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Uversky VN, Madeira PP, Zaslavsky BY. What Can Be Learned from the Partitioning Behavior of Proteins in Aqueous Two-Phase Systems? Int J Mol Sci 2024; 25:6339. [PMID: 38928046 PMCID: PMC11203663 DOI: 10.3390/ijms25126339] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2024] [Revised: 05/31/2024] [Accepted: 06/03/2024] [Indexed: 06/28/2024] Open
Abstract
This review covers the analytical applications of protein partitioning in aqueous two-phase systems (ATPSs). We review the advancements in the analytical application of protein partitioning in ATPSs that have been achieved over the last two decades. Multiple examples of different applications, such as the quality control of recombinant proteins, analysis of protein misfolding, characterization of structural changes as small as a single-point mutation, conformational changes upon binding of different ligands, detection of protein-protein interactions, and analysis of structurally different isoforms of a protein are presented. The new approach to discovering new drugs for a known target (e.g., a receptor) is described when one or more previous drugs are already available with well-characterized biological efficacy profiles.
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Affiliation(s)
- Vladimir N. Uversky
- Department of Molecular Medicine, Byrd Alzheimer’s Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA;
| | - Pedro P. Madeira
- Centro de Investigacao em Materiais Ceramicos e Compositos, Department of Chemistry, 3810-193 Aveiro, Portugal;
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MutTMPredictor: Robust and accurate cascade XGBoost classifier for prediction of mutations in transmembrane proteins. Comput Struct Biotechnol J 2021; 19:6400-6416. [PMID: 34938415 PMCID: PMC8649221 DOI: 10.1016/j.csbj.2021.11.024] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Revised: 11/05/2021] [Accepted: 11/15/2021] [Indexed: 12/11/2022] Open
Abstract
Prediction of mutations in transmembrane proteins is of significance for diseases diagnosis. Building on the evolutionary information, proposed the Gaussian WAPSSM algorithm. Based on WAPSSM and sequence and structure-based features, proposed the cascade XGBoost algorithm. Webserver is freely at (http://csbio.njust.edu.cn/bioinf/ffmsresmutp/). Implement MutTMPredictor to predict mutations in transmembrane proteins.
Transmembrane proteins have critical biological functions and play a role in a multitude of cellular processes including cell signaling, transport of molecules and ions across membranes. Approximately 60% of transmembrane proteins are considered as drug targets. Missense mutations in such proteins can lead to many diverse diseases and disorders, such as neurodegenerative diseases and cystic fibrosis. However, there are limited studies on mutations in transmembrane proteins. In this work, we first design a new feature encoding method, termed weight attenuation position-specific scoring matrix (WAPSSM), which builds upon the protein evolutionary information. Then, we propose a new mutation prediction algorithm (cascade XGBoost) by leveraging the idea learned from consensus predictors and gcForest. Multi-level experiments illustrate the effectiveness of WAPSSM and cascade XGBoost algorithms. Finally, based on WAPSSM and other three types of features, in combination with the cascade XGBoost algorithm, we develop a new transmembrane protein mutation predictor, named MutTMPredictor. We benchmark the performance of MutTMPredictor against several existing predictors on seven datasets. On the 546 mutations dataset, MutTMPredictor achieves the accuracy (ACC) of 0.9661 and the Matthew’s Correlation Coefficient (MCC) of 0.8950. While on the 67,584 dataset, MutTMPredictor achieves an MCC of 0.7523 and area under curve (AUC) of 0.8746, which are 0.1625 and 0.0801 respectively higher than those of the existing best predictor (fathmm). Besides, MutTMPredictor also outperforms two specific predictors on the Pred-MutHTP datasets. The results suggest that MutTMPredictor can be used as an effective method for predicting and prioritizing missense mutations in transmembrane proteins. The MutTMPredictor webserver and datasets are freely accessible at http://csbio.njust.edu.cn/bioinf/muttmpredictor/ for academic use.
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Key Words
- 1000 Genomes, 1000 genomes project consortium
- APOGEE, pathogenicity prediction through the logistic model tree
- BorodaTM, boosted regression trees for disease-associated mutations in transmembrane proteins
- COSMIC, catalogue of somatic mutations in cancer
- Cascade XGBoost
- ClinVar, clinical variants
- Condel, consensus deleteriousness score of missense mutations
- Disease-associated mutations
- Entprise, entropy and predicted protein structure
- ExAC, the exome aggregation consortium
- Meta-SNP, meta single nucleotide polymorphism
- Mutation prediction
- PROVEAN, protein variation effect analyzer
- PolyPhen, polymorphism phenotyping
- PolyPhen-2, polymorphism phenotyping v2
- Pred-MutHTP, prediction of mutations in human transmembrane proteins
- PredictSNP1, predict single nucleotide polymorphism v1
- Protein evolutionary information
- REVEL, rare exome variant ensemble learner
- SDM, site-directed mutate
- SIFT, sorting intolerant from tolerant
- SNAP, screening for non-acceptable polymorphisms
- SNP&GO, single nucleotide polymorphisms and gene ontology annotations
- SwissVar, variants in UniProtKB/Swiss-Prot
- TMSNP, transmembrane single nucleotide polymorphisms
- Transmembrane protein
- WEKA, waikato environment for knowledge analysis
- fathmm, functional analysis through hidden markov models
- humsavar, human polymorphisms and disease mutations
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Wang C, Scott SM, Sun S, Zhao P, Hutt DM, Shao H, Gestwicki JE, Balch WE. Individualized management of genetic diversity in Niemann-Pick C1 through modulation of the Hsp70 chaperone system. Hum Mol Genet 2020; 29:1-19. [PMID: 31509197 DOI: 10.1093/hmg/ddz215] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Revised: 08/05/2019] [Accepted: 09/02/2019] [Indexed: 12/21/2022] Open
Abstract
Genetic diversity provides a rich repository for understanding the role of proteostasis in the management of the protein fold in human biology. Failure in proteostasis can trigger multiple disease states, affecting both human health and lifespan. Niemann-Pick C1 (NPC1) disease is a rare genetic disorder triggered by mutations in NPC1, a multi-spanning transmembrane protein that is trafficked through the exocytic pathway to late endosomes (LE) and lysosomes (Ly) (LE/Ly) to globally manage cholesterol homeostasis. Defects triggered by >300 NPC1 variants found in the human population inhibit export of NPC1 protein from the endoplasmic reticulum (ER) and/or function in downstream LE/Ly, leading to cholesterol accumulation and onset of neurodegeneration in childhood. We now show that the allosteric inhibitor JG98, that targets the cytosolic Hsp70 chaperone/co-chaperone complex, can significantly improve the trafficking and post-ER protein level of diverse NPC1 variants. Using a new approach to model genetic diversity in human disease, referred to as variation spatial profiling, we show quantitatively how JG98 alters the Hsp70 chaperone/co-chaperone system to adjust the spatial covariance (SCV) tolerance and set-points on an amino acid residue-by-residue basis in NPC1 to differentially regulate variant trafficking, stability, and cholesterol homeostasis, results consistent with the role of BCL2-associated athanogene family co-chaperones in managing the folding status of NPC1 variants. We propose that targeting the cytosolic Hsp70 system by allosteric regulation of its chaperone/co-chaperone based client relationships can be used to adjust the SCV tolerance of proteostasis buffering capacity to provide an approach to mitigate systemic and neurological disease in the NPC1 population.
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Affiliation(s)
- Chao Wang
- Department of Molecular Medicine, Scripps Research, La Jolla, CA 92037, USA
| | - Samantha M Scott
- Department of Molecular Medicine, Scripps Research, La Jolla, CA 92037, USA
| | - Shuhong Sun
- Department of Molecular Medicine, Scripps Research, La Jolla, CA 92037, USA
| | - Pei Zhao
- Department of Molecular Medicine, Scripps Research, La Jolla, CA 92037, USA
| | - Darren M Hutt
- Department of Molecular Medicine, Scripps Research, La Jolla, CA 92037, USA
| | - Hao Shao
- Department of Pharmaceutical Chemistry, University of California at San Francisco, San Francisco, CA 94158, USA
| | - Jason E Gestwicki
- Department of Pharmaceutical Chemistry, University of California at San Francisco, San Francisco, CA 94158, USA
| | - William E Balch
- Department of Molecular Medicine, Scripps Research, La Jolla, CA 92037, USA.,The Skaggs Institute for Chemical Biology, Scripps Research, La Jolla, CA 92037, USA
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4
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Tang H, Xue S, Zhao G, Fang C, Cai L, Shi Z, Fu W, Qian R, Zhang P, Tang X, Guo D. CLOCK disruption aggravates carotid artery stenosis through endoplasmic reticulum stress-induced endothelial-mesenchymal transition. Am J Transl Res 2020; 12:7885-7898. [PMID: 33437367 PMCID: PMC7791501] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2020] [Accepted: 11/18/2020] [Indexed: 06/12/2023]
Abstract
Carotid artery stenosis is a leading cause of ischemic stroke, but the underlying mechanism remains unclear. We aimed to determine the molecular mechanisms of carotid plaque progression. We analyzed the molecular and morphometric characteristics of carotid plaque samples obtained from 30 patients who underwent carotid endarterectomy. Additionally, we established a mouse model of carotid atherosclerosis by partially ligating the left common carotid arteries of male ClockΔ19/Δ19 (Clk) and wild-type (WT) C57BL/6J mice fed a high-fat diet. Clk and WT primary mouse aortic endothelial cells (pMAECs) were exposed to disturbed flow (DF) or undisturbed flow (UF) with or without treatment with the IRE-1α inhibitor STF-083010 or the PERK inhibitor GSK2606414. In human carotid artery plaques, CLOCK expression was lower in the lipid-rich necrotic core than in transitional regions, especially in the endothelium. Decreased CLOCK mRNA levels were associated with more extensive stenosis, intraplaque hemorrhage, and complex plaque in human carotid plaques. In mice, the ClockΔ19/Δ19 mutation significantly increased neointima formation and neovascularization but decreased collagen content and lumen area in partially ligated carotid arteries. In addition, ClockΔ19/Δ19 mutants exhibited significantly decreased Cdh5 expression and increased expression of endothelial-mesenchymal transition (EndMT) and endoplasmic reticulum (ER) stress markers in mice with partially ligated carotid arteries and pMAECs exposed to DF. Notably, inhibition of the IRE1α-XBP1 axis abrogated the increased EndMT caused by ClockΔ19/Δ19 mutation and DF in pMAECs. In conclusion, the disruption of CLOCK function aggravates EndMT via the IRE1α-XBP1 axis, contributing to carotid artery stenosis.
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Affiliation(s)
- Hanfei Tang
- Department of Vascular Surgery, Institute of Vascular Surgery, Zhongshan Hospital, Fudan UniversityShanghai, China
| | - Song Xue
- Department of Vascular Surgery, Institute of Vascular Surgery, Zhongshan Hospital, Fudan UniversityShanghai, China
| | - Gefei Zhao
- Department of Thoracic and Cardiovascular Surgery, The Affiliated Drum Tower Hospital, Medical School of Nanjing UniversityNanjing, Jiangsu, China
| | - Chao Fang
- Department of Vascular Surgery, Institute of Vascular Surgery, Zhongshan Hospital, Fudan UniversityShanghai, China
| | - Liang Cai
- Department of Vascular Surgery, Institute of Vascular Surgery, Zhongshan Hospital, Fudan UniversityShanghai, China
| | - Zhenyu Shi
- Department of Vascular Surgery, Institute of Vascular Surgery, Zhongshan Hospital, Fudan UniversityShanghai, China
| | - Weiguo Fu
- Department of Vascular Surgery, Institute of Vascular Surgery, Zhongshan Hospital, Fudan UniversityShanghai, China
| | - Ruizhe Qian
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Shanghai Key Laboratory of Clinical Geriatric Medicine, Fudan UniversityShanghai, China
| | - Pengfei Zhang
- Department of Thoracic and Cardiovascular Surgery, The Affiliated Drum Tower Hospital, Medical School of Nanjing UniversityNanjing, Jiangsu, China
| | - Xiao Tang
- Department of Vascular Surgery, Institute of Vascular Surgery, Zhongshan Hospital, Fudan UniversityShanghai, China
| | - Daqiao Guo
- Department of Vascular Surgery, Institute of Vascular Surgery, Zhongshan Hospital, Fudan UniversityShanghai, China
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Pharmacoproteomics pinpoints HSP70 interaction for correction of the most frequent Wilson disease-causing mutant of ATP7B. Proc Natl Acad Sci U S A 2020; 117:32453-32463. [PMID: 33288711 DOI: 10.1073/pnas.2006648117] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Pathogenic mutations in the copper transporter ATP7B have been hypothesized to affect its protein interaction landscape contributing to loss of function and, thereby, to hepatic copper toxicosis in Wilson disease. Although targeting mutant interactomes was proposed as a therapeutic strategy, druggable interactors for rescue of ATP7B mutants remain elusive. Using proteomics, we found that the frequent H1069Q substitution promotes ATP7B interaction with HSP70, thus accelerating endoplasmic reticulum (ER) degradation of the mutant protein and consequent copper accumulation in hepatic cells. This prompted us to use an HSP70 inhibitor as bait in a bioinformatics search for structurally similar Food and Drug Administration-approved drugs. Among the hits, domperidone emerged as an effective corrector that recovered trafficking and function of ATP7B-H1069Q by impairing its exposure to the HSP70 proteostatic network. Our findings suggest that HSP70-mediated degradation can be safely targeted with domperidone to rescue ER-retained ATP7B mutants and, hence, to counter the onset of Wilson disease.
