451
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Olszewski MM, Williams C, Dong KC, Martin A. The Cdc48 unfoldase prepares well-folded protein substrates for degradation by the 26S proteasome. Commun Biol 2019; 2:29. [PMID: 30675527 PMCID: PMC6340886 DOI: 10.1038/s42003-019-0283-z] [Citation(s) in RCA: 82] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Accepted: 12/28/2018] [Indexed: 11/09/2022] Open
Abstract
Cdc48/p97 is an essential and highly conserved AAA+ ATPase that uses its protein-unfoldase activity to extract ubiquitinated polypeptides from macromolecular complexes and membranes. This motor has also been implicated in protein-degradation pathways, yet its exact role in acting upstream of the 26S proteasome remains elusive. Ubiquitinated proteins destined for degradation by the proteasome require an unstructured initiation region to engage with the proteasomal translocation machinery, and Cdc48 was proposed to generate these unfolded segments, yet direct evidence has been missing. Here, we used an in vitro reconstituted system to demonstrate the collaboration of Cdc48 and the 26S proteasome from S. cerevisiae in degrading ubiquitinated, well-folded proteins that lack unstructured segments. Our data indicate that a critical role for Cdc48 in the ubiquitin-proteasome system is to create flexible initiation regions in compact substrates that otherwise would be refractory to engagement and degradation by the proteasome.
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Affiliation(s)
- Michal M. Olszewski
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720 USA
- California Institute for Quantitative Biosciences, University of California, Berkeley, CA 94720 USA
| | - Cameron Williams
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720 USA
- California Institute for Quantitative Biosciences, University of California, Berkeley, CA 94720 USA
- Biophysics Graduate Group, University of California, Berkeley, CA 94720 USA
| | - Ken C. Dong
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720 USA
- California Institute for Quantitative Biosciences, University of California, Berkeley, CA 94720 USA
- Howard Hughes Medical Institute, University of California, Berkeley, CA 94720 USA
| | - Andreas Martin
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720 USA
- California Institute for Quantitative Biosciences, University of California, Berkeley, CA 94720 USA
- Howard Hughes Medical Institute, University of California, Berkeley, CA 94720 USA
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452
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Interplay between Autophagy and the Ubiquitin-Proteasome System and Its Role in the Pathogenesis of Age-Related Macular Degeneration. Int J Mol Sci 2019; 20:ijms20010210. [PMID: 30626110 PMCID: PMC6337628 DOI: 10.3390/ijms20010210] [Citation(s) in RCA: 83] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Revised: 12/21/2018] [Accepted: 01/02/2019] [Indexed: 12/20/2022] Open
Abstract
Age-related macular degeneration (AMD) is a complex eye disease with many pathogenesis factors, including defective cellular waste management in retinal pigment epithelium (RPE). Main cellular waste in AMD are: all-trans retinal, drusen and lipofuscin, containing unfolded, damaged and unneeded proteins, which are degraded and recycled in RPE cells by two main machineries—the ubiquitin-proteasome system (UPS) and autophagy. Recent findings show that these systems can act together with a significant role of the EI24 (etoposide-induced protein 2.4 homolog) ubiquitin ligase in their action. On the other hand, E3 ligases are essential in both systems, but E3 is degraded by autophagy. The interplay between UPS and autophagy was targeted in several diseases, including Alzheimer disease. Therefore, cellular waste clearing in AMD should be considered in the context of such interplay rather than either of these systems singly. Aging and oxidative stress, two major AMD risk factors, reduce both UPS and autophagy. In conclusion, molecular mechanisms of UPS and autophagy can be considered as a target in AMD prevention and therapeutic perspective. Further work is needed to identify molecules and effects important for the coordination of action of these two cellular waste management systems.
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453
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Wang R, Wang G. Protein Modification and Autophagy Activation. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1206:237-259. [PMID: 31776989 DOI: 10.1007/978-981-15-0602-4_12] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Protein modification refers to the chemical modification of proteins after their biosynthesis, which is also called posttranslational modification (PTM). PTM causes changes in protein properties and functions. PTM includes an attachment of addition of functional groups, such as methylation, acetylation, glycosylation and phosphorylation; a covalent coupling of small peptides or proteins, such as ubiquitination and SUMOylation; or chemical changes in amino acids, such as citrullination (conversion of arginine to citrulline). Protein modification plays an important role in cellular processes. Since a protein can be modified in different ways, such as acetylation, methylation and phosphorylation, the functions of proteins are different under different modification states. Moreover, the same modification at different sites may have completely different effects on protein function. For example, phosphorylation at some sites in a protein may lead to a functional activation, while phosphorylation at other sites may cause an inhibition of the functions. Thus, different modifications, combinations and sites changes lead to different functional regulations of a protein, resulting in different effects in the cells. In autophagy, PTMs are widely involved in the regulation of autophagy, including ubiquitination, phosphorylation and acetylation. Ubiquitination is the covalent conjugation of ubiquitin to the substrates through a series of enzymes. Phosphorylation refers to an attachment of a phosphoryl group into a protein, primarily on serine, threonine and tyrosine, which is catalyzed by the kinases. Phosphorylation, a common modification, regulates protein function and localization. Phosphorylation in autophagy regulates the activity of autophagy-associated proteins and the initiation and progression of autophagy by regulating signaling pathways. Acetylation means the addition of acetyl groups onto lysine or N-terminal segment of target proteins through acetyltransferases. Acetylation and deacetylation are both involved in the regulation of autophagy initiation and selective autophagy by controlling the acetylation level of important proteins in the autophagy process. In this chapter, we will focus on the regulation of ubiquitination and phosphorylation in autophagy.
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Affiliation(s)
- Rui Wang
- Laboratory of Molecular Neuropathology, Jiangsu Key Laboratory of Neuropsychiatric Diseases & Department of Pharmacology, College of Pharmaceutical Sciences, Soochow University, Suzhou, 215123, China
| | - Guanghui Wang
- Laboratory of Molecular Neuropathology, Jiangsu Key Laboratory of Neuropsychiatric Diseases & Department of Pharmacology, College of Pharmaceutical Sciences, Soochow University, Suzhou, 215123, China.
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454
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Delorme-Axford E, Klionsky DJ. On the edge of degradation: Autophagy regulation by RNA decay. WILEY INTERDISCIPLINARY REVIEWS-RNA 2018; 10:e1522. [PMID: 30560575 DOI: 10.1002/wrna.1522] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Revised: 11/21/2018] [Accepted: 11/27/2018] [Indexed: 12/21/2022]
Abstract
Cells must dynamically adapt to altered environmental conditions, particularly during times of stress, to ensure their ability to function effectively and survive. The macroautophagy/autophagy pathway is highly conserved across eukaryotic cells and promotes cell survival during stressful conditions. In general, basal autophagy occurs at a low level to sustain cellular homeostasis and metabolism. However, autophagy is robustly upregulated in response to nutrient deprivation, pathogen infection and increased accumulation of potentially toxic protein aggregates and superfluous organelles. Within the cell, RNA decay maintains quality control to remove aberrant transcripts and regulate appropriate levels of gene expression. Recent evidence has identified components of the cellular mRNA decay machinery as novel regulators of autophagy. Here, we review current findings that demonstrate how autophagy is modulated through RNA decay. This article is categorized under: RNA Turnover and Surveillance > Turnover/Surveillance Mechanisms RNA Turnover and Surveillance > Regulation of RNA Stability.
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Affiliation(s)
| | - Daniel J Klionsky
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan
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455
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Wang C, Fu J, Wang M, Cai Y, Hua X, Du Y, Yang Z, Li Y, Wang Z, Sheng H, Yin N, Liu X, Koehler JE, Yuan C. Bartonella quintana type IV secretion effector BepE-induced selective autophagy by conjugation with K63 polyubiquitin chain. Cell Microbiol 2018; 21:e12984. [PMID: 30463105 DOI: 10.1111/cmi.12984] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Revised: 11/08/2018] [Accepted: 11/14/2018] [Indexed: 12/20/2022]
Abstract
Bartonella effector proteins (named Beps) are substrates of VirB type IV secretion system for translocation into host cells evolved in Bartonella spp. Among these, BepE has been shown to protect cells from fragmentation effects triggered by other Beps and to promote in vivo dissemination of bacteria from the dermal site of inoculation to the bloodstream. Bacterial pathogens secreted effectors to modulate the interplay with host autophagy, either to combat autophagy to escape its bactericidal effect or to exploit autophagy to benefit intracellular replication. Here, we reported a distinct phenotype that selective autophagy in host cells is activated as a countermeasure, to attack BepE via conjugation with K63 polyubiquitin chain on BepE. We found that ectopic expression of Bartonella quintana BepE specifically induced punctate structures that colocalised with an autophagy marker (LC3-II) in host cells, in addition to filopodia and membrane ruffle formation. Two tandemly arranged Bartonella Intracellular Delivery (BID) domains in the BepE C-terminus, where ubiquitination of sister pairs of lysine residues was confirmed, were essential to activate host cell autophagy. Multiple polyubiquitin chain linkages of K27, K29, K33, and K63 were found to be conjugated at sites of K222 and K365 on BepE, of which K63 polyubiquitination on BepE K365 determined the selective autophagy (p62/SQSTM1 positive autophagy) independent of the PI3K pathway. Colocalisation of BepE with LAMP1 confirmed the maturation of BepE-induced autophagosomes in which BepE were targeted for degradation. Moreover, host cells employed selective autophagy to counter-attack BepE to rescue cells from BepE-induced endocytosis deficiency.
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Affiliation(s)
- Chunyan Wang
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Jiaqi Fu
- Institute of Analytical Chemistry and Synthetic and Functional Biomolecules Center, College of Chemistry and Molecular Engineering, Peking University, Beijing, China
| | - Meng Wang
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Yuhao Cai
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Xiuguo Hua
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Yuming Du
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Zhibiao Yang
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Yan Li
- Shanghai General Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Zhenxia Wang
- Shanghai General Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Huiming Sheng
- Tongren hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Na Yin
- Xinhua hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Xiaoyun Liu
- Institute of Analytical Chemistry and Synthetic and Functional Biomolecules Center, College of Chemistry and Molecular Engineering, Peking University, Beijing, China
| | - Jane E Koehler
- Department of Medicine, Division of Infectious Diseases, and the Microbial Pathogenesis and Host Defense Program, University of California, San Francisco, California, USA
| | - Congli Yuan
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China.,Shanghai Key Laboratory of Veterinary Medicine, Shanghai Jiao Tong University, Shanghai, China
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456
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Lopes‐Coelho F, Silva F, Hipólito A, Cardoso BA, Serpa J. Acetylation drives hepatocyte nuclear factor 1β stability by blocking proteasome‐mediated degradation. J Cell Biochem 2018; 120:9337-9344. [DOI: 10.1002/jcb.28209] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Accepted: 11/15/2018] [Indexed: 12/11/2022]
Affiliation(s)
- Filipa Lopes‐Coelho
- CEDOC, Chronic Diseases Research Centre, NOVA Medical School, Faculdade de Ciências Médicas, Universidade NOVA de Lisboa, Campo dos Mártires da Pátria Lisboa Portugal
- Unidade de Investigação em Patobiologia Molecular do Instituto Português de Oncologia de Lisboa Francisco Gentil (IPOLFG) Lisboa Portugal
| | - Fernanda Silva
- CEDOC, Chronic Diseases Research Centre, NOVA Medical School, Faculdade de Ciências Médicas, Universidade NOVA de Lisboa, Campo dos Mártires da Pátria Lisboa Portugal
- Unidade de Investigação em Patobiologia Molecular do Instituto Português de Oncologia de Lisboa Francisco Gentil (IPOLFG) Lisboa Portugal
| | - Ana Hipólito
- CEDOC, Chronic Diseases Research Centre, NOVA Medical School, Faculdade de Ciências Médicas, Universidade NOVA de Lisboa, Campo dos Mártires da Pátria Lisboa Portugal
- Unidade de Investigação em Patobiologia Molecular do Instituto Português de Oncologia de Lisboa Francisco Gentil (IPOLFG) Lisboa Portugal
| | - Bruno A. Cardoso
- CEDOC, Chronic Diseases Research Centre, NOVA Medical School, Faculdade de Ciências Médicas, Universidade NOVA de Lisboa, Campo dos Mártires da Pátria Lisboa Portugal
- Unidade de Investigação em Patobiologia Molecular do Instituto Português de Oncologia de Lisboa Francisco Gentil (IPOLFG) Lisboa Portugal
| | - Jacinta Serpa
- CEDOC, Chronic Diseases Research Centre, NOVA Medical School, Faculdade de Ciências Médicas, Universidade NOVA de Lisboa, Campo dos Mártires da Pátria Lisboa Portugal
- Unidade de Investigação em Patobiologia Molecular do Instituto Português de Oncologia de Lisboa Francisco Gentil (IPOLFG) Lisboa Portugal
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457
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Li J, Yu T, Yan M, Zhang X, Liao L, Zhu M, Lin H, Pan H, Yao M. DCUN1D1 facilitates tumor metastasis by activating FAK signaling and up-regulates PD-L1 in non-small-cell lung cancer. Exp Cell Res 2018; 374:304-314. [PMID: 30528265 DOI: 10.1016/j.yexcr.2018.12.001] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Revised: 11/09/2018] [Accepted: 12/03/2018] [Indexed: 12/24/2022]
Abstract
E3 ubiquitin ligases, which are key enzymes in the ubiquitin proteasome system, catalyze the ubiquitination of proteins to target them for proteasomal degradation. Emerging evidence suggests that E3 ubiquitin ligases play important roles in the development and progression of lung cancer. In our study, we characterized the gene expression landscape of lung cancer using data obtained from TCGA to explore the changes in E3 ubiquitin ligase containing the regulators of E3 ubiquitin ligase activity. Overall, most gene expression changes occurred in NSCLC tissues compared with adjacent normal ones. In total, 48 E3 ubiquitin ligases containing the regulators were up-regulated in NSCLC tissues compared with their levels in normal tissues. We analyzed the expression of up-regulated E3 ubiquitin ligases containing the regulators in two publicly available transcriptome data sets (GSE13213 and GSE30219). We found that four E3 ubiquitin ligases (UHRF1, BRCA1, TRAIP and HLTF) and one regulator of ubiquitin E3 activity DCUN1D1 that were dramatically up-regulated in cancer were significantly associated with tumor metastasis and patient's poor prognosis both in two transcriptome data sets. Next, clinical analysis indicated that the expression levels of DCUN1D1 correlated with clinical stage and lymph node metastasis in NSCLC patients as determined by quantitative reverse transcription-PCR. Furthermore, functional assays showed that DCUN1D1 promoted NSCLC cell invasion and migration as determined by transwell assay in vitro. Mechanistically, we found that the C-terminal Cullin binding domain leads to oncogenic activity and the UBA domain acts as a negative regulator of DCUN1D1 function in NSCLC. Moreover, DCUN1D1 activated the FAK oncogenic signaling pathway and up-regulated PD-L1. Taken together, our results demonstrate that DCUN1D1 is a metastasis regulator and suggest a new therapeutic option for NSCLC metastasis.
