Berke S, Paulson H (2003) Protein aggregation and the ubiquitin 29. Rao SN, Maity R, Sharma J, Dey P, Shankar SK, Satishchandra P, proteasome pathway: gaining the UPPer hand on neurodegenera- Jana NR (2010) Sequestration of chaperones and proteasome into tion. Curr Opin Genet Dev 13(3):253–314 Lafora bodies and proteasomal dysfunction induced by Lafora 47. Heck J, Cheung S, Hampton R (2010) Cytoplasmic protein qual- disease-associated mutations of malin. Hum Mol Genet 19 ity control degradation mediated by parallel actions of the E3 (23):4726–4734. doi:10.1093/hmg/ddq407 ubiquitin ligases Ubr1 and San1. Proc Natl Acad Sci U S A 107 30. Singh S, Satishchandra P, Shankar SK, Ganesh S (2008) Lafora (3):1106–1117. doi:10.1073/pnas.0910591107 disease in the Indian population: EPM2A and NHLRC1 gene 48. Matsuo Y, Kishimoto H, Tanae K, Kitamura K, Katayama S, mutations and their impact on subcellular localization of laforin Kawamukai M (2011) Nuclear protein quality is regulated by and malin. Hum Mutat 29(6):E1–12. doi:10.1002/humu.20737 the ubiquitin-proteasome system through the activity of Ubc4 31. Kahle PJ, Haass C (2004) How does parkin ligate ubiquitin to and San1 in fission yeast. J Biol Chem 286(15):13775–13865. Parkinson’s disease? EMBO Rep 5(7):681–685. doi:10.1038/ doi:10.1074/jbc.M110.169953 sj.embor.74001887400188 49. Hampton R (2011) San1-mediated quality control: substrate rec- 32. Lenartowski R, Gumowski K, Goc A (2008) The multifunction- ognition “sans” chaperones. Mol Cell 41(1):2–5. doi:10.1016/ ality of CHIP protein in the protein quality-control system. Post- j.molcel.2010.12.022 epy Hig Med Dosw (Online) 62:297–308 50. Rosenbaum J, Fredrickson E, Oeser M, Garrett-Engele C, Locke 33. Chhangani D, Joshi AP, Mishra A (2012) E3 ubiquitin ligases in M, Richardson L, Nelson Z, Hetrick E, Milac T, Gottschling D, protein quality control mechanism. Mol Neurobiol 45(3):571– Gardner R (2011) Disorder targets misorder in nuclear quality 585. doi:10.1007/s12035-012-8273-x control degradation: a disordered ubiquitin ligase directly recog- 34. Fu L, Gao Y-S, Sztul E (2005) Transcriptional repression and cell nizes its misfolded substrates. Mol Cell 41(1):93–199. death induced by nuclear aggregates of non-polyglutamine protein. doi:10.1016/j.molcel.2010.12.004 Neurobiol Dis 20(3):656–721. doi:10.1016/j.nbd.2005.05.015 51. Bashan A, Yonath A (2008) Correlating ribosome function with 35. Mishra A, Dikshit P, Purkayastha S, Sharma J, Nukina N, Jana high-resolution structures. Trends Microbiol 16(7):326–361. NR (2008) E6-AP promotes misfolded polyglutamine proteins doi:10.1016/j.tim.2008.05.001 Mol Neurobiol

52. Brandt F, Etchells S, Ortiz J, Elcock A, Hartl F, Baumeister W 70. Mishra A, Godavarthi SK, Maheshwari M, Goswami A, Jana NR (2009) The native 3D organization of bacterial polysomes. Cell (2009) The ubiquitin ligase E6-AP is induced and recruited to 136(2):261–332. doi:10.1016/j.cell.2008.11.016 aggresomes in response to proteasome inhibition and may be in- 53. Koplin A, Preissler S, Ilina Y, Koch M, Scior A, Erhardt M, volved in the ubiquitination of Hsp70-bound misfolded proteins. J Deuerling E (2010) A dual