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Combined Use of CFTR Correctors in LGMD2D Myotubes Improves Sarcoglycan Complex Recovery. Int J Mol Sci 2020; 21:ijms21051813. [PMID: 32155735 PMCID: PMC7084537 DOI: 10.3390/ijms21051813] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Accepted: 02/28/2020] [Indexed: 12/28/2022] Open
Abstract
Sarcoglycanopathies are rare limb girdle muscular dystrophies, still incurable, even though symptomatic treatments may slow down the disease progression. Most of the disease-causing defects are missense mutations leading to a folding defective protein, promptly removed by the cell’s quality control, even if possibly functional. Recently, we repurposed small molecules screened for cystic fibrosis as potential therapeutics in sarcoglycanopathy. Indeed, cystic fibrosis transmembrane regulator (CFTR) correctors successfully recovered the defective sarcoglycan-complex in vitro. Our aim was to test the combined administration of some CFTR correctors with C17, the most effective on sarcoglycans identified so far, and evaluate the stability of the rescued sarcoglycan-complex. We treated differentiated myogenic cells from both sarcoglycanopathy and healthy donors, evaluating the global rescue and the sarcolemma localization of the mutated protein, by biotinylation assays and western blot analyses. We observed the additive/synergistic action of some compounds, gathering the first ideas on possible mechanism/s of action. Our data also suggest that a defective α-sarcoglycan is competent for assembly into the complex that, if helped in cell traffic, can successfully reach the sarcolemma. In conclusion, our results strengthen the idea that CFTR correctors, acting probably as proteostasis modulators, have the potential to progress as therapeutics for sarcoglycanopathies caused by missense mutations.
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7
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Landi C, Luddi A, Bianchi L, Pannuzzo G, Pavone V, Piomboni P, Bini L. Proteostasis network alteration in lysosomal storage disorders: Insights from the mouse model of Krabbe disease. J Neurosci Res 2019; 98:718-733. [PMID: 31797419 DOI: 10.1002/jnr.24558] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Revised: 10/09/2019] [Accepted: 10/29/2019] [Indexed: 12/19/2022]
Abstract
In Krabbe disease, a mutation in GALC gene causes widespread demyelination determining cell death by apoptosis, mainly in oligodendrocytes and Schwann cells. Less is known on the molecular mechanisms induced by this deficiency. Here, we report an impairment in protein synthesis and degradation and in proteasomal clearance with a potential accumulation of the misfolded proteins and induction of the endoplasmic reticulum stress in the brain of 6-day-old twitcher mice (TM) (model of Krabbe disease). In particular, an imbalance of the immunoproteasome function was highlighted, useful for shaping adaptive immune response by neurological cells. Moreover, our data show an involvement of cytoskeleton remodeling in Krabbe pathogenesis, with a lamin meshwork disaggregation in twitcher oligodendrocytes in 6-day-old TM. This study provides interesting protein targets and mechanistic insight on the early onset of Krabbe disease that may be promising options to be tested in combination with currently available therapies to rescue Krabbe phenotype.
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Affiliation(s)
- Claudia Landi
- Department of Life Sciences, University of Siena, Siena, Italy
| | - Alice Luddi
- Department of Molecular and Developmental Medicine, University of Siena, Siena, Italy
| | - Laura Bianchi
- Department of Life Sciences, University of Siena, Siena, Italy
| | - Giovanna Pannuzzo
- Department of Biomedical and Biotechnological Sciences, Section of Physiology, University of Catania, Catania, Italy
| | - Valentina Pavone
- Department of Molecular and Developmental Medicine, University of Siena, Siena, Italy
| | - Paola Piomboni
- Department of Molecular and Developmental Medicine, University of Siena, Siena, Italy
| | - Luca Bini
- Department of Life Sciences, University of Siena, Siena, Italy
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8
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Investigating the effects of different natural molecules on the structure and oligomerization propensity of hen egg-white lysozyme. Int J Biol Macromol 2019; 134:189-201. [DOI: 10.1016/j.ijbiomac.2019.05.048] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Revised: 04/25/2019] [Accepted: 05/07/2019] [Indexed: 12/17/2022]
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9
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Boczek E, Gaglia G, Olshina M, Sarraf S. The first Autumn School on Proteostasis: from molecular mechanisms to organismal consequences. Cell Stress Chaperones 2019; 24:481-492. [PMID: 31073902 PMCID: PMC6527634 DOI: 10.1007/s12192-019-00998-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/15/2019] [Indexed: 12/12/2022] Open
Abstract
The first Autumn School on Proteostasis was held at the Mediterranean Institute for Life Sciences (MedILS) in Split, Croatia, from November 12th-16th, 2018, bringing together 44 graduate students and postdoctoral fellows and 22 principal investigators from around the world. This meeting was geared towards providing students with an in-depth understanding of the field of proteostasis, with the aim of broadening their perspectives of the field. Session topics covered multiple aspects of cellular and organismal proteostasis, including fundamental principles, responses to heat shock, aging and disease, and protein folding, misfolding, and degradation. The structure of the meeting and the restricted number of participants afforded the students and postdocs the opportunity to interact with principal investigators to discuss not only their latest research, but also their career prospects and progression in a close, supportive environment.
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Affiliation(s)
- Edgar Boczek
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Giorgio Gaglia
- Brigham Women’s Hospital, Harvard Medical School, Boston, MA USA
| | - Maya Olshina
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Shireen Sarraf
- National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD USA
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10
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Yuan G, Hua B, Cai T, Xu L, Li E, Huang Y, Sun N, Yan Z, Lu C, Qian R. Clock mediates liver senescence by controlling ER stress. Aging (Albany NY) 2019; 9:2647-2665. [PMID: 29283886 PMCID: PMC5764397 DOI: 10.18632/aging.101353] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2017] [Accepted: 12/17/2017] [Indexed: 12/18/2022]
Abstract
Accumulated evidence indicates that circadian genes regulate cell damage and senescence in most mammals. Endoplasmic reticulum (ER) stress and reactive oxygen species (ROS) regulate longevity in many organisms. However, the specific mechanisms of the relationship between the circadian clock and the two stress processes in organisms are poorly understood. Here, we show that Clock-mediated Pdia3 expression is required to sustain reactive oxidative reagents and ER stress. First, ER stress and ROS are strongly activated in the liver tissue of ClockΔ19 mutant mice, which exhibit a significant aging phenotype. Next, transcription of Pdia3 is mediated by the circadian gene Clock, but this process is affected by the ClockΔ19 mutant due to the low affinity of the E-box motif in the promoter. Finally, ablation of Pdia3 with siRNA causes ER stress with sustained phosphorylation of PERK and eIF1α, resulting in exaggerated up-regulation of UPR target genes and increased apoptosis as well as ROS. Moreover, the combined effects result in an imbalance of cell homeostasis and ultimately lead to cell damage and senescence. Taken together, this study identified the circadian gene Clock as a regulator of ER stress and senescence, which will provide a reference for the clinical prevention of aging.
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Affiliation(s)
- Gongsheng Yuan
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Fudan University, Shanghai, 200032, China.,Shanghai Key Laboratory of Clinical Geriatric Medicine, Research Center on Aging and Medicine, Fudan University, Shanghai, 200032, China
| | - Bingxuan Hua
- Department of Orthopedics, Zhongshan Hospital, Fudan University, Shanghai, 200032, China
| | - Tingting Cai
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Fudan University, Shanghai, 200032, China
| | - Lirong Xu
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Fudan University, Shanghai, 200032, China
| | - Ermin Li
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Fudan University, Shanghai, 200032, China
| | - Yiqing Huang
- Shanghai Key Laboratory of Clinical Geriatric Medicine, Research Center on Aging and Medicine, Fudan University, Shanghai, 200032, China.,Department of Gastroenterology, Huadong Hospital, Shanghai Medical College of Fudan University, Shanghai, 200040, China
| | - Ning Sun
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Fudan University, Shanghai, 200032, China.,Shanghai Key Laboratory of Clinical Geriatric Medicine, Research Center on Aging and Medicine, Fudan University, Shanghai, 200032, China.,State Key Laboratory of Medical Neurobiology, Fudan University, Shanghai, 200032, China
| | - Zuoqin Yan
- Department of Orthopedics, Zhongshan Hospital, Fudan University, Shanghai, 200032, China
| | - Chao Lu
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Fudan University, Shanghai, 200032, China.,Shanghai Key Laboratory of Clinical Geriatric Medicine, Research Center on Aging and Medicine, Fudan University, Shanghai, 200032, China
| | - Ruizhe Qian
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Fudan University, Shanghai, 200032, China.,Shanghai Key Laboratory of Clinical Geriatric Medicine, Research Center on Aging and Medicine, Fudan University, Shanghai, 200032, China
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11
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Thomas R, Kermode AR. Enzyme enhancement therapeutics for lysosomal storage diseases: Current status and perspective. Mol Genet Metab 2019; 126:83-97. [PMID: 30528228 DOI: 10.1016/j.ymgme.2018.11.011] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Revised: 11/20/2018] [Accepted: 11/21/2018] [Indexed: 01/28/2023]
Abstract
Small-molecule- enzyme enhancement therapeutics (EETs) have emerged as attractive agents for the treatment of lysosomal storage diseases (LSDs), a broad group of genetic diseases caused by mutations in genes encoding lysosomal enzymes, or proteins required for lysosomal function. The underlying enzyme deficiencies characterizing LSDs cause a block in the stepwise degradation of complex macromolecules (e.g. glycosaminoglycans, glycolipids and others), such that undegraded or partially degraded substrates progressively accumulate in lysosomal and non-lysosomal compartments, a process leading to multisystem pathology via primary and secondary mechanisms. Missense mutations underlie many of the LSDs; the resultant mutant variant enzyme hydrolase is often impaired in its folding and maturation making it subject to rapid disposal by endoplasmic reticulum (ER)-associated degradation (ERAD). Enzyme deficiency in the lysosome is the result, even though the mutant enzyme may retain significant catalytic functioning. Small molecule modulators - pharmacological chaperones (PCs), or proteostasis regulators (PRs) are being identified through library screens and computational tools, as they may offer a less costly approach than enzyme replacement therapy (ERT) for LSDs, and potentially treat neuronal forms of the diseases. PCs, capable of directly stabilizing the mutant protein, and PRs, which act on other cellular elements to enhance protein maturation, both allow a proportion of the synthesized variant protein to reach the lysosome and function. Proof-of-principle for PCs and PRs as therapeutic agents has been demonstrated for several LSDs, yet definitive data of their efficacy in disease models and/or in downstream clinical studies in many cases has yet to be achieved. Basic research to understand the cellular consequences of protein misfolding such as perturbed organellar crosstalk, redox status, and calcium balance is needed. Likewise, an elucidation of the early in cellulo pathogenic events underlying LSDs is vital and may lead to the discovery of new small molecule modulators and/or to other therapeutic approaches for driving proteostasis toward protein rescue.
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Affiliation(s)
- Ryan Thomas
- Department of Biological Sciences, Simon Fraser University, 8888 University Dr., Burnaby B.C. V5A 1S6, Canada
| | - Allison R Kermode
- Department of Biological Sciences, Simon Fraser University, 8888 University Dr., Burnaby B.C. V5A 1S6, Canada.