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Affiliation(s)
- Jing Li
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Tao Yu
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Mingxia Yan
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xiao Zhang
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Li Liao
- Department of Oncology, Huashan Hospital Fudan University, Shanghai, China
| | - Miaoxin Zhu
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Hechun Lin
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Hongyu Pan
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital Shanghai Jiao Tong University School of Medicine, Shanghai, China.
| | - Ming Yao
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital Shanghai Jiao Tong University School of Medicine, Shanghai, China.
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458
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Pustylnikov S, Costabile F, Beghi S, Facciabene A. Targeting mitochondria in cancer: current concepts and immunotherapy approaches. Transl Res 2018; 202:35-51. [PMID: 30144423 PMCID: PMC6456045 DOI: 10.1016/j.trsl.2018.07.013] [Citation(s) in RCA: 84] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Revised: 07/24/2018] [Accepted: 07/25/2018] [Indexed: 12/12/2022]
Abstract
An essential advantage during eukaryotic cell evolution was the acquisition of a network of mitochondria as a source of energy for cell metabolism and contrary to conventional wisdom, functional mitochondria are essential for the cancer cell. Multiple aspects of mitochondrial biology beyond bioenergetics support transformation including mitochondrial biogenesis, fission and fusion dynamics, cell death susceptibility, oxidative stress regulation, metabolism, and signaling. In cancer, the metabolism of cells is reprogrammed for energy generation from oxidative phosphorylation to aerobic glycolysis and impacts cancer mitochondrial function. Furthermore cancer cells can also modulate energy metabolism within the cancer microenvironment including immune cells and induce "metabolic anergy" of antitumor immune response. Classical approaches targeting the mitochondria of cancer cells usually aim at inducing changing energy metabolism or directly affecting functions of mitochondrial antiapoptotic proteins but most of such approaches miss the required specificity of action and carry important side effects. Several types of cancers harbor somatic mitochondrial DNA mutations and specific immune response to mutated mitochondrial proteins has been observed. An attractive alternative way to target the mitochondria in cancer cells is the induction of an adaptive immune response against mutated mitochondrial proteins. Here, we review the cancer cell-intrinsic and cell-extrinsic mechanisms through which mitochondria influence all steps of oncogenesis, with a focus on the therapeutic potential of targeting mitochondrial DNA mutations or Tumor Associated Mitochondria Antigens using the immune system.
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Affiliation(s)
- Sergey Pustylnikov
- Department of Radiation Oncology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Francesca Costabile
- Department of Radiation Oncology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Silvia Beghi
- Department of Radiation Oncology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Andrea Facciabene
- Department of Radiation Oncology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania; Ovarian Cancer Research Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania.
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459
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Iruka Eliminates Dysfunctional Argonaute by Selective Ubiquitination of Its Empty State. Mol Cell 2018; 73:119-129.e5. [PMID: 30503771 DOI: 10.1016/j.molcel.2018.10.033] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Revised: 08/31/2018] [Accepted: 10/19/2018] [Indexed: 12/13/2022]
Abstract
MicroRNAs (miRNAs) are loaded into the Argonaute subfamily of proteins (AGO) to form an effector complex that silences target genes. Empty but not miRNA-loaded AGO is selectively degraded across species. However, the mechanism and biological significance of selective AGO degradation remain unclear. We discovered a RING-type E3 ubiquitin ligase we named Iruka (Iru), which selectively ubiquitinates the empty form of Drosophila Ago1 to trigger its degradation. Iru preferentially binds empty Ago1 and ubiquitinates Lys514 in the L2 linker, which is predicted to be inaccessible in the miRNA-loaded state. Depletion of Iru results in global impairment of miRNA-mediated silencing of target genes and in the accumulation of aberrant Ago1 that is dysfunctional for canonical protein-protein interactions and miRNA loading. Our findings reveal a sophisticated mechanism for the selective degradation of empty AGO that underlies a quality control process to ensure AGO function.
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460
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A new reporter cell line for studies with proteasome inhibitors in Trypanosoma brucei. Mol Biochem Parasitol 2018; 227:15-18. [PMID: 30444978 DOI: 10.1016/j.molbiopara.2018.11.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Revised: 11/08/2018] [Accepted: 11/09/2018] [Indexed: 11/22/2022]
Abstract
A Trypanosoma brucei cell line is described that produces a visual readout of proteasome activity. The cell line contains an integrated transgene encoding an ubiquitin-green fluorescent protein (GFP) fusion polypeptide responsive to the addition of proteasome inhibitors. A modified version of T. brucei ubiquitin unable to be recognized by deubiquitinases (UbG76V) was fused to eGFP and constitutively expressed. The fusion protein is unstable but addition of the proteasome inhibitor lactacystin stabilizes it and leads to visually detectable GFP. This cell line can be widely used to monitor the efficiency of inhibitor treatment through detection of GFP accumulation in studies involving proteasome-mediated proteolysis, screening of proteasome inhibitors or other events related to the ubiquitin-proteasome pathway.
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461
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Estrogen-dependent DLL1-mediated Notch signaling promotes luminal breast cancer. Oncogene 2018; 38:2092-2107. [PMID: 30442981 PMCID: PMC6756232 DOI: 10.1038/s41388-018-0562-z] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Revised: 09/23/2018] [Accepted: 10/10/2018] [Indexed: 12/13/2022]
Abstract
Aberrant Notch signaling is implicated in several cancers, including breast cancer. However, the mechanistic details of the specific receptors and function of ligand-mediated Notch signaling that promote breast cancer remains elusive. In our studies we show that DLL1, a Notch signaling ligand, is significantly overexpressed in ERα+ luminal breast cancer. Intriguingly, DLL1 overexpression correlates with poor prognosis in ERα+ luminal breast cancer, but not in other subtypes of breast cancer. In addition, this effect is specific to DLL1, as other Notch ligands (DLL3, JAGGED1, and JAGGED2) do not influence the clinical outcome of ERα+ patients. Genetic studies show that DLL1-mediated Notch signaling in breast cancer is important for tumor cell proliferation, angiogenesis, and cancer stem cell function. Consistent with prognostic clinical data, we found the tumor-promoting function of DLL1 is exclusive to ERα+ luminal breast cancer, as loss of DLL1 inhibits both tumor growth and lung metastasis of luminal breast cancer. Importantly, we find that estrogen signaling stabilizes DLL1 protein by preventing its proteasomal and lysososmal degradations. Moreover, estrogen inhibits ubiquitination of DLL1. Together, our results highlight an unexpected and novel subtype-specific function of DLL1 in promoting luminal breast cancer that is regulated by estrogen signaling. Our studies also emphasize the critical role of assessing subtype-specific mechanisms driving tumor growth and metastasis to generate effective subtype-specific therapeutics.
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462
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Sharma V, Verma S, Seranova E, Sarkar S, Kumar D. Selective Autophagy and Xenophagy in Infection and Disease. Front Cell Dev Biol 2018; 6:147. [PMID: 30483501 PMCID: PMC6243101 DOI: 10.3389/fcell.2018.00147] [Citation(s) in RCA: 168] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Accepted: 10/10/2018] [Indexed: 12/29/2022] Open
Abstract
Autophagy, a cellular homeostatic process, which ensures cellular survival under various stress conditions, has catapulted to the forefront of innate defense mechanisms during intracellular infections. The ability of autophagy to tag and target intracellular pathogens toward lysosomal degradation is central to this key defense function. However, studies involving the role and regulation of autophagy during intracellular infections largely tend to ignore the housekeeping function of autophagy. A growing number of evidences now suggest that the housekeeping function of autophagy, rather than the direct pathogen degradation function, may play a decisive role to determine the outcome of infection and immunological balance. We discuss herein the studies that establish the homeostatic and anti-inflammatory function of autophagy, as well as role of bacterial effectors in modulating and coopting these functions. Given that the core autophagy machinery remains largely the same across diverse cargos, how selectivity plays out during intracellular infection remains intriguing. We explore here, the contrasting role of autophagy adaptors being both selective as well as pleotropic in functions and discuss whether E3 ligases could bring in the specificity to cargo selectivity.
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Affiliation(s)
- Vartika Sharma
- Cellular Immunology Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
| | - Surbhi Verma
- Cellular Immunology Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
| | - Elena Seranova
- Institute of Cancer and Genomic Sciences, Institute of Biomedical Research, College of Medical and Dental Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Sovan Sarkar
- Institute of Cancer and Genomic Sciences, Institute of Biomedical Research, College of Medical and Dental Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Dhiraj Kumar
- Cellular Immunology Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
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463
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Junqueira SC, Centeno EGZ, Wilkinson KA, Cimarosti H. Post-translational modifications of Parkinson's disease-related proteins: Phosphorylation, SUMOylation and Ubiquitination. Biochim Biophys Acta Mol Basis Dis 2018; 1865:2001-2007. [PMID: 30412791 DOI: 10.1016/j.bbadis.2018.10.025] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Revised: 10/12/2018] [Accepted: 10/19/2018] [Indexed: 12/11/2022]
Abstract
Parkinson's disease (PD) is a neurodegenerative disorder characterized by loss of dopaminergic neurons in the nigrostriatal pathway. The etiology of PD remains unclear and most cases are sporadic, however genetic mutations in more than 20 proteins have been shown to cause inherited forms of PD. Many of these proteins are linked to mitochondrial function, defects in which are a central characteristic of PD. Post-translational modifications (PTMs) allow rapid and reversible control over protein function. Largely focussing on mitochondrial dysfunction in PD, here we review findings on the PTMs phosphorylation, SUMOylation and ubiquitination that have been shown to affect PD-related proteins.
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Affiliation(s)
- Stella C Junqueira
- Department of Pharmacology, Federal University of Santa Catarina, Florianopolis, Brazil
| | - Eduarda G Z Centeno
- Department of Pharmacology, Federal University of Santa Catarina, Florianopolis, Brazil
| | - Kevin A Wilkinson
- School of Biochemistry, Centre for Synaptic Plasticity, University of Bristol, Bristol, UK.
| | - Helena Cimarosti
- Department of Pharmacology, Federal University of Santa Catarina, Florianopolis, Brazil.
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464
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Tan P, Ye Y, He L, Xie J, Jing J, Ma G, Pan H, Han L, Han W, Zhou Y. TRIM59 promotes breast cancer motility by suppressing p62-selective autophagic degradation of PDCD10. PLoS Biol 2018; 16:e3000051. [PMID: 30408026 PMCID: PMC6245796 DOI: 10.1371/journal.pbio.3000051] [Citation(s) in RCA: 63] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Revised: 11/20/2018] [Accepted: 10/23/2018] [Indexed: 12/12/2022] Open
Abstract
Cancer cells adopt various modes of migration during metastasis. How the ubiquitination machinery contributes to cancer cell motility remains underexplored. Here, we report that tripartite motif (TRIM) 59 is frequently up-regulated in metastatic breast cancer, which is correlated with advanced clinical stages and reduced survival among breast cancer patients. TRIM59 knockdown (KD) promoted apoptosis and inhibited tumor growth, while TRIM59 overexpression led to the opposite effects. Importantly, we uncovered TRIM59 as a key regulator of cell contractility and adhesion to control the plasticity of metastatic tumor cells. At the molecular level, we identified programmed cell death protein 10 (PDCD10) as a target of TRIM59. TRIM59 stabilized PDCD10 by suppressing RING finger and transmembrane domain-containing protein 1 (RNFT1)-induced lysine 63 (K63) ubiquitination and subsequent phosphotyrosine-independent ligand for the Lck SH2 domain of 62 kDa (p62)-selective autophagic degradation. TRIM59 promoted PDCD10-mediated suppression of Ras homolog family member A (RhoA)-Rho-associated coiled-coil kinase (ROCK) 1 signaling to control the transition between amoeboid and mesenchymal invasiveness. PDCD10 overexpression or administration of a ROCK inhibitor reversed TRIM59 loss-induced contractile phenotypes, thereby accelerating cell migration, invasion, and tumor formation. These findings establish the rationale for targeting deregulated TRIM59/PDCD10 to treat breast cancer.