function for chaperones SSB-RAC Biol Chem 284(16):10537–10545. doi:10.1074/jbc.M806804200 and the NAC nascent polypeptide-associated complex on ribo- 71. Ying Z, Wang H, Fan H, Zhu X, Zhou J, Fei E, Wang G (2009) somes. J Cell Biol 189(1):57–68. doi:10.1083/jcb.200910074 Gp78, an ER associated E3, promotes SOD1 and ataxin-3 degrada- 54. Kramer G, Boehringer D, Ban N, Bukau B (2009) The ribosome tion. Hum Mol Genet 18(22):4268–4349. doi:10.1093/hmg/ddp380 as a platform for co-translational processing, folding and target- 72. Morito D, Hirao K, Oda Y, Hosokawa N, Tokunaga F, Cyr DM, ing of newly synthesized proteins. Nat Struct Mol Biol 16 Tanaka K, Iwai K, Nagata K (2008) Gp78 cooperates with RMA1 in (6):589–686. doi:10.1038/nsmb.1614 endoplasmic reticulum-associated degradation of CFTRDeltaF508. 55. Rauch T, Hundley H, Pfund C, Wegrzyn R, Walter W, Kramer G, Mol Biol Cell 19(4):1328–1336. doi:10.1091/mbc.E07-06-0601 Kim S-Y, Craig E, Deuerling E (2005) Dissecting functional 73. Zhu H, Kavsak P, Abdollah S, Wrana JL, Thomsen GH (1999) A similarities of ribosome-associated chaperones from Saccharomy- SMAD ubiquitin ligase targets the BMP pathway and affects embry- ces cerevisiae and Escherichia coli. Mol Microbiol 57(2):357– onic pattern formation. Nature 400(6745):687–693. doi:10.1038/23293 422. doi:10.1111/j.1365-2958.2005.04690.x 74. Guo X, Shen S, Song S, He S, Cui Y, Xing G, Wang J, Yin Y, Fan 56. Bengtson MH, Joazeiro CA (2010) Role of a ribosome-associated L, He F, Zhang L (2011) The E3 ligase Smurf1 regulates Wolfram E3 ubiquitin ligase in protein quality control. Nature 467 syndrome protein stability at the endoplasmic reticulum. J Biol (7314):470–473. doi:10.1038/nature09371 Chem 286(20):18037–18047. doi:10.1074/jbc.M111.225615 57. Chu J, Hong N, Masuda C, Jenkins B, Nelms K, Goodnow C, 75. Xu C, Bailly-Maitre B, Reed JC (2005) Endoplasmic reticulum Glynne R, Wu H, Masliah E, Joazeiro C, Kay S (2009) A mouse stress: cell life and death decisions. J Clin Invest 115(10):2656– forward genetics screen identifies LISTERIN as an E3 ubiquitin 2664. doi:10.1172/JCI26373 ligase involved in neurodegeneration. Proc Natl Acad Sci U S A 76. Egger L, Madden DT, Rheme C, Rao RV, Bredesen DE (2007) 106(7):2097–2200. doi:10.1073/pnas.0812819106 Endoplasmic reticulum stress-induced cell death mediated by the 58. Verma R, Chen S, Feldman R, Schieltz D, Yates J, Dohmen J, proteasome. Cell Death Differ 14(6):1172–1180. doi:10.1038/ Deshaies R (2000) Proteasomal : identification of sj.cdd.4402125 nucleotide-sensitive proteasome-interacting proteins by mass 77. Roth W, Kermer P, Krajewska M, Welsh K, Davis S, Krajewski S, spectrometric analysis of affinity-purified proteasomes. Mol Biol Reed JC (2003) Bifunctional apoptosis inhibitor (BAR) protects 11(10):3425–3464 neurons from diverse cell death pathways. Cell Death Differ 10 59. Collart M (2003) Global control of in yeast by (10):1178–1187. doi:10.1038/sj.cdd.44012874401287 the Ccr4-Not complex. Gene 313:1–17 78. Deak PM, Wolf DH (2001) Membrane topology and function of 60. Panasenko O, Collart M (2012) Presence of Not5 and ubiquitinated Der3/Hrd1p as a ubiquitin-protein ligase (E3) involved in endo- Rps7A in polysome fractions depends upon the Not4 E3 ligase. Mol plasmic reticulum degradation. J Biol Chem 276(14):10663– Microbiol 83(3):640–693. doi:10.1111/j.1365-2958.2011.07957.x 10669. doi:10.1074/jbc.M008608200M008608200 61. Gao X, Hu H (2008) Quality control of the proteins associated 79. Lerner M, Corcoran M, Cepeda D, Nielsen M, Zubarev R, Pontén with neurodegenerative diseases. Acta Biochim Biophys Sin F, Uhlén M, Hober S, Grandér D, Sangfelt O (2007) The RBCC (Shanghai) 40(7):612–618 gene RFP2 (Leu5) encodes a novel transmembrane E3 ubiquitin 62. Ellis J (1987) Proteins as molecular chaperones. Nature 328:378– ligase involved in ERAD. Mol Biol Cell 18(5):1670–1752. 387. doi:10.1038/328378a0 doi:10.1091/mbc.E06-03-0248 63. Bercovich B, Stancovski I, Mayer A, Blumenfeld N, Laszlo A, 80. Maruyama Y, Yamada M, Takahashi K (2008) Ubiquitin ligase Schwartz AL, Ciechanover A (1997) Ubiquitin-dependent degra- Kf-1 is involved in the endoplasmic reticulum-associated degra- dation of certain protein substrates in vitro requires the molecular dation pathway. Biochem Biophys Res Commun 374(4):737– chaperone Hsc70. J Biol Chem 272(14):9002–9010 741. doi:10.1016/j.bbrc.2008.07.126 64. Lee D, Sherman M, Goldberg A (1996) Involvement of the 81. Yasojima K, Tsujimura A, Mizuno T, Shigeyoshi Y, Inazawa J, molecular chaperone Ydj1 in the ubiquitin-dependent degrada- Kikuno R, Kuma K, Ohkubo K, Hosokawa Y, Ibata Y, Abe T, tion of short-lived and abnormal proteins in Saccharomyces cer- Miyata T, Matsubara K, Nakajima K, Hashimoto-Gotoh T (1997) evisiae. Mol Cell Biol 16(9):4773–4854 Cloning of human and mouse cDNAs encoding novel zinc finger 65. McClellan A, Frydman J (2001) Molecular chaperones and the art proteins expressed in cerebellum and . Biochem of recognizing a lost cause. Nat Cell Biol 3(2):E51–3. doi:10.1038/ Biophys Res Commun 231(2):481–487 35055162 82. Kreft SG, Wang L, Hochstrasser M (2006) Membrane topology 66. Plemper R, Böhmler S, Bordallo J, Sommer T, Wolf D (1997) of the yeast endoplasmic reticulum-localized ubiquitin ligase Mutant analysis links the translocon and BiP to retrograde protein Doa10 and comparison with its human ortholog TEB4 transport for ER degradation. Nature 388(6645):891–896. (MARCH-VI). J Biol Chem 281(8):4646–4653. doi:10.1074/ doi:10.1038/42276 jbc.M512215200 67. Ballinger C, Connell P, Wu Y, Hu Z, Thompson L, Yin L, 83. Zavacki AM, Arrojo EDR, Freitas BC, Chung M, Harney JW, Egri Patterson C (1999) Identification of CHIP, a novel tetratricopep- P, Wittmann G, Fekete C, Gereben B, Bianco AC (2009) The E3 tide repeat-containing protein that interacts with heat shock pro- ubiquitin ligase TEB4 mediates degradation of type 2 iodothyronine teins and negatively regulates chaperone functions. Mol Cell Biol deiodinase. Mol Cell Biol 29(19):5339–5347. doi:10.1128/ 19(6):4535–4580 MCB.01498-08 68. Murata S, Minami Y, Minami M, Chiba T, Tanaka K (2001) CHIP is 84. Shah IM, Di Napoli M (2007) The ubiquitin-proteasome system a chaperone-dependent E3 ligase that ubiquitylates unfolded protein. and proteasome inhibitors in central nervous system diseases. EMBO Rep 