1
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Zheng M, Chen X, Xu Z, Ye Z, Zhong L, Chen Z, Chen G, Cai B. Comprehensive analysis of PSMG3 in pan-cancer and validation of its role in hepatocellular carcinoma. Clin Transl Oncol 2024:10.1007/s12094-024-03580-8. [PMID: 38967739 DOI: 10.1007/s12094-024-03580-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2024] [Accepted: 06/19/2024] [Indexed: 07/06/2024]
Abstract
BACKGROUND Proteasome assembly chaperone 3 (PSMG3), a subunit of proteasome, has been found to be associated with lung cancer. However, the role of PSMG3 in other cancers has not been elucidated. The objective of this study was to explore the immune role of PSMG3 in pan-cancer and confirm the oncogenic significance in liver hepatocellular carcinoma (LIHC). METHODS We examined the differential expression of PSMG3 across various cancer types using data from The Cancer Genome Atlas (TCGA) and the Genotype-Tissue Expression (GTEx) databases. We investigated the prognostic value of PSMG3 and examined its relationship with tumor mutation burden (TMB), microsatellite instability (MSI), and immune infiltration. The functional enrichment analysis was performed to explore the potential molecular mechanism of PSMG3. To elucidate the biological function of PSMG3, we conducted in vitro experiments using liver cancer cell lines. RESULTS PSMG3 was highly expressed in most cancers. The high PSMG3 expression value of PSMG3 was closely related to poor prognosis. We observed correlations between PSMG3 and TMB, and MSI immune infiltration. PSMG3 may be involved in metabolic reprogramming, cell cycle, and PPAR pathways. The over-expression of PSMG3 promoted the proliferation, migration, and invasion capabilities of liver cancer cells. CONCLUSION Our study demonstrated that PSMG3 was a pivotal oncogene in multiple cancers. PSMG3 contributed to the progression and immune infiltration in pan-cancer, especially in LIHC.
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Affiliation(s)
- Mengli Zheng
- Department of Gastroenterology, The Tenth Affiliated Hospital, Southern Medical University (Dongguan People's Hospital), Dongguan, China
| | - Xiaochun Chen
- Department of Gastroenterology, The Tenth Affiliated Hospital, Southern Medical University (Dongguan People's Hospital), Dongguan, China
| | - Zhe Xu
- Department of Gastroenterology, The Tenth Affiliated Hospital, Southern Medical University (Dongguan People's Hospital), Dongguan, China
| | - Zhitao Ye
- Department of Nephrology, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Lixian Zhong
- Department of Gastroenterology, The Tenth Affiliated Hospital, Southern Medical University (Dongguan People's Hospital), Dongguan, China
| | - Zhicao Chen
- Department of Gastroenterology, The Tenth Affiliated Hospital, Southern Medical University (Dongguan People's Hospital), Dongguan, China
| | - Guiquan Chen
- Department of Gastroenterology, The Tenth Affiliated Hospital, Southern Medical University (Dongguan People's Hospital), Dongguan, China.
| | - Boyong Cai
- Department of Gastroenterology, The Tenth Affiliated Hospital, Southern Medical University (Dongguan People's Hospital), Dongguan, China.
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2
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Neshat A, Mahdavi A, Yousefshahi MR, Cheraghi M, Mousavizadeh Mobarakeh A, Mohammadi S, Eigner V, Kucerakova M, Dusek M, Kaboudin B. Homobimetallic Au(I)-Au(I) and Heterotrimetallic Au(I)-Fe(II)-Au(I) Complexes with Dialkyldithiophosphates and Phosphine Ligands: Structural Characterization, DFT Analysis, and Tyrosinase Inhibitory and Biological Effects. ACS OMEGA 2023; 8:20423-20439. [PMID: 37332817 PMCID: PMC10268621 DOI: 10.1021/acsomega.3c00645] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Accepted: 04/21/2023] [Indexed: 06/20/2023]
Abstract
The role of bridging and terminal ligand electronic and steric properties on the structure and antiproliferative activity of two-coordinated gold(I) complexes was investigated on seven novel binuclear and trinuclear gold(I) complexes synthesized by the reaction of either Au2(dppm)Cl2, Au2(dppe)Cl2, or Au2(dppf)Cl2 with potassium diisopropyldithiophosphate, K[(S-OiPr)2], potassium dicyclohexyldithiophosphate, K[(S-OCy)2], or sodium bis(methimazolyl)borate, Na(S-Mt)2, which afforded air-stable gold(I) complexes. In 1-7, the gold(I) centers adopt a two-coordinated linear geometry and are structurally similar. However, their structural features and antiproliferative properties highly depend upon subtle ligand substituent changes. All complexes were validated by 1H, 13C{1H}, 31P NMR, and IR spectroscopy. The solid-state structures of 1, 2, 3, 6, and 7 were confirmed using single-crystal X-ray diffraction. A density functional theory geometry optimization calculation was used to extract further structural and electronic information. To investigate the possible cytotoxicities of 2, 3, and 7, in vitro cellular tests were carried out on the human cancerous breast cell line MCF-7. 2 and 7 show promising cytotoxicity.
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Affiliation(s)
- Abdollah Neshat
- Department
of Chemistry, Institute for Advanced Studies
in Basic Sciences (IASBS), 444 Prof. Sobouti Blvd., Gava Zang, Zanjan 45137-66731, Iran
| | - Atiyeh Mahdavi
- Department
of Biological Sciences, Institute for Advanced
Studies in Basic Sciences (IASBS), 444 Prof. Sobouti Blvd., Gava Zang, Zanjan 45137-66731, Iran
| | - Mohammad Reza Yousefshahi
- Department
of Chemistry, Institute for Advanced Studies
in Basic Sciences (IASBS), 444 Prof. Sobouti Blvd., Gava Zang, Zanjan 45137-66731, Iran
| | - Mahdi Cheraghi
- Department
of Chemistry, Institute for Advanced Studies
in Basic Sciences (IASBS), 444 Prof. Sobouti Blvd., Gava Zang, Zanjan 45137-66731, Iran
| | - Ali Mousavizadeh Mobarakeh
- Department
of Chemistry, Institute for Advanced Studies
in Basic Sciences (IASBS), 444 Prof. Sobouti Blvd., Gava Zang, Zanjan 45137-66731, Iran
| | - Saiedeh Mohammadi
- Department
of Biological Sciences, Institute for Advanced
Studies in Basic Sciences (IASBS), 444 Prof. Sobouti Blvd., Gava Zang, Zanjan 45137-66731, Iran
| | - Vaclav Eigner
- Institute
of Physics of the Czech Academy of Sciences, Na Slovance 2, 18221 Prague 8, The Czech Republic
| | - Monika Kucerakova
- Institute
of Physics of the Czech Academy of Sciences, Na Slovance 2, 18221 Prague 8, The Czech Republic
| | - Michal Dusek
- Institute
of Physics of the Czech Academy of Sciences, Na Slovance 2, 18221 Prague 8, The Czech Republic
| | - Babak Kaboudin
- Department
of Chemistry, Institute for Advanced Studies
in Basic Sciences (IASBS), 444 Prof. Sobouti Blvd., Gava Zang, Zanjan 45137-66731, Iran
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3
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Kang D, Baek Y, Lee JS. Mechanisms of RNA and Protein Quality Control and Their Roles in Cellular Senescence and Age-Related Diseases. Cells 2022; 11:cells11244062. [PMID: 36552825 PMCID: PMC9777292 DOI: 10.3390/cells11244062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Revised: 12/04/2022] [Accepted: 12/13/2022] [Indexed: 12/23/2022] Open
Abstract
Cellular senescence, a hallmark of aging, is defined as irreversible cell cycle arrest in response to various stimuli. It plays both beneficial and detrimental roles in cellular homeostasis and diseases. Quality control (QC) is important for the proper maintenance of cellular homeostasis. The QC machineries regulate the integrity of RNA and protein by repairing or degrading them, and are dysregulated during cellular senescence. QC dysfunction also contributes to multiple age-related diseases, including cancers and neurodegenerative, muscle, and cardiovascular diseases. In this review, we describe the characters of cellular senescence, discuss the major mechanisms of RNA and protein QC in cellular senescence and aging, and comprehensively describe the involvement of these QC machineries in age-related diseases. There are many open questions regarding RNA and protein QC in cellular senescence and aging. We believe that a better understanding of these topics could propel the development of new strategies for addressing age-related diseases.
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Affiliation(s)
- Donghee Kang
- Research Center for Controlling Intercellular Communication (RCIC), College of Medicine, Inha University, Incheon 22212, Republic of Korea
- Department of Molecular Medicine, College of Medicine, Inha University, Incheon 22212, Republic of Korea
| | - Yurim Baek
- Research Center for Controlling Intercellular Communication (RCIC), College of Medicine, Inha University, Incheon 22212, Republic of Korea
- Department of Molecular Medicine, College of Medicine, Inha University, Incheon 22212, Republic of Korea
- Program in Biomedical Science & Engineering, Inha University, Incheon 22212, Republic of Korea
| | - Jae-Seon Lee
- Research Center for Controlling Intercellular Communication (RCIC), College of Medicine, Inha University, Incheon 22212, Republic of Korea
- Department of Molecular Medicine, College of Medicine, Inha University, Incheon 22212, Republic of Korea
- Program in Biomedical Science & Engineering, Inha University, Incheon 22212, Republic of Korea
- Correspondence: ; Tel.: +82-32-860-9832; Fax: +82-32-885-8302
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4
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Kim L, Lee BG, Kim M, Kim MK, Kwon DH, Kim H, Brötz-Oesterhelt H, Roh SH, Song HK. Structural insights into ClpP protease side exit pore-opening by a pH drop coupled with substrate hydrolysis. EMBO J 2022; 41:e109755. [PMID: 35593068 DOI: 10.15252/embj.2021109755] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2021] [Revised: 04/27/2022] [Accepted: 04/29/2022] [Indexed: 11/09/2022] Open
Abstract
The ClpP serine peptidase is a tetradecameric degradation molecular machine involved in many physiological processes. It becomes a competent ATP-dependent protease when coupled with Clp-ATPases. Small chemical compounds, acyldepsipeptides (ADEPs), are known to cause the dysregulation and activation of ClpP without ATPases and have potential as novel antibiotics. Previously, structural studies of ClpP from various species revealed its structural details, conformational changes, and activation mechanism. Although product release through side exit pores has been proposed, the detailed driving force for product release remains elusive. Herein, we report crystal structures of ClpP from Bacillus subtilis (BsClpP) in unforeseen ADEP-bound states. Cryo-electron microscopy structures of BsClpP revealed various conformational states under different pH conditions. To understand the conformational change required for product release, we investigated the relationship between substrate hydrolysis and the pH-lowering process. The production of hydrolyzed peptides from acidic and basic substrates by proteinase K and BsClpP lowered the pH values. Our data, together with those of previous findings, provide insight into the molecular mechanism of product release by the ClpP self-compartmentalizing protease.