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Affiliation(s)
- Peng Tan
- Department of Medical Oncology and Biomedical Research Center, Sir Run Run Shaw Hospital, College of Medicine, Zhejiang University, Hangzhou, China
- Center for Translational Cancer Research, Institute of Biosciences and Technology, College of Medicine, Texas A&M University, Houston, Texas, United States of America
| | - Youqiong Ye
- Department of Biochemistry and Molecular Biology, University of Texas Health Science Center at Houston McGovern Medical School, Houston, Texas, United States of America
| | - Lian He
- Center for Translational Cancer Research, Institute of Biosciences and Technology, College of Medicine, Texas A&M University, Houston, Texas, United States of America
| | - Jiansheng Xie
- Department of Medical Oncology and Biomedical Research Center, Sir Run Run Shaw Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Ji Jing
- Center for Translational Cancer Research, Institute of Biosciences and Technology, College of Medicine, Texas A&M University, Houston, Texas, United States of America
| | - Guolin Ma
- Center for Translational Cancer Research, Institute of Biosciences and Technology, College of Medicine, Texas A&M University, Houston, Texas, United States of America
| | - Hongming Pan
- Department of Medical Oncology and Biomedical Research Center, Sir Run Run Shaw Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Leng Han
- Department of Biochemistry and Molecular Biology, University of Texas Health Science Center at Houston McGovern Medical School, Houston, Texas, United States of America
| | - Weidong Han
- Department of Medical Oncology and Biomedical Research Center, Sir Run Run Shaw Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Yubin Zhou
- Center for Translational Cancer Research, Institute of Biosciences and Technology, College of Medicine, Texas A&M University, Houston, Texas, United States of America
- Department of Medical Physiology, College of Medicine, Texas A&M University, Temple, Texas, United States of America
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465
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Samant RS, Livingston CM, Sontag EM, Frydman J. Distinct proteostasis circuits cooperate in nuclear and cytoplasmic protein quality control. Nature 2018; 563:407-411. [PMID: 30429547 PMCID: PMC6707801 DOI: 10.1038/s41586-018-0678-x] [Citation(s) in RCA: 115] [Impact Index Per Article: 19.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2017] [Accepted: 09/04/2018] [Indexed: 11/09/2022]
Abstract
Protein misfolding is linked to a wide array of human disorders, including Alzheimer's disease, Parkinson's disease and type II diabetes1,2. Protective cellular protein quality control (PQC) mechanisms have evolved to selectively recognize misfolded proteins and limit their toxic effects3-9, thus contributing to the maintenance of the proteome (proteostasis). Here we examine how molecular chaperones and the ubiquitin-proteasome system cooperate to recognize and promote the clearance of soluble misfolded proteins. Using a panel of PQC substrates with distinct characteristics and localizations, we define distinct chaperone and ubiquitination circuitries that execute quality control in the cytoplasm and nucleus. In the cytoplasm, proteasomal degradation of misfolded proteins requires tagging with mixed lysine 48 (K48)- and lysine 11 (K11)-linked ubiquitin chains. A distinct combination of E3 ubiquitin ligases and specific chaperones is required to achieve each type of linkage-specific ubiquitination. In the nucleus, however, proteasomal degradation of misfolded proteins requires only K48-linked ubiquitin chains, and is thus independent of K11-specific ligases and chaperones. The distinct ubiquitin codes for nuclear and cytoplasmic PQC appear to be linked to the function of the ubiquilin protein Dsk2, which is specifically required to clear nuclear misfolded proteins. Our work defines the principles of cytoplasmic and nuclear PQC as distinct, involving combinatorial recognition by defined sets of cooperating chaperones and E3 ligases. A better understanding of how these organelle-specific PQC requirements implement proteome integrity has implications for our understanding of diseases linked to impaired protein clearance and proteostasis dysfunction.
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Affiliation(s)
- Rahul S Samant
- Department of Biology, Stanford University, Stanford, CA, USA.
| | - Christine M Livingston
- Department of Biology, Stanford University, Stanford, CA, USA. .,Janssen Research and Development, Spring House, PA, USA.
| | - Emily M Sontag
- Department of Biology, Stanford University, Stanford, CA, USA
| | - Judith Frydman
- Department of Biology, Stanford University, Stanford, CA, USA. .,Department of Genetics, Stanford University, Stanford, CA, USA.
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466
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Kocaturk NM, Gozuacik D. Crosstalk Between Mammalian Autophagy and the Ubiquitin-Proteasome System. Front Cell Dev Biol 2018; 6:128. [PMID: 30333975 PMCID: PMC6175981 DOI: 10.3389/fcell.2018.00128] [Citation(s) in RCA: 271] [Impact Index Per Article: 45.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Accepted: 09/13/2018] [Indexed: 12/16/2022] Open
Abstract
Autophagy and the ubiquitin-proteasome system (UPS) are the two major intracellular quality control and recycling mechanisms that are responsible for cellular homeostasis in eukaryotes. Ubiquitylation is utilized as a degradation signal by both systems, yet, different mechanisms are in play. The UPS is responsible for the degradation of short-lived proteins and soluble misfolded proteins whereas autophagy eliminates long-lived proteins, insoluble protein aggregates and even whole organelles (e.g., mitochondria, peroxisomes) and intracellular parasites (e.g., bacteria). Both the UPS and selective autophagy recognize their targets through their ubiquitin tags. In addition to an indirect connection between the two systems through ubiquitylated proteins, recent data indicate the presence of connections and reciprocal regulation mechanisms between these degradation pathways. In this review, we summarize these direct and indirect interactions and crosstalks between autophagy and the UPS, and their implications for cellular stress responses and homeostasis.
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Affiliation(s)
- Nur Mehpare Kocaturk
- Molecular Biology, Genetics and Bioengineering Program, Faculty of Engineering and Natural Sciences, Sabanci University, Istanbul, Turkey
| | - Devrim Gozuacik
- Molecular Biology, Genetics and Bioengineering Program, Faculty of Engineering and Natural Sciences, Sabanci University, Istanbul, Turkey
- Center of Excellence for Functional Surfaces and Interfaces for Nano Diagnostics (EFSUN), Sabanci University, Istanbul, Turkey
- Nanotechnology Research and Application Center (SUNUM), Sabanci University, Istanbul, Turkey
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467
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E3 ligase FBXW7 aggravates TMPD-induced systemic lupus erythematosus by promoting cell apoptosis. Cell Mol Immunol 2018; 15:1057-1070. [PMID: 30275535 DOI: 10.1038/s41423-018-0167-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Accepted: 08/17/2018] [Indexed: 12/11/2022] Open
Abstract
Systemic lupus erythematosus (SLE) is a systemic autoimmune disease, and the pathogenesis of SLE has not been fully elucidated. The E3 ubiquitin ligase FBXW7 has been well characterized in cancer as a tumor suppressor that can promote the ubiquitination and subsequent degradation of various oncoproteins; however, the potential role of FBXW7 in autoimmune diseases is unclear. In the present study, we identified that FBXW7 is a crucial exacerbating factor for SLE development and progression in a mouse model induced by 2, 6, 10, 14-tetramethylpentadecane (TMPD). Myeloid cell-specific FBXW7-deficient (Lysm+FBXW7f/f) C57BL/6 mice showed decreased immune complex accumulation, glomerulonephritis, glomerular mesangial cell proliferation, and base-membrane thickness in the kidney. Lysm+FBXW7f/f mice produced fewer anti-Sm/RNP and anti-ANA autoantibodies and showed a decreased MHC II expression in B cells. In Lysm+FBXW7f/f mice, we observed that cell apoptosis was reduced and that fewer CD11b+Ly6Chi inflammatory monocytes were recruited to the peritoneal cavity. Consistently, diffuse pulmonary hemorrhage (DPH) was also decreased in Lysm+FBXW7f/f mice. Mechanistically, we clarified that FBXW7 promoted TMPD-induced cell apoptosis by catalyzing MCL1 degradation through K48-linked ubiquitination. Our work revealed that FBXW7 expression in myeloid cells played a crucial role in TMPD-induced SLE progression in mice, which may provide novel ideas and theoretical support for understanding the pathogenesis of SLE.
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468
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Cheng J, North BJ, Zhang T, Dai X, Tao K, Guo J, Wei W. The emerging roles of protein homeostasis-governing pathways in Alzheimer's disease. Aging Cell 2018; 17:e12801. [PMID: 29992725 PMCID: PMC6156496 DOI: 10.1111/acel.12801] [Citation(s) in RCA: 75] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Accepted: 06/04/2018] [Indexed: 12/22/2022] Open
Abstract
Pathways governing protein homeostasis are involved in maintaining the structural, quantitative, and functional stability of intracellular proteins and involve the ubiquitin-proteasome system, autophagy, endoplasmic reticulum, and mTOR pathway. Due to the broad physiological implications of protein homeostasis pathways, dysregulation of proteostasis is often involved in the development of multiple pathological conditions, including Alzheimer's disease (AD). Similar to other neurodegenerative diseases that feature pathogenic accumulation of misfolded proteins, Alzheimer's disease is characterized by two pathological hallmarks, amyloid-β (Aβ) plaques and tau aggregates. Knockout or transgenic overexpression of various proteostatic components in mice results in AD-like phenotypes. While both Aβ plaques and tau aggregates could in turn enhance the dysfunction of these proteostatic pathways, eventually leading to apoptotic or necrotic neuronal death and pathogenesis of Alzheimer's disease. Therefore, targeting the components of proteostasis pathways may be a promising therapeutic strategy against Alzheimer's disease.
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Affiliation(s)
- Ji Cheng
- Department of Gastrointestinal SurgeryUnion HospitalTongji Medical CollegeHuazhong University of Science and TechnologyWuhanChina
- Department of PathologyBeth Israel Deaconess Medical CenterHarvard Medical SchoolBostonMassachusetts
| | - Brian J. North
- Department of PathologyBeth Israel Deaconess Medical CenterHarvard Medical SchoolBostonMassachusetts
| | - Tao Zhang
- Department of PathologyBeth Israel Deaconess Medical CenterHarvard Medical SchoolBostonMassachusetts
| | - Xiangpeng Dai
- Department of PathologyBeth Israel Deaconess Medical CenterHarvard Medical SchoolBostonMassachusetts
| | - Kaixiong Tao
- Department of Gastrointestinal SurgeryUnion HospitalTongji Medical CollegeHuazhong University of Science and TechnologyWuhanChina
| | - Jianping Guo
- Department of PathologyBeth Israel Deaconess Medical CenterHarvard Medical SchoolBostonMassachusetts
| | - Wenyi Wei
- Department of PathologyBeth Israel Deaconess Medical CenterHarvard Medical SchoolBostonMassachusetts
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469
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Monda JK, Cheeseman IM. Dynamic regulation of dynein localization revealed by small molecule inhibitors of ubiquitination enzymes. Open Biol 2018; 8:rsob.180095. [PMID: 30257893 PMCID: PMC6170511 DOI: 10.1098/rsob.180095] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Accepted: 08/29/2018] [Indexed: 11/27/2022] Open
Abstract
Cytoplasmic dynein is a minus-end-directed microtubule-based motor that acts at diverse subcellular sites. During mitosis, dynein localizes simultaneously to the mitotic spindle, spindle poles, kinetochores and the cell cortex. However, it is unclear what controls the relative targeting of dynein to these locations. As dynein is heavily post-translationally modified, we sought to test a role for these modifications in regulating dynein localization. We find that dynein rapidly and strongly accumulates at mitotic spindle poles following treatment with NSC697923, a small molecule that inhibits the ubiquitin E2 enzyme, Ubc13, or treatment with PYR-41, a ubiquitin E1 inhibitor. Subsets of dynein regulators such as Lis1, ZW10 and Spindly accumulate at the spindle poles, whereas others do not, suggesting that NSC697923 differentially affects specific dynein populations. We additionally find that dynein relocalization induced by NSC697923 or PYR-41 can be suppressed by simultaneous treatment with the non-selective deubiquitinase inhibitor, PR-619. However, we did not observe altered dynein localization following treatment with the selective E1 inhibitor, TAK-243. Although it is possible that off-target effects of NSC697923 and PYR-41 are responsible for the observed changes in dynein localization, the rapid relocalization upon drug treatment highlights the highly dynamic nature of dynein regulation during mitosis.
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Affiliation(s)
- Julie K Monda
- Whitehead Institute for Biomedical Research, 455 Main Street, Cambridge, MA 02142, USA.,Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Iain M Cheeseman
- Whitehead Institute for Biomedical Research, 455 Main Street, Cambridge, MA 02142, USA .,Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
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470
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Demasi M, da Cunha FM. The physiological role of the free 20S proteasome in protein degradation: A critical review. Biochim Biophys Acta Gen Subj 2018; 1862:2948-2954. [PMID: 30297324 DOI: 10.1016/j.bbagen.2018.09.009] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2018] [Revised: 08/27/2018] [Accepted: 09/12/2018] [Indexed: 01/26/2023]
Abstract
BACKGROUND It has been almost three decades since the removal of oxidized proteins by the free 20S catalytic unit of the proteasome (20SPT) was proposed. Since then, experimental evidence suggesting a physiological role of proteolysis mediated by the free 20SPT has being gathered. SCOPE OF REVIEW Experimental data that favors the hypothesis of free 20SPT as playing a role in proteolysis are critically reviewed. MAJOR CONCLUSIONS Protein degradation by the proteasome may proceed through multiple proteasome complexes with different requirements though the unequivocal role of the free 20SPT in cellular proteolysis towards native or oxidized proteins remains to be demonstrated. GENERAL SIGNIFICANCE The biological significance of proteolysis mediated by the free 20SPT has been elusive since its discovery. The present review critically analyzes the available experimental data supporting the proteolytic role of the free or single capped 20SPT.