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12
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State-of-the-Art Fluorescence Fluctuation-Based Spectroscopic Techniques for the Study of Protein Aggregation. Int J Mol Sci 2018; 19:ijms19040964. [PMID: 29570669 PMCID: PMC5979297 DOI: 10.3390/ijms19040964] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2018] [Revised: 03/17/2018] [Accepted: 03/21/2018] [Indexed: 02/07/2023] Open
Abstract
Neurodegenerative diseases, including amyotrophic lateral sclerosis (ALS), Alzheimer’s disease, Parkinson’s disease, and Huntington’s disease, are devastating proteinopathies with misfolded protein aggregates accumulating in neuronal cells. Inclusion bodies of protein aggregates are frequently observed in the neuronal cells of patients. Investigation of the underlying causes of neurodegeneration requires the establishment and selection of appropriate methodologies for detailed investigation of the state and conformation of protein aggregates. In the current review, we present an overview of the principles and application of several methodologies used for the elucidation of protein aggregation, specifically ones based on determination of fluctuations of fluorescence. The discussed methods include fluorescence correlation spectroscopy (FCS), imaging FCS, image correlation spectroscopy (ICS), photobleaching ICS (pbICS), number and brightness (N&B) analysis, super-resolution optical fluctuation imaging (SOFI), and transient state (TRAST) monitoring spectroscopy. Some of these methodologies are classical protein aggregation analyses, while others are not yet widely used. Collectively, the methods presented here should help the future development of research not only into protein aggregation but also neurodegenerative diseases.
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13
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Hadizadeh Esfahani A, Sverchkova A, Saez-Rodriguez J, Schuppert AA, Brehme M. A systematic atlas of chaperome deregulation topologies across the human cancer landscape. PLoS Comput Biol 2018; 14:e1005890. [PMID: 29293508 PMCID: PMC5766242 DOI: 10.1371/journal.pcbi.1005890] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2017] [Revised: 01/12/2018] [Accepted: 11/23/2017] [Indexed: 01/17/2023] Open
Abstract
Proteome balance is safeguarded by the proteostasis network (PN), an intricately regulated network of conserved processes that evolved to maintain native function of the diverse ensemble of protein species, ensuring cellular and organismal health. Proteostasis imbalances and collapse are implicated in a spectrum of human diseases, from neurodegeneration to cancer. The characteristics of PN disease alterations however have not been assessed in a systematic way. Since the chaperome is among the central components of the PN, we focused on the chaperome in our study by utilizing a curated functional ontology of the human chaperome that we connect in a high-confidence physical protein-protein interaction network. Challenged by the lack of a systems-level understanding of proteostasis alterations in the heterogeneous spectrum of human cancers, we assessed gene expression across more than 10,000 patient biopsies covering 22 solid cancers. We derived a novel customized Meta-PCA dimension reduction approach yielding M-scores as quantitative indicators of disease expression changes to condense the complexity of cancer transcriptomics datasets into quantitative functional network topographies. We confirm upregulation of the HSP90 family and also highlight HSP60s, Prefoldins, HSP100s, ER- and mitochondria-specific chaperones as pan-cancer enriched. Our analysis also reveals a surprisingly consistent strong downregulation of small heat shock proteins (sHSPs) and we stratify two cancer groups based on the preferential upregulation of ATP-dependent chaperones. Strikingly, our analyses highlight similarities between stem cell and cancer proteostasis, and diametrically opposed chaperome deregulation between cancers and neurodegenerative diseases. We developed a web-based Proteostasis Profiler tool (Pro2) enabling intuitive analysis and visual exploration of proteostasis disease alterations using gene expression data. Our study showcases a comprehensive profiling of chaperome shifts in human cancers and sets the stage for a systematic global analysis of PN alterations across the human diseasome towards novel hypotheses for therapeutic network re-adjustment in proteostasis disorders. Protein homeostasis, or proteostasis, is maintained by the proteostasis network (PN), an intricately regulated modular network of interacting processes that evolved to balance the native proteome, supporting cellular and organismal health throughout lifespan. Imbalances and collapse of cellular proteostasis capacity, the capacity to buffer against cytotoxic damage and stress, is increasingly implicated in some of the most challenging diseases of our time, including neurodegeneration and cancers. The systems-level PN alterations in these diseases are not understood to date. Here, we address this challenge, focussing on the human chaperome, the ensemble of chaperones and co-chaperones, which represents a central conserved PN functional arm. We devised a novel data dimensionality reduction approach enabling quantitative contextual visualization of chaperome alterations in the heterogeneous spectrum of cancers based on gene expression data from thousands of patient biopsies. We developed Proteostasis Profiler (Pro2), a new web-tool enabling intuitive visualisation of cancer chaperome deregulation maps. We stratify two cancer groups based on diverging chaperome deregulation and highlight similarities between cancer and stem cell proteostasis. Our study also exposes drastically opposed shifts between cancers and neurodegenerative diseases. Collectively, this study sets the stage for a systematic global analysis of PN alterations across the human diseasome.
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Affiliation(s)
- Ali Hadizadeh Esfahani
- Joint Research Center for Computational Biomedicine (JRC-COMBINE), RWTH Aachen University, Aachen, Germany
- Aachen Institute for Advanced Study in Computational Engineering Science (AICES), RWTH Aachen University, Aachen, Germany
| | - Angelina Sverchkova
- Joint Research Center for Computational Biomedicine (JRC-COMBINE), RWTH Aachen University, Faculty of Medicine, Aachen, Germany
| | - Julio Saez-Rodriguez
- Joint Research Center for Computational Biomedicine (JRC-COMBINE), RWTH Aachen University, Faculty of Medicine, Aachen, Germany
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, United Kingdom
| | - Andreas A. Schuppert
- Joint Research Center for Computational Biomedicine (JRC-COMBINE), RWTH Aachen University, Aachen, Germany
- Aachen Institute for Advanced Study in Computational Engineering Science (AICES), RWTH Aachen University, Aachen, Germany
| | - Marc Brehme
- Joint Research Center for Computational Biomedicine (JRC-COMBINE), RWTH Aachen University, Aachen, Germany
- * E-mail:
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14
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Ulloa-Aguirre A, Zariñán T, Gutiérrez-Sagal R, Dias JA. Intracellular Trafficking of Gonadotropin Receptors in Health and Disease. Handb Exp Pharmacol 2018; 245:1-39. [PMID: 29063275 DOI: 10.1007/164_2017_49] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Gonadotropin receptors belong to the highly conserved subfamily of the G protein-coupled receptor (GPCR) superfamily, the so-called Rhodopsin-like family (class A), which is the largest class of GPCRs and currently a major drug target. Both the follicle-stimulating hormone receptor (FSHR) and the luteinizing hormone/chorionic gonadotropin hormone receptor (LHCGR) are mainly located in the gonads where they play key functions associated to essential reproductive functions. As any other protein, gonadotropin receptors must be properly folded into a mature tertiary conformation compatible with quaternary assembly and endoplasmic reticulum export to the cell surface plasma membrane. Several primary and secondary structural features, including presence of particular amino acid residues and short motifs and in addition, posttranslational modifications, regulate intracellular trafficking of gonadotropin receptors to the plasma membrane as well as internalization and recycling of the receptor back to the cell surface after activation by agonist. Inactivating mutations of gonadotropin receptors may derive from receptor misfolding and lead to absent or reduced plasma membrane expression of the altered receptor, thereby manifesting an array of phenotypical abnormalities mostly characterized by reproductive failure and/or abnormal or absence of development of secondary sex characteristics. In this chapter we review the structural requirements necessary for intracellular trafficking of the gonadotropin receptors, and describe how mutations in these receptors may lead to receptor misfolding and disease in humans.
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Affiliation(s)
- Alfredo Ulloa-Aguirre
- Red de Apoyo a la Investigación (RAI), Universidad Nacional Autónoma de México-Instituto Nacional de Ciencias Médicas y Nutrición SZ, Vasco de Quiroga 15, Tlalpan, Mexico City, 14000, Mexico.
| | - Teresa Zariñán
- Red de Apoyo a la Investigación (RAI), Universidad Nacional Autónoma de México-Instituto Nacional de Ciencias Médicas y Nutrición SZ, Vasco de Quiroga 15, Tlalpan, Mexico City, 14000, Mexico
| | - Rubén Gutiérrez-Sagal
- Red de Apoyo a la Investigación (RAI), Universidad Nacional Autónoma de México-Instituto Nacional de Ciencias Médicas y Nutrición SZ, Vasco de Quiroga 15, Tlalpan, Mexico City, 14000, Mexico
| | - James A Dias
- Department of Biomedical Sciences, School of Public Health, University at Albany, Albany, NY, USA
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15
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Cutrona MB, Morgan NE, Simpson JC. Heritable Skeletal Disorders Arising from Defects in Processing and Transport of Type I Procollagen from the ER: Perspectives on Possible Therapeutic Approaches. Handb Exp Pharmacol 2018; 245:191-225. [PMID: 29071510 DOI: 10.1007/164_2017_67] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Rare bone disorders are a heterogeneous group of diseases, initially associated with mutations in type I procollagen (PC) genes. Recent developments from dissection at the molecular and cellular level have expanded the list of disease-causing proteins, revealing that disruption of the machinery that handles protein secretion can lead to failure in PC secretion and in several cases result in skeletal dysplasia. In parallel, cell-based in vitro studies of PC trafficking pathways offer clues to the identification of new disease candidate genes. Together, this raises the prospect of heritable bone disorders as a paradigm for biosynthetic protein traffic-related diseases, and an avenue through which therapeutic strategies can be explored.Here, we focus on human syndromes linked to defects in type I PC secretion with respect to the landscape of biosynthetic and protein transport steps within the early secretory pathway. We provide a perspective on possible therapeutic interventions for associated heritable craniofacial and skeletal disorders, considering different orders of complexity, from the cellular level by manipulation of proteostasis pathways to higher levels involving cell-based therapies for bone repair and regeneration.
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Affiliation(s)
- Meritxell B Cutrona
- School of Biology and Environmental Science, Conway Institute of Biomolecular and Biomedical Research, University College Dublin (UCD), Dublin, Ireland
| | - Niamh E Morgan
- School of Biology and Environmental Science, Conway Institute of Biomolecular and Biomedical Research, University College Dublin (UCD), Dublin, Ireland
| | - Jeremy C Simpson
- School of Biology and Environmental Science, Conway Institute of Biomolecular and Biomedical Research, University College Dublin (UCD), Dublin, Ireland.
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16
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Nigi I, Fairall L, Schwabe JWR. Expression and Purification of Protein Complexes Suitable for Structural Studies Using Mammalian HEK 293F Cells. ACTA ACUST UNITED AC 2017; 90:5.28.1-5.28.16. [PMID: 29091272 DOI: 10.1002/cpps.44] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Prokaryotic expression systems have been widely used to express proteins for structural studies. Such expression systems have the advantage of being economical, straightforward and fast. However, for many eukaryotic proteins and particularly protein complexes, bacterial expression systems do not produce significant yields of soluble protein. This may result from failure to efficiently transcribe/translate the required protein or may result from the formation of insoluble aggregates known as inclusion bodies. Mammalian expression systems can often produce natively folded proteins, sometimes with native post-translational modifications. However, such expression systems are underutilized due to the perception that they are costly, technically challenging and result in limited protein yields. In fact, HEK 293F cells are straightforward to grow, transfect with high efficiency and often produce significant yields of recombinant proteins. In this unit, we describe a method to express and purify milligram quantities of a human protein complex from HEK 293F cells grown in suspension transiently transfected with the appropriate plasmids. © 2017 by John Wiley & Sons, Inc.
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Affiliation(s)
- Irene Nigi
- Leicester Institute of Structural and Chemical Biology, Department of Molecular and Cell Biology, University of Leicester, Leicester, United Kingdom
| | - Louise Fairall
- Leicester Institute of Structural and Chemical Biology, Department of Molecular and Cell Biology, University of Leicester, Leicester, United Kingdom
| | - John W R Schwabe
- Leicester Institute of Structural and Chemical Biology, Department of Molecular and Cell Biology, University of Leicester, Leicester, United Kingdom
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17
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Cornejo VH, Luarte A, Couve A. Global and local mechanisms sustain axonal proteostasis of transmembrane proteins. Traffic 2017; 18:255-266. [PMID: 28220989 DOI: 10.1111/tra.12472] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2016] [Revised: 02/02/2017] [Accepted: 02/16/2017] [Indexed: 12/22/2022]
Abstract
The control of neuronal protein homeostasis or proteostasis is tightly regulated both spatially and temporally, assuring accurate and integrated responses to external or intrinsic stimuli. Local or autonomous responses in dendritic and axonal compartments are crucial to sustain function during development, physiology and in response to damage or disease. Axons are responsible for generating and propagating electrical impulses in neurons, and the establishment and maintenance of their molecular composition are subject to extreme constraints exerted by length and size. Proteins that require the secretory pathway, such as receptors, transporters, ion channels or cell adhesion molecules, are fundamental for axonal function, but whether axons regulate their abundance autonomously and how they achieve this is not clear. Evidence supports the role of three complementary mechanisms to maintain proteostasis of these axonal proteins, namely vesicular transport, local translation and trafficking and transfer from supporting cells. Here, we review these mechanisms, their molecular machineries and contribution to neuronal function. We also examine the signaling pathways involved in local translation and their role during development and nerve injury. We discuss the relative contributions of a transport-controlled proteome directed by the soma (global regulation) versus a local-controlled proteome based on local translation or cell transfer (local regulation).