2(12):1133–1141. doi:10.1093/embo-reports/kve246 Cardiovasc Hematol Disord Drug Targets 7(4):250–273 69. Ehrlich E, Wang T, Luo K, Xiao Z, Niewiadomska A, Martinez T, 85. Kwon Y, Reiss Y, Fried V, Hershko A, Yoon J, Gonda D, Sangan Xu W, Neckers L, Yu X-F (2009) Regulation of Hsp90 client P, Copeland N, Jenkins N, Varshavsky A (1998) The mouse and proteins by a Cullin5-RING E3 ubiquitin ligase. Proc Natl Acad human genes encoding the recognition component of the N-end Sci U S A 106(48):20330–20335. doi:10.1073/pnas.0810571106 rule pathway. Proc Natl Acad Sci U S A 95(14):7898–8801 Mol Neurobiol

86. Zenker M, Mayerle J, Lerch M, Tagariello A, Zerres K, Durie P, 101. Chan E, Young E, Ianzano L, Munteanu I, Zhao X, Christopoulos C, Beier M, Hülskamp G, Guzman C, Rehder H, Beemer F, Hamel Avanzini G, Elia M, Ackerley C, Jovic N, Bohlega S, Andermann E, B, Vanlieferinghen P, Gershoni-Baruch R, Vieira M, Dumic M, Rouleau G, Delgado-Escueta A, Minassian B, Scherer S (2003) Auslender R, Gil-da-Silva-Lopes V, Steinlicht S, Rauh M, Shalev Mutations in NHLRC1 cause progressive myoclonus epilepsy. Nat S, Thiel C, Ekici A, Winterpacht A, Kwon Y, Varshavsky A, Reis Genet 35(2):125–132. doi:10.1038/ng1238 A (2005) Deficiency of UBR1, a ubiquitin ligase of the N-end 102. Mittal S, Dubey D, Yamakawa K, Ganesh S (2007) Lafora rule pathway, causes pancreatic dysfunction, malformations and disease proteins malin and laforin are recruited to aggresomes mental retardation (Johanson–Blizzard syndrome). Nat Genet 37 in response to proteasomal impairment. Hum Mol Genet 16 (12):1345–1395. doi:10.1038/ng1681 (7):753–815. doi:10.1093/hmg/ddm006 87. Johnson E, Ma P, Ota I, Varshavsky A (1995) A proteolytic 103. Junn E, Lee S, Suhr U, Mouradian M (2002) Parkin accumulation pathway that recognizes ubiquitin as a degradation signal. J Biol in aggresomes due to proteasome impairment. J Biol Chem 277 Chem 270(29):17442–17498 (49):47870–47877. doi:10.1074/jbc.M203159200 88. Koegl M, Hoppe T, Schlenker S, Ulrich H, Mayer T, Jentsch S 104. Muqit M, Davidson S, Payne Smith M, MacCormac L, Kahns S, (1999) A novel ubiquitination factor, E4, is involved in multi- Jensen P, Wood N, Latchman D (2004) Parkin is recruited into ubiquitin chain assembly. Cell 96(5):635–679 aggresomes in a stress-specific manner: over-expression of parkin 89. Hwang CS, Shemorry A, Varshavsky A (2009) Two proteolytic reduces aggresome formation but can be dissociated from par- pathways regulate DNA repair by cotargeting the Mgt1 alkylgua- kin’s effect on neuronal survival. Hum Mol Genet 13(1):117–152. nine . Proc Natl Acad Sci U S A 106(7):2142–2147. doi:10.1093/hmg/ddh012 doi:10.1073/pnas.0812316106 105. Zhao J, Ren Y, Jiang Q, Feng J (2003) Parkin is recruited to the 90. Hwang CS, Shemorry A, Auerbach D, Varshavsky A (2010) The centrosome in response to inhibition of proteasomes. J Cell Sci N-end rule pathway is mediated by a complex of the RING-type 116(Pt 19):4011–4020. doi:10.1242/jcs.00700 Ubr1 and HECT-type Ufd4 ubiquitin ligases. Nat Cell Biol 12 106. Ellgaard L, Molinari M, Helenius A (1999) Setting the (12):1177–1262. doi:10.1038/ncb2121 standards: quality control in the