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Affiliation(s)
- Marilene Demasi
- Laboratório de Bioquímica e Biofísica, Instituto Butantan, São Paulo, SP, Brazil.
| | - Fernanda Marques da Cunha
- Departamento de Bioquímica, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, SP, Brazil.
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471
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Roles of ubiquitin in autophagy and cell death. Semin Cell Dev Biol 2018; 93:125-135. [PMID: 30195063 PMCID: PMC6854449 DOI: 10.1016/j.semcdb.2018.09.004] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Revised: 08/28/2018] [Accepted: 09/03/2018] [Indexed: 01/12/2023]
Abstract
The balance between cell survival and cell death is often lost in human pathologies such as inflammation and cancer. Autophagy plays a critical role in cell survival: essential nutrients are generated by autophagy-dependent degradation and recycling of cellular garbage. On the other hand, cell death is induced by different programs, such as apoptosis, pyroptosis, and necroptosis. Emerging evidence is revealing how cell survival and cell death pathways are coordinated to determine cell fate. For instance, posttranslational modification of proteins with ubiquitin regulates many steps of autophagy and cell death pathways. In this review article, we will discuss how the ubiquitin system influences cell death and autophagy.
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472
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Insights into degradation mechanism of N-end rule substrates by p62/SQSTM1 autophagy adapter. Nat Commun 2018; 9:3291. [PMID: 30120248 PMCID: PMC6098011 DOI: 10.1038/s41467-018-05825-x] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2018] [Accepted: 07/27/2018] [Indexed: 02/06/2023] Open
Abstract
p62/SQSTM1 is the key autophagy adapter protein and the hub of multi-cellular signaling. It was recently reported that autophagy and N-end rule pathways are linked via p62. However, the exact recognition mode of degrading substrates and regulation of p62 in the autophagic pathway remain unknown. Here, we present the complex structures between the ZZ-domain of p62 and various type-1 and type-2 N-degrons. The binding mode employed in the interaction of the ZZ-domain with N-degrons differs from that employed by classic N-recognins. It was also determined that oligomerization via the PB1 domain can control functional affinity to the R-BiP substrate. Unexpectedly, we found that self-oligomerization and disassembly of p62 are pH-dependent. These findings broaden our understanding of the functional repertoire of the N-end rule pathway and provide an insight into the regulation of p62 during the autophagic pathway. The autophagy adapter p62/SQSTM1 plays a key role in selective autophagy and also recognizes N-end rule substrates. Here the authors provide molecular insights into p62 N-end rule substrate recognition by solving the structures of the p62 ZZ-domain in complex with various type 1 and type 2 degrons and also show the pH dependent oligomerization of p62.
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473
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Mohan J, Wollert T. Human ubiquitin-like proteins as central coordinators in autophagy. Interface Focus 2018; 8:20180025. [PMID: 30443326 DOI: 10.1098/rsfs.2018.0025] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/11/2018] [Indexed: 02/07/2023] Open
Abstract
Autophagy is one of the most versatile recycling systems of eukaryotic cells. It degrades diverse cytoplasmic components such as organelles, protein aggregates, ribosomes and multi-enzyme complexes. Not surprisingly, any failure of autophagy or reduced activity of the pathway contributes to the onset of various pathologies, including neurodegeneration, cancer and metabolic disorders such as diabetes or immune diseases. Furthermore, autophagy contributes to the innate immune response and combats bacterial or viral pathogens. The hallmark of macroautophagy is the formation of a membrane sack that sequesters cytoplasmic cargo and delivers it to lysosomes for degradation. More than 40 autophagy-related (ATG) proteins have so far been identified. A unique protein-conjugation system represents one of the core components of this highly elaborate machinery. It conjugates six homologous ATG8 family proteins to the autophagic membrane. In this review, we summarize the current knowledge regarding the various functions of ATG8 proteins in autophagy and briefly discuss how physical approaches and in vitro reconstitution contributed in deciphering their function.
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Affiliation(s)
- Jagan Mohan
- Membrane Biochemistry and Transport, Institute Pasteur, 28 rue du Dr Roux, 75015 Paris, France
| | - Thomas Wollert
- Membrane Biochemistry and Transport, Institute Pasteur, 28 rue du Dr Roux, 75015 Paris, France
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474
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The immunoproteasome and thymoproteasome: functions, evolution and human disease. Nat Immunol 2018; 19:923-931. [PMID: 30104634 DOI: 10.1038/s41590-018-0186-z] [Citation(s) in RCA: 198] [Impact Index Per Article: 33.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Revised: 07/12/2018] [Accepted: 07/19/2018] [Indexed: 01/12/2023]
Abstract
The basic principle of adaptive immunity is to strictly discriminate between self and non-self, and a central challenge to overcome is the enormous variety of pathogens that might be encountered. In cell-mediated immunity, immunological discernment takes place at a molecular or cellular level. Central to both mechanisms of discernment is the generation of antigenic peptides associated with MHC class I molecules, which is achieved by a proteolytic complex called the proteasome. To adequately accomplish the discrimination between self and non-self that is essential for adaptive immunity and self-tolerance, two proteasome subtypes have evolved via gene duplication: the immunoproteasome and the thymoproteasome. In this Review, we describe various aspects of these immunity-dedicated proteasomes, from their discovery to recent findings.
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475
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Ubiquitin, SUMO, and NEDD8: Key Targets of Bacterial Pathogens. Trends Cell Biol 2018; 28:926-940. [PMID: 30107971 DOI: 10.1016/j.tcb.2018.07.005] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2018] [Revised: 07/13/2018] [Accepted: 07/17/2018] [Indexed: 01/09/2023]
Abstract
Manipulation of host protein post-translational modifications (PTMs) is used by various pathogens to interfere with host cell functions. Among these modifications, ubiquitin (UBI) and ubiquitin-like proteins (UBLs) constitute key targets because they are regulators of pathways essential for the host cell. In particular, these PTM modifiers control pathways that have been described as crucial for infection such as pathogen entry, replication, propagation, or detection by the host. Although bacterial pathogens lack eucaryotic-like UBI or UBL systems, many of them produce proteins that specifically interfere with these host PTMs during infection. In this review we discuss the different mechanisms used by bacteria to interfere with host UBI and the two UBLs, SUMO and NEDD8.
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476
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Koganti P, Levy-Cohen G, Blank M. Smurfs in Protein Homeostasis, Signaling, and Cancer. Front Oncol 2018; 8:295. [PMID: 30116722 PMCID: PMC6082930 DOI: 10.3389/fonc.2018.00295] [Citation(s) in RCA: 71] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Accepted: 07/16/2018] [Indexed: 12/13/2022] Open
Abstract
Protein ubiquitination is an evolutionary conserved highly-orchestrated enzymatic cascade essential for normal cellular functions and homeostasis maintenance. This pathway relies on a defined set of cellular enzymes, among them, substrate-specific E3 ubiquitin ligases (E3s). These ligases are the most critical players, as they define the spatiotemporal nature of ubiquitination and confer specificity to this cascade. Smurf1 and Smurf2 (Smurfs) are the C2-WW-HECT-domain E3 ubiquitin ligases, which recently emerged as important determinants of pivotal cellular processes. These processes include cell proliferation and differentiation, chromatin organization and dynamics, DNA damage response and genomic integrity maintenance, gene expression, cell stemness, migration, and invasion. All these processes are intimately connected and profoundly altered in cancer. Initially, Smurf proteins were identified as negative regulators of the bone morphogenetic protein (BMP) and the transforming growth factor beta (TGF-β) signaling pathways. However, recent studies have extended the scope of Smurfs' biological functions beyond the BMP/TGF-β signaling regulation. Here, we provide a critical literature overview and updates on the regulatory roles of Smurfs in molecular and cell biology, with an emphasis on cancer. We also highlight the studies demonstrating the impact of Smurf proteins on tumor cell sensitivity to anticancer therapies. Further in-depth analyses of Smurfs' biological functions and influences on molecular pathways could provide novel therapeutic targets and paradigms for cancer diagnosis and treatment.
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Affiliation(s)
- Praveen Koganti
- Laboratory of Molecular and Cellular Cancer Biology, Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel
| | - Gal Levy-Cohen
- Laboratory of Molecular and Cellular Cancer Biology, Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel
| | - Michael Blank
- Laboratory of Molecular and Cellular Cancer Biology, Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel
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477
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Tanghe G, Urwyler-Rösselet C, De Groote P, Dejardin E, De Bock PJ, Gevaert K, Vandenabeele P, Declercq W. RIPK4 activity in keratinocytes is controlled by the SCF β-TrCP ubiquitin ligase to maintain cortical actin organization. Cell Mol Life Sci 2018; 75:2827-2841. [PMID: 29435596 PMCID: PMC11105318 DOI: 10.1007/s00018-018-2763-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2017] [Revised: 01/22/2018] [Accepted: 01/25/2018] [Indexed: 01/20/2023]
Abstract
RIPK4 is a key player in epidermal differentiation and barrier formation. RIPK4 signaling pathways controlling keratinocyte proliferation and differentiation depend on its kinase activity leading to Dvl2, Pkp1 and IRF6 phosphorylation and NF-κB activation. However, the mechanism regulating RIPK4 activity levels remains elusive. We show that cultured keratinocytes display constitutive active phosphorylated RIPK4 while PKC signaling can trigger RIPK4 activation in various non-keratinocyte cell lines, in which RIPK4 is present in a non-phosphorylated state. Interestingly, we identified the SCFβ-TrCP ubiquitin E3 ligase complex responsible for regulating the active RIPK4 protein level. The SCFβ-TrCP complex binds to a conserved phosphodegron motif in the intermediate domain of RIPK4, subsequently leading to K48-linked ubiquitinylation and degradation. The recruitment of β-TrCP is dependent on RIPK4 activation and trans-autophosphorylation. β-TrCP knock-down resulted in RIPK4-dependent formation of actin stress fibers, cell scattering and increased cell motility, suggesting that tight control of RIPK4 activity levels is crucial to maintain cell shape and behavior in keratinocytes.
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Affiliation(s)
- Giel Tanghe
- Molecular Signaling and Cell Death Unit, VIB-UGent Center for Inflammation Research, Technologiepark 927, 9052, Gent, Belgium
- Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | - Corinne Urwyler-Rösselet
- Molecular Signaling and Cell Death Unit, VIB-UGent Center for Inflammation Research, Technologiepark 927, 9052, Gent, Belgium
- Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
- Department of Biology, Institute of Molecular Health Sciences, ETH Zurich, Zurich, Switzerland
| | - Philippe De Groote
- Molecular Signaling and Cell Death Unit, VIB-UGent Center for Inflammation Research, Technologiepark 927, 9052, Gent, Belgium
- Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | - Emmanuel Dejardin
- Laboratory of Molecular Immunology and Signal Transduction, GIGA-Institute, University of Liège, Liège, Belgium
| | - Pieter-Jan De Bock
- VIB-UGent Center for Medical Biotechnology, Ghent, Belgium
- Department of Biochemistry, Ghent University, Ghent, Belgium
| | - Kris Gevaert
- VIB-UGent Center for Medical Biotechnology, Ghent, Belgium
- Department of Biochemistry, Ghent University, Ghent, Belgium
| | - Peter Vandenabeele
- Molecular Signaling and Cell Death Unit, VIB-UGent Center for Inflammation Research, Technologiepark 927, 9052, Gent, Belgium
- Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | - Wim Declercq
- Molecular Signaling and Cell Death Unit, VIB-UGent Center for Inflammation Research, Technologiepark 927, 9052, Gent, Belgium.
- Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium.
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478
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Aim for the core: suitability of the ubiquitin-independent 20S proteasome as a drug target in neurodegeneration. Transl Res 2018; 198:48-57. [PMID: 30244692 PMCID: PMC6154511 DOI: 10.1016/j.trsl.2018.05.002] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/08/2018] [Revised: 05/14/2018] [Accepted: 05/15/2018] [Indexed: 02/06/2023]
Abstract
Neurodegenerative diseases are a class of age-associated proteopathies characterized by the accumulation of misfolded and/or aggregation-prone proteins. This imbalance has been attributed, in part, to an age-dependent decay in the capacity of protein turnover. Most proteins are degraded by the ubiquitin-proteasome system (UPS), which is composed of ubiquitin ligases and regulatory particles, such as the 19S, that deliver cargo to the proteolytically active 20S proteasome (20S) core. However, a subset of clients, especially intrinsically disordered proteins (IDPs), are also removed by the action of the ubiquitin-independent proteasome system (UIPS). What are the specific contributions of the UPS and UIPS in the context of neurodegeneration? Here, we explore how age-associated changes in the relative contribution of the UPS and UIPS, combined with the IDP-like structure of many neurodegenerative disease-associated proteins, might contribute. Strikingly, the 20S has been shown to predominate in older neurons and to preferentially act on relevant substrates, such as synuclein and tau. Moreover, pharmacological activation of the 20S has been shown to accelerate removal of aggregation-prone proteins in some models. Together, these recent studies are turning attention to the 20S and the UIPS as potential therapeutic targets in neurodegeneration.