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Affiliation(s)
- Víctor Hugo Cornejo
- Program of Physiology and Biophysics, ICBM, Faculty of Medicine, Universidad de Chile, Santiago, Chile.,Biomedical Neuroscience Institute, Universidad de Chile, Santiago, Chile
| | - Alejandro Luarte
- Program of Physiology and Biophysics, ICBM, Faculty of Medicine, Universidad de Chile, Santiago, Chile.,Biomedical Neuroscience Institute, Universidad de Chile, Santiago, Chile
| | - Andrés Couve
- Program of Physiology and Biophysics, ICBM, Faculty of Medicine, Universidad de Chile, Santiago, Chile.,Biomedical Neuroscience Institute, Universidad de Chile, Santiago, Chile
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18
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Pipalia NH, Subramanian K, Mao S, Ralph H, Hutt DM, Scott SM, Balch WE, Maxfield FR. Histone deacetylase inhibitors correct the cholesterol storage defect in most Niemann-Pick C1 mutant cells. J Lipid Res 2017; 58:695-708. [PMID: 28193631 DOI: 10.1194/jlr.m072140] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2016] [Revised: 01/24/2017] [Indexed: 02/05/2023] Open
Abstract
Niemann-Pick C (NPC) disease is an autosomal recessive disorder that leads to excessive storage of cholesterol and other lipids in late endosomes and lysosomes. The large majority of NPC disease is caused by mutations in NPC1, a large polytopic membrane protein that functions in late endosomes. There are many disease-associated mutations in NPC1, and most patients are compound heterozygotes. The most common mutation, NPC1I1061T, has been shown to cause endoplasmic reticulum-associated degradation of the NPC1 protein. Treatment of patient-derived NPC1I1061T fibroblasts with histone deacetylase inhibitors (HDACis) vorinostat or panobinostat increases expression of the mutant NPC1 protein and leads to correction of the cholesterol storage. Here, we show that several other human NPC1 mutant fibroblast cell lines can also be corrected by vorinostat or panobinostat and that treatment with vorinostat extends the lifetime of the NPC1I1061T protein. To test effects of HDACi on a large number of NPC1 mutants, we engineered a U2OS cell line to suppress NPC1 expression by shRNA and then transiently transfected these cells with 60 different NPC1 mutant constructs. The mutant NPC1 did not significantly reduce cholesterol accumulation, but approximately 85% of the mutants showed reduced cholesterol accumulation when treated with vorinostat or panobinostat.
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Affiliation(s)
- Nina H Pipalia
- Department of Biochemistry, Weill Cornell Medical College, New York, NY 10065; and Department of Chemical Physiology and Cell and Molecular Biology
| | - Kanagaraj Subramanian
- The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA, 92037
| | - Shu Mao
- Department of Biochemistry, Weill Cornell Medical College, New York, NY 10065; and Department of Chemical Physiology and Cell and Molecular Biology
| | - Harold Ralph
- Department of Biochemistry, Weill Cornell Medical College, New York, NY 10065; and Department of Chemical Physiology and Cell and Molecular Biology
| | - Darren M Hutt
- The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA, 92037
| | - Samantha M Scott
- The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA, 92037
| | - William E Balch
- The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA, 92037.
| | - Frederick R Maxfield
- Department of Biochemistry, Weill Cornell Medical College, New York, NY 10065; and Department of Chemical Physiology and Cell and Molecular Biology,.
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19
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Hegde RN, Subramanian A, Pothukuchi P, Parashuraman S, Luini A. Rare ER protein misfolding-mistrafficking disorders: Therapeutic developments. Tissue Cell 2017; 49:175-185. [PMID: 28222887 DOI: 10.1016/j.tice.2017.02.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2016] [Revised: 02/02/2017] [Accepted: 02/04/2017] [Indexed: 12/16/2022]
Abstract
The presence of a functional protein at the appropriate location in the cell is the result of the processes of transcription, translation, folding and trafficking to the correct destination. There are numerous diseases that are caused by protein misfolding, mainly due to mutations in the respective gene. The consequences of this misfolding may be that proteins effectively lose their function, either by being removed by the cellular quality control machinery or by accumulating at the incorrect intracellular or extracellular location. A number of mutations that lead to protein misfolding and affect trafficking to the final destination, e.g. Cystic fibrosis, Wilson's disease, and Progressive Familial Intrahepatic 1 cholestasis, result in proteins that retain partial function if their folding and trafficking is restored either by molecular or pharmacological means. In this review, we discuss several mutant proteins within this class of misfolding diseases and provide an update on the status of molecular and therapeutic developments and potential therapeutic strategies being developed to counter these diseases.
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Affiliation(s)
| | - Advait Subramanian
- Institute of Protein Biochemistry, National Research Council, Naples, Italy
| | | | | | - Alberto Luini
- Institute of Protein Biochemistry, National Research Council, Naples, Italy; Istituto di Ricovero e Cura a Carattere Scientifico SDN, Naples, Italy
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20
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Dabbah M, Attar-Schneider O, Zismanov V, Tartakover Matalon S, Lishner M, Drucker L. Multiple myeloma cells promote migration of bone marrow mesenchymal stem cells by altering their translation initiation. J Leukoc Biol 2016; 100:761-770. [DOI: 10.1189/jlb.3a1115-510rr] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2015] [Accepted: 04/26/2016] [Indexed: 12/26/2022] Open
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21
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Genereux JC, Wiseman RL. Regulating extracellular proteostasis capacity through the unfolded protein response. Prion 2016; 9:10-21. [PMID: 25946012 DOI: 10.1080/19336896.2015.1011887] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
The extracellular aggregation of proteins into proteotoxic oligomers and amyloid fibrils is implicated in the onset and pathology of numerous diseases referred to as amyloid diseases. All of the proteins that aggregate extracellularly in association with amyloid disease pathogenesis originate in the endoplasmic reticulum (ER) and are secreted through the secretory pathway. Disruptions in ER protein homeostasis or proteostasis (i.e., ER stress) can facilitate the aberrant secretion of misfolded protein conformations to the extracellular space and exacerbate pathologic protein aggregation into proteotoxic species. Activation of an ER stress-responsive signaling pathway, the Unfolded Protein Response (UPR), restores ER proteostasis through the transcriptional regulation of ER proteostasis pathways. In contrast, the functional role for the UPR in regulating extracellular proteostasis during ER stress is poorly defined. We recently identified ERdj3 as a UPR-regulated secreted chaperone that increases extracellular proteostasis capacity in response to ER stress, revealing a previously-unanticipated direct mechanism by which the UPR impacts extracellular proteostasis. Here, we discuss the functional implications of ERdj3 secretion on extracellular proteostasis maintenance and define the mechanisms by which ERdj3 secretion coordinates intra- and extracellular proteostasis environments during ER stress.
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Affiliation(s)
- Joseph C Genereux
- a Department of Molecular & Experimental Medicine; Department of Chemical Physiology ; The Scripps Research Institute ; La Jolla , CA USA
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22
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Amaral MD, Balch WE. Hallmarks of therapeutic management of the cystic fibrosis functional landscape. J Cyst Fibros 2015; 14:687-99. [PMID: 26526359 PMCID: PMC4644672 DOI: 10.1016/j.jcf.2015.09.006] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2015] [Revised: 09/16/2015] [Accepted: 09/16/2015] [Indexed: 01/29/2023]
Abstract
The cystic fibrosis (CF) transmembrane conductance regulator (CFTR) protein does not operate in isolation, rather in a dynamic network of interacting components that impact its synthesis, folding, stability, intracellular location and function, referred to herein as the 'CFTR Functional Landscape (CFFL)'. For the prominent F508del mutation, many of these interactors are deeply connected to a protein fold management system, the proteostasis network (PN). However, CF encompasses an additional 2000 CFTR variants distributed along its entire coding sequence (referred to as CFTR2), and each variant contributes a differential liability to PN management of CFTR and to a protein 'social network' (SN) that directs the probability of the (patho)physiologic events that impact ion transport in each cell, tissue and patient in health and disease. Recognition of the importance of the PN and SN in driving the unique patient CFFL leading to disease highlights the importance of precision medicine in therapeutic management of disease progression. We take the view herein that it is not CFTR, rather the PN/SN, and their impact on the CFFL, that are the key physiologic forces driving onset and clinical progression of CF. We posit that a deep understanding of each patients PN/SN gained by merging genomic, proteomic (mass spectrometry (MS)), and high-content microscopy (HCM) technologies in the context of novel network learning algorithms will lead to a paradigm shift in CF clinical management. This should allow for generation of new classes of patient specific PN/SN directed therapeutics for personalized management of the CFFL in the clinic.
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Affiliation(s)
- Margarida D Amaral
- University of Lisboa, Faculty of Sciences, BioISI - Biosystems & Integrative Sciences Institute, Lisboa, Portugal.
| | - William E Balch
- Department of Chemical Physiology, Department of Cell and Molecular Biology, The Skaggs Institute of Chemical Biology, The Scripps Research Institute, La Jolla, CA, USA.
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23
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Vignaud H, Cullin C, Bouchecareilh M. [Alpha-1 antitrypsin deficiency: A model of alteration of protein homeostasis or proteostasis]. Rev Mal Respir 2015; 32:1059-71. [PMID: 26386628 DOI: 10.1016/j.rmr.2015.05.013] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2014] [Accepted: 05/08/2015] [Indexed: 10/23/2022]
Abstract
Chronic obstructive pulmonary disease (COPD) is currently the ninth leading cause of death in France and is predicted to become the third leading cause of worldwide morbidity and mortality by 2020. Risk factors for COPD include exposure to tobacco, dusts and chemicals, asthma and alpha-1 antitrypsin deficiency. This genetic disease, significantly under-diagnosed and under-recognized, affects 1 in 2500 live births and is an important cause of lung and, occasionally, liver disease. Alpha-1 antitrypsin deficiency is a pathology of proteostasis-mediated protein folding and trafficking pathways. To date, there are only palliative therapeutic approaches for the symptoms associated with this hereditary disorder. Therefore, a more detailed understanding is required of the folding and trafficking biology governing alpha-1 antitrypsin biogenesis and its response to drugs. Here, we review the cell biological, biochemical and biophysical properties of alpha-1 antitrypsin and its variants, and we suggest that alpha-1 antitrypsin deficiency is an example of cell autonomous and non-autonomous challenges to proteostasis. Finally, we review emerging strategies that may be used to enhance the proteostasis system and protect the lung from alpha-1 antitrypsin deficiency.
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Affiliation(s)
- H Vignaud
- Institut de biochimie et génétique cellulaires, CNRS UMR 5095, université de Bordeaux, 1, rue Camille-Saint-Saëns, 33077 Bordeaux cedex, France
| | - C Cullin
- Institut de biochimie et génétique cellulaires, CNRS UMR 5095, université de Bordeaux, 1, rue Camille-Saint-Saëns, 33077 Bordeaux cedex, France
| | - M Bouchecareilh
- Institut de biochimie et génétique cellulaires, CNRS UMR 5095, université de Bordeaux, 1, rue Camille-Saint-Saëns, 33077 Bordeaux cedex, France.