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Affiliation(s)
- Leehyeon Kim
- Department of Life Sciences, Korea University, Seoul, South Korea
| | - Byung-Gil Lee
- Department of Life Sciences, Korea University, Seoul, South Korea
| | - Minki Kim
- Department of Life Sciences, Korea University, Seoul, South Korea
| | - Min Kyung Kim
- Department of Life Sciences, Korea University, Seoul, South Korea
| | - Do Hoon Kwon
- Department of Life Sciences, Korea University, Seoul, South Korea
| | - Hyunmin Kim
- School of Biological Sciences, Institute of Molecular Biology and Genetics, Seoul National University, Seoul, South Korea
| | - Heike Brötz-Oesterhelt
- Department of Microbial Bioactive Compounds, Interfaculty Institute of Microbiology and Infection Medicine, University of Tuebingen, Tuebingen, Germany.,Cluster of Excellence Controlling Microbes to Fight Infection, University of Tuebingen, Tuebingen, Germany
| | - Soung-Hun Roh
- School of Biological Sciences, Institute of Molecular Biology and Genetics, Seoul National University, Seoul, South Korea
| | - Hyun Kyu Song
- Department of Life Sciences, Korea University, Seoul, South Korea
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5
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Costa G, Caputi FF, Serra M, Simola N, Rullo L, Stamatakos S, Sanna F, Germain M, Martinoli MG, Candeletti S, Morelli M, Romualdi P. Activation of Antioxidant and Proteolytic Pathways in the Nigrostriatal Dopaminergic System After 3,4-Methylenedioxymethamphetamine Administration: Sex-Related Differences. Front Pharmacol 2021; 12:713486. [PMID: 34512343 PMCID: PMC8430399 DOI: 10.3389/fphar.2021.713486] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2021] [Accepted: 07/12/2021] [Indexed: 12/29/2022] Open
Abstract
3,4-Methylenedioxymethamphetamine (MDMA, “ecstasy”) is an amphetamine-related drug that may damage the dopaminergic nigrostriatal system. To investigate the mechanisms that sustain this toxic effect and ascertain their sex-dependence, we evaluated in the nigrostriatal system of MDMA-treated (4 × 20 mg/kg, 2 h apart) male and female mice the activity of superoxide dismutase (SOD), the gene expression of SOD type 1 and 2, together with SOD1/2 co-localization with tyrosine hydroxylase (TH)-positive neurons. In the same mice and brain areas, activity of glutathione peroxidase (GPx) and of β2/β5 subunits of the ubiquitin-proteasome system (UPS) were also evaluated. After MDMA, SOD1 increased in striatal TH-positive terminals, but not nigral neurons, of males and females, while SOD2 increased in striatal TH-positive terminals and nigral neurons of males only. Moreover, after MDMA, SOD1 gene expression increased in the midbrain of males and females, whereas SOD2 increased only in males. Finally, MDMA increased the SOD activity in the midbrain of females, without affecting GPx activity, decreased the β2/β5 activities in the striatum of males and the β2 activity in the midbrain of females. These results suggest that the mechanisms of MDMA-induced neurotoxic effects are sex-dependent and dopaminergic neurons of males could be more sensitive to SOD2- and UPS-mediated toxic effects.
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Affiliation(s)
- Giulia Costa
- Department of Biomedical Sciences, Section of Neuroscience, University of Cagliari, Cagliari, Italy
| | - Francesca Felicia Caputi
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum-University of Bologna, Bologna, Italy
| | - Marcello Serra
- Department of Biomedical Sciences, Section of Neuroscience, University of Cagliari, Cagliari, Italy
| | - Nicola Simola
- Department of Biomedical Sciences, Section of Neuroscience, University of Cagliari, Cagliari, Italy
| | - Laura Rullo
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum-University of Bologna, Bologna, Italy
| | - Serena Stamatakos
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum-University of Bologna, Bologna, Italy
| | - Fabrizio Sanna
- Department of Biomedical Sciences, Section of Neuroscience, University of Cagliari, Cagliari, Italy
| | - Marc Germain
- Department of Medical Biology, Université du Québec à Trois-Rivières, Trois-Rivières, QC, Canada.,CERMO-FC UQAM, Québec, QC, Canada
| | - Maria-Grazia Martinoli
- Department of Medical Biology, Université du Québec à Trois-Rivières, Trois-Rivières, QC, Canada.,Department of Psychiatry and Neuroscience, Université Laval and CHU Research Center, Québec, QC, Canada
| | - Sanzio Candeletti
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum-University of Bologna, Bologna, Italy
| | - Micaela Morelli
- Department of Biomedical Sciences, Section of Neuroscience, University of Cagliari, Cagliari, Italy.,National Research Council of Italy, Neuroscience Institute, Cagliari, Italy
| | - Patrizia Romualdi
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum-University of Bologna, Bologna, Italy
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6
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Determination of Proteasomal Unfolding Ability. Methods Mol Biol 2021. [PMID: 34432247 DOI: 10.1007/978-1-0716-1665-9_12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/19/2023]
Abstract
We use an in vitro degradation assay with a model substrate to assess proteasomal unfolding ability. Our substrate has an unstructured region that is the site of ubiquitination, followed by an easy-to-unfold domain and a difficult-to-unfold domain. Degradation proceeds through the unstructured and easy-to-unfold domains, but the difficult-to-unfold domain can be degraded completely or, if the proteasome stalls, can be released as a partially degraded fragment. The ratio between these two possible outcomes allows us to quantify the unfolding ability and determine how processively the proteasome degrades its substrates.
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7
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Ren S, Bian Y, Hou Y, Wang Z, Zuo Z, Liu Z, Teng Y, Fu J, Wang H, Xu Y, Zhang Q, Chen Y, Pi J. The roles of NFE2L1 in adipocytes: Structural and mechanistic insight from cell and mouse models. Redox Biol 2021; 44:102015. [PMID: 34058615 PMCID: PMC8170497 DOI: 10.1016/j.redox.2021.102015] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Revised: 05/07/2021] [Accepted: 05/16/2021] [Indexed: 12/12/2022] Open
Abstract
Adipocytes play pivotal roles in maintaining energy homeostasis by storing lipids in adipose tissue (AT), regulating the flux of lipids between AT and the circulation in response to the body's energy requirements and secreting a variety of hormones, cytokines and other factors. Proper AT development and function ensure overall metabolic health. Nuclear factor erythroid 2-related factor 1 (NFE2L1, also known as NRF1) belongs to the CNC-bZIP family and plays critical roles in regulating a wide range of essential cellular functions and varies stress responses in many cells and tissues. Human and rodent Nfe2l1 genes can be transcribed into multiple splice variants resulting in various protein isoforms, which may be further modified by a variety of post-translational mechanisms. While the long isoforms of NFE2L1 have been established as master regulators of cellular adaptive antioxidant response and proteasome homeostasis, the exact tissue distribution and physiological function of NFE2L1 isoforms, the short isoforms in particular, are still under intense investigation. With regard to key roles of NFE2L1 in adipocytes, emerging data indicates that deficiency of Nfe2l1 results in aberrant adipogenesis and impaired AT functioning. Intriguingly, a single nucleotide polymorphism (SNP) of the human NFE2L1 gene is associated with obesity. In this review, we summarize the most significant findings regarding the specific roles of the multiple isoforms of NFE2L1 in AT formation and function. We highlight that NFE2L1 plays a fundamental regulatory role in the expression of multiple genes that are crucial to AT metabolism and function and thus could be an important target to improve disease states involving aberrant adipose plasticity and lipid homeostasis.
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Affiliation(s)
- Suping Ren
- Program of Environmental Toxicology, School of Public Health, China Medical University. No. 77 Puhe Road, Shenyang North New Area, Shenyang, Liaoning, 110122, China
| | - Yiying Bian
- Program of Environmental Toxicology, School of Public Health, China Medical University. No. 77 Puhe Road, Shenyang North New Area, Shenyang, Liaoning, 110122, China
| | - Yongyong Hou
- Program of Environmental Toxicology, School of Public Health, China Medical University. No. 77 Puhe Road, Shenyang North New Area, Shenyang, Liaoning, 110122, China
| | - Zhendi Wang
- Program of Environmental Toxicology, School of Public Health, China Medical University. No. 77 Puhe Road, Shenyang North New Area, Shenyang, Liaoning, 110122, China
| | - Zhuo Zuo
- Program of Environmental Toxicology, School of Public Health, China Medical University. No. 77 Puhe Road, Shenyang North New Area, Shenyang, Liaoning, 110122, China
| | - Zhiyuan Liu
- Program of Environmental Toxicology, School of Public Health, China Medical University. No. 77 Puhe Road, Shenyang North New Area, Shenyang, Liaoning, 110122, China
| | - Yue Teng
- Department of Hepatopancreatobiliary Surgery, The Forth Affiliated Hospital, Harbin Medical University, Harbin, China
| | - Jingqi Fu
- Program of Environmental Toxicology, School of Public Health, China Medical University. No. 77 Puhe Road, Shenyang North New Area, Shenyang, Liaoning, 110122, China
| | - Huihui Wang
- Group of Chronic Disease and Environmental Genomics, School of Public Health, China Medical University, No. 77 Puhe Road, Shenyang North New Area, Shenyang, Liaoning, 110122, China
| | - Yuanyuan Xu
- Group of Chronic Disease and Environmental Genomics, School of Public Health, China Medical University, No. 77 Puhe Road, Shenyang North New Area, Shenyang, Liaoning, 110122, China
| | - Qiang Zhang
- Gangarosa Department of Environmental Health, Rollins School of Public Health, Emory University, GA, 30322, USA
| | - Yanyan Chen
- The First Affiliated Hospital, China Medical University, No. 155 Nanjing North Road, Heping Area, Shenyang, Liaoning, 110001, China.
| | - Jingbo Pi
- Program of Environmental Toxicology, School of Public Health, China Medical University. No. 77 Puhe Road, Shenyang North New Area, Shenyang, Liaoning, 110122, China.
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8
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Computational Design of Novel Allosteric Inhibitors for Plasmodium falciparum DegP. Molecules 2021; 26:molecules26092742. [PMID: 34066964 PMCID: PMC8141111 DOI: 10.3390/molecules26092742] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Revised: 03/24/2021] [Accepted: 03/31/2021] [Indexed: 11/23/2022] Open
Abstract
The serine protease, DegP exhibits proteolytic and chaperone activities, essential for cellular protein quality control and normal cell development in eukaryotes. The P. falciparum DegP is essential for the parasite survival and required to combat the oscillating thermal stress conditions during the infection, protein quality checks and protein homeostasis in the extra-cytoplasmic compartments, thereby establishing it as a potential target for drug development against malaria. Previous studies have shown that diisopropyl fluorophosphate (DFP) and the peptide SPMFKGV inhibit E. coli DegP protease activity. To identify novel potential inhibitors specific to PfDegP allosteric and the catalytic binding sites, we performed a high throughput in silico screening using Malaria Box, Pathogen Box, Maybridge library, ChEMBL library and the library of FDA approved compounds. The screening helped identify five best binders that showed high affinity to PfDegP allosteric (T0873, T2823, T2801, RJC02337, CD00811) and the catalytic binding site (T0078L, T1524, T2328, BTB11534 and 552691). Further, molecular dynamics simulation analysis revealed RJC02337, BTB11534 as the best hits forming a stable complex. WaterMap and electrostatic complementarity were used to evaluate the novel bio-isosteric chemotypes of RJC02337, that led to the identification of 231 chemotypes that exhibited better binding affinity. Further analysis of the top 5 chemotypes, based on better binding affinity, revealed that the addition of electron donors like nitrogen and sulphur to the side chains of butanoate group are more favoured than the backbone of butanoate group. In a nutshell, the present study helps identify novel, potent and Plasmodium specific inhibitors, using high throughput in silico screening and bio-isosteric replacement, which may be experimentally validated.