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479
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Magnani ND, Dada LA, Sznajder JI. Ubiquitin-proteasome signaling in lung injury. Transl Res 2018; 198:29-39. [PMID: 29752900 PMCID: PMC6986356 DOI: 10.1016/j.trsl.2018.04.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Revised: 04/15/2018] [Accepted: 04/16/2018] [Indexed: 12/21/2022]
Abstract
Cell homeostasis requires precise coordination of cellular proteins function. Ubiquitination is a post-translational modification that modulates protein half-life and function and is tightly regulated by ubiquitin E3 ligases and deubiquitinating enzymes. Lung injury can progress to acute respiratory distress syndrome that is characterized by an inflammatory response and disruption of the alveolocapillary barrier resulting in alveolar edema accumulation and hypoxemia. Ubiquitination plays an important role in the pathobiology of acute lung injury as it regulates the proteins modulating the alveolocapillary barrier and the inflammatory response. Better understanding of the signaling pathways regulated by ubiquitination may lead to novel therapeutic approaches by targeting specific elements of the ubiquitination pathways.
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Affiliation(s)
- Natalia D Magnani
- Pulmonary and Critical Care Division, Northwestern Feinberg School of Medicine, Chicago, Illinois
| | - Laura A Dada
- Pulmonary and Critical Care Division, Northwestern Feinberg School of Medicine, Chicago, Illinois
| | - Jacob I Sznajder
- Pulmonary and Critical Care Division, Northwestern Feinberg School of Medicine, Chicago, Illinois.
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480
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Mavor D, Barlow KA, Asarnow D, Birman Y, Britain D, Chen W, Green EM, Kenner LR, Mensa B, Morinishi LS, Nelson CA, Poss EM, Suresh P, Tian R, Arhar T, Ary BE, Bauer DP, Bergman ID, Brunetti RM, Chio CM, Dai SA, Dickinson MS, Elledge SK, Helsell CVM, Hendel NL, Kang E, Kern N, Khoroshkin MS, Kirkemo LL, Lewis GR, Lou K, Marin WM, Maxwell AM, McTigue PF, Myers-Turnbull D, Nagy TL, Natale AM, Oltion K, Pourmal S, Reder GK, Rettko NJ, Rohweder PJ, Schwarz DMC, Tan SK, Thomas PV, Tibble RW, Town JP, Tsai MK, Ugur FS, Wassarman DR, Wolff AM, Wu TS, Bogdanoff D, Li J, Thorn KS, O'Conchúir S, Swaney DL, Chow ED, Madhani HD, Redding S, Bolon DN, Kortemme T, DeRisi JL, Kampmann M, Fraser JS. Extending chemical perturbations of the ubiquitin fitness landscape in a classroom setting reveals new constraints on sequence tolerance. Biol Open 2018; 7:7/7/bio036103. [PMID: 30037883 PMCID: PMC6078352 DOI: 10.1242/bio.036103] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Although the primary protein sequence of ubiquitin (Ub) is extremely stable over evolutionary time, it is highly tolerant to mutation during selection experiments performed in the laboratory. We have proposed that this discrepancy results from the difference between fitness under laboratory culture conditions and the selective pressures in changing environments over evolutionary timescales. Building on our previous work (Mavor et al., 2016), we used deep mutational scanning to determine how twelve new chemicals (3-Amino-1,2,4-triazole, 5-fluorocytosine, Amphotericin B, CaCl2, Cerulenin, Cobalt Acetate, Menadione, Nickel Chloride, p-Fluorophenylalanine, Rapamycin, Tamoxifen, and Tunicamycin) reveal novel mutational sensitivities of ubiquitin residues. Collectively, our experiments have identified eight new sensitizing conditions for Lys63 and uncovered a sensitizing condition for every position in Ub except Ser57 and Gln62. By determining the ubiquitin fitness landscape under different chemical constraints, our work helps to resolve the inconsistencies between deep mutational scanning experiments and sequence conservation over evolutionary timescales.
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Affiliation(s)
- David Mavor
- Biophysics Graduate Group, University of California, San Francisco 94158, USA
| | - Kyle A Barlow
- Bioinformatics Graduate Group, University of California, San Francisco 94158, USA
| | - Daniel Asarnow
- Biophysics Graduate Group, University of California, San Francisco 94158, USA
| | - Yuliya Birman
- Biophysics Graduate Group, University of California, San Francisco 94158, USA
| | - Derek Britain
- Biophysics Graduate Group, University of California, San Francisco 94158, USA
| | - Weilin Chen
- Bioinformatics Graduate Group, University of California, San Francisco 94158, USA
| | - Evan M Green
- Biophysics Graduate Group, University of California, San Francisco 94158, USA
| | - Lillian R Kenner
- Biophysics Graduate Group, University of California, San Francisco 94158, USA
| | - Bruk Mensa
- Chemistry and Chemical Biology Graduate Program, University of California, San Francisco 94158, USA
| | - Leanna S Morinishi
- Bioinformatics Graduate Group, University of California, San Francisco 94158, USA
| | - Charlotte A Nelson
- Bioinformatics Graduate Group, University of California, San Francisco 94158, USA
| | - Erin M Poss
- Chemistry and Chemical Biology Graduate Program, University of California, San Francisco 94158, USA
| | - Pooja Suresh
- Biophysics Graduate Group, University of California, San Francisco 94158, USA
| | - Ruilin Tian
- Biophysics Graduate Group, University of California, San Francisco 94158, USA
| | - Taylor Arhar
- Chemistry and Chemical Biology Graduate Program, University of California, San Francisco 94158, USA
| | - Beatrice E Ary
- Chemistry and Chemical Biology Graduate Program, University of California, San Francisco 94158, USA
| | - David P Bauer
- Biophysics Graduate Group, University of California, San Francisco 94158, USA
| | - Ian D Bergman
- Chemistry and Chemical Biology Graduate Program, University of California, San Francisco 94158, USA
| | - Rachel M Brunetti
- Biophysics Graduate Group, University of California, San Francisco 94158, USA
| | - Cynthia M Chio
- Chemistry and Chemical Biology Graduate Program, University of California, San Francisco 94158, USA
| | - Shizhong A Dai
- Chemistry and Chemical Biology Graduate Program, University of California, San Francisco 94158, USA
| | - Miles S Dickinson
- Chemistry and Chemical Biology Graduate Program, University of California, San Francisco 94158, USA
| | - Susanna K Elledge
- Chemistry and Chemical Biology Graduate Program, University of California, San Francisco 94158, USA
| | - Cole V M Helsell
- Biophysics Graduate Group, University of California, San Francisco 94158, USA
| | - Nathan L Hendel
- Bioinformatics Graduate Group, University of California, San Francisco 94158, USA
| | - Emily Kang
- Chemistry and Chemical Biology Graduate Program, University of California, San Francisco 94158, USA
| | - Nadja Kern
- Biophysics Graduate Group, University of California, San Francisco 94158, USA
| | - Matvei S Khoroshkin
- Bioinformatics Graduate Group, University of California, San Francisco 94158, USA
| | - Lisa L Kirkemo
- Chemistry and Chemical Biology Graduate Program, University of California, San Francisco 94158, USA
| | - Greyson R Lewis
- Biophysics Graduate Group, University of California, San Francisco 94158, USA
| | - Kevin Lou
- Chemistry and Chemical Biology Graduate Program, University of California, San Francisco 94158, USA
| | - Wesley M Marin
- Bioinformatics Graduate Group, University of California, San Francisco 94158, USA
| | - Alison M Maxwell
- Chemistry and Chemical Biology Graduate Program, University of California, San Francisco 94158, USA
| | - Peter F McTigue
- Chemistry and Chemical Biology Graduate Program, University of California, San Francisco 94158, USA
| | | | - Tamas L Nagy
- Bioinformatics Graduate Group, University of California, San Francisco 94158, USA
| | - Andrew M Natale
- Biophysics Graduate Group, University of California, San Francisco 94158, USA
| | - Keely Oltion
- Chemistry and Chemical Biology Graduate Program, University of California, San Francisco 94158, USA
| | - Sergei Pourmal
- Chemistry and Chemical Biology Graduate Program, University of California, San Francisco 94158, USA
| | - Gabriel K Reder
- Biophysics Graduate Group, University of California, San Francisco 94158, USA
| | - Nicholas J Rettko
- Chemistry and Chemical Biology Graduate Program, University of California, San Francisco 94158, USA
| | - Peter J Rohweder
- Chemistry and Chemical Biology Graduate Program, University of California, San Francisco 94158, USA
| | - Daniel M C Schwarz
- Chemistry and Chemical Biology Graduate Program, University of California, San Francisco 94158, USA
| | - Sophia K Tan
- Biophysics Graduate Group, University of California, San Francisco 94158, USA
| | - Paul V Thomas
- Biophysics Graduate Group, University of California, San Francisco 94158, USA
| | - Ryan W Tibble
- Chemistry and Chemical Biology Graduate Program, University of California, San Francisco 94158, USA
| | - Jason P Town
- Bioinformatics Graduate Group, University of California, San Francisco 94158, USA
| | - Mary K Tsai
- Chemistry and Chemical Biology Graduate Program, University of California, San Francisco 94158, USA
| | - Fatima S Ugur
- Chemistry and Chemical Biology Graduate Program, University of California, San Francisco 94158, USA
| | - Douglas R Wassarman
- Chemistry and Chemical Biology Graduate Program, University of California, San Francisco 94158, USA
| | - Alexander M Wolff
- Biophysics Graduate Group, University of California, San Francisco 94158, USA
| | - Taia S Wu
- Chemistry and Chemical Biology Graduate Program, University of California, San Francisco 94158, USA
| | - Derek Bogdanoff
- Department of Biochemistry and Biophysics, University of California, San Francisco 94158, USA
| | - Jennifer Li
- Department of Chemistry Undergraduate Program, University of California, Davis 95616, USA
| | - Kurt S Thorn
- Department of Biochemistry and Biophysics, University of California, San Francisco 94158, USA
| | - Shane O'Conchúir
- Department of Bioengineering and Therapeutic Sciences, California Institute for Quantitative Biology (QBI), San Francisco 94158, USA
| | - Danielle L Swaney
- Department of Cellular and Molecular Pharmacology, California Institute for Quantitative Biology (QBI), San Francisco 94158, USA
| | - Eric D Chow
- Department of Biochemistry and Biophysics, University of California, San Francisco 94158, USA
| | - Hiten D Madhani
- Department of Biochemistry and Biophysics, University of California, San Francisco 94158, USA
| | - Sy Redding
- Department of Biochemistry and Biophysics, University of California, San Francisco 94158, USA
| | - Daniel N Bolon
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester 01655, USA
| | - Tanja Kortemme
- Department of Bioengineering and Therapeutic Sciences, California Institute for Quantitative Biology (QBI), San Francisco 94158, USA
| | - Joseph L DeRisi
- Department of Biochemistry and Biophysics, University of California, San Francisco 94158, USA
| | - Martin Kampmann
- Department of Biochemistry and Biophysics, University of California, San Francisco 94158, USA .,Institute for Neurodegenerative Diseases, University of California, San Francisco 94158, USA
| | - James S Fraser
- Department of Bioengineering and Therapeutic Sciences, California Institute for Quantitative Biology (QBI), San Francisco 94158, USA
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481
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Lee DH, Kim D, Kim ST, Jeong S, Kim JL, Shim SM, Heo AJ, Song X, Guo ZS, Bartlett DL, Oh SC, Lee J, Saito Y, Kim BY, Kwon YT, Lee YJ. PARK7 modulates autophagic proteolysis through binding to the N-terminally arginylated form of the molecular chaperone HSPA5. Autophagy 2018; 14:1870-1885. [PMID: 29976090 PMCID: PMC6152518 DOI: 10.1080/15548627.2018.1491212] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2018] [Accepted: 06/07/2018] [Indexed: 02/08/2023] Open
Abstract
Macroautophagy is induced under various stresses to remove cytotoxic materials, including misfolded proteins and their aggregates. These protein cargoes are collected by specific autophagic receptors such as SQSTM1/p62 (sequestosome 1) and delivered to phagophores for lysosomal degradation. To date, little is known about how cells sense and react to diverse stresses by inducing the activity of SQSTM1. Here, we show that the peroxiredoxin-like redox sensor PARK7/DJ-1 modulates the activity of SQSTM1 and the targeting of ubiquitin (Ub)-conjugated proteins to macroautophagy under oxidative stress caused by TNFSF10/TRAIL (tumor necrosis factor [ligand] superfamily, member 10). In this mechanism, TNFSF10 induces the N-terminal arginylation (Nt-arginylation) of the endoplasmic reticulum (ER)-residing molecular chaperone HSPA5/BiP/GRP78, leading to cytosolic accumulation of Nt-arginylated HSPA5 (R-HSPA5). In parallel, TNFSF10 induces the oxidation of PARK7. Oxidized PARK7 acts as a co-chaperone-like protein that binds the ER-derived chaperone R-HSPA5, a member of the HSPA/HSP70 family. By forming a complex with PARK7 (and possibly misfolded protein cargoes), R-HSPA5 binds SQSTM1 through its Nt-Arg, facilitating self-polymerization of SQSTM1 and the targeting of SQSTM1-cargo complexes to phagophores. The 3-way interaction among PARK7, R-HSPA5, and SQSTM1 is stabilized by the Nt-Arg residue of R-HSPA5. PARK7-deficient cells are impaired in the targeting of R-HSPA5 and SQSTM1 to phagophores and the removal of Ub-conjugated cargoes. Our results suggest that PARK7 functions as a co-chaperone for R-HSPA5 to modulate autophagic removal of misfolded protein cargoes generated by oxidative stress.