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Friebe S, Deuquet J, van der Goot FG. Differential dependence on N-glycosylation of anthrax toxin receptors CMG2 and TEM8. PLoS One 2015; 10:e0119864. [PMID: 25781883 PMCID: PMC4363784 DOI: 10.1371/journal.pone.0119864] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2014] [Accepted: 01/16/2015] [Indexed: 11/29/2022] Open
Abstract
ANTXR 1 and 2, also known as TEM8 and CMG2, are two type I membrane proteins, which have been extensively studied for their role as anthrax toxin receptors, but with a still elusive physiological function. Here we have analyzed the importance of N-glycosylation on folding, trafficking and ligand binding of these closely related proteins. We find that TEM8 has a stringent dependence on N-glycosylation. The presence of at least one glycan on each of its two extracellular domains, the vWA and Ig-like domains, is indeed necessary for efficient trafficking to the cell surface. In the absence of any N-linked glycans, TEM8 fails to fold correctly and is recognized by the ER quality control machinery. Expression of N-glycosylation mutants reveals that CMG2 is less vulnerable to sugar loss. The absence of N-linked glycans in one of the extracellular domains indeed has little impact on folding, trafficking or receptor function of the wild type protein expressed in tissue culture cells. N-glycans do, however, seem required in primary fibroblasts from human patients. Here, the presence of N-linked sugars increases the tolerance to mutations in cmg2 causing the rare genetic disease Hyaline Fibromatosis Syndrome. It thus appears that CMG2 glycosylation provides a buffer towards genetic variation by promoting folding of the protein in the ER lumen.
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Affiliation(s)
- Sarah Friebe
- Faculty of Life Sciences, Global Health Institute, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Julie Deuquet
- Faculty of Life Sciences, Global Health Institute, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - F. Gisou van der Goot
- Faculty of Life Sciences, Global Health Institute, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
- * E-mail:
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25
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Protein traffic disorders: an effective high-throughput fluorescence microscopy pipeline for drug discovery. Sci Rep 2015; 5:9038. [PMID: 25762484 PMCID: PMC4356983 DOI: 10.1038/srep09038] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2015] [Accepted: 02/13/2015] [Indexed: 12/12/2022] Open
Abstract
Plasma membrane proteins are essential molecules in the cell which mediate interactions with the exterior milieu, thus representing key drug targets for present pharma. Not surprisingly, protein traffic disorders include a large range of diseases sharing the common mechanism of failure in the respective protein to reach the plasma membrane. However, specific therapies for these diseases are remarkably lacking. Herein, we report a robust platform for drug discovery applied to a paradigmatic genetic disorder affecting intracellular trafficking – Cystic Fibrosis. This platform includes (i) two original respiratory epithelial cellular models incorporating an inducible double-tagged traffic reporter; (ii) a plasma membrane protein traffic assay for high-throughput microscopy screening; and (iii) open-source image analysis software to quantify plasma membrane protein traffic. By allowing direct scoring of compounds rescuing the basic traffic defect, this platform enables an effective drug development pipeline, which can be promptly adapted to any traffic disorder-associated protein and leverage therapy development efforts.
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26
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Shah K, Cheng Y, Hahn B, Bridges R, Bradbury NA, Mueller DM. Synonymous codon usage affects the expression of wild type and F508del CFTR. J Mol Biol 2015; 427:1464-1479. [PMID: 25676312 DOI: 10.1016/j.jmb.2015.02.003] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2014] [Revised: 02/03/2015] [Accepted: 02/04/2015] [Indexed: 10/24/2022]
Abstract
The cystic fibrosis transmembrane conductance regulator (CFTR) is an anion channel composed of 1480 amino acids. The major mutation responsible for cystic fibrosis results in loss of amino acid residue, F508 (F508del). Loss of F508 in CFTR alters the folding pathway resulting in endoplasmic-reticulum-associated degradation. This study investigates the role of synonymous codon in the expression of CFTR and CFTR F508del in human HEK293 cells. DNA encoding the open reading frame (ORF) for CFTR containing synonymous codon replacements was expressed using a heterologous vector integrated into the genome. The results indicate that the codon usage greatly affects the expression of CFTR. While the promoter strength driving expression of the ORFs was largely unchanged and the mRNA half-lives were unchanged, the steady-state levels of the mRNA varied by as much as 30-fold. Experiments support that this apparent inconsistency is attributed to nonsense mediated decay independent of exon junction complex. The ratio of CFTR/mRNA indicates that mRNA containing native codons was more efficient in expressing mature CFTR as compared to mRNA containing synonymous high-expression codons. However, when F508del CFTR was expressed after codon optimization, a greater percentage of the protein escaped endoplasmic-reticulum-associated degradation resulting in considerable levels of mature F508del CFTR on the plasma membrane, which showed channel activity. These results indicate that codon usage has an effect on mRNA levels and protein expression, for CFTR, and likely on chaperone-assisted folding pathway, for F508del CFTR.
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Affiliation(s)
- Kalpit Shah
- Department of Biochemistry and Molecular Biology, Rosalind Franklin University, The Chicago Medical School, North Chicago, IL 60064, USA; Department of Physiology and Biophysics, Rosalind Franklin University, The Chicago Medical School, North Chicago, IL 60064, USA
| | - Yi Cheng
- Department of Physiology and Biophysics, Rosalind Franklin University, The Chicago Medical School, North Chicago, IL 60064, USA
| | - Brian Hahn
- Department of Biochemistry and Molecular Biology, Rosalind Franklin University, The Chicago Medical School, North Chicago, IL 60064, USA
| | - Robert Bridges
- Department of Physiology and Biophysics, Rosalind Franklin University, The Chicago Medical School, North Chicago, IL 60064, USA
| | - Neil A Bradbury
- Department of Physiology and Biophysics, Rosalind Franklin University, The Chicago Medical School, North Chicago, IL 60064, USA
| | - David M Mueller
- Department of Biochemistry and Molecular Biology, Rosalind Franklin University, The Chicago Medical School, North Chicago, IL 60064, USA.
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27
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Roth DM, Hutt DM, Tong J, Bouchecareilh M, Wang N, Seeley T, Dekkers JF, Beekman JM, Garza D, Drew L, Masliah E, Morimoto RI, Balch WE. Modulation of the maladaptive stress response to manage diseases of protein folding. PLoS Biol 2014; 12:e1001998. [PMID: 25406061 PMCID: PMC4236052 DOI: 10.1371/journal.pbio.1001998] [Citation(s) in RCA: 75] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2014] [Accepted: 10/07/2014] [Indexed: 12/31/2022] Open
Abstract
Diseases of protein folding arise because of the inability of an altered peptide sequence to properly engage protein homeostasis components that direct protein folding and function. To identify global principles of misfolding disease pathology we examined the impact of the local folding environment in alpha-1-antitrypsin deficiency (AATD), Niemann-Pick type C1 disease (NPC1), Alzheimer's disease (AD), and cystic fibrosis (CF). Using distinct models, including patient-derived cell lines and primary epithelium, mouse brain tissue, and Caenorhabditis elegans, we found that chronic expression of misfolded proteins not only triggers the sustained activation of the heat shock response (HSR) pathway, but that this sustained activation is maladaptive. In diseased cells, maladaptation alters protein structure-function relationships, impacts protein folding in the cytosol, and further exacerbates the disease state. We show that down-regulation of this maladaptive stress response (MSR), through silencing of HSF1, the master regulator of the HSR, restores cellular protein folding and improves the disease phenotype. We propose that restoration of a more physiological proteostatic environment will strongly impact the management and progression of loss-of-function and gain-of-toxic-function phenotypes common in human disease.
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Affiliation(s)
- Daniela Martino Roth
- Department of Cell Biology, The Scripps Research Institute, La Jolla, California, United States of America
| | - Darren M. Hutt
- Department of Cell Biology, The Scripps Research Institute, La Jolla, California, United States of America
| | - Jiansong Tong
- Department of Cell Biology, The Scripps Research Institute, La Jolla, California, United States of America
| | - Marion Bouchecareilh
- Department of Cell Biology, The Scripps Research Institute, La Jolla, California, United States of America
| | - Ning Wang
- Department of Molecular Biosciences, Rice Institute for Biomedical Research, Northwestern University, Evanston, Illinois, United States of America
| | - Theo Seeley
- Department of Cell Biology, The Scripps Research Institute, La Jolla, California, United States of America
| | - Johanna F. Dekkers
- Department of Pediatric Pulmonology, Wilhelmina Children's Hospital, University Medical Centre, Utrecht, The Netherlands
- Laboratory of Translational Immunology, Wilhelmina Children's Hospital, University Medical Centre, Utrecht, The Netherlands
| | - Jeffrey M. Beekman
- Department of Pediatric Pulmonology, Wilhelmina Children's Hospital, University Medical Centre, Utrecht, The Netherlands
- Laboratory of Translational Immunology, Wilhelmina Children's Hospital, University Medical Centre, Utrecht, The Netherlands
| | - Dan Garza
- Proteostasis Therapeutics Inc., Cambridge, Massachusetts, United States of America
| | - Lawrence Drew
- Proteostasis Therapeutics Inc., Cambridge, Massachusetts, United States of America
| | - Eliezer Masliah
- Department of Neurosciences, University of California, San Diego, La Jolla, California, United States of America
| | - Richard I. Morimoto
- Department of Molecular Biosciences, Rice Institute for Biomedical Research, Northwestern University, Evanston, Illinois, United States of America
| | - William E. Balch
- Department of Cell Biology, The Scripps Research Institute, La Jolla, California, United States of America
- The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, California, United States of America
- Department of Chemical Physiology, The Scripps Research Institute, La Jolla, California, United States of America
- The Institute for Childhood and Neglected Diseases, The Scripps Research Institute, La Jolla, California, United States of America
- * E-mail:
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28
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Lotfy M, Singh J, Rashed H, Tariq S, Zilahi E, Adeghate E. The effect of glucagon-like peptide-1 in the management of diabetes mellitus: cellular and molecular mechanisms. Cell Tissue Res 2014; 358:343-58. [PMID: 25115772 DOI: 10.1007/s00441-014-1959-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2014] [Accepted: 07/03/2014] [Indexed: 12/20/2022]
Abstract
Incretins, such as glucagon-like peptide-1 (GLP)-1, have been shown to elevate plasma insulin concentration. The purpose of this study is to investigate the cellular and molecular basis of the beneficial effects of GLP-1. Normal and diabetic male Wistar rats were treated with GLP-1 (50 ng/kg body weight) for 10 weeks. At the end of the experiment, pancreatic tissues were taken for immunohistochemistry, immunoelectron microscopy and real-time polymerase chain reaction studies. Samples of blood were retrieved from the animals for the measurement of enzymes and insulin. The results show that treatment of diabetic rats with GLP-1 caused significant (P < 0.05) reduction in body weight gain and blood glucose level. GLP-1 (10(-12)-10(-6) M) induced significant (P < 0.01) dose-dependent increases in insulin release from the pancreas of normal and diabetic rats compared to basal. Diabetes-induced abnormal liver (aspartate aminotransferase and alanine aminotransferase) and kidney (blood urea nitrogen and uric acid) parameters were corrected in GLP-1-treated rats compared to controls. GLP-1 treatment induced significant (P < 0.05) elevation in the expression of pancreatic duodenal homeobox-1, heat shock protein-70, glutathione peroxidase, insulin receptor and GLP-1-receptor genes in diabetic animals compared to controls. GLP-1 is present in pancreatic beta cells and significantly (P < 0.05) increased the number of insulin-, glutathione reductase- and catalase-immunoreactive islet cells. The results of this study show that GLP-1 is co-localized with insulin and seems to exert its beneficial effects by increasing cellular concentrations of endogenous antioxidant genes and other genes involved in the maintenance of pancreatic beta cell structure and function.
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Affiliation(s)
- Mohamed Lotfy
- Department of Biology, College of Science, United Arab Emirates University, P.O. Box 17666, Al Ain, United Arab Emirates
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29
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Babajani G, Kermode AR. Alteration of the proteostasis network of plant cells promotes the post-endoplasmic reticulum trafficking of recombinant mutant (L444P) human β-glucocerebrosidase. PLANT SIGNALING & BEHAVIOR 2014; 9:e28714. [PMID: 24713615 PMCID: PMC4091198 DOI: 10.4161/psb.28714] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2014] [Revised: 03/30/2014] [Accepted: 03/31/2014] [Indexed: 06/03/2023]
Abstract
Gaucher disease is a prevalent lysosomal storage disease characterized by a deficiency in the activity of lysosomal acid β-glucosidase (glucocerebrosidase, GCase, EC 3.2.1.45). One of the most prevalent disease-causing mutations in humans is a L444P missense mutation in the GCase protein, which results in its disrupted folding in the endoplasmic reticulum (ER) and impaired post-ER trafficking. To determine whether the post-ER trafficking of this severely malfolded protein can be restored, we expressed the mutant L444P GCase as a recombinant protein in transgenic tobacco (Nicotiana tabacum L. cv Bright Yellow 2 [BY2]) cells, in which the GCase variant was equipped with a plant signal peptide to allow for secretion upon rescued trafficking out of the ER. The recombinant L444P mutant GCase was retained in the plant endoplasmic reticulum (ER). Kifunensine and Eeyarestatin I, both inhibitors of ER-associated degradation (ERAD), and the proteostasis regulators, celastrol and MG-132, increased the steady-state levels of the mutant protein inside the plant cells and further promoted the post-ER trafficking of L444P GCase, as indicated by endoglycosidase-H sensitivity- and secretion- analyses. Transcript profiling of genes encoding ER-molecular chaperones, ER stress responsive proteins, and cytoplasmic heat shock response proteins, revealed insignificant or only very modest changes in response to the ERAD inhibitors and proteostasis regulators. An exception was the marked response to celastrol which reduced the steady-state levels of cytoplasmic HSP90 transcripts and protein. As Hsp90 participates in the targeting of misfolded proteins to the proteasome pathway, its down-modulation in response to celastrol may partly account for the mechanism of improved homeostasis of L444P GCase mediated by this triterpene.