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9
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Hsieh FC, Chang LK, Tsai CH, Kuan JE, Wu KF, Wu C, Wu WF. Roles of double-loop (130~159 aa and 175~209 aa) in ClpY(HslU)-I domain for SulA substrate degradation by ClpYQ(HslUV) protease in Escherichia coli. J GEN APPL MICROBIOL 2021; 66:297-306. [PMID: 32435002 DOI: 10.2323/jgam.2019.12.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
An Escherichia coli ATP-dependent two-component protease, ClpYQ(HslUV), targets the SulA molecule, an SOS induced protein. ClpY recognizes, unfolds and translocates the substrates into the proteolytic site of ClpQ for degradation. ClpY is divided into three domains N, I and C. The N domain is an ATPase; the C domain allows for oligomerization, while the I domain coordinates substrate binding. In the ClpYQ complex, two layer pore sites, pore I and II, are in the center of its hexameric rings. However, the actual roles of two outer-loop (130~159 aa, L1 and 175~209 aa, L2) of the ClpY-I domain for the degradation of SulA are unclear. In this study, with ATP, the MBP-SulA molecule was bound to ClpY oligomer(s). ClpYΔL1 (ClpY deleted of loop 1) oligomers revealed an excessive SulA-binding activity. With ClpQ, it showed increased proteolytic activity for SulA degradation. Yet, ClpYΔL2 formed fewer oligomers that retained less proteolytic activity, but still had increased SulA-binding activity. In contrast, ClpYΔpore I had a lower SulA-binding activity. ClpYΔ pore I ΔL2 showed the lowest SulA-binding activity. In addition, ClpY (Q198L, Q200L), with a double point mutation in loop 2, formed stable oligomers. It also had a subtle increase in SulA-binding activity, but displayed less proteolytic activity. As a result, loop 2 has an effect on ClpY oligomerization, substrate binding and delivery. Loop 1 has a role as a gate, to prevent excessive substrate binding. Thus, accordingly, ClpY permits the formation of SulA-ClpY(6x), with ATP(s), and this complex then docks through ClpQ(6x) for ultimate proteolytic degradation.
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Affiliation(s)
- Fan-Ching Hsieh
- Department of Agricultural Chemistry, College of Bio-Resource and Agriculture, National Taiwan University
| | - Lu-Kao Chang
- Department of Agricultural Chemistry, College of Bio-Resource and Agriculture, National Taiwan University
| | - Chih-Hsuan Tsai
- Department of Agricultural Chemistry, College of Bio-Resource and Agriculture, National Taiwan University
| | - Jung-En Kuan
- Department of Agricultural Chemistry, College of Bio-Resource and Agriculture, National Taiwan University
| | - Ke-Feng Wu
- Department of Agricultural Chemistry, College of Bio-Resource and Agriculture, National Taiwan University
| | - Cindy Wu
- Department of Agricultural Chemistry, College of Bio-Resource and Agriculture, National Taiwan University
| | - Whei-Fen Wu
- Department of Agricultural Chemistry, College of Bio-Resource and Agriculture, National Taiwan University
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10
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Hubbell GE, Tepe JJ. Natural product scaffolds as inspiration for the design and synthesis of 20S human proteasome inhibitors. RSC Chem Biol 2020; 1:305-332. [PMID: 33791679 PMCID: PMC8009326 DOI: 10.1039/d0cb00111b] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Accepted: 09/01/2020] [Indexed: 12/13/2022] Open
Abstract
The 20S proteasome is a valuable target for the treatment of a number of diseases including cancer, neurodegenerative disease, and parasitic infection. In an effort to discover novel inhibitors of the 20S proteasome, many reseaarchers have looked to natural products as potential leads for drug discovery. The following review discusses the efforts made in the field to isolate and identify natural products as inhibitors of the proteasome. In addition, we describe some of the modifications made to natural products in order to discover more potent and selective inhibitors for potential disease treatment.
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Affiliation(s)
- Grace E. Hubbell
- Department of Chemistry, Michigan State UniversityEast LansingMI 48823USA
| | - Jetze J. Tepe
- Department of Chemistry, Michigan State UniversityEast LansingMI 48823USA
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11
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The active second-generation proteasome inhibitor oprozomib reverts the oxaliplatin-induced neuropathy symptoms. Biochem Pharmacol 2020; 182:114255. [PMID: 33010214 DOI: 10.1016/j.bcp.2020.114255] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 09/28/2020] [Accepted: 09/28/2020] [Indexed: 02/06/2023]
Abstract
Oxaliplatin-induced neuropathy (OXAIN) is a major adverse effect of this antineoplastic drug, widely used in the treatment of colorectal cancer. Although its molecular mechanisms remain poorly understood, recent evidence suggest that maladaptive neuroplasticity and oxidative stress may participate to the development of this neuropathy. Given the role played on protein remodeling by ubiquitin-proteasome system (UPS) in response to oxidative stress and in neuropathic pain, we investigated whether oxaliplatin might cause alterations in the UPS-mediated degradation pathway, in order to identify new pharmacological tools useful in OXAIN. In a rat model of OXAIN (2.4 mg kg-1 i.p., daily for 10 days), a significant increase in chymotrypsin-(β5) like activity of the constitutive proteasome 26S was observed in the thalamus (TH) and somatosensory cortex (SSCx). In addition, the selective up-regulation of β5 and LMP7 (β5i) subunit gene expression was assessed in the SSCx. Furthermore, this study revealed that oprozomib, a selective β5 subunit proteasome inhibitor, is able to normalize the spinal prodynorphin gene expression upregulation induced by oxaliplatin, as well as to revert mechanical allodynia and thermal hyperalgesia observed in oxaliplatin-treated rats. These results underline the relevant role of UPS in the OXAIN and suggest new pharmacological targets to counteract this severe adverse effect. This preclinical study reveals the involvement of the proteasome in the oxaliplatin-induced neuropathy and adds useful information to better understand the molecular mechanism underlying this pain condition. Moreover, although further evidence is required, these findings suggest that oprozomib could be a therapeutic option to counteract chemotherapy-induced neuropathy.
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Dickson P, Simanski S, Ngundu JM, Kodadek T. Mechanistic Studies of the Multiple Myeloma and Melanoma Cell-Selective Toxicity of the Rpn13-Binding Peptoid KDT-11. Cell Chem Biol 2020; 27:1383-1395.e5. [PMID: 32857986 DOI: 10.1016/j.chembiol.2020.08.008] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Revised: 05/22/2020] [Accepted: 08/07/2020] [Indexed: 12/12/2022]
Abstract
We previously reported a peptoid ligand for the proteasomal ubiquitin receptor Rpn13 called KDT-11 and demonstrated that this compound is toxic to multiple myeloma cells, but not non-malignant cells. Here, we show that KDT-11 decreases the viability of a variety of cancer cell lines, especially melanomas and various blood cancers. The peptoid induces selective G1 cell-cycle arrest, resulting in eventual apoptosis. While KDT-11 does not antagonize any of the known protein-protein interactions involving Rpn13, the peptoid inhibits the ability of Rpn13 to stimulate the activity of an associated deubiquitylase Uch37/UCHL5 in vitro, suggesting a high level of Uch37 activity might be important for cancer cell proliferation. However, a variety of experiments in SK-MEL-5 melanoma cells suggest that KDT-11's cytotoxic effects are mediated by interactions with proteins other than Rpn13.
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Affiliation(s)
- Paige Dickson
- Department of Chemistry, The Scripps Research Institute, 130 Scripps Way, Jupiter, FL 33458, USA
| | - Scott Simanski
- Department of Chemistry, The Scripps Research Institute, 130 Scripps Way, Jupiter, FL 33458, USA
| | - John Maina Ngundu
- Department of Chemistry, The Scripps Research Institute, 130 Scripps Way, Jupiter, FL 33458, USA
| | - Thomas Kodadek
- Department of Chemistry, The Scripps Research Institute, 130 Scripps Way, Jupiter, FL 33458, USA.
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13
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Guzmán-Téllez P, Martínez-Valencia D, Silva-Olivares A, Del Ángel RM, Serrano-Luna J, Shibayama M. Naegleria fowleri and Naegleria gruberi 20S proteasome: identification and characterization. Eur J Cell Biol 2020; 99:151085. [PMID: 32646643 DOI: 10.1016/j.ejcb.2020.151085] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Revised: 04/17/2020] [Accepted: 05/07/2020] [Indexed: 11/26/2022] Open
Abstract
The Naegleria are ubiquitous free-living amoebae and are characterized by the presence of three phases in their biological cycle: trophozoite, cyst and flagellate. Of this genus, only Naegleria fowleri has been reported as pathogenic to humans. The proteasome is a multi-catalytic complex and is considered to be the most important structure responsible for the degradation of intracellular proteins. This structure is related to the maintenance of cellular homeostasis and, in pathogenic microorganisms, to the modulation of their virulence. Until now, the proteasome and its function have not been described for the Naegleria genus. In the current study, using bioinformatic analysis, protein sequences homologous to those reported for the subunits of the 20S proteasome in other organisms were found, and virtual modelling was used to determine their three-dimensional structure. The presence of structural and catalytic subunits of the 20S proteasome was detected by Western and dot blot assays. Its localization was observed by immunofluorescence microscopy to be mainly in the cytoplasm, and a leading role of the chymotrypsin-like catalytic activity was determined using fluorogenic peptidase assays and specific proteasome inhibitors. Finally, the role of the 20S proteasome in the proliferation and differentiation of Naegleria genus trophozoites was demonstrated.
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Affiliation(s)
- Paula Guzmán-Téllez
- Department of Infectomics and Molecular Pathogenesis, Center for Research and Advanced Studies of the National Polytechnic Institute, Av. IPN 2508, 07360 Mexico City, Mexico
| | - Diana Martínez-Valencia
- Department of Infectomics and Molecular Pathogenesis, Center for Research and Advanced Studies of the National Polytechnic Institute, Av. IPN 2508, 07360 Mexico City, Mexico
| | - Angélica Silva-Olivares
- Department of Infectomics and Molecular Pathogenesis, Center for Research and Advanced Studies of the National Polytechnic Institute, Av. IPN 2508, 07360 Mexico City, Mexico
| | - Rosa M Del Ángel
- Department of Infectomics and Molecular Pathogenesis, Center for Research and Advanced Studies of the National Polytechnic Institute, Av. IPN 2508, 07360 Mexico City, Mexico
| | - Jesús Serrano-Luna
- Department of Cell Biology, Center for Research and Advanced Studies of the National Polytechnic Institute, Av. IPN 2508, 07360 Mexico City, Mexico.
| | - Mineko Shibayama
- Department of Infectomics and Molecular Pathogenesis, Center for Research and Advanced Studies of the National Polytechnic Institute, Av. IPN 2508, 07360 Mexico City, Mexico.
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Giletto MB, Osmulski PA, Jones CL, Gaczynska ME, Tepe JJ. Pipecolic esters as minimized templates for proteasome inhibition. Org Biomol Chem 2020; 17:2734-2746. [PMID: 30778435 DOI: 10.1039/c9ob00122k] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Allosteric regulators of clinically important enzymes are gaining popularity as alternatives to competitive inhibitors. This is also the case for the proteasome, a major intracellular protease and a target of anti-cancer drugs. All clinically used proteasome inhibitors bind to the active sites in catalytic chamber and display a competitive mechanism. Unfortunately, inevitable resistance associated with this type of inhibition drives the search for non-competitive agents. The multisubunit and multicatalytic "proteolytic machine" such as the proteasome is occasionally found to be affected by agents with other primary targets. For example the immunosuppressive agent rapamycin has been shown to allosterically inhibit the proteasome albeit at levels far higher than its mTOR related efficacy. As part of an ongoing program to search for novel proteasome-targeting pharmacophores, we identified the binding domain of rapamycin as required for proteasome inhibition even without the macrocyclic context of the parent compound. By subsequent structure-activity relationship studies, we generated a pipecolic ester derivative compound 3 representing a new class of proteasome inhibitors. Compound 3 affects the core proteasome activities and proliferation of cancer cells with low micromolar/high nanomolar efficacy. Molecular modeling, atomic force microscopy imaging and biochemical data suggest that compound 3 binds into one of intersubunit pockets in the proteasomal α ring and destabilizes the α face and the gate. The α face is used as a docking area for proteasome-regulating protein modules and the gate is critical for controlling access to the catalytic chamber. Thus, the pipecolic ester template elicits a new and attractive mechanism for proteasome inhibition distinct from classical competitive drugs.