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Affiliation(s)
- Dae-Hee Lee
- Department of Oncology, Korea University Guro Hospital, Seoul, Republic of Korea
- Graduate School of Medicine, Korea University College of Medicine, Seoul, Republic of Korea
- Department of Surgery, School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Daeho Kim
- Protein Metabolism Medical Research Center and Department of Biomedical Sciences, College of Medicine, Seoul National University, Seoul, Republic of Korea
- Department of Biophysics and Chemical Biology, College of Natural Sciences, Seoul National University, Seoul, Republic of Korea
| | - Sung Tae Kim
- Protein Metabolism Medical Research Center and Department of Biomedical Sciences, College of Medicine, Seoul National University, Seoul, Republic of Korea
- Center for Pharmacogenetics and Department of Pharmaceutical Sciences, School of Pharmacy, University of Pittsburgh, Pittsburgh, PA, USA
| | - Soyeon Jeong
- Department of Oncology, Korea University Guro Hospital, Seoul, Republic of Korea
| | - Jung Lim Kim
- Department of Oncology, Korea University Guro Hospital, Seoul, Republic of Korea
| | - Sang Mi Shim
- Protein Metabolism Medical Research Center and Department of Biomedical Sciences, College of Medicine, Seoul National University, Seoul, Republic of Korea
| | - Ah Jung Heo
- Protein Metabolism Medical Research Center and Department of Biomedical Sciences, College of Medicine, Seoul National University, Seoul, Republic of Korea
| | - Xinxin Song
- Department of Surgery, School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Zong Sheng Guo
- Department of Surgery, School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - David L. Bartlett
- Department of Surgery, School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Sang Cheul Oh
- Department of Oncology, Korea University Guro Hospital, Seoul, Republic of Korea
- Graduate School of Medicine, Korea University College of Medicine, Seoul, Republic of Korea
| | - Junho Lee
- Department of Biophysics and Chemical Biology, College of Natural Sciences, Seoul National University, Seoul, Republic of Korea
- The Institute of Molecular Biology and Genetics, Department of Biological Sciences, Seoul National University, Seoul, Republic of Korea
| | - Yoshiro Saito
- Department of Medical Life Systems, Faculty of Life and Medical Sciences, Doshisha University, Kyoto, Japan
| | - Bo Yeon Kim
- World Class Institute, Korea Research Institute of Bioscience and Biotechnology, Cheongju-si, Republic of Korea
| | - Yong Tae Kwon
- Protein Metabolism Medical Research Center and Department of Biomedical Sciences, College of Medicine, Seoul National University, Seoul, Republic of Korea
- Ischemic/Hypoxic Disease Institute, College of Medicine, Seoul National University, Seoul, Republic of Korea
| | - Yong J. Lee
- Department of Surgery, School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
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482
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Santarriaga S, Haver HN, Kanack AJ, Fikejs AS, Sison SL, Egner JM, Bostrom JR, Seminary ER, Hill RB, Link BA, Ebert AD, Scaglione KM. SRCP1 Conveys Resistance to Polyglutamine Aggregation. Mol Cell 2018; 71:216-228.e7. [PMID: 30029002 PMCID: PMC6091221 DOI: 10.1016/j.molcel.2018.07.008] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Revised: 05/24/2018] [Accepted: 06/18/2018] [Indexed: 12/18/2022]
Abstract
The polyglutamine (polyQ) diseases are a group of nine neurodegenerative diseases caused by the expansion of a polyQ tract that results in protein aggregation. Unlike other model organisms, Dictyostelium discoideum is a proteostatic outlier, naturally encoding long polyQ tracts yet resistant to polyQ aggregation. Here we identify serine-rich chaperone protein 1 (SRCP1) as a molecular chaperone that is necessary and sufficient to suppress polyQ aggregation. SRCP1 inhibits aggregation of polyQ-expanded proteins, allowing for their degradation via the proteasome, where SRCP1 is also degraded. SRCP1's C-terminal domain is essential for its activity in cells, and peptides that mimic this domain suppress polyQ aggregation in vitro. Together our results identify a novel type of molecular chaperone and reveal how nature has dealt with the problem of polyQ aggregation.
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Affiliation(s)
| | - Holly N Haver
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Adam J Kanack
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Alicia S Fikejs
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Samantha L Sison
- Department of Cell Biology, Neurobiology, and Anatomy, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - John M Egner
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Jonathan R Bostrom
- Department of Cell Biology, Neurobiology, and Anatomy, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Emily R Seminary
- Department of Cell Biology, Neurobiology, and Anatomy, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - R Blake Hill
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Brian A Link
- Department of Cell Biology, Neurobiology, and Anatomy, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Allison D Ebert
- Department of Cell Biology, Neurobiology, and Anatomy, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - K Matthew Scaglione
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI 53226, USA.
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483
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Park D, Goh CJ, Kim H, Lee JS, Hahn Y. Loss of conserved ubiquitylation sites in conserved proteins during human evolution. Int J Mol Med 2018; 42:2203-2212. [PMID: 30015863 DOI: 10.3892/ijmm.2018.3772] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Accepted: 07/06/2018] [Indexed: 11/06/2022] Open
Abstract
Ubiquitylation of lysine residues in proteins serves a pivotal role in the efficient removal of misfolded or unused proteins and in the control of various regulatory pathways by monitoring protein activity that may lead to protein degradation. The loss of ubiquitylated lysines may affect the ubiquitin‑mediated regulatory network and result in the emergence of novel phenotypes. The present study analyzed mouse ubiquitylation data and orthologous proteins from 62 mammals to identify 193 conserved ubiquitylation sites from 169 proteins that were lost in the Euarchonta lineage leading to humans. A total of 8 proteins, including betaine homocysteine S‑methyltransferase, clin and CBS domain divalent metal cation transport mediator 3, ribosome‑binding protein 1 and solute carrier family 37 member 4, lost 1 conserved lysine residue, which was ubiquitylated in the mouse ortholog, following the human‑chimpanzee divergence. A total of 17 of the lost ubiquitylated lysines are also known to be modified by acetylation and/or succinylation in mice. In 8 cases, a novel lysine evolved at positions flanking the lost conserved lysine residues, potentially as a method of compensation. We hypothesize that the loss of ubiquitylation sites during evolution may lead to the development of advantageous phenotypes, which are then fixed by selection. The ancestral ubiquitylation sites identified in the present study may be a useful resource for investigating the association between loss of ubiquitylation sites and the emergence of novel phenotypes during evolution towards modern humans.
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Affiliation(s)
- Dongbin Park
- Department of Life Science, Chung‑Ang University, Seoul 06974, Republic of Korea
| | - Chul Jun Goh
- Department of Life Science, Chung‑Ang University, Seoul 06974, Republic of Korea
| | - Hyein Kim
- Department of Life Science, Chung‑Ang University, Seoul 06974, Republic of Korea
| | - Ji Seok Lee
- Department of Life Science, Chung‑Ang University, Seoul 06974, Republic of Korea
| | - Yoonsoo Hahn
- Department of Life Science, Chung‑Ang University, Seoul 06974, Republic of Korea
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484
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Zhang W, Xu W, Chen W, Zhou Q. Interplay of Autophagy Inducer Rapamycin and Proteasome Inhibitor MG132 in Reduction of Foam Cell Formation and Inflammatory Cytokine Expression. Cell Transplant 2018; 27:1235-1248. [PMID: 30001636 PMCID: PMC6434468 DOI: 10.1177/0963689718786229] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
MG132 is a pivotal inhibitor of the ubiquitin-proteasome system (UPS), and rapamycin (RAPA) is an important inducer of autophagy. MG132 and RAPA have been shown to be effective agents that can cure multiple autoimmune diseases by reducing inflammation. Although individual MG132 and RAPA showed protective effects for atherosclerosis (AS), the combined effect of these two drugs and its molecular mechanism are still unclear. In this article we investigate the regulation of oxidative modification of low-density lipoprotein (ox-LDL) stress and foam cell formation in the presence of both proteasome inhibitor MG132 and the autophagy inducer RAPA to uncover the molecular mechanism underlying this process. We established the foam cells model by ox-LDL and an animal model. Then, we tested six experimental groups of MG132, RAPA, and 3MA drugs. As a result, RAPA-induced autophagy reduces accumulation of polyubiquitinated proteins and apoptosis of foam cells. The combination of MG132 with RAPA not only suppressed expression of the inflammatory cytokines and formation of macrophage foam cells, but also significantly affected the NF-κB signaling pathway and the polarization of RAW 264.7 cells. These data suggest that the combination of proteasome inhibitor and autophagy inducer ameliorates the inflammatory response and reduces the formation of macrophage foam cells during development of AS. Our research provides a new way to suppress vascular inflammation and stabilize plaques of late atherosclerosis.
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Affiliation(s)
- Wei Zhang
- 1 MOE Key Laboratory of Laser Life Science & Institute of Laser Life Science, South China Normal University, Guangzhou, China.,2 College of Biophotonics, South China Normal University, Guangzhou, China
| | - Wan Xu
- 1 MOE Key Laboratory of Laser Life Science & Institute of Laser Life Science, South China Normal University, Guangzhou, China.,2 College of Biophotonics, South China Normal University, Guangzhou, China
| | - Wenli Chen
- 1 MOE Key Laboratory of Laser Life Science & Institute of Laser Life Science, South China Normal University, Guangzhou, China.,2 College of Biophotonics, South China Normal University, Guangzhou, China
| | - Quan Zhou
- 3 Department of Radiology, The Third Affiliated Hospital of Southern Medical University, Guangzhou, China
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485
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Farrawell NE, Lambert-Smith I, Mitchell K, McKenna J, McAlary L, Ciryam P, Vine KL, Saunders DN, Yerbury JJ. SOD1 A4V aggregation alters ubiquitin homeostasis in a cell model of ALS. J Cell Sci 2018; 131:jcs.209122. [PMID: 29748379 DOI: 10.1242/jcs.209122] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Accepted: 05/01/2018] [Indexed: 12/11/2022] Open
Abstract
A hallmark of amyotrophic lateral sclerosis (ALS) pathology is the accumulation of ubiquitylated protein inclusions within motor neurons. Recent studies suggest the sequestration of ubiquitin (Ub) into inclusions reduces the availability of free Ub, which is essential for cellular function and survival. However, the dynamics of the Ub landscape in ALS have not yet been described. Here, we show that Ub homeostasis is altered in a cell model of ALS induced by expressing mutant SOD1 (SOD1A4V). By monitoring the distribution of Ub in cells expressing SOD1A4V, we show that Ub is present at the earliest stages of SOD1A4V aggregation, and that cells containing SOD1A4V aggregates have greater ubiquitin-proteasome system (UPS) dysfunction. Furthermore, SOD1A4V aggregation is associated with the redistribution of Ub and depletion of the free Ub pool. Ubiquitomics analysis indicates that expression of SOD1A4V is associated with a shift of Ub to a pool of supersaturated proteins, including those associated with oxidative phosphorylation and metabolism, corresponding with altered mitochondrial morphology and function. Taken together, these results suggest that misfolded SOD1 contributes to UPS dysfunction and that Ub homeostasis is an important target for monitoring pathological changes in ALS.This article has an associated First Person interview with the first author of the paper.
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Affiliation(s)
- Natalie E Farrawell
- Illawarra Health and Medical Research Institute, Wollongong, NSW, Australia 2522.,Molecular Horizons and School of Chemistry & Molecular Bioscience, University of Wollongong, NSW, Australia 2522
| | - Isabella Lambert-Smith
- Illawarra Health and Medical Research Institute, Wollongong, NSW, Australia 2522.,Molecular Horizons and School of Chemistry & Molecular Bioscience, University of Wollongong, NSW, Australia 2522
| | - Kristen Mitchell
- Illawarra Health and Medical Research Institute, Wollongong, NSW, Australia 2522.,Molecular Horizons and School of Chemistry & Molecular Bioscience, University of Wollongong, NSW, Australia 2522
| | - Jessie McKenna
- School of Medical Sciences, Faculty of Medicine, UNSW Australia 2052
| | - Luke McAlary
- Illawarra Health and Medical Research Institute, Wollongong, NSW, Australia 2522.,Molecular Horizons and School of Chemistry & Molecular Bioscience, University of Wollongong, NSW, Australia 2522.,Department of Physics & Astronomy, University of British Columbia, Vancouver, British Columbia, Canada V6T 2B5
| | - Prajwal Ciryam
- Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, UK.,Department of Molecular Biosciences, Rice Institute for Biomedical Research, Northwestern University, Evanston, IL 60208-3500, USA.,Department of Neurology, Columbia University College of Physicians & Surgeons, New York, NY 10032-3784, USA
| | - Kara L Vine
- Illawarra Health and Medical Research Institute, Wollongong, NSW, Australia 2522.,Molecular Horizons and School of Chemistry & Molecular Bioscience, University of Wollongong, NSW, Australia 2522
| | - Darren N Saunders
- School of Medical Sciences, Faculty of Medicine, UNSW Australia 2052
| | - Justin J Yerbury
- Illawarra Health and Medical Research Institute, Wollongong, NSW, Australia 2522 .,Molecular Horizons and School of Chemistry & Molecular Bioscience, University of Wollongong, NSW, Australia 2522
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486
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Kim L, Kwon DH, Kim BH, Kim J, Park MR, Park ZY, Song HK. Structural and Biochemical Study of the Mono-ADP-Ribosyltransferase Domain of SdeA, a Ubiquitylating/Deubiquitylating Enzyme from Legionella pneumophila. J Mol Biol 2018; 430:2843-2856. [PMID: 29870726 DOI: 10.1016/j.jmb.2018.05.043] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2018] [Revised: 05/24/2018] [Accepted: 05/27/2018] [Indexed: 11/18/2022]
Abstract
Conventional ubiquitylation occurs through an ATP-dependent three-enzyme cascade (E1, E2, and E3) that mediates the covalent conjugation of the C-terminus of ubiquitin to a lysine on the substrate. SdeA, which belongs to the SidE effector family of Legionella pneumophila, can transfer ubiquitin to endoplasmic reticulum-associated Rab-family GTPases in a manner independent of E1 and E2 enzymes. The novel ubiquitin-modifying enzyme SdeA utilizes NAD+ as a cofactor to attach ubiquitin to a serine residue of the substrate. Here, to elucidate the coupled enzymatic reaction of NAD+ hydrolysis and ADP-ribosylation of ubiquitin in SdeA, we characterized the mono-ADP-ribosyltransferase domain of SdeA and show that it consists of two sub-domains termed mART-N and mART-C. The crystal structure of the mART-C domain of SdeA was also determined in free form and in complex with NAD+ at high resolution. Furthermore, the spatial orientations of the N-terminal deubiquitylase, phosphodiesterase, mono-ADP-ribosyltransferase, and C-terminal coiled-coil domains within the 180-kDa full-length SdeA were determined. These results provide insight into the unusual ubiquitylation mechanism of SdeA and expand our knowledge on the structure-function of mono-ADP-ribosyltransferases.