secretory pathway. Science 91. Nillegoda N, Theodoraki M, Mandal A, Mayo K, Ren H, Sultana R, 286(5446):1882–1888 Wu K, Johnson J, Cyr D, Caplan A (2010) Ubr1 and Ubr2 function in a 107. Fiedler K, Simons K (1995) The role of N-glycans in the secre- quality control pathway for degradation of unfolded cytosolic proteins. tory pathway. Cell 81(3):309–312 MolBiolCell21(13):2102–2118. doi:10.1091/mbc.E10-02-0098 108. Helenius A, Aebi M (2001) Intracellular functions of N-linked 92. Eisele F, Wolf DH (2008) Degradation of misfolded protein in the glycans. Science 291(5512):2364–2369 cytoplasm is mediated by the ubiquitin ligase Ubr1. FEBS Lett 109. Yoshida Y, Chiba T, Tokunaga F, Kawasaki H, Iwai K, Suzuki T, 582(30):4143–4146. doi:10.1016/j.febslet.2008.11.015 Ito Y, Matsuoka K, Yoshida M, Tanaka K, Tai T (2002) E3 93. Varshavsky A Recent studies of the ubiquitin system and the N- ubiquitin ligase that recognizes sugar chains. Nature 418 end rule pathway. Harvey Lect 96:93-209 (6896):438–442. doi:10.1038/nature00890 94. Varshavsky A (2005) Regulated protein degradation. Trends Bio- 110. Thalmann R, Henzl MT, Thalmann I (1997) Specific proteins of chem Sci 30(6):283–289. doi:10.1016/j.tibs.2005.04.005 the organ of Corti. Acta Otolaryngol 117(2):265–268 95. Vashist S, Kim W, Belden W, Spear E, Barlowe C, Ng D (2001) 111. Nelson RF, Glenn KA, Zhang Y, Wen H, Knutson T, Gouvion Distinct retrieval and retention mechanisms are required for the CM, Robinson BK, Zhou Z, Yang B, Smith RJ, Paulson HL quality control of endoplasmic reticulum protein folding. J Cell (2007) Selective cochlear degeneration in mice lacking the F-box Biol 155(3):355–423. doi:10.1083/jcb.200106123 protein, Fbx2, a glycoprotein-specific ubiquitin ligase subunit. J 96. Wilhovsky S, Gardner R, Hampton R (2000) HRD gene depen- Neurosci 27(19):5163–5171. doi:10.1523/JNEUROSCI.0206- dence of endoplasmic reticulum-associated degradation. Mol Biol 07.2007 Cell 11(5):1697–2405 112. Yoshida Y, Tokunaga F, Chiba T, Iwai K, Tanaka K, Tai T (2003) 97. Ross C, Poirier M (2004) Protein aggregation and neurodegener- Fbs2 is a new member of the E3 ubiquitin ligase family that ative disease. Nat Med 10(Suppl):S10–7. doi:10.1038/nm1066 recognizes sugar chains. J Biol Chem 278(44):43877–43884. 98. Nakamura T, Lipton S (2009) Cell death: protein misfolding and doi:10.1074/jbc.M304157200 neurodegenerative diseases. Apoptosis 14(4):455–523. doi:10.1007/ 113. Yoshida Y, Adachi E, Fukiya K, Iwai K, Tanaka K (2005) s10495-008-0301-y Glycoprotein-specific ubiquitin ligases recognize N-glycans in 99. Kubota H (2009) Quality control against misfolded proteins in unfolded substrates. EMBO Rep 6(3):239–244. doi:10.1038/ the cytosol: a network for cell survival. J Biochem 146(5):609– sj.embor.7400351 625. doi:10.1093/jb/mvp139 114. Groisman B, Avezov E, Lederkremer GZ (2006) The E3 ubiquitin 100. Kishino T, Lalande M, Wagstaff J (1997) UBE3A/E6-AP muta- ligases HRD1 and SCFFbs2 recognize the protein moiety and tions cause . Nat Genet 15(1):70–73. sugar chains, respectively, of an ER-associated degradation sub- doi:10.1038/ng0197-70 strate. Israel Journal of Chemistry 46(2):189–196