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Affiliation(s)
- Matthew B Giletto
- Department of Chemistry, Michigan State University, East Lansing, Michigan 48824, USA.
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Panagiotidou E, Chondrogianni N. We Are What We Eat: Ubiquitin–Proteasome System (UPS) Modulation Through Dietary Products. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2020; 1233:329-348. [DOI: 10.1007/978-3-030-38266-7_15] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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16
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Xie SC, Dick LR, Gould A, Brand S, Tilley L. The proteasome as a target for protozoan parasites. Expert Opin Ther Targets 2019; 23:903-914. [PMID: 31679410 DOI: 10.1080/14728222.2019.1685981] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Introduction: The proteasome is a multi-subunit enzyme complex responsible for the turnover of short-lived, abnormal or damaged proteins in eukaryotic cells. As organisms that undergo rapid growth and cell division, protozoan parasites exist on the knife-edge of proteotoxic catastrophe and thus rely heavily on their protein quality control machinery for survival. Because of this, the proteasome has recently emerged as a desirable drug target.Area covered: This review focuses on efforts to identify protozoan parasite-specific proteasome inhibitors using substrate profiling, library screening, and in vitro evolution of resistance approaches to inform medicinal chemistry. Targeting the parasite's 20S proteasome chymotrypsin-like (β5) activity and selectively inhibiting protein turnover in parasites compared to human cells are critical properties of potent, selective inhibitors.Expert opinion: Proteasome inhibitors have the potential for rapid action against all stages, all species and all strains of plasmodium and kinetoplastid parasites. Given the high level of conservation of proteasome active sites in eukaryotes, an important challenge is achieving inhibitors that show sufficient selectivity while maintaining properties consistent with drug development.
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Affiliation(s)
- Stanley C Xie
- Department of Biochemistry and Molecular Biology Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, Australia
| | | | - Alexandra Gould
- Oncology Chemistry, Takeda Pharmaceuticals International Co., Cambridge, MA, USA
| | - Stephen Brand
- Medicines for Malaria Venture, CH-1215 Geneva 15, Switzerland
| | - Leann Tilley
- Department of Biochemistry and Molecular Biology Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, Australia
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17
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Abstract
Proteasomes are multienzyme complexes that maintain protein homeostasis (proteostasis) and important cellular functions through the degradation of misfolded, redundant, and damaged proteins. It is well established that aging is associated with the accumulation of damaged and misfolded proteins. This phenomenon is paralleled by declined proteasome activity. When the accumulation of redundant proteins exceed degradation, undesirable signaling and/or aggregation occurs and are the hallmarks of neurodegenerative diseases and many cancers. Thus, increasing proteasome activity has been recognized as a new approach to delay the onset or ameliorate the symptoms of neurodegenerative and other proteotoxic disorders. Enhancement of proteasome activity has many therapeutic potentials but is still a relatively unexplored field. In this perspective, we review current approaches, genetic manipulation, posttranslational modification, and small molecule proteasome agonists used to increase proteasome activity, challenges facing the field, and applications beyond aging and neurodegenerative diseases.
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Affiliation(s)
- Evert Njomen
- Department of Chemistry, and Pharmacology & Toxicology, Michigan State University, East Lansing, Michigan 48824, United States
| | - Jetze J. Tepe
- Department of Chemistry, and Pharmacology & Toxicology, Michigan State University, East Lansing, Michigan 48824, United States
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18
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Chaves CF, Mazzotti DR, Cendoroglo MS, Ramos LR, Tufik S, Silva VCD, D'Almeida V. Genes related to maintenance of autophagy and successful aging. ARQUIVOS DE NEURO-PSIQUIATRIA 2019; 76:831-839. [PMID: 30698207 DOI: 10.1590/0004-282x20180142] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Accepted: 09/25/2018] [Indexed: 01/11/2023]
Abstract
Considering aging as a phenomenon in which there is a decline in essential processes for cell survival, we investigated the autophagic and proteasome pathways in three different groups: young, older and oldest old male adults. The expression profile of autophagic pathway-related genes was carried out in peripheral blood, and the proteasome quantification was performed in plasma. No significant changes were found in plasma proteasome concentrations or in correlations between proteasome concentrations and ages. However, some autophagy- and/or apoptosis-related genes were differentially expressed. In addition, the network and enrichment analysis showed an interaction between four of the five differentially expressed genes and an association of these genes with the transcriptional process. Considering that the oldest old individuals maintained both the expression of genes linked to the autophagic machinery, and the proteasome levels, when compared with the older group, we concluded that these factors could be considered crucial for successful aging.
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Affiliation(s)
| | - Diego Robles Mazzotti
- Universidade Federal de São Paulo, Departamento de Psicobiologia, São Paulo SP, Brasil
| | | | - Luiz Roberto Ramos
- Universidade Federal de São Paulo, Departamento de Medicina Preventiva, São Paulo SP, Brasil
| | - Sergio Tufik
- Universidade Federal de São Paulo, Departamento de Psicobiologia, São Paulo SP, Brasil
| | | | - Vânia D'Almeida
- Universidade Federal de São Paulo, Departamento de Psicobiologia, São Paulo SP, Brasil
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Kudriaeva AA, Belogurov AA. Proteasome: a Nanomachinery of Creative Destruction. BIOCHEMISTRY (MOSCOW) 2019; 84:S159-S192. [PMID: 31213201 DOI: 10.1134/s0006297919140104] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
In the middle of the 20th century, it was postulated that degradation of intracellular proteins is a stochastic process. More than fifty years of intense studies have finally proven that protein degradation is a very complex and tightly regulated in time and space process that plays an incredibly important role in the vast majority of metabolic pathways. Degradation of more than a half of intracellular proteins is controlled by a hierarchically aligned and evolutionarily perfect system consisting of many components, the main ones being ubiquitin ligases and proteasomes, together referred to as the ubiquitin-proteasome system (UPS). The UPS includes more than 1000 individual components, and most of them are critical for the cell functioning and survival. In addition to the well-known signaling functions of ubiquitination, such as modification of substrates for proteasomal degradation and DNA repair, polyubiquitin (polyUb) chains are involved in other important cellular processes, e.g., cell cycle regulation, immunity, protein degradation in mitochondria, and even mRNA stability. This incredible variety of ubiquitination functions is related to the ubiquitin ability to form branching chains through the ε-amino group of any of seven lysine residues in its sequence. Deubiquitination is accomplished by proteins of the deubiquitinating enzyme family. The second main component of the UPS is proteasome, a multisubunit proteinase complex that, in addition to the degradation of functionally exhausted and damaged proteins, regulates many important cellular processes through controlled degradation of substrates, for example, transcription factors and cyclins. In addition to the ubiquitin-dependent-mediated degradation, there is also ubiquitin-independent degradation, when the proteolytic signal is either an intrinsic protein sequence or shuttle molecule. Protein hydrolysis is a critically important cellular function; therefore, any abnormalities in this process lead to systemic impairments further transforming into serious diseases, such as diabetes, malignant transformation, and neurodegenerative disorders (multiple sclerosis, Alzheimer's disease, Parkinson's disease, Creutzfeldt-Jakob disease and Huntington's disease). In this review, we discuss the mechanisms that orchestrate all components of the UPS, as well as the plurality of the fine-tuning pathways of proteasomal degradation.
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Affiliation(s)
- A A Kudriaeva
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia.
| | - A A Belogurov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia. .,Lomonosov Moscow State University, Moscow, 119991, Russia
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20
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Pilla SP, R B, Bahadur RP. Dissecting protein‐protein interactions in proteasome assembly: Implication to its self‐assembly. J Mol Recognit 2019; 32:e2784. [DOI: 10.1002/jmr.2784] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2018] [Revised: 03/07/2019] [Accepted: 03/19/2019] [Indexed: 01/18/2023]
Affiliation(s)
- Smita P. Pilla
- Computational Structural Biology Laboratory, Department of BiotechnologyIndian Institute of Technology Kharagpur Kharagpur India
| | - Babu R
- Computational Structural Biology Laboratory, Department of BiotechnologyIndian Institute of Technology Kharagpur Kharagpur India
| | - Ranjit P. Bahadur
- Computational Structural Biology Laboratory, Department of BiotechnologyIndian Institute of Technology Kharagpur Kharagpur India
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21
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The HslV Protease from Leishmania major and Its Activation by C-terminal HslU Peptides. Int J Mol Sci 2019; 20:ijms20051021. [PMID: 30813632 PMCID: PMC6429459 DOI: 10.3390/ijms20051021] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Revised: 02/11/2019] [Accepted: 02/20/2019] [Indexed: 12/31/2022] Open
Abstract
HslVU is an ATP-dependent proteolytic complex present in certain bacteria and in the mitochondrion of some primordial eukaryotes, including deadly parasites such as Leishmania. It is formed by the dodecameric protease HslV and the hexameric ATPase HslU, which binds via the C-terminal end of its subunits to HslV and activates it by a yet unclear allosteric mechanism. We undertook the characterization of HslV from Leishmania major (LmHslV), a trypanosomatid that expresses two isoforms for HslU, LmHslU1 and LmHslU2. Using a novel and sensitive peptide substrate, we found that LmHslV can be activated by peptides derived from the C-termini of both LmHslU1 and LmHslU2. Truncations, Ala- and D-scans of the C-terminal dodecapeptide of LmHslU2 (LmC12-U2) showed that five out of the six C-terminal residues of LmHslU2 are essential for binding to and activating HslV. Peptide cyclisation with a lactam bridge allowed shortening of the peptide without loss of potency. Finally, we found that dodecapeptides derived from HslU of other parasites and bacteria are able to activate LmHslV with similar or even higher efficiency. Importantly, using electron microscopy approaches, we observed that the activation of LmHslV was accompanied by a large conformational remodeling, which represents a yet unidentified layer of control of HslV activation.
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Schramm FD, Heinrich K, Thüring M, Bernhardt J, Jonas K. An essential regulatory function of the DnaK chaperone dictates the decision between proliferation and maintenance in Caulobacter crescentus. PLoS Genet 2017; 13:e1007148. [PMID: 29281627 PMCID: PMC5760092 DOI: 10.1371/journal.pgen.1007148] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2017] [Revised: 01/09/2018] [Accepted: 12/11/2017] [Indexed: 11/19/2022] Open
Abstract
Hsp70 chaperones are well known for their important functions in maintaining protein homeostasis during thermal stress conditions. In many bacteria the Hsp70 homolog DnaK is also required for growth in the absence of stress. The molecular reasons underlying Hsp70 essentiality remain in most cases unclear. Here, we demonstrate that DnaK is essential in the α-proteobacterium Caulobacter crescentus due to its regulatory function in gene expression. Using a suppressor screen we identified mutations that allow growth in the absence of DnaK. All mutations reduced the activity of the heat shock sigma factor σ32, demonstrating that the DnaK-dependent inactivation of σ32 is a growth requirement. While most mutations occurred in the rpoH gene encoding σ32, we also identified mutations affecting σ32 activity or stability in trans, providing important new insight into the regulatory mechanisms controlling σ32 activity. Most notably, we describe a mutation in the ATP dependent protease HslUV that induces rapid degradation of σ32, and a mutation leading to increased levels of the house keeping σ70 that outcompete σ32 for binding to the RNA polymerase. We demonstrate that σ32 inhibits growth and that its unrestrained activity leads to an extensive reprogramming of global gene expression, resulting in upregulation of repair and maintenance functions and downregulation of the growth-promoting functions of protein translation, DNA replication and certain metabolic processes. While this re-allocation from proliferative to maintenance functions could provide an advantage during heat stress, it leads to growth defects under favorable conditions. We conclude that Caulobacter has co-opted the DnaK chaperone system as an essential regulator of gene expression under conditions when its folding activity is dispensable. Molecular chaperones of the Hsp70 family belong to the most conserved cellular machineries throughout the tree of life. These proteins play key roles in maintaining protein homeostasis, especially under heat stress conditions. In diverse bacteria the Hsp70 homolog DnaK is essential for growth even in the absence of stress. However, the molecular mechanisms underlying the essential nature of DnaK have in most cases not been studied. We found in the α-proteobacterium Caulobacter crescentus that the function of DnaK as a folding catalyst is dispensable in the absence of stress. Instead, its sole essential function under such conditions is to inhibit the activity of the heat shock sigma factor σ32. Our findings highlight that some bacteria have co-opted chaperones as essential regulators of gene expression under conditions when their folding activity is not required. Furthermore, our work illustrates that essential genes can perform different essential functions in discrete growth conditions.