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Affiliation(s)
- Leehyeon Kim
- Department of Life Sciences, Korea University, 145 Anam-ro, Seongbuk-gu, Seoul 02841, Korea
| | - Do Hoon Kwon
- Department of Life Sciences, Korea University, 145 Anam-ro, Seongbuk-gu, Seoul 02841, Korea
| | - Bong Heon Kim
- Department of Life Sciences, Korea University, 145 Anam-ro, Seongbuk-gu, Seoul 02841, Korea
| | - Jiyeon Kim
- School of Life Sciences, Gwangju Institute of Science and Technology, Gwangju 61005, Korea
| | - Mi Rae Park
- Department of Life Sciences, Korea University, 145 Anam-ro, Seongbuk-gu, Seoul 02841, Korea
| | - Zee-Yong Park
- School of Life Sciences, Gwangju Institute of Science and Technology, Gwangju 61005, Korea
| | - Hyun Kyu Song
- Department of Life Sciences, Korea University, 145 Anam-ro, Seongbuk-gu, Seoul 02841, Korea.
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487
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Targeted protein degradation and the enzymology of degraders. Curr Opin Chem Biol 2018; 44:47-55. [DOI: 10.1016/j.cbpa.2018.05.004] [Citation(s) in RCA: 73] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Accepted: 05/03/2018] [Indexed: 02/06/2023]
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488
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Koren I, Timms RT, Kula T, Xu Q, Li MZ, Elledge SJ. The Eukaryotic Proteome Is Shaped by E3 Ubiquitin Ligases Targeting C-Terminal Degrons. Cell 2018; 173:1622-1635.e14. [PMID: 29779948 DOI: 10.1016/j.cell.2018.04.028] [Citation(s) in RCA: 185] [Impact Index Per Article: 30.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Revised: 03/03/2018] [Accepted: 04/20/2018] [Indexed: 01/18/2023]
Abstract
Degrons are minimal elements that mediate the interaction of proteins with degradation machineries to promote proteolysis. Despite their central role in proteostasis, the number of known degrons remains small, and a facile technology to characterize them is lacking. Using a strategy combining global protein stability (GPS) profiling with a synthetic human peptidome, we identify thousands of peptides containing degron activity. Employing CRISPR screening, we establish that the stability of many proteins is regulated through degrons located at their C terminus. We characterize eight Cullin-RING E3 ubiquitin ligase (CRL) complex adaptors that regulate C-terminal degrons, including six CRL2 and two CRL4 complexes, and computationally implicate multiple non-CRLs in end recognition. Proteome analysis revealed that the C termini of eukaryotic proteins are depleted for C-terminal degrons, suggesting an E3-ligase-dependent modulation of proteome composition. Thus, we propose that a series of "C-end rules" operate to govern protein stability and shape the eukaryotic proteome.
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Affiliation(s)
- Itay Koren
- Department of Genetics, Harvard Medical School and Division of Genetics, Brigham and Women's Hospital, Howard Hughes Medical Institute, 77 Avenue Louis Pasteur, Boston, MA 02115, USA
| | - Richard T Timms
- Department of Genetics, Harvard Medical School and Division of Genetics, Brigham and Women's Hospital, Howard Hughes Medical Institute, 77 Avenue Louis Pasteur, Boston, MA 02115, USA
| | - Tomasz Kula
- Department of Genetics, Harvard Medical School and Division of Genetics, Brigham and Women's Hospital, Howard Hughes Medical Institute, 77 Avenue Louis Pasteur, Boston, MA 02115, USA
| | - Qikai Xu
- Department of Genetics, Harvard Medical School and Division of Genetics, Brigham and Women's Hospital, Howard Hughes Medical Institute, 77 Avenue Louis Pasteur, Boston, MA 02115, USA
| | - Mamie Z Li
- Department of Genetics, Harvard Medical School and Division of Genetics, Brigham and Women's Hospital, Howard Hughes Medical Institute, 77 Avenue Louis Pasteur, Boston, MA 02115, USA
| | - Stephen J Elledge
- Department of Genetics, Harvard Medical School and Division of Genetics, Brigham and Women's Hospital, Howard Hughes Medical Institute, 77 Avenue Louis Pasteur, Boston, MA 02115, USA.
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489
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Bustamante HA, González AE, Cerda-Troncoso C, Shaughnessy R, Otth C, Soza A, Burgos PV. Interplay Between the Autophagy-Lysosomal Pathway and the Ubiquitin-Proteasome System: A Target for Therapeutic Development in Alzheimer's Disease. Front Cell Neurosci 2018; 12:126. [PMID: 29867359 PMCID: PMC5954036 DOI: 10.3389/fncel.2018.00126] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Accepted: 04/20/2018] [Indexed: 12/14/2022] Open
Abstract
Alzheimer’s disease (AD) is the most common cause of age-related dementia leading to severe irreversible cognitive decline and massive neurodegeneration. While therapeutic approaches for managing symptoms are available, AD currently has no cure. AD associates with a progressive decline of the two major catabolic pathways of eukaryotic cells—the autophagy-lysosomal pathway (ALP) and the ubiquitin-proteasome system (UPS)—that contributes to the accumulation of harmful molecules implicated in synaptic plasticity and long-term memory impairment. One protein recently highlighted as the earliest initiator of these disturbances is the amyloid precursor protein (APP) intracellular C-terminal membrane fragment β (CTFβ), a key toxic agent with deleterious effects on neuronal function that has become an important pathogenic factor for AD and a potential biomarker for AD patients. This review focuses on the involvement of regulatory molecules and specific post-translational modifications (PTMs) that operate in the UPS and ALP to control a single proteostasis network to achieve protein balance. We discuss how these aspects can contribute to the development of novel strategies to strengthen the balance of key pathogenic proteins associated with AD.
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Affiliation(s)
- Hianara A Bustamante
- Institute of Physiology, Faculty of Medicine, Universidad Austral de Chile, Valdivia, Chile.,Center for Interdisciplinary Studies on the Nervous System (CISNe), Universidad Austral de Chile, Valdivia, Chile
| | - Alexis E González
- Institute of Physiology, Faculty of Medicine, Universidad Austral de Chile, Valdivia, Chile.,Fundación Ciencia y Vida, Santiago, Chile
| | - Cristobal Cerda-Troncoso
- Centro de Biología Celular y Biomedicina (CEBICEM), Facultad de Medicina y Ciencia, Universidad San Sebastián, Santiago, Chile
| | - Ronan Shaughnessy
- Centro de Biología Celular y Biomedicina (CEBICEM), Facultad de Medicina y Ciencia, Universidad San Sebastián, Santiago, Chile.,Center for Aging and Regeneration (CARE), Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Carola Otth
- Center for Interdisciplinary Studies on the Nervous System (CISNe), Universidad Austral de Chile, Valdivia, Chile.,Institute of Clinical Microbiology, Faculty of Medicine, Universidad Austral de Chile, Valdivia, Chile
| | - Andrea Soza
- Centro de Biología Celular y Biomedicina (CEBICEM), Facultad de Medicina y Ciencia, Universidad San Sebastián, Santiago, Chile.,Center for Aging and Regeneration (CARE), Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Patricia V Burgos
- Institute of Physiology, Faculty of Medicine, Universidad Austral de Chile, Valdivia, Chile.,Centro de Biología Celular y Biomedicina (CEBICEM), Facultad de Medicina y Ciencia, Universidad San Sebastián, Santiago, Chile.,Center for Aging and Regeneration (CARE), Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
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490
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Ceelen JJM, Schols AMWJ, Thielen NGM, Haegens A, Gray DA, Kelders MCJM, de Theije CC, Langen RCJ. Pulmonary inflammation-induced loss and subsequent recovery of skeletal muscle mass require functional poly-ubiquitin conjugation. Respir Res 2018; 19:80. [PMID: 29720191 PMCID: PMC5932886 DOI: 10.1186/s12931-018-0753-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2017] [Accepted: 03/18/2018] [Indexed: 01/24/2023] Open
Abstract
BACKGROUND Pulmonary inflammation in response to respiratory infections can evoke muscle wasting. Increased activity of the ubiquitin (Ub)-proteasome system (UPS) and the autophagy lysosome pathway (ALP) have been implicated in inflammation-induced muscle atrophy. Since poly-Ub conjugation is required for UPS-mediated proteolysis and has been implicated in the ALP, we assessed the effect of impaired ubiquitin conjugation on muscle atrophy and recovery following pulmonary inflammation, and compared activation and suppression of these proteolytic systems to protein synthesis regulation. METHODS Pulmonary inflammation was induced in mice by an intratracheal instillation of LPS. Proteolysis (UPS and ALP) and synthesis signaling were examined in gastrocnemius muscle homogenates. Ub-conjugation-dependency of muscle atrophy and recovery was addressed using Ub-K48R (K48R) mice with attenuated poly-ubiquitin conjugation, and compared to UBWT control mice. RESULTS Pulmonary inflammation caused a decrease in skeletal muscle mass which was accompanied by a rapid increase in expression of UPS and ALP constituents and reduction in protein synthesis signaling acutely after LPS. Muscle atrophy was attenuated in K48R mice, while ALP and protein synthesis signaling were not affected. Muscle mass recovery starting 72 h post LPS, correlated with reduced expression of UPS and ALP constituents and restoration of protein synthesis signaling. K48R mice however displayed impaired recovery of muscle mass. CONCLUSION Pulmonary inflammation-induced muscle atrophy is in part attributable to UPS-mediated proteolysis, as activation of ALP- and suppression of protein synthesis signaling occur independently of poly-Ub conjugation during muscle atrophy. Recovery of muscle mass following pulmonary inflammation involves inverse regulation of proteolysis and protein synthesis signaling, and requires a functional poly-Ub conjugation.
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Affiliation(s)
- Judith J. M. Ceelen
- Department of Respiratory Medicine, School of Nutrition and Translational Research in Metabolism (NUTRIM), Maastricht University Medical Centre (MUMC+), Maastricht, the Netherlands
| | - Annemie M. W. J. Schols
- Department of Respiratory Medicine, School of Nutrition and Translational Research in Metabolism (NUTRIM), Maastricht University Medical Centre (MUMC+), Maastricht, the Netherlands
| | - Nathalie G. M. Thielen
- Department of Respiratory Medicine, School of Nutrition and Translational Research in Metabolism (NUTRIM), Maastricht University Medical Centre (MUMC+), Maastricht, the Netherlands
| | - Astrid Haegens
- Department of Respiratory Medicine, School of Nutrition and Translational Research in Metabolism (NUTRIM), Maastricht University Medical Centre (MUMC+), Maastricht, the Netherlands
| | - Douglas A. Gray
- Department of Biochemistry, Microbiology and Immunology, Ottawa Hospital Research Institute, Ottawa, Canada
| | - Marco C. J. M. Kelders
- Department of Respiratory Medicine, School of Nutrition and Translational Research in Metabolism (NUTRIM), Maastricht University Medical Centre (MUMC+), Maastricht, the Netherlands
| | - Chiel C. de Theije
- Department of Respiratory Medicine, School of Nutrition and Translational Research in Metabolism (NUTRIM), Maastricht University Medical Centre (MUMC+), Maastricht, the Netherlands
| | - Ramon C. J. Langen
- Department of Respiratory Medicine, School of Nutrition and Translational Research in Metabolism (NUTRIM), Maastricht University Medical Centre (MUMC+), Maastricht, the Netherlands
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491
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Xu C, Zhang W, Liu S, Wu W, Qin M, Huang J. Activation of the SphK1/ERK/p-ERK pathway promotes autophagy in colon cancer cells. Oncol Lett 2018; 15:9719-9724. [PMID: 29928348 PMCID: PMC6004663 DOI: 10.3892/ol.2018.8588] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2017] [Accepted: 03/16/2018] [Indexed: 12/22/2022] Open
Abstract
Sphingosine kinase 1 (SphK1) is a master kinase that catalyzes the synthesis of sphingosine 1 phosphate and participates in the regulation of cell proliferation and autophagy. The present study aimed to assess the effects of the activation of the SphK1/extracellular signal-regulated kinase (ERK)/phosphorylated (p-)ERK pathway in the regulation of autophagy in colon cancer (HT-29) cells. Inverted fluorescence microscopy was used to detect the expression of green fluorescent protein (GFP) in the SphK1-overexpressing HT-29 cells [SphK1(+)-HT-29] and the negative control HT-29 cells (NC-HT-29). Western blotting was used to detect the protein expression levels of SphK1, ERK1/2, p-ERK1/2, as well as those of the autophagy-associated markers LC3A, ATG5, and ULK1. Protein localization and expression of the LC3A antibody were detected by immunofluorescence. The results demonstrated that GFP was similarly expressed in SphK1(+)-HT-29 and NC-HT-29 cells. However, significantly increased SphK1 mRNA and protein expression levels were detected in SphK1(+)-HT-29 cells compared with in NC-HT-29 cells, which resulted in upregulated ERK/p-ERK. Furthermore, the protein expression levels of the three autophagy-associated markers increased. LC3A protein was localized in the cytoplasm of SphK1(+)-HT-29 cells, indicating autophagy. In summary, the findings of the present study suggested that activation of the SphK1/ERK/p-ERK pathway promotes autophagy in colon cancer HT-29 cells.