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Affiliation(s)
- Gholamreza Babajani
- Department of Biological Sciences; Simon Fraser University; Burnaby, BC Canada
| | - Allison R Kermode
- Department of Biological Sciences; Simon Fraser University; Burnaby, BC Canada
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30
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Park S, Jang I, Zuber C, Lee Y, Cho JW, Matsuo I, Ito Y, Roth J. ERADication of EDEM1 occurs by selective autophagy and requires deglycosylation by cytoplasmic peptide N-glycanase. Histochem Cell Biol 2014; 142:153-69. [PMID: 24664425 DOI: 10.1007/s00418-014-1204-3] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/22/2014] [Indexed: 11/30/2022]
Abstract
ER degradation-enhancing α-mannosidase-like 1 protein (EDEM1) is involved in the routing of misfolded glycoproteins for degradation in the cytoplasm. Previously, we reported that EDEM1 leaves the endoplasmic reticulum via non-COPII vesicles (Zuber et al. in Proc Natl Acad Sci USA 104:4407-4412, 2007) and becomes degraded by basal autophagy (Le Fourn et al. in Cell Mol Life Sci 66:1434-1445, 2009). However, it is unknown which type of autophagy is involved. Likewise, how EDEM1 is targeted to autophagosomes remains elusive. We now show that EDEM1 is degraded by selective autophagy. It colocalizes with the selective autophagy cargo receptors p62/SQSTM1, neighbor of BRCA1 gene 1 (NBR1) and autophagy-linked FYVE (Alfy) protein, and becomes engulfed by autophagic isolation membranes. The interaction with p62/SQSTM1 and NBR1 is required for routing of EDEM1 to autophagosomes since it can be blocked by short inhibitory RNA knockdown of the cargo receptors. Furthermore, p62/SQSTM1 interacts only with deglycosylated EDEM1 that is also ubiquitinated. The deglycosylation of EDEM1 occurs by the cytosolic peptide N-glycanase and is a prerequisite for interaction and aggregate formation with p62/SQSTM1 as demonstrated by the effect of peptide N-glycanase inhibitors on the formation of protein aggregates. Conversely, aggregation of p62/SQSTM1 and EDEM1 occurs independent of cytoplasmic histone deacetylase. These data provide novel insight into the mechanism of autophagic degradation of the ER-associated protein degradation (ERAD) component EDEM1 and disclose hitherto unknown parallels with the clearance of cytoplasmic aggregates of misfolded proteins by selective autophagy.
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Affiliation(s)
- Sujin Park
- WCU Program, Department of Integrated OMICS for Biomedical Science, Yonsei University Graduate School, Seoul, 120-749, Korea
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31
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Ulloa-Aguirre A, Zariñán T, Dias JA, Conn PM. Mutations in G protein-coupled receptors that impact receptor trafficking and reproductive function. Mol Cell Endocrinol 2014; 382:411-423. [PMID: 23806559 PMCID: PMC3844050 DOI: 10.1016/j.mce.2013.06.024] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/15/2013] [Revised: 05/28/2013] [Accepted: 06/17/2013] [Indexed: 11/15/2022]
Abstract
G protein coupled receptors (GPCRs) are a large superfamily of integral cell surface plasma membrane proteins that play key roles in transducing extracellular signals, including sensory stimuli, hormones, neurotransmitters, or paracrine factors into the intracellular environment through the activation of one or more heterotrimeric G proteins. Structural alterations provoked by mutations or variations in the genes coding for GPCRs may lead to misfolding, altered plasma membrane expression of the receptor protein and frequently to disease. A number of GPCRs regulate reproductive function at different levels; these receptors include the gonadotropin-releasing hormone receptor (GnRHR) and the gonadotropin receptors (follicle-stimulating hormone receptor and luteinizing hormone receptor), which regulate the function of the pituitary-gonadal axis. Loss-of-function mutations in these receptors may lead to hypogonadotropic or hypergonadotropic hypogonadism, which encompass a broad spectrum of clinical phenotypes. In this review we describe mutations that provoke misfolding and failure of these receptors to traffick from the endoplasmic reticulum to the plasma membrane. We also discuss some aspects related to the therapeutic potential of some target-specific drugs that selectively bind to and rescue function of misfolded mutant GnRHR and gonadotropin receptors, and that represent potentially valuable strategies to treat diseases caused by inactivating mutations of these receptors.
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Affiliation(s)
- Alfredo Ulloa-Aguirre
- Division of Reproductive Health, Research Center in Population Health, National Institute of Public Health, Cuernavaca, Mexico; Divisions of Reproductive Sciences and Neuroscience, Oregon National Primate Research Center, Oregon Health and Science University, Beaverton, OR 97006, USA.
| | - Teresa Zariñán
- Research Unit in Reproductive Medicine, UMAE Hospital de Ginecobstetricia "Luis Castelazo Ayala", Mexico, DF, Mexico
| | - James A Dias
- Department of Biomedical Sciences, School of Public Health, University at Albany, Albany, NY, USA
| | - P Michael Conn
- Divisions of Reproductive Sciences and Neuroscience, Oregon National Primate Research Center, Oregon Health and Science University, Beaverton, OR 97006, USA; Department of Pharmacology and Physiology, Oregon Health and Science University, Beaverton, OR 97006, USA; Department of Cell and Developmental Biology, Oregon Health and Science University, Beaverton, OR 97006, USA; Department of Obstetrics and Gynecology, Oregon Health and Science University, Beaverton, OR 97006, USA
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32
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Ciryam P, Tartaglia GG, Morimoto RI, Dobson CM, Vendruscolo M. Widespread aggregation and neurodegenerative diseases are associated with supersaturated proteins. Cell Rep 2013; 5:781-90. [PMID: 24183671 PMCID: PMC3883113 DOI: 10.1016/j.celrep.2013.09.043] [Citation(s) in RCA: 209] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2013] [Revised: 08/12/2013] [Accepted: 09/27/2013] [Indexed: 12/19/2022] Open
Abstract
The maintenance of protein solubility is a fundamental aspect of cellular homeostasis because protein aggregation is associated with a wide variety of human diseases. Numerous proteins unrelated in sequence and structure, however, can misfold and aggregate, and widespread aggregation can occur in living systems under stress or aging. A crucial question in this context is why only certain proteins appear to aggregate readily in vivo, whereas others do not. We identify here the proteins most vulnerable to aggregation as those whose cellular concentrations are high relative to their solubilities. We find that these supersaturated proteins represent a metastable subproteome involved in pathological aggregation during stress and aging and are overrepresented in biochemical processes associated with neurodegenerative disorders. Consequently, such cellular processes become dysfunctional when the ability to keep intrinsically supersaturated proteins soluble is compromised. Thus, the simultaneous analysis of abundance and solubility can rationalize the diverse cellular pathologies linked to neurodegenerative diseases and aging.
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Affiliation(s)
- Prajwal Ciryam
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
- Department of Biochemistry, Molecular Biology and Cell Biology, Rice Institute for Biomedical Research, Northwestern University, Evanston, IL 60208-3500, USA
| | | | - Richard I. Morimoto
- Department of Biochemistry, Molecular Biology and Cell Biology, Rice Institute for Biomedical Research, Northwestern University, Evanston, IL 60208-3500, USA
| | - Christopher M. Dobson
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
| | - Michele Vendruscolo
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
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33
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Hutt DM, Balch WE. Expanding proteostasis by membrane trafficking networks. Cold Spring Harb Perspect Biol 2013; 5:cshperspect.a013383. [PMID: 23426524 DOI: 10.1101/cshperspect.a013383] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The folding biology common to all three kingdoms of life (Archaea, Bacteria, and Eukarya) is proteostasis. The proteostasis network (PN) functions as a "cloud" to generate, protect, and degrade the proteome. Whereas microbes (Bacteria, Archaea) have a single compartment, Eukarya have numerous subcellular compartments. We examine evidence that Eukarya compartments use coat, tether, and fusion (CTF) membrane trafficking components to form an evolutionarily advanced arm of the PN that we refer to as the "trafficking PN" (TPN). We suggest that the TPN builds compartments by generating a mosaic of integrated cargo-specific trafficking signatures (TRaCKS). TRaCKS control the temporal and spatial features of protein-folding biology based on the Anfinsen principle that the local environment plays a critical role in managing protein structure. TPN-generated endomembrane compartments apply a "quinary" level of structural control to modify the secondary, tertiary, and quaternary structures defined by the primary polypeptide-chain sequence. The development of Anfinsen compartments provides a unifying foundation for understanding the purpose of endomembrane biology and its capacity to drive extant Eukarya function and diversity.
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Affiliation(s)
- Darren M Hutt
- Department of Cell Biology and Department of Chemical Physiology, The Skaggs Institute for Chemical Biology and the Dorris Institute for Neurological Diseases, The Scripps Research Institute, La Jolla, California 92037, USA
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34
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Disease-relevant proteostasis regulation of cystic fibrosis transmembrane conductance regulator. Cell Death Differ 2013; 20:1101-15. [PMID: 23686137 DOI: 10.1038/cdd.2013.46] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2012] [Revised: 04/09/2013] [Accepted: 04/10/2013] [Indexed: 01/20/2023] Open
Abstract
Mismanaged protein trafficking by the proteostasis network contributes to several conformational diseases, including cystic fibrosis, the most frequent lethal inherited disease in Caucasians. Proteostasis regulators, as cystamine, enable the beneficial action of cystic fibrosis transmembrane conductance regulator (CFTR) potentiators in ΔF508-CFTR airways beyond drug washout. Here we tested the hypothesis that functional CFTR protein can sustain its own plasma membrane (PM) stability. Depletion or inhibition of wild-type CFTR present in bronchial epithelial cells reduced the availability of the small GTPase Rab5 by causing Rab5 sequestration within the detergent-insoluble protein fraction together with its accumulation in aggresomes. CFTR depletion decreased the recruitment of the Rab5 effector early endosome antigen 1 to endosomes, thus reducing the local generation of phosphatidylinositol-3-phosphate. This diverts recycling of surface proteins, including transferrin receptor and CFTR itself. Inhibiting CFTR function also resulted in its ubiquitination and interaction with SQSTM1/p62 at the PM, favoring its disposal. Addition of cystamine prevented the recycling defect of CFTR by enhancing BECN1 expression and reducing SQSTM1 accumulation. Our results unravel an unexpected link between CFTR protein and function, the latter regulating the levels of CFTR surface expression in a positive feed-forward loop, and highlight CFTR as a pivot of proteostasis in bronchial epithelial cells.
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35
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Diversity in the origins of proteostasis networks--a driver for protein function in evolution. Nat Rev Mol Cell Biol 2013; 14:237-48. [PMID: 23463216 DOI: 10.1038/nrm3542] [Citation(s) in RCA: 166] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Although the sequence of a protein largely determines its function, proteins can adopt different folding states in response to changes in the environment, some of which may be deleterious to the organism. All organisms--Bacteria, Archaea and Eukarya--have evolved a protein homeostasis, or proteostasis, network comprising chaperones and folding factors, degradation components, signalling pathways and specialized compartmentalized modules that manage protein folding in response to environmental stimuli and variation. Surveying the origins of proteostasis networks reveals that they have co-evolved with the proteome to regulate the physiological state of the cell, reflecting the unique stresses that different cells or organisms experience, and that they have a key role in driving evolution by closely managing the link between the phenotype and the genotype.