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Affiliation(s)
- Frederic D. Schramm
- Science for Life Laboratory, Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
- LOEWE Center for Synthetic Microbiology (SYNMIKRO), Philipps University Marburg, Marburg, Germany
| | - Kristina Heinrich
- Science for Life Laboratory, Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
- LOEWE Center for Synthetic Microbiology (SYNMIKRO), Philipps University Marburg, Marburg, Germany
| | - Marietta Thüring
- LOEWE Center for Synthetic Microbiology (SYNMIKRO), Philipps University Marburg, Marburg, Germany
| | - Jörg Bernhardt
- Institute of Microbiology, Ernst-Moritz-Arndt University Greifswald, Greifswald, Germany
| | - Kristina Jonas
- Science for Life Laboratory, Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
- LOEWE Center for Synthetic Microbiology (SYNMIKRO), Philipps University Marburg, Marburg, Germany
- * E-mail:
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Ng’ong’a F, Nyanjom S, Adunga V, Wamunyokoli F. Computational identification of tricorn protease interacting factor 3 in Trypanosoma brucei brucei. ACTA ACUST UNITED AC 2017. [DOI: 10.1093/biohorizons/hzx012] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Affiliation(s)
- Florence Ng’ong’a
- Department of Biochemistry, Jomo Kenyatta University of Agriculture and Technology, P.O. Box 62000-00200, Nairobi, Kenya
- International Centre of Insect Physiology and Ecology (ICIPE), P.O. Box 30772-00100 Nairobi, Kenya
| | - Steven Nyanjom
- Department of Biochemistry, Jomo Kenyatta University of Agriculture and Technology, P.O. Box 62000-00200, Nairobi, Kenya
| | - Vincent Adunga
- International Centre of Insect Physiology and Ecology (ICIPE), P.O. Box 30772-00100 Nairobi, Kenya
- Department of Biochemistry, Egerton University, P.O. Box 536 Njoro, Kenya
| | - Fred Wamunyokoli
- Department of Biochemistry, Jomo Kenyatta University of Agriculture and Technology, P.O. Box 62000-00200, Nairobi, Kenya
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Gaczynska M, Osmulski PA. Targeting Protein-Protein Interactions in the Ubiquitin-Proteasome Pathway. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2017; 110:123-165. [PMID: 29412995 DOI: 10.1016/bs.apcsb.2017.09.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The ubiquitin-proteasome pathway (UPP) is a major venue for controlled intracellular protein degradation in Eukaryota. The machinery of several hundred proteins is involved in recognizing, tagging, transporting, and cleaving proteins, all in a highly regulated manner. Short-lived transcription factors, misfolded translation products, stress-damaged polypeptides, or worn-out long-lived proteins, all can be found among the substrates of UPP. Carefully choreographed protein-protein interactions (PPI) are involved in each step of the pathway. For many of the steps small-molecule inhibitors have been identified and often they directly or indirectly target PPI. The inhibitors may destabilize intracellular proteostasis and trigger apoptosis. So far this is the most explored option used as an anticancer strategy. Alternatively, substrate-specific polyubiquitination may be regulated for a precise intervention aimed at a particular metabolic pathway. This very attractive opportunity is moving close to clinical application. The best known drug target in UPP is the proteasome: the end point of the journey of a protein destined for degradation. The proteasome alone is a perfect object to study the mechanisms and roles of PPI on many levels. This giant protease is built from multisubunit modules and additionally utilizes a service from transient protein ligands, for example, delivering substrates. An elaborate set of PPI within the highest-order proteasome assembly is involved in substrate recognition and processing. Below we will outline PPI involved in the UPP and discuss the growing prospects for their utilization in pharmacological interventions.
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Affiliation(s)
- Maria Gaczynska
- Institute of Biotechnology, University of Texas Health Science Center at San Antonio, San Antonio, TX, United States.
| | - Pawel A Osmulski
- Institute of Biotechnology, University of Texas Health Science Center at San Antonio, San Antonio, TX, United States
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25
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Broekaart DWM, van Scheppingen J, Geijtenbeek KW, Zuidberg MRJ, Anink JJ, Baayen JC, Mühlebner A, Aronica E, Gorter JA, van Vliet EA. Increased expression of (immuno)proteasome subunits during epileptogenesis is attenuated by inhibition of the mammalian target of rapamycin pathway. Epilepsia 2017. [DOI: 10.1111/epi.13823] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Diede W. M. Broekaart
- Department of (Neuro)Pathology; Academic Medical Center; University of Amsterdam; Amsterdam The Netherlands
| | - Jackelien van Scheppingen
- Department of (Neuro)Pathology; Academic Medical Center; University of Amsterdam; Amsterdam The Netherlands
| | - Karlijne W. Geijtenbeek
- Department of (Neuro)Pathology; Academic Medical Center; University of Amsterdam; Amsterdam The Netherlands
| | - Mark R. J. Zuidberg
- Department of (Neuro)Pathology; Academic Medical Center; University of Amsterdam; Amsterdam The Netherlands
| | - Jasper J. Anink
- Department of (Neuro)Pathology; Academic Medical Center; University of Amsterdam; Amsterdam The Netherlands
| | - Johannes C. Baayen
- Department of Neurosurgery; VU University Medical Center; Vrije Universiteit; Amsterdam The Netherlands
| | - Angelika Mühlebner
- Department of (Neuro)Pathology; Academic Medical Center; University of Amsterdam; Amsterdam The Netherlands
| | - Eleonora Aronica
- Department of (Neuro)Pathology; Academic Medical Center; University of Amsterdam; Amsterdam The Netherlands
- Swammerdam Institute for Life Sciences; Center for Neuroscience; University of Amsterdam; Amsterdam The Netherlands
- Stichting Epilepsie Instellingen Nederland (SEIN); Heemstede The Netherlands
| | - Jan A. Gorter
- Swammerdam Institute for Life Sciences; Center for Neuroscience; University of Amsterdam; Amsterdam The Netherlands
| | - Erwin A. van Vliet
- Department of (Neuro)Pathology; Academic Medical Center; University of Amsterdam; Amsterdam The Netherlands
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26
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High-resolution cryo-EM structure of the proteasome in complex with ADP-AlFx. Cell Res 2017; 27:373-385. [PMID: 28106073 DOI: 10.1038/cr.2017.12] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2016] [Revised: 12/05/2016] [Accepted: 12/23/2016] [Indexed: 12/12/2022] Open
Abstract
The 26S proteasome is an ATP-dependent dynamic 2.5 MDa protease that regulates numerous essential cellular functions through degradation of ubiquitinated substrates. Here we present a near-atomic-resolution cryo-EM map of the S. cerevisiae 26S proteasome in complex with ADP-AlFx. Our biochemical and structural data reveal that the proteasome-ADP-AlFx is in an activated state, displaying a distinct conformational configuration especially in the AAA-ATPase motor region. Noteworthy, this map demonstrates an asymmetric nucleotide binding pattern with four consecutive AAA-ATPase subunits bound with nucleotide. The remaining two subunits, Rpt2 and Rpt6, with empty or only partially occupied nucleotide pocket exhibit pronounced conformational changes in the AAA-ATPase ring, which may represent a collective result of allosteric cooperativity of all the AAA-ATPase subunits responding to ATP hydrolysis. This collective motion of Rpt2 and Rpt6 results in an elevation of their pore loops, which could play an important role in substrate processing of proteasome. Our data also imply that the nucleotide occupancy pattern could be related to the activation status of the complex. Moreover, the HbYX tail insertion may not be sufficient to maintain the gate opening of 20S core particle. Our results provide new insights into the mechanisms of nucleotide-driven allosteric cooperativity of the complex and of the substrate processing by the proteasome.
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Cecarini V, Bonfili L, Cuccioloni M, Mozzicafreddo M, Angeletti M, Keller JN, Eleuteri AM. The fine-tuning of proteolytic pathways in Alzheimer's disease. Cell Mol Life Sci 2016; 73:3433-51. [PMID: 27120560 PMCID: PMC11108445 DOI: 10.1007/s00018-016-2238-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2015] [Revised: 03/31/2016] [Accepted: 04/21/2016] [Indexed: 11/28/2022]
Abstract
Several integrated proteolytic systems contribute to the maintenance of cellular homeostasis through the continuous removal of misfolded, aggregated or oxidized proteins and damaged organelles. Among these systems, the proteasome and autophagy play the major role in protein quality control, which is a fundamental issue in non-proliferative cells such as neurons. Disturbances in the functionality of these two pathways are frequently observed in neurodegenerative diseases, like Alzheimer's disease, and reflect the accumulation of protease-resistant, deleterious protein aggregates. In this review, we explored the sophisticated crosstalk between the ubiquitin-proteasome system and autophagy in the removal of the harmful structures that characterize Alzheimer's disease neurons. We also dissected the role of the numerous shuttle factors and chaperones that, directly or indirectly interacting with ubiquitin and LC3, are used for cargo selection and delivery to one pathway or the other.
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Affiliation(s)
- Valentina Cecarini
- Department of Biosciences and Veterinary Medicine, School of Biosciences and Veterinary Medicine, University of Camerino, Via Gentile III da Varano, 62032, Camerino, Italy.
| | - Laura Bonfili
- Department of Biosciences and Veterinary Medicine, School of Biosciences and Veterinary Medicine, University of Camerino, Via Gentile III da Varano, 62032, Camerino, Italy
| | - Massimiliano Cuccioloni
- Department of Biosciences and Veterinary Medicine, School of Biosciences and Veterinary Medicine, University of Camerino, Via Gentile III da Varano, 62032, Camerino, Italy
| | - Matteo Mozzicafreddo
- Department of Biosciences and Veterinary Medicine, School of Biosciences and Veterinary Medicine, University of Camerino, Via Gentile III da Varano, 62032, Camerino, Italy
| | - Mauro Angeletti
- Department of Biosciences and Veterinary Medicine, School of Biosciences and Veterinary Medicine, University of Camerino, Via Gentile III da Varano, 62032, Camerino, Italy
| | - Jeffrey N Keller
- Pennington Biomedical Research Centre, Louisiana State University System, Baton Rouge, LA, 70808, USA
| | - Anna Maria Eleuteri
- Department of Biosciences and Veterinary Medicine, School of Biosciences and Veterinary Medicine, University of Camerino, Via Gentile III da Varano, 62032, Camerino, Italy
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Caputi FF, Carboni L, Mazza D, Candeletti S, Romualdi P. Cocaine and ethanol target 26S proteasome activity and gene expression in neuroblastoma cells. Drug Alcohol Depend 2016; 161:265-75. [PMID: 26922280 DOI: 10.1016/j.drugalcdep.2016.02.012] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/10/2015] [Revised: 01/26/2016] [Accepted: 02/05/2016] [Indexed: 10/22/2022]
Abstract
BACKGROUND Ethanol and cocaine are widely abused drugs triggering long-lasting changes in neuronal circuits and synaptic transmission through the regulation of enzyme activity and gene expression. Compelling evidence indicates that the ubiquitin-proteasome system plays a role in the molecular changes induced by addictive substances, impacting on several mechanisms implicated in abuse. The goal of these studies was to evaluate the effects of cocaine or ethanol on proteasome activity in neuroblastoma cells. Moreover, the gene expression of specific subunits was assessed. METHODS Chymotrypsin-like activity was measured after 2 h, 24 h, and 48 h exposure to 5 μM cocaine or 40 mM ethanol. Proteasome subunit transcripts were evaluated by qPCR at the same time-points. RESULTS Treatments modified proteasome function in opposite directions, since cocaine increased and ethanol reduced chymotrypsin-like activity. Interestingly, we observed gene expression alterations induced by these drugs. In the core particle, the β1 and α5 subunits were mainly up-regulated by cocaine, whereas α6 transcripts were mostly decreased. β2 and β5 did not change. Similarly, ethanol exposure generally increased β1 and α5 mRNAs. Moreover, the β2 subunit was significantly up-regulated by ethanol only. The β5 and α6 subunits were not altered. In the regulatory particle, Rpt3 was increased by cocaine exposure, whereas it was reduced by ethanol. No significant Rpn9 alterations were observed. CONCLUSIONS These findings support the notion that addictive substances regulate proteasome function, contributing to the dysregulations related to drug abuse since the availability of adequate subunit amounts is necessary for proper complex assembly and function.