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Affiliation(s)
- Chunyan Xu
- Department of Gastroenterology, The Second Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi 530007, P.R. China
| | - Wenlu Zhang
- Department of Respiratory Medicine, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi 530021, P.R. China
| | - Shiquan Liu
- Department of Gastroenterology, The Second Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi 530007, P.R. China
| | - Wenhong Wu
- Department of Gastroenterology, The Second Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi 530007, P.R. China
| | - Mengbin Qin
- Department of Gastroenterology, The Second Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi 530007, P.R. China
| | - Jiean Huang
- Department of Gastroenterology, The Second Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi 530007, P.R. China
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492
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Courtois G, Fauvarque MO. The Many Roles of Ubiquitin in NF-κB Signaling. Biomedicines 2018; 6:E43. [PMID: 29642643 PMCID: PMC6027159 DOI: 10.3390/biomedicines6020043] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Revised: 03/31/2018] [Accepted: 04/02/2018] [Indexed: 12/24/2022] Open
Abstract
The nuclear factor κB (NF-κB) signaling pathway ubiquitously controls cell growth and survival in basic conditions as well as rapid resetting of cellular functions following environment changes or pathogenic insults. Moreover, its deregulation is frequently observed during cell transformation, chronic inflammation or autoimmunity. Understanding how it is properly regulated therefore is a prerequisite to managing these adverse situations. Over the last years evidence has accumulated showing that ubiquitination is a key process in NF-κB activation and its resolution. Here, we examine the various functions of ubiquitin in NF-κB signaling and more specifically, how it controls signal transduction at the molecular level and impacts in vivo on NF-κB regulated cellular processes.
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493
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The expression pattern and potential functions of PHB in the spermiogenesis of Phascolosoma esculenta. Gene 2018; 652:25-38. [DOI: 10.1016/j.gene.2018.01.056] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2017] [Revised: 01/11/2018] [Accepted: 01/16/2018] [Indexed: 11/20/2022]
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494
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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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495
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Verheijen BM, Oyanagi K, van Leeuwen FW. Dysfunction of Protein Quality Control in Parkinsonism-Dementia Complex of Guam. Front Neurol 2018; 9:173. [PMID: 29615966 PMCID: PMC5869191 DOI: 10.3389/fneur.2018.00173] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2017] [Accepted: 03/06/2018] [Indexed: 12/12/2022] Open
Abstract
Guam parkinsonism–dementia complex (G-PDC) is an enigmatic neurodegenerative disease that is endemic to the Pacific island of Guam. G-PDC patients are clinically characterized by progressive cognitive impairment and parkinsonism. Neuropathologically, G-PDC is characterized by abundant neurofibrillary tangles, which are composed of hyperphosphorylated tau, marked deposition of 43-kDa TAR DNA-binding protein, and neuronal loss. Although both genetic and environmental factors have been implicated, the etiology and pathogenesis of G-PDC remain unknown. Recent neuropathological studies have provided new clues about the pathomechanisms involved in G-PDC. For example, deposition of abnormal components of the protein quality control system in brains of G-PDC patients indicates a role for proteostasis imbalance in the disease. This opens up promising avenues for new research on G-PDC and could have important implications for the study of other neurodegenerative disorders.
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Affiliation(s)
- Bert M Verheijen
- Department of Translational Neuroscience, Brain Center Rudolf Magnus, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands.,Department of Neurology and Neurosurgery, Brain Center Rudolf Magnus, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands
| | - Kiyomitsu Oyanagi
- Division of Neuropathology, Department of Brain Disease Research, Shinshu University School of Medicine, Nagano, Japan.,Brain Research Laboratory, Hatsuishi Hospital, Chiba, Japan
| | - Fred W van Leeuwen
- Department of Neuroscience, Faculty of Health, Medicine and Life Sciences, Maastricht University, Maastricht, Netherlands
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496
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Subcellular localisation modulates ubiquitylation and degradation of Ascl1. Sci Rep 2018; 8:4625. [PMID: 29545540 PMCID: PMC5854709 DOI: 10.1038/s41598-018-23056-4] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2018] [Accepted: 03/01/2018] [Indexed: 12/31/2022] Open
Abstract
The proneural transcription factor Ascl1 is a master regulator of neurogenesis, coordinating proliferation and differentiation in the central nervous system. While its expression is well characterised, post-translational regulation is much less well understood. Here we demonstrate that a population of chromatin-bound Ascl1 can be found associated with short chains of ubiquitin while cytoplasmic Ascl1 harbours much longer ubiquitin chains. Only cytoplasmic ubiquitylation targets Ascl1 for destruction, which occurs by conjugation of ubiquitin to lysines in the basic helix-loop-helix domain of Ascl1 and requires the E3 ligase Huwe1. In contrast, chromatin-bound Ascl1 associated with short ubiquitin-chains, which can occur on lysines within the N-terminal region or the bHLH domain and is not mediated by Huwe1, is not targeted for ubiquitin-mediated destruction. We therefore offer further insights into post-translational regulation of Ascl1, highlighting complex regulation of ubiquitylation and degradation in the cytoplasm and on chromatin.
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497
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Penke B, Bogár F, Crul T, Sántha M, Tóth ME, Vígh L. Heat Shock Proteins and Autophagy Pathways in Neuroprotection: from Molecular Bases to Pharmacological Interventions. Int J Mol Sci 2018; 19:E325. [PMID: 29361800 PMCID: PMC5796267 DOI: 10.3390/ijms19010325] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Revised: 01/15/2018] [Accepted: 01/18/2018] [Indexed: 02/07/2023] Open
Abstract
Neurodegenerative diseases (NDDs) such as Alzheimer's disease, Parkinson's disease and Huntington's disease (HD), amyotrophic lateral sclerosis, and prion diseases are all characterized by the accumulation of protein aggregates (amyloids) into inclusions and/or plaques. The ubiquitous presence of amyloids in NDDs suggests the involvement of disturbed protein homeostasis (proteostasis) in the underlying pathomechanisms. This review summarizes specific mechanisms that maintain proteostasis, including molecular chaperons, the ubiquitin-proteasome system (UPS), endoplasmic reticulum associated degradation (ERAD), and different autophagic pathways (chaperon mediated-, micro-, and macro-autophagy). The role of heat shock proteins (Hsps) in cellular quality control and degradation of pathogenic proteins is reviewed. Finally, putative therapeutic strategies for efficient removal of cytotoxic proteins from neurons and design of new therapeutic targets against the progression of NDDs are discussed.
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Affiliation(s)
- Botond Penke
- Department of Medical Chemistry, University of Szeged, H-6720 Szeged, Dóm Square 8, Hungary.
| | - Ferenc Bogár
- Department of Medical Chemistry, University of Szeged, H-6720 Szeged, Dóm Square 8, Hungary.
- MTA-SZTE Biomimetic Systems Research Group, University of Szeged, H-6720 Szeged, Dóm Square 8, Hungary.
| | - Tim Crul
- Institute of Biochemistry, Biological Research Centre, Hungarian Academy of Sciences, H-6726 Szeged, Temesvári krt. 62, Hungary.
| | - Miklós Sántha
- Institute of Biochemistry, Biological Research Centre, Hungarian Academy of Sciences, H-6726 Szeged, Temesvári krt. 62, Hungary.
| | - Melinda E Tóth
- Institute of Biochemistry, Biological Research Centre, Hungarian Academy of Sciences, H-6726 Szeged, Temesvári krt. 62, Hungary.
| | - László Vígh
- Institute of Biochemistry, Biological Research Centre, Hungarian Academy of Sciences, H-6726 Szeged, Temesvári krt. 62, Hungary.
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498
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Nam T, Han JH, Devkota S, Lee HW. Emerging Paradigm of Crosstalk between Autophagy and the Ubiquitin-Proteasome System. Mol Cells 2017; 40:897-905. [PMID: 29237114 PMCID: PMC5750708 DOI: 10.14348/molcells.2017.0226] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Revised: 11/13/2017] [Accepted: 11/23/2017] [Indexed: 02/08/2023] Open
Abstract
Cellular protein homeostasis is maintained by two major degradation pathways, namely the ubiquitin-proteasome system (UPS) and autophagy. Until recently, the UPS and autophagy were considered to be largely independent systems targeting proteins for degradation in the proteasome and lysosome, respectively. However, the identification of crucial roles of molecular players such as ubiquitin and p62 in both of these pathways as well as the observation that blocking the UPS affects autophagy flux and vice versa has generated interest in studying crosstalk between these pathways. Here, we critically review the current understanding of how the UPS and autophagy execute coordinated protein degradation at the molecular level, and shed light on our recent findings indicating an important role of an autophagy-associated transmembrane protein EI24 as a bridging molecule between the UPS and autophagy that functions by regulating the degradation of several E3 ligases with Really Interesting New Gene (RING)-domains.
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Affiliation(s)
- Taewook Nam
- Department of Biochemistry, College of Life Science and Biotechnology and Yonsei Laboratory Animal Research Center, Yonsei University, Seoul 03722,
Republic of Korea
| | - Jong Hyun Han
- Department of Biochemistry, College of Life Science and Biotechnology and Yonsei Laboratory Animal Research Center, Yonsei University, Seoul 03722,
Republic of Korea
| | - Sushil Devkota
- Section of Cell and Developmental Biology, University of California San Diego, La Jolla, CA,
USA
| | - Han-Woong Lee
- Department of Biochemistry, College of Life Science and Biotechnology and Yonsei Laboratory Animal Research Center, Yonsei University, Seoul 03722,
Republic of Korea
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499
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Gut Symbiont Bacteroides fragilis Secretes a Eukaryotic-Like Ubiquitin Protein That Mediates Intraspecies Antagonism. mBio 2017; 8:mBio.01902-17. [PMID: 29184019 PMCID: PMC5705921 DOI: 10.1128/mbio.01902-17] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Human gut Bacteroides species produce different types of toxins that antagonize closely related members of the gut microbiota. Some are toxic effectors delivered by type VI secretion systems, and others are non-contact-dependent secreted antimicrobial proteins. Many strains of Bacteroides fragilis secrete antimicrobial molecules, but only one of these toxins has been described to date (Bacteroidales secreted antimicrobial protein 1 [BSAP-1]). In this study, we describe a novel secreted protein produced by B. fragilis strain 638R that mediated intraspecies antagonism. Using transposon mutagenesis and deletion mutation, we identified a gene encoding a eukaryotic-like ubiquitin protein (BfUbb) necessary for toxin activity against a subset of B. fragilis strains. The addition of ubb into a heterologous background strain conferred toxic activity on that strain. We found this gene to be one of the most highly expressed in the B. fragilis genome. The mature protein is 84% similar to human ubiquitin but has an N-terminal signal peptidase I (SpI) signal sequence and is secreted extracellularly. We found that the mature 76-amino-acid synthetic protein has very potent activity, confirming that BfUbb mediates the activity. Analyses of human gut metagenomic data sets revealed that ubb is present in 12% of the metagenomes that have evidence of B. fragilis. As 638R produces both BSAP-1 and BfUbb, we performed a comprehensive analysis of the toxin activity of BSAP-1 and BfUbb against a set of 40 B. fragilis strains, revealing that 75% of B. fragilis strains are targeted by one or the other of these two secreted proteins of strain 638R. We are just beginning to understand some of the important interactions that occur between microbes of the human gut microbiota that dictate the composition and abundance of its constituent members. The ability of one member to produce molecules that directly kill a coresident member has been shown among minor gut species and is just starting to be studied in the abundant Bacteroides species. Here, we show that some strains of Bacteroides fragilis have acquired a gene encoding a secreted eukaryotic-like ubiquitin protein with potent inhibitory activity against other B. fragilis stains. This is the first bacterially encoded ubiquitin-like molecule shown to function like a bacterial toxin. This molecule is an example of a gut symbiont acquiring and adapting a eukaryotic molecule likely to increase its competitiveness in the mammalian gut. Understanding antagonistic factors produced by abundant gut symbionts is an important prerequisite to properly engineer strains to colonize the gut for health benefits.
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