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36
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Villella VR, Esposito S, Bruscia EM, Maiuri MC, Raia V, Kroemer G, Maiuri L. Targeting the Intracellular Environment in Cystic Fibrosis: Restoring Autophagy as a Novel Strategy to Circumvent the CFTR Defect. Front Pharmacol 2013; 4:1. [PMID: 23346057 PMCID: PMC3549520 DOI: 10.3389/fphar.2013.00001] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2012] [Accepted: 01/01/2013] [Indexed: 12/18/2022] Open
Abstract
Cystic fibrosis (CF) patients harboring the most common deletion mutation of the CF transmembrane conductance regulator (CFTR), F508del, are poor responders to potentiators of CFTR channel activity which can be used to treat a small subset of CF patients who genetically carry plasma membrane (PM)-resident CFTR mutants. The misfolded F508del-CFTR protein is unstable in the PM even if rescued by pharmacological agents that prevent its intracellular retention and degradation. CF is a conformational disease in which defective CFTR induces an impressive derangement of general proteostasis resulting from disabled autophagy. In this review, we discuss how rescuing Beclin 1 (BECN1), a major player of autophagosome formation, either by means of direct gene transfer or indirectly by administration of proteostasis regulators, could stabilize F508del-CFTR at the PM. We focus on the relationship between the improvement of peripheral proteostasis and CFTR PM stability in F508del-CFTR homozygous bronchial epithelia or mouse lungs. Moreover, this article reviews recent pre-clinical evidence indicating that targeting the intracellular environment surrounding the misfolded mutant CFTR instead of protein itself could constitute an attractive therapeutic option to sensitize patients carrying the F508del-CFTR mutation to the beneficial action of CFTR potentiators on lung inflammation.
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Affiliation(s)
- Valeria Rachela Villella
- European Institute for Research in Cystic Fibrosis, San Raffaele Scientific Institute Milan, Italy
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37
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Chanoux RA, Rubenstein RC. Molecular Chaperones as Targets to Circumvent the CFTR Defect in Cystic Fibrosis. Front Pharmacol 2012; 3:137. [PMID: 22822398 PMCID: PMC3398409 DOI: 10.3389/fphar.2012.00137] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2012] [Accepted: 06/25/2012] [Indexed: 01/07/2023] Open
Abstract
Cystic Fibrosis (CF) is the most common autosomal recessive lethal disorder among Caucasian populations. CF results from mutations and resulting dysfunction of the Cystic Fibrosis Transmembrane Conductance Regulator (CFTR). CFTR is a cyclic AMP-dependent chloride channel that is localized to the apical membrane in epithelial cells where it plays a key role in salt and water homeostasis. An intricate network of molecular chaperone proteins regulates CFTR’s proper maturation and trafficking to the apical membrane. Understanding and manipulation of this network may lead to therapeutics for CF in cases where mutant CFTR has aberrant trafficking.
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Affiliation(s)
- Rebecca A Chanoux
- Division of Pulmonary Medicine and Cystic Fibrosis Center, The Children's Hospital of Philadelphia Philadelphia, PA, USA
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38
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Coppinger JA, Hutt DM, Razvi A, Koulov AV, Pankow S, Yates JR, Balch WE. A chaperone trap contributes to the onset of cystic fibrosis. PLoS One 2012; 7:e37682. [PMID: 22701530 PMCID: PMC3365120 DOI: 10.1371/journal.pone.0037682] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2011] [Accepted: 04/26/2012] [Indexed: 12/29/2022] Open
Abstract
Protein folding is the primary role of proteostasis network (PN) where chaperone interactions with client proteins determine the success or failure of the folding reaction in the cell. We now address how the Phe508 deletion in the NBD1 domain of the cystic fibrosis (CF) transmembrane conductance regulator (CFTR) protein responsible for cystic fibrosis (CF) impacts the binding of CFTR with cellular chaperones. We applied single ion reaction monitoring mass spectrometry (SRM-MS) to quantitatively characterize the stoichiometry of the heat shock proteins (Hsps) in CFTR folding intermediates in vivo and mapped the sites of interaction of the NBD1 domain of CFTR with Hsp90 in vitro. Unlike folding of WT-CFTR, we now demonstrate the presence of ΔF508-CFTR in a stalled folding intermediate in stoichiometric association with the core Hsps 40, 70 and 90, referred to as a ‘chaperone trap’. Culturing cells at 30 C resulted in correction of ΔF508-CFTR trafficking and function, restoring the sub-stoichiometric association of core Hsps observed for WT-CFTR. These results support the interpretation that ΔF508-CFTR is restricted to a chaperone-bound folding intermediate, a state that may contribute to its loss of trafficking and increased targeting for degradation. We propose that stalled folding intermediates could define a critical proteostasis pathway branch-point(s) responsible for the loss of function in misfolding diseases as observed in CF.
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Affiliation(s)
- Judith A Coppinger
- Department of Cell Biology, The Scripps Research Institute, La Jolla, California, United States of America
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39
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Bortezomib a safe treatment for patients with multiple myeloma and cystic fibrosis. Mediterr J Hematol Infect Dis 2012; 4:e2012035. [PMID: 22708050 PMCID: PMC3375716 DOI: 10.4084/mjhid.2012.035] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2012] [Accepted: 05/02/2012] [Indexed: 12/23/2022] Open
Abstract
Introduction: Bortezomib is a proteasome inhibitor that targets myeloma cell and its bone marrow microenvironment. Intravenous Bortezomib with or without dexamethasone, is effective and well tolerated in patients with relapsed/refractory multiple myeloma (MM). Methods: We used Bortezomib without corticosteroids, to avoid the risk of lung infection reactivations due to patient’s Pseudomonas aeruginosa colonization, in a MM patient with Cystic Fibrosis. Four 21-day cycles of Bortezomib were administrated at 1.3 mg/m2 on days 1,4,8 and 11 with a 10 day rest period. Treatment response and toxicity were evaluated. Results: After four cycles of therapy the patient achieved a very good partial response (VGPR) according to the IMWG response criteria, without clinically significant side effects. Conclusions: Bortezomib can be successfully utilized for the management of this difficult disease situation.
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40
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Hutt DM, Roth DM, Chalfant MA, Youker RT, Matteson J, Brodsky JL, Balch WE. FK506 binding protein 8 peptidylprolyl isomerase activity manages a late stage of cystic fibrosis transmembrane conductance regulator (CFTR) folding and stability. J Biol Chem 2012; 287:21914-25. [PMID: 22474283 DOI: 10.1074/jbc.m112.339788] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Cystic fibrosis (CF) is caused by mutations in the apical chloride channel cystic fibrosis transmembrane conductance regulator (CFTR) with 90% of patients carrying at least one deletion of the F508 (ΔF508) allele. This mutant form of CFTR is characterized by a folding and trafficking defect that prevents exit from the endoplasmic reticulum. We previously reported that ΔF508 CFTR can be recovered in a complex with Hsp90 and its co-chaperones as an on-pathway folding intermediate, suggesting that Δ508 CF disease arises due to a failure of the proteostasis network (PN), which manages protein folding and degradation in the cell. We have now examined the role of FK506-binding protein 8 (FKBP8), a component of the CFTR interactome, during the biogenesis of wild-type and ΔF508 CFTR. FKBP8 is a member of the peptidylprolyl isomerase family that mediates the cis/trans interconversion of peptidyl prolyl bonds. Our results suggest that FKBP8 is a key PN factor required at a post-Hsp90 step in CFTR biogenesis. In addition, changes in its expression level or alteration of its activity by a peptidylprolyl isomerase inhibitor alter CFTR stability and transport. We propose that CF is caused by the sequential failure of the prevailing PN pathway to stabilize ΔF508-CFTR for endoplasmic reticulum export, a pathway that can be therapeutically managed.
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Affiliation(s)
- Darren M Hutt
- Department of Cell Biology, The Scripps Research Institute, La Jolla, California 92037, USA
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41
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Pharmacological chaperones correct misfolded GPCRs and rescue function: protein trafficking as a therapeutic target. Subcell Biochem 2012; 63:263-89. [PMID: 23161143 DOI: 10.1007/978-94-007-4765-4_14] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
G-protein-coupled receptors (GPCRs) are a large superfamily of plasma membrane proteins that play central roles in transducing endocrine, neural and -sensory signals. In humans, more than 30 disorders are associated with mutations in GPCRs and these proteins are common drug development targets, with 30-50% of drugs targeting them. GPCR mutants are frequently misfolded, recognized as defective by the cellular quality control system, retained in the endoplasmic reticulum and do not traffic to the plasma membrane. The use of small molecules chaperones (pharmacological chaperones or "pharmacoperones") to rescue misfolded GPCRs has provided a new approach for treatment of human diseases caused by misfolding and misrouting. This chapter provides an overview of the molecular basis of this approach using the human gonadotropin-releasing hormone receptor (hGnRHR) as model for treatment of conformational diseases provoked by -misfolded GPCRs.
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42
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Hetz C, Martinon F, Rodriguez D, Glimcher LH. The unfolded protein response: integrating stress signals through the stress sensor IRE1α. Physiol Rev 2011; 91:1219-43. [PMID: 22013210 DOI: 10.1152/physrev.00001.2011] [Citation(s) in RCA: 443] [Impact Index Per Article: 34.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Stress induced by accumulation of unfolded proteins at the endoplasmic reticulum (ER) is a classic feature of secretory cells and is observed in many tissues in human diseases including cancer, diabetes, obesity, and neurodegeneration. Cellular adaptation to ER stress is achieved by the activation of the unfolded protein response (UPR), an integrated signal transduction pathway that transmits information about the protein folding status at the ER to the nucleus and cytosol to restore ER homeostasis. Inositol-requiring transmembrane kinase/endonuclease-1 (IRE1α), the most conserved UPR stress sensor, functions as an endoribonuclease that processes the mRNA of the transcription factor X-box binding protein-1 (XBP1). IRE1α signaling is a highly regulated process, controlled by the formation of a dynamic scaffold onto which many regulatory components assemble, here referred to as the UPRosome. Here we provide an overview of the signaling and regulatory mechanisms underlying IRE1α function and discuss the emerging role of the UPR in adaptation to protein folding stress in specialized secretory cells and in pathological conditions associated with alterations in ER homeostasis.
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Affiliation(s)
- Claudio Hetz
- Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston, MA, USA.
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43
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Abstract
The endoplasmic reticulum (ER) uses an elaborate surveillance system called the ER quality control (ERQC) system. The ERQC facilitates folding and modification of secretory and membrane proteins and eliminates terminally misfolded polypeptides through ER-associated degradation (ERAD) or autophagic degradation. This mechanism of ER protein surveillance is closely linked to redox and calcium homeostasis in the ER, whose balance is presumed to be regulated by a specific cellular compartment. The potential to modulate proteostasis and metabolism with chemical compounds or targeted siRNAs may offer an ideal option for the treatment of disease.
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44
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Needham PG, Mikoluk K, Dhakarwal P, Khadem S, Snyder AC, Subramanya AR, Brodsky JL. The thiazide-sensitive NaCl cotransporter is targeted for chaperone-dependent endoplasmic reticulum-associated degradation. J Biol Chem 2011; 286:43611-43621. [PMID: 22027832 DOI: 10.1074/jbc.m111.288928] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
The thiazide-sensitive NaCl cotransporter (NCC, SLC12A3) mediates salt reabsorption in the distal nephron of the kidney and is the target of thiazide diuretics, which are commonly prescribed to treat hypertension. Mutations in NCC also give rise to Gitelman syndrome, a hereditary salt-wasting disorder thought in most cases to arise from impaired NCC biogenesis through enhanced endoplasmic reticulum-associated degradation (ERAD). Because the machinery that mediates NCC quality control is completely undefined, we employed yeast as a model heterologous expression system to identify factors involved in NCC degradation. We confirmed that NCC was a bona fide ERAD substrate in yeast, as the majority of NCC polypeptide was integrated into ER membranes, and its turnover rate was sensitive to proteasome inhibition. NCC degradation was primarily dependent on the ER membrane-associated E3 ubiquitin ligase Hrd1. Whereas several ER luminal chaperones were dispensable for NCC ERAD, NCC ubiquitination and degradation required the activity of Ssa1, a cytoplasmic Hsp70 chaperone. Compatible findings were observed when NCC was expressed in mammalian kidney cells, as the cotransporter was polyubiquitinated and degraded by the proteasome, and mammalian cytoplasmic Hsp70 (Hsp72) coexpression stimulated the degradation of newly synthesized NCC. Hsp70 also preferentially associated with the ER-localized NCC glycosylated species, indicating that cytoplasmic Hsp70 plays a critical role in selecting immature forms of NCC for ERAD. Together, these results provide the first survey of components involved in the ERAD of a mammalian SLC12 cation chloride cotransporter and provide a framework for future studies on NCC ER quality control.