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Affiliation(s)
- Francesca Felicia Caputi
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum-University of Bologna, Irnerio 48, 40126 Bologna, Italy.
| | - Lucia Carboni
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum-University of Bologna, Irnerio 48, 40126 Bologna, Italy
| | - Daria Mazza
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum-University of Bologna, Irnerio 48, 40126 Bologna, Italy
| | - Sanzio Candeletti
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum-University of Bologna, Irnerio 48, 40126 Bologna, Italy
| | - Patrizia Romualdi
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum-University of Bologna, Irnerio 48, 40126 Bologna, Italy
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Kim HM, Han JW, Chan JY. Nuclear Factor Erythroid-2 Like 1 (NFE2L1): Structure, function and regulation. Gene 2016; 584:17-25. [PMID: 26947393 DOI: 10.1016/j.gene.2016.03.002] [Citation(s) in RCA: 76] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2015] [Revised: 02/18/2016] [Accepted: 03/01/2016] [Indexed: 02/06/2023]
Abstract
Nrf1 (also referred to as NFE2L1) is a member of the CNC-bZIP family of transcription factors that are characterized by a highly conserved CNC-domain, and a basic-leucine zipper domain required for dimerization and DNA binding. Nrf1 is ubiquitously expressed across tissue and cell types as various isoforms, and is induced by stress signals from a broad spectrum of stimuli. Evidence indicates that Nrf1 plays an important role in regulating a range of cellular functions including oxidative stress response, differentiation, inflammatory response, metabolism, and maintaining proteostasis. Thus, Nrf1 has been implicated in the pathogenesis of various disease processes including cancer development, and degenerative and metabolic disorders. This review summarizes our current understanding of Nrf1 and the molecular mechanism underlying its regulation and action in different cellular functions.
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Affiliation(s)
- Hyun Min Kim
- Department of Laboratory Medicine and Pathology, University of California, Irvine, D440 Medical Sciences, Irvine, CA 92697, USA
| | - Jeong Woo Han
- Department of Laboratory Medicine and Pathology, University of California, Irvine, D440 Medical Sciences, Irvine, CA 92697, USA
| | - Jefferson Y Chan
- Department of Laboratory Medicine and Pathology, University of California, Irvine, D440 Medical Sciences, Irvine, CA 92697, USA.
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Papaevgeniou N, Chondrogianni N. UPS Activation in the Battle Against Aging and Aggregation-Related Diseases: An Extended Review. Methods Mol Biol 2016; 1449:1-70. [PMID: 27613027 DOI: 10.1007/978-1-4939-3756-1_1] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Aging is a biological process accompanied by gradual increase of damage in all cellular macromolecules, i.e., nucleic acids, lipids, and proteins. When the proteostasis network (chaperones and proteolytic systems) cannot reverse the damage load due to its excess as compared to cellular repair/regeneration capacity, failure of homeostasis is established. This failure is a major hallmark of aging and/or aggregation-related diseases. Dysfunction of the major cellular proteolytic machineries, namely the proteasome and the lysosome, has been reported during the progression of aging and aggregation-prone diseases. Therefore, activation of these pathways is considered as a possible preventive or therapeutic approach against the progression of these processes. This chapter focuses on UPS activation studies in cellular and organismal models and the effects of such activation on aging, longevity and disease prevention or reversal.
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Affiliation(s)
- Nikoletta Papaevgeniou
- Institute of Biology, Medicinal Chemistry and Biotechnology, National Hellenic Research Foundation, 48 Vassileos Constantinou Ave., Athens, 11635, Greece
| | - Niki Chondrogianni
- Institute of Biology, Medicinal Chemistry and Biotechnology, National Hellenic Research Foundation, 48 Vassileos Constantinou Ave., Athens, 11635, Greece.
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Proteomics in Traditional Chinese Medicine with an Emphasis on Alzheimer's Disease. EVIDENCE-BASED COMPLEMENTARY AND ALTERNATIVE MEDICINE 2015; 2015:393510. [PMID: 26557146 PMCID: PMC4628675 DOI: 10.1155/2015/393510] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/24/2015] [Accepted: 07/27/2015] [Indexed: 12/12/2022]
Abstract
In recent years, there has been an increasing worldwide interest in traditional Chinese medicine (TCM). This increasing demand for TCM needs to be accompanied by a deeper understanding of the mechanisms of action of TCM-based therapy. However, TCM is often described as a concept of Chinese philosophy, which is incomprehensible for Western medical society, thereby creating a gap between TCM and Western medicine (WM). In order to meet this challenge, TCM research has applied proteomics technologies for exploring the mechanisms of action of TCM treatment. Proteomics enables TCM researchers to oversee various pathways that are affected by treatment, as well as the dynamics of their interactions with one another. This review discusses the utility of comparative proteomics to better understand how TCM treatment may be used as a complementary therapy for Alzheimer's disease (AD). Additionally, we review the data from comparative AD-related TCM proteomics studies and establish the relevance of the data with available AD hypotheses, most notably regarding the ubiquitin proteasome system (UPS).
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Chondrogianni N, Voutetakis K, Kapetanou M, Delitsikou V, Papaevgeniou N, Sakellari M, Lefaki M, Filippopoulou K, Gonos ES. Proteasome activation: An innovative promising approach for delaying aging and retarding age-related diseases. Ageing Res Rev 2015; 23:37-55. [PMID: 25540941 DOI: 10.1016/j.arr.2014.12.003] [Citation(s) in RCA: 74] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2014] [Revised: 12/09/2014] [Accepted: 12/15/2014] [Indexed: 11/16/2022]
Abstract
Aging is a natural process accompanied by a progressive accumulation of damage in all constituent macromolecules (nucleic acids, lipids and proteins). Accumulation of damage in proteins leads to failure of proteostasis (or vice versa) due to increased levels of unfolded, misfolded or aggregated proteins and, in turn, to aging and/or age-related diseases. The major cellular proteolytic machineries, namely the proteasome and the lysosome, have been shown to dysfunction during aging and age-related diseases. Regarding the proteasome, it is well established that it can be activated either through genetic manipulation or through treatment with natural or chemical compounds that eventually result to extension of lifespan or deceleration of the progression of age-related diseases. This review article focuses on proteasome activation studies in several species and cellular models and their effects on aging and longevity. Moreover, it summarizes findings regarding proteasome activation in the major age-related diseases as well as in progeroid syndromes.
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Affiliation(s)
- Niki Chondrogianni
- National Hellenic Research Foundation, Institute of Biology, Medicinal Chemistry and Biotechnology, 48 Vas. Constantinou Ave., 116 35 Athens, Greece.
| | - Konstantinos Voutetakis
- National Hellenic Research Foundation, Institute of Biology, Medicinal Chemistry and Biotechnology, 48 Vas. Constantinou Ave., 116 35 Athens, Greece
| | - Marianna Kapetanou
- National Hellenic Research Foundation, Institute of Biology, Medicinal Chemistry and Biotechnology, 48 Vas. Constantinou Ave., 116 35 Athens, Greece
| | - Vasiliki Delitsikou
- National Hellenic Research Foundation, Institute of Biology, Medicinal Chemistry and Biotechnology, 48 Vas. Constantinou Ave., 116 35 Athens, Greece
| | - Nikoletta Papaevgeniou
- National Hellenic Research Foundation, Institute of Biology, Medicinal Chemistry and Biotechnology, 48 Vas. Constantinou Ave., 116 35 Athens, Greece
| | - Marianthi Sakellari
- National Hellenic Research Foundation, Institute of Biology, Medicinal Chemistry and Biotechnology, 48 Vas. Constantinou Ave., 116 35 Athens, Greece; Örebro University, Medical School, Örebro, Sweden
| | - Maria Lefaki
- National Hellenic Research Foundation, Institute of Biology, Medicinal Chemistry and Biotechnology, 48 Vas. Constantinou Ave., 116 35 Athens, Greece
| | - Konstantina Filippopoulou
- National Hellenic Research Foundation, Institute of Biology, Medicinal Chemistry and Biotechnology, 48 Vas. Constantinou Ave., 116 35 Athens, Greece
| | - Efstathios S Gonos
- National Hellenic Research Foundation, Institute of Biology, Medicinal Chemistry and Biotechnology, 48 Vas. Constantinou Ave., 116 35 Athens, Greece; Örebro University, Medical School, Örebro, Sweden.
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Slutskaya E, Artemova N, Kleymenov S, Petrova T, Popov V. Heat-induced conformational changes of TET peptidase from crenarchaeon Desulfurococcus kamchatkensis. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2015. [PMID: 26219412 DOI: 10.1007/s00249-015-1064-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
The effects of heating on the structure and stability of multimeric TET aminopeptidase (APDkam589) were studied by differential scanning calorimetry, tryptophan fluorescence quenching, and dynamic light scattering. Thermally induced structural changes in APDkam589 were found to occur in two phases: local conformational changes, which occur below 70 °C and are not associated with thermal denaturation of the protein, and global structural changes (above 70 °C) induced by irreversible thermal unfolding of the protein accompanied by its spontaneous aggregation. These results may explain the bell-shaped temperature dependence with a maximum at ~70 °C previously observed for enzymatic activity of APDkam589. Interestingly, the thermal unfolding of APDkam589 at about 81.2 °C is accompanied by a so-called blue-shift of about 10 nm-a shift of the Trp fluorescence spectrum toward shorter wavelength. From this point of view, APDkam589 is quite different from most proteins, which are characterized by a long wavelength shift of the spectrum ("red-shift") upon denaturation. The blue-shift of the Trp fluorescence spectrum reflects the changes in the environment of Trp residues, which becomes more hydrophobic upon denaturation. The molecular structure of APDkam589 was determined by X-ray diffraction. The monomer of APDkam589 has six Trp residues, five of which are on the external surface of the dodecamer. Therefore, the blue-shift of the Trp fluorescence spectrum can be explained, at least partly, by aggregation of APDkam589, which occurs simultaneously with its thermal denaturation and probably makes the environment of these Trp residues more hydrophobic.
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Affiliation(s)
- Elvira Slutskaya
- A.N. Bakh Institute of Biochemistry, Russian Academy of Sciences, Leninsky pr. 33, Moscow, 119071, Russian Federation.
| | - Natalia Artemova
- A.N. Bakh Institute of Biochemistry, Russian Academy of Sciences, Leninsky pr. 33, Moscow, 119071, Russian Federation
| | - Sergey Kleymenov
- A.N. Bakh Institute of Biochemistry, Russian Academy of Sciences, Leninsky pr. 33, Moscow, 119071, Russian Federation.,N.K. Koltsov Institute of Developmental Biology, Russian Academy of Sciences, Vavilova str. 26, Moscow, 119334, Russian Federation
| | - Tatiana Petrova
- Institute of Mathematical Problems of Biology, RAS, Institutskaja str., 4, Pushchino, 142290, Russian Federation
| | - Vladimir Popov
- A.N. Bakh Institute of Biochemistry, Russian Academy of Sciences, Leninsky pr. 33, Moscow, 119071, Russian Federation.,Russian National Research Centre "Kurchatov Institute", Akademika Kurchatova sq. 1, Moscow, 123182, Russian Federation
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Pramanik S, Kutzner A, Heese K. 3D Structure, Dimerization Modeling, and Lead Discovery by Ligand-protein Interaction Analysis of p60 Transcription Regulator Protein (p60TRP). Mol Inform 2015; 35:99-108. [DOI: 10.1002/minf.201500035] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2015] [Accepted: 05/20/2015] [Indexed: 12/28/2022]
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Increasing Avermectin Production in Streptomyces avermitilis by Manipulating the Expression of a Novel TetR-Family Regulator and Its Target Gene Product. Appl Environ Microbiol 2015; 81:5157-73. [PMID: 26002902 DOI: 10.1128/aem.00868-15] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2015] [Accepted: 05/18/2015] [Indexed: 11/20/2022] Open
Abstract
Avermectins produced by Streptomyces avermitilis are commercially important anthelmintic agents. The detailed regulatory mechanisms of avermectin biosynthesis remain unclear. Here, we identified SAV3619, a TetR-family transcriptional regulator designated AveT, to be an activator for both avermectin production and morphological differentiation in S. avermitilis. AveT was shown to indirectly stimulate avermectin production by affecting transcription of the cluster-situated activator gene aveR. AveT directly repressed transcription of its own gene (aveT), adjacent gene pepD2 (sav_3620), sav_7490 (designated aveM), and sav_7491 by binding to an 18-bp perfect palindromic sequence (CGAAACGKTKYCGTTTCG, where K is T or G and Y is T or C and where the underlining indicates inverted repeats) within their promoter regions. aveM (which encodes a putative transmembrane efflux protein belonging to the major facilitator superfamily [MFS]), the important target gene of AveT, had a striking negative effect on avermectin production and morphological differentiation. Overexpression of aveT and deletion of aveM in wild-type and industrial strains of S. avermitilis led to clear increases in the levels of avermectin production. In vitro gel-shift assays suggested that C-5-O-B1, the late pathway precursor of avermectin B1, acts as an AveT ligand. Taken together, our findings indicate positive-feedback regulation of aveT expression and avermectin production by a late pathway intermediate and provide the basis for an efficient strategy to increase avermectin production in S. avermitilis by manipulation of AveT and its target gene product, AveM.
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Dogovski C, Xie SC, Burgio G, Bridgford J, Mok S, McCaw JM, Chotivanich K, Kenny S, Gnädig N, Straimer J, Bozdech Z, Fidock DA, Simpson JA, Dondorp AM, Foote S, Klonis N, Tilley L. Targeting the cell stress response of Plasmodium falciparum to overcome artemisinin resistance. PLoS Biol 2015; 13:e1002132. [PMID: 25901609 PMCID: PMC4406523 DOI: 10.1371/journal.pbio.1002132] [Citation(s) in RCA: 221] [Impact Index Per Article: 24.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2014] [Accepted: 03/16/2015] [Indexed: 11/30/2022] Open
Abstract
Successful control of falciparum malaria depends greatly on treatment with artemisinin combination therapies. Thus, reports that resistance to artemisinins (ARTs) has emerged, and that the prevalence of this resistance is increasing, are alarming. ART resistance has recently been linked to mutations in the K13 propeller protein. We undertook a detailed kinetic analysis of the drug responses of K13 wild-type and mutant isolates of Plasmodium falciparum sourced from a region in Cambodia (Pailin). We demonstrate that ART treatment induces growth retardation and an accumulation of ubiquitinated proteins, indicative of a cellular stress response that engages the ubiquitin/proteasome system. We show that resistant parasites exhibit lower levels of ubiquitinated proteins and delayed onset of cell death, indicating an enhanced cell stress response. We found that the stress response can be targeted by inhibiting the proteasome. Accordingly, clinically used proteasome inhibitors strongly synergize ART activity against both sensitive and resistant parasites, including isogenic lines expressing mutant or wild-type K13. Synergy is also observed against Plasmodium berghei in vivo. We developed a detailed model of parasite responses that enables us to infer, for the first time, in vivo parasite clearance profiles from in vitro assessments of ART sensitivity. We provide evidence that the clinical marker of resistance (delayed parasite clearance) is an indirect measure of drug efficacy because of the persistence of unviable parasites with unchanged morphology in the circulation, and we suggest alternative approaches for the direct measurement of viability. Our model predicts that extending current three-day ART treatment courses to four days, or splitting the doses, will efficiently clear resistant parasite infections. This work provides a rationale for improving the detection of ART resistance in the field and for treatment strategies that can be employed in areas with ART resistance. Resistance to artemisinin antimalarial drugs is jeopardizing malaria control. This study shows that proteasome-mediated stress responses can be targeted to overcome artemisinin resistance and suggests alternate therapeutic regimens and monitoring strategies. Resistance to artemisinin antimalarials, some of the most effective antimalarial drugs, has emerged in Southeast Asia, jeopardizing malaria control. We have undertaken a detailed study of artemisinin-sensitive and-resistant strains of Plasmodium falciparum, the parasite responsible for malaria, taken directly from the field in a region where resistance is developing. We compared these strains to lab strains engineered with either mutant or wild-type resistance alleles. We demonstrate that in sensitive P. falciparum, artemisinin induces growth retardation and accumulation of ubiquitinated proteins, indicating that the drugs activate the cellular stress response. Resistant parasites, on the other hand, exhibit reduced protein ubiquitination and delayed onset of cell death following drug exposure. We show that proteasome inhibitors strongly synergize artemisinin activity, offering a means of overcoming artemisinin resistance. We have developed a detailed model of parasite responses and have modelled in vivo clearance profiles. Our data indicate that extending artemisinin treatment from the standard three-day treatment to a four-day treatment will clear resistant parasites, thus preserving the use of this critical therapy in areas experiencing artemisinin resistance.
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Affiliation(s)
- Con Dogovski
- Department of Biochemistry and Molecular Biology and ARC Centre of Excellence for Coherent X-ray Science, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, Victoria, Australia
| | - Stanley C Xie
- Department of Biochemistry and Molecular Biology and ARC Centre of Excellence for Coherent X-ray Science, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, Victoria, Australia
| | - Gaetan Burgio
- John Curtin School of Medical Research, the Australian National University, Canberra, Australian Capital Territory, Australia; Australian School of Advanced Medicine, Macquarie University, Sydney, New South Wales, Australia
| | - Jess Bridgford
- Department of Biochemistry and Molecular Biology and ARC Centre of Excellence for Coherent X-ray Science, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, Victoria, Australia
| | - Sachel Mok
- School of Biological Sciences, Nanyang Technological University, Singapore
| | - James M McCaw
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, University of Melbourne, Parkville, Victoria, Australia; Murdoch Childrens Research Institute, Royal Childrens Hospital, Victoria, Australia
| | | | - Shannon Kenny
- Department of Biochemistry and Molecular Biology and ARC Centre of Excellence for Coherent X-ray Science, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, Victoria, Australia
| | - Nina Gnädig
- Department of Microbiology and Immunology, Columbia University Medical Center, New York, New York, United States of America
| | - Judith Straimer
- Department of Microbiology and Immunology, Columbia University Medical Center, New York, New York, United States of America
| | - Zbynek Bozdech
- School of Biological Sciences, Nanyang Technological University, Singapore
| | - David A Fidock
- Department of Microbiology and Immunology, Columbia University Medical Center, New York, New York, United States of America; Division of Infectious Diseases, Department of Medicine, Columbia University Medical Center, New York, New York, United States of America
| | - Julie A Simpson
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, University of Melbourne, Parkville, Victoria, Australia
| | - Arjen M Dondorp
- Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand; Centre for Tropical Medicine, Nuffield Department of Clinical Medicine, Oxford, United Kingdom
| | - Simon Foote
- John Curtin School of Medical Research, the Australian National University, Canberra, Australian Capital Territory, Australia
| | - Nectarios Klonis
- Department of Biochemistry and Molecular Biology and ARC Centre of Excellence for Coherent X-ray Science, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, Victoria, Australia
| | - Leann Tilley
- Department of Biochemistry and Molecular Biology and ARC Centre of Excellence for Coherent X-ray Science, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, Victoria, Australia
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Gaczynska M, Osmulski PA. Harnessing proteasome dynamics and allostery in drug design. Antioxid Redox Signal 2014; 21:2286-301. [PMID: 24410482 PMCID: PMC4241894 DOI: 10.1089/ars.2013.5816] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/30/2013] [Accepted: 01/12/2014] [Indexed: 12/14/2022]
Abstract
SIGNIFICANCE The proteasome is the essential protease that is responsible for regulated cleavage of the bulk of intracellular proteins. Its central role in cellular physiology has been exploited in therapies against aggressive cancers where proteasome-specific competitive inhibitors that block proteasome active centers are very effectively used. However, drugs regulating this essential protease are likely to have broader clinical usefulness. The non-catalytic sites of the proteasome emerge as an attractive alternative target in search of highly specific and diverse proteasome regulators. RECENT ADVANCES Crystallographic models of the proteasome leave the false impression of fixed structures with minimal molecular dynamics lacking long-distance allosteric signaling. However, accumulating biochemical and structural observations strongly support the notion that the proteasome is regulated by precise allosteric interactions arising from protein dynamics, encouraging the active search for allosteric regulators. Here, we discuss properties of several promising compounds that affect substrate gating and processing in antechambers, and interactions of the catalytic core with regulatory proteins. CRITICAL ISSUES Given the structural complexity of proteasome assemblies, it is a painstaking process to better understand their allosteric regulation and molecular dynamics. Here, we discuss the challenges and achievements in this field. We place special emphasis on the role of atomic force microscopy imaging in probing the allostery and dynamics of the proteasome, and in dissecting the mechanisms involving small-molecule allosteric regulators. FUTURE DIRECTIONS New small-molecule allosteric regulators may become a next generation of drugs targeting the proteasome, which is critical to the development of new therapies in cancers and other diseases.