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Affiliation(s)
- Patrick G Needham
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania 15261
| | - Kasia Mikoluk
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania 15261
| | - Pradeep Dhakarwal
- Department of Medicine, Renal-Electrolyte Division, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15261
| | - Shaheen Khadem
- Department of Medicine, Renal-Electrolyte Division, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15261; Veterans Affairs Pittsburgh Healthcare System, Pittsburgh, Pennsylvania 15261
| | - Avin C Snyder
- Department of Medicine, Renal-Electrolyte Division, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15261
| | - Arohan R Subramanya
- Department of Medicine, Renal-Electrolyte Division, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15261; Veterans Affairs Pittsburgh Healthcare System, Pittsburgh, Pennsylvania 15261.
| | - Jeffrey L Brodsky
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania 15261
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45
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Ng DP, Poulsen BE, Deber CM. Membrane protein misassembly in disease. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2011; 1818:1115-22. [PMID: 21840297 DOI: 10.1016/j.bbamem.2011.07.046] [Citation(s) in RCA: 67] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2011] [Revised: 07/28/2011] [Accepted: 07/29/2011] [Indexed: 11/19/2022]
Abstract
Helix-helix interactions play a central role in the folding and assembly of integral α-helical membrane proteins and are fundamentally dictated by the amino acid sequence of the TM domain. It is not surprising then that missense mutations that target these residues are often linked to disease. In this review, we focus on the molecular mechanisms through which missense mutations lead to aberrant folding and/or assembly of these proteins, and then discuss pharmacological approaches that may potentially mitigate or reverse the negative effects of these mutations. Improving our understanding of how missense mutations affect the interactions between TM α-helices will increase our capability to develop effective therapeutic approaches to counter the misassembly of these proteins and, ultimately, disease. This article is part of a Special Issue entitled: Protein Folding in Membranes.
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Affiliation(s)
- Derek P Ng
- Division of Molecular Structure & Function, Research Institute, Hospital for Sick Children, Toronto, Ontario, Canada
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46
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Hutt DM, Olsen CA, Vickers CJ, Herman D, Chalfant MA, Montero A, Leman LJ, Burkle R, Maryanoff BE, Balch WE, Ghadiri MR. Potential Agents for Treating Cystic Fibrosis: Cyclic Tetrapeptides that Restore Trafficking and Activity of ΔF508-CFTR. ACS Med Chem Lett 2011; 2:703-707. [PMID: 21984958 DOI: 10.1021/ml200136e] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Cystic fibrosis (CF) is a loss-of-function disease caused by mutations in the CF transmembrane conductance regulator (CFTR) protein, a chloride ion channel that localizes to the apical plasma membrane of epithelial cells. The most common form of the disease results from the deletion of phenylalanine-508 (ΔF508), leading to the accumulation of CFTR in the endoplasmic reticulum with a concomitant loss of chloride flux. We discovered that cyclic tetrapeptides, such as 11, 14, and 15, are able to correct the trafficking defect and restore cell surface activity of ΔF508-CFTR. Although this class of cyclic tetrapeptides is known to contain inhibitors of certain histone deacetylase (HDAC) isoforms, their HDAC inhibitory potencies did not directly correlate with their ability to rescue ΔF508-CFTR. In full HDAC profiling, 15 strongly inhibited HDACs 1, 2, 3, 10 and 11, but not HDACs 4-9. Although 15 had less potent IC(50) values than reference agent vorinostat (2) in HDAC profiling, it was markedly more potent than 2 in rescuing ΔF508-CFTR. We suggest that specific HDACs can have a differential influence on correcting ΔF508-CFTR, which may reflect both deacetylase and protein scaffolding actions.
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Affiliation(s)
- Darren M. Hutt
- Departments of †Cell Biology, ‡Chemical Physiology, and §Chemistry, and ∥The Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Christian A. Olsen
- Departments of †Cell Biology, ‡Chemical Physiology, and §Chemistry, and ∥The Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Chris J. Vickers
- Departments of †Cell Biology, ‡Chemical Physiology, and §Chemistry, and ∥The Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - David Herman
- Departments of †Cell Biology, ‡Chemical Physiology, and §Chemistry, and ∥The Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Monica A. Chalfant
- Departments of †Cell Biology, ‡Chemical Physiology, and §Chemistry, and ∥The Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Ana Montero
- Departments of †Cell Biology, ‡Chemical Physiology, and §Chemistry, and ∥The Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Luke J. Leman
- Departments of †Cell Biology, ‡Chemical Physiology, and §Chemistry, and ∥The Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Renner Burkle
- Departments of †Cell Biology, ‡Chemical Physiology, and §Chemistry, and ∥The Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Bruce E. Maryanoff
- Departments of †Cell Biology, ‡Chemical Physiology, and §Chemistry, and ∥The Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - William E. Balch
- Departments of †Cell Biology, ‡Chemical Physiology, and §Chemistry, and ∥The Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - M. Reza Ghadiri
- Departments of †Cell Biology, ‡Chemical Physiology, and §Chemistry, and ∥The Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
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47
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Matsumura Y, David LL, Skach WR. Role of Hsc70 binding cycle in CFTR folding and endoplasmic reticulum-associated degradation. Mol Biol Cell 2011; 22:2797-809. [PMID: 21697503 PMCID: PMC3154877 DOI: 10.1091/mbc.e11-02-0137] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Hsc70 plays a productive role during cotranslational cystic fibrosis transmembrane conductance regulator folding that is outweighed by its dominant contribution to posttranslational targeting to the ubiquitin-proteasome system. Moreover, the outcome of Hsc70 binding appears highly sensitive to the duration of its binding cycle, which is governed by regulatory cochaperones. The Hsp/c70 cytosolic chaperone system facilitates competing pathways of protein folding and degradation. Here we use a reconstituted cell-free system to investigate the mechanism and extent to which Hsc70 contributes to these co- and posttranslational decisions for the membrane protein cystic fibrosis transmembrane conductance regulator (CFTR). Hsc70 binding to CFTR was destabilized by the C-terminal domain of Bag-1 (CBag), which stimulates client release by accelerating ADP-ATP exchange. Addition of CBag during CFTR translation slightly increased susceptibility of the newly synthesized protein to degradation, consistent with a profolding function for Hsc70. In contrast, posttranslational destabilization of Hsc70 binding nearly completely blocked CFTR ubiquitination, dislocation from the endoplasmic reticulum, and proteasome-mediated cleavage. This effect required molar excess of CBag relative to Hsc70 and was completely reversed by the CBag-binding subdomain of Hsc70. These results demonstrate that the profolding role of Hsc70 during cotranslational CFTR folding is counterbalanced by a dominant and essential role in posttranslational targeting to the ubiquitin-proteasome system. Moreover, the degradative outcome of Hsc70 binding appears highly sensitive to the duration of its binding cycle, which is in turn governed by the integrated expression of regulatory cochaperones.
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Affiliation(s)
- Yoshihiro Matsumura
- Department of Biochemistry and Molecular Biology, Oregon Health and Science University, Portland, OR 97239, USA
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48
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Bouchecareilh M, Balch WE. Proteostasis: a new therapeutic paradigm for pulmonary disease. PROCEEDINGS OF THE AMERICAN THORACIC SOCIETY 2011; 8:189-95. [PMID: 21543800 PMCID: PMC3131838 DOI: 10.1513/pats.201008-055ms] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2011] [Accepted: 02/01/2011] [Indexed: 01/10/2023]
Abstract
Among lung pathologies, α1AT, chronic obstructive pulmonary disease (COPD), emphysema, and asthma are diseases triggered by local environmental stress in the airway that we refer to herein collectively as airway stress diseases (ASDs). A deficiency of α-1-antitrypsin (α1AT) is an inherited genetic disorder that is a consequence of the misfolding of α1AT during protein synthesis in liver hepatocytes, reducing secretion to the plasma and delivery to the lung. Deficiency of α1AT in the lung triggers a similar pathological phenotype to other ASDs. Moreover, the loss of α1AT in the lung is a well-known environmental risk factor for COPD/emphysema. To date there are no effective therapeutic approaches to address ASDs, which reflects a general lack of understanding of their cellular basis. Herein, we propose that ASDs are disorders of proteostasis. That is, they are initiated and propagated by a common theme-a challenge to protein folding capacity maintained by the proteostasis network (PN) (see Balch et al., Science 2008;319:916-919). The PN is a network of chaperones and degradative components that generates and manages protein folding pathways responsible for normal human physiology. In ASD, we suggest that the PN system fails to respond to the increased burden of unfolded proteins due to genetic and environmental stresses, thus triggering pulmonary pathophysiology. We introduce the enabling concept of proteostasis regulators (PRs), small molecules that regulate signaling pathways that control the composition and activity of PN components, as a new and general approach for therapeutic management of ASDs.
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Affiliation(s)
- Marion Bouchecareilh
- Department of Cell Biology, The Skaggs Institute for Chemical Biology, Department of Chemical Physiology and the Institute for Childhood and Neglected Diseases, The Scripps Research Institute, La Jolla, California
| | - William E. Balch
- Department of Cell Biology, The Skaggs Institute for Chemical Biology, Department of Chemical Physiology and the Institute for Childhood and Neglected Diseases, The Scripps Research Institute, La Jolla, California
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49
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Shouldice SR, Heras B, Walden PM, Totsika M, Schembri MA, Martin JL. Structure and function of DsbA, a key bacterial oxidative folding catalyst. Antioxid Redox Signal 2011; 14:1729-60. [PMID: 21241169 DOI: 10.1089/ars.2010.3344] [Citation(s) in RCA: 86] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Since its discovery in 1991, the bacterial periplasmic oxidative folding catalyst DsbA has been the focus of intense research. Early studies addressed why it is so oxidizing and how it is maintained in its less stable oxidized state. The crystal structure of Escherichia coli DsbA (EcDsbA) revealed that the oxidizing periplasmic enzyme is a distant evolutionary cousin of the reducing cytoplasmic enzyme thioredoxin. Recent significant developments have deepened our understanding of DsbA function, mechanism, and interactions: the structure of the partner membrane protein EcDsbB, including its complex with EcDsbA, proved a landmark in the field. Studies of DsbA machineries from bacteria other than E. coli K-12 have highlighted dramatic differences from the model organism, including a striking divergence in redox parameters and surface features. Several DsbA structures have provided the first clues to its interaction with substrates, and finally, evidence for a central role of DsbA in bacterial virulence has been demonstrated in a range of organisms. Here, we review current knowledge on DsbA, a bacterial periplasmic protein that introduces disulfide bonds into diverse substrate proteins and which may one day be the target of a new class of anti-virulence drugs to treat bacterial infection.
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Affiliation(s)
- Stephen R Shouldice
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Australia
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50
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Koga H, Kaushik S, Cuervo AM. Protein homeostasis and aging: The importance of exquisite quality control. Ageing Res Rev 2011; 10:205-15. [PMID: 20152936 DOI: 10.1016/j.arr.2010.02.001] [Citation(s) in RCA: 305] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2010] [Revised: 01/25/2010] [Accepted: 02/01/2010] [Indexed: 01/12/2023]
Abstract
All cells count on precise mechanisms that regulate protein homeostasis to maintain a stable and functional proteome. A progressive deterioration in the ability of cells to preserve the stability of their proteome occurs with age and contributes to the functional loss characteristic of old organisms. Molecular chaperones and the proteolytic systems are responsible for this cellular quality control by assuring continuous renewal of intracellular proteins. When protein damage occurs, such as during cellular stress, the coordinated action of these cellular surveillance systems allows detection and repair of the damaged structures or, in many instances, leads to the complete elimination of the altered proteins from inside cells. Dysfunction of the quality control mechanisms and intracellular accumulation of abnormal proteins in the form of protein inclusions and aggregates occur in almost all tissues of an aged organism. Preservation or enhancement of the activity of these surveillance systems until late in life improves their resistance to stress and is sufficient to slow down aging. In this work, we review recent advances on our understanding of the contribution of chaperones and proteolytic systems to the maintenance of cellular homeostasis, the cellular response to stress and ultimately to longevity.
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Affiliation(s)
- Hiroshi Koga
- Department of Developmental and Molecular Biology, Marion Bessin Liver Research Center, Institute for Aging Research, Albert Einstein College of Medicine, Bronx, NY 10461, USA
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