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Affiliation(s)
- Maria Gaczynska
- Department of Molecular Medicine, Institute of Biotechnology, University of Texas Health Science Center at San Antonio , San Antonio, Texas
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Appolaire A, Durá MA, Ferruit M, Andrieu JP, Godfroy A, Gribaldo S, Franzetti B. The TET2 and TET3 aminopeptidases fromPyrococcus horikoshiiform a hetero-subunit peptidasome with enhanced peptide destruction properties. Mol Microbiol 2014; 94:803-14. [DOI: 10.1111/mmi.12775] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/25/2014] [Indexed: 11/28/2022]
Affiliation(s)
- Alexandre Appolaire
- Univ. Grenoble Alpes; Institut de Biologie Structurale (IBS); F-38027 Grenoble France
- CNRS, IBS; F-38027 Grenoble France
- CEA, DSV, IBS; F-38027 Grenoble France
| | - M. Asunción Durá
- Univ. Grenoble Alpes; Institut de Biologie Structurale (IBS); F-38027 Grenoble France
- CNRS, IBS; F-38027 Grenoble France
- CEA, DSV, IBS; F-38027 Grenoble France
| | - Mylène Ferruit
- Univ. Grenoble Alpes; Institut de Biologie Structurale (IBS); F-38027 Grenoble France
- CNRS, IBS; F-38027 Grenoble France
- CEA, DSV, IBS; F-38027 Grenoble France
| | - Jean-Pierre Andrieu
- Univ. Grenoble Alpes; Institut de Biologie Structurale (IBS); F-38027 Grenoble France
- CNRS, IBS; F-38027 Grenoble France
- CEA, DSV, IBS; F-38027 Grenoble France
| | - Anne Godfroy
- Ifremer, UMR6197; Laboratoire de Microbiologie des Environnements Extrêmes; 29280 Plouzané France
| | - Simonetta Gribaldo
- Institut Pasteur; Unité Biologie Moléculaire du Gène chez les Extremophiles; Département de Microbiologie; 75724 Paris Cedex 15 France
| | - Bruno Franzetti
- Univ. Grenoble Alpes; Institut de Biologie Structurale (IBS); F-38027 Grenoble France
- CNRS, IBS; F-38027 Grenoble France
- CEA, DSV, IBS; F-38027 Grenoble France
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Pramanik S, Kutzner A, Heese K. Lead discovery and in silico 3D structure modeling of tumorigenic FAM72A (p17). Tumour Biol 2014; 36:239-49. [PMID: 25234718 DOI: 10.1007/s13277-014-2620-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2014] [Accepted: 09/09/2014] [Indexed: 12/30/2022] Open
Abstract
FAM72A (p17) is a novel neuronal protein that has been linked to tumorigenic effects in non-neuronal tissue. Using state of the art in silico physicochemical analyses (e.g., I-TASSER, RaptorX, and Modeller), we determined the three-dimensional (3D) protein structure of FAM72A and further identified potential ligand-protein interactions. Our data indicate a Zn(2+)/Fe(3+)-containing 3D protein structure, based on a 3GA3_A model template, which potentially interacts with the organic molecule RSM ((2s)-2-(acetylamino)-N-methyl-4-[(R)-methylsulfinyl] butanamide). The discovery of RSM may serve as potential lead for further anti-FAM72A drug screening tests in the pharmaceutical industry because interference with FAM72A's activities via RSM-related molecules might be a novel option to influence the tumor suppressor protein p53 signaling pathways for the treatment of various types of cancers.
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Affiliation(s)
- Subrata Pramanik
- Graduate School of Biomedical Science and Engineering, Hanyang University, 222 Wangsimni-ro, Seongdong-gu, Seoul, 133-791, Republic of Korea
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40
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Shi X, Yan L, Zhang H, Sun K, Chang Z, Fu X. Differential degradation for small heat shock proteins IbpA and IbpB is synchronized in Escherichia coli: Implications for their functional cooperation in substrate refolding. Biochem Biophys Res Commun 2014; 452:402-7. [DOI: 10.1016/j.bbrc.2014.08.084] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2014] [Accepted: 08/18/2014] [Indexed: 11/30/2022]
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Ando R, Noda K, Tomaru U, Kamoshita M, Ozawa Y, Notomi S, Hisatomi T, Noda M, Kanda A, Ishibashi T, Kasahara M, Ishida S. Decreased proteasomal activity causes photoreceptor degeneration in mice. Invest Ophthalmol Vis Sci 2014; 55:4682-90. [PMID: 24994871 DOI: 10.1167/iovs.13-13272] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
PURPOSE To study the retinal degeneration caused by decreased proteasomal activity in β5t transgenic (β5t-Tg) mice, an animal model of senescence acceleration. METHODS β5t-Tg mice and age-matched littermate control (WT) mice were used. Proteasomal activities and protein level of poly-ubiquitinated protein in retinal extracts were quantified. Fundus images of β5t-Tg mice were taken and their features were assessed. For histologic evaluation, the thicknesses of inner nuclear layer (INL), outer nuclear layer (ONL), and photoreceptor outer segment (OS) were measured. For functional analysis, ERG was recorded under scotopic and photopic illumination conditions. Immunofluorescence (IF) staining and TUNEL were performed to investigate the mechanism of photoreceptor degeneration. RESULTS Chymotrypsin-like activity was partially suppressed in retinal tissues of β5t-Tg mice. Retinal degenerative changes with arterial attenuation were present in β5t-Tg, but not in WT mice. Inner nuclear layer thickness showed no significant change between β5t-Tg and WT mice at 1, 3, 6, and 9 months of age. By contrast, thicknesses of ONL and OS in β5t-Tg mice were significantly decreased at 3, 6, and 9 months compared with those in WT mice. Electroretinograms showed decrease of scotopic a-wave amplitude in β5t-Tg mice. The number of TUNEL-positive cells in ONL were significantly increased in β5t-Tg mice and colocalized with apoptosis-inducing factor, but not with cleaved caspase-3 and -9, indicating that the photoreceptor cell death was induced via a caspase-independent pathway. CONCLUSIONS The current data showed that impaired proteasomal function causes photoreceptor degeneration.
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Affiliation(s)
- Ryo Ando
- Laboratory of Ocular Cell Biology & Visual Science, Hokkaido University Graduate School of Medicine, Sapporo, Japan Department of Ophthalmology, Hokkaido University Graduate School of Medicine, Sapporo, Japan
| | - Kousuke Noda
- Laboratory of Ocular Cell Biology & Visual Science, Hokkaido University Graduate School of Medicine, Sapporo, Japan Department of Ophthalmology, Hokkaido University Graduate School of Medicine, Sapporo, Japan
| | - Utano Tomaru
- Department of Pathology, Hokkaido University Graduate School of Medicine, Sapporo, Japan
| | - Mamoru Kamoshita
- Department of Ophthalmology, Keio University School of Medicine, Tokyo, Japan
| | - Yoko Ozawa
- Department of Ophthalmology, Keio University School of Medicine, Tokyo, Japan
| | - Shoji Notomi
- Department of Ophthalmology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Toshio Hisatomi
- Department of Ophthalmology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Mika Noda
- Department of Ophthalmology, Hokkaido University Graduate School of Medicine, Sapporo, Japan
| | - Atsuhiro Kanda
- Laboratory of Ocular Cell Biology & Visual Science, Hokkaido University Graduate School of Medicine, Sapporo, Japan Department of Ophthalmology, Hokkaido University Graduate School of Medicine, Sapporo, Japan
| | - Tatsuro Ishibashi
- Department of Ophthalmology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Masanori Kasahara
- Department of Pathology, Hokkaido University Graduate School of Medicine, Sapporo, Japan
| | - Susumu Ishida
- Laboratory of Ocular Cell Biology & Visual Science, Hokkaido University Graduate School of Medicine, Sapporo, Japan Department of Ophthalmology, Hokkaido University Graduate School of Medicine, Sapporo, Japan
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Chondrogianni N, Sakellari M, Lefaki M, Papaevgeniou N, Gonos ES. Proteasome activation delays aging in vitro and in vivo. Free Radic Biol Med 2014; 71:303-320. [PMID: 24681338 DOI: 10.1016/j.freeradbiomed.2014.03.031] [Citation(s) in RCA: 63] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/30/2014] [Revised: 03/18/2014] [Accepted: 03/18/2014] [Indexed: 02/02/2023]
Abstract
Aging is a natural biological process that is characterized by a progressive accumulation of macromolecular damage. In the proteome, aging is accompanied by decreased protein homeostasis and function of the major cellular proteolytic systems, leading to the accumulation of unfolded, misfolded, or aggregated proteins. In particular, the proteasome is responsible for the removal of normal as well as damaged or misfolded proteins. Extensive work during the past several years has clearly demonstrated that proteasome activation by either genetic means or use of compounds significantly retards aging. Importantly, this represents a common feature across evolution, thereby suggesting proteasome activation to be an evolutionarily conserved mechanism of aging and longevity regulation. This review article reports on the means of function of these proteasome activators and how they regulate aging in various species.
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Affiliation(s)
- Niki Chondrogianni
- National Hellenic Research Foundation, Institute of Biology, Medicinal Chemistry, and Biotechnology, 116 35 Athens, Greece.
| | - Marianthi Sakellari
- National Hellenic Research Foundation, Institute of Biology, Medicinal Chemistry, and Biotechnology, 116 35 Athens, Greece; Örebro University Medical School, Örebro, Sweden
| | - Maria Lefaki
- National Hellenic Research Foundation, Institute of Biology, Medicinal Chemistry, and Biotechnology, 116 35 Athens, Greece
| | - Nikoletta Papaevgeniou
- National Hellenic Research Foundation, Institute of Biology, Medicinal Chemistry, and Biotechnology, 116 35 Athens, Greece
| | - Efstathios S Gonos
- National Hellenic Research Foundation, Institute of Biology, Medicinal Chemistry, and Biotechnology, 116 35 Athens, Greece; Örebro University Medical School, Örebro, Sweden
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43
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General Characteristics and Important Model Organisms. ARCHAEA-AN INTERNATIONAL MICROBIOLOGICAL JOURNAL 2014. [DOI: 10.1128/9781555815516.ch2] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Mbang-Benet DE, Sterkers Y, Morelle C, Kebe NM, Crobu L, Portalès P, Coux O, Hernandez JF, Meghamla S, Pagès M, Bastien P. The bacterial-like HslVU protease complex subunits are involved in the control of different cell cycle events in trypanosomatids. Acta Trop 2014; 131:22-31. [PMID: 24299926 DOI: 10.1016/j.actatropica.2013.11.017] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2013] [Revised: 11/16/2013] [Accepted: 11/21/2013] [Indexed: 02/08/2023]
Abstract
The trypanosomatid parasites Leishmania and Trypanosoma are responsible for the most important WHO-designated neglected tropical diseases, for which the need for cost-effective new drugs is urgent. In addition to the classical eukaryotic 20S and 26S proteasomes, these unconventional eukaryotes possess a bacterial-like protease complex, HslVU, made of proteolytic (HslV) and regulatory (HslU) subunits. In trypanosomatids, two paralogous genes are co-expressed: HslU1 and HslU2. Conflicting reports have been published with respect to subcellular localization, functional redundancy and putative roles of the different subunits of this complex in trypanosomatids. Here, we definitively established the mitochondrial localization of HslVU in L. major procyclic promastigotes and of HslV in T. brucei bloodstream trypomastigotes, the latter being the form responsible for the disease in the mammalian host. Moreover, our data demonstrate for the first time the essential nature of HslVU in the bloodstream trypomastigotes of T. brucei, in spite of mitochondrial repression at this stage. Interestingly, our work also allows distinguishing a specific role for the different members of the complex, as HslV and HslU1 appear to be involved in the control of different cell cycle events. Finally, these data validate HslVU as a promising drug target against these parasitic diseases of wide medical and economical importance.
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Broad-spectrum antimalarial activity of peptido sulfonyl fluorides, a new class of proteasome inhibitors. Antimicrob Agents Chemother 2013; 57:3576-84. [PMID: 23689711 DOI: 10.1128/aac.00742-12] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Despite declining numbers of cases and deaths, malaria remains a major public health problem in many parts of the world. Today, case management relies heavily on a single class of antimalarial compounds: artemisinins. Hence, development of resistance against artemisinins may destroy current malaria control strategies. Beyond malaria control are elimination and eradication programs that will require drugs with good activity against acute infection but also with preventive and transmission-blocking properties. Consequently, new antimalarials are needed not only to ensure malaria control but also for elimination and eradication efforts. In this study, we introduce peptido sulfonyl fluorides (PSF) as a new class of compounds with antiplasmodial activity. We show that PSF target the plasmodial proteasome and act on all asexual stages of the intraerythrocytic cycle and on gametocytes. PSF showed activities at concentrations as low as 20 nM against multidrug-resistant and chloroquine-sensitive Plasmodium falciparum laboratory strains and clinical isolates from Gabon. Structural requirements for activity were identified, and cytotoxicity in human HeLa or HEK 293 cells was low. The lead PSF PW28 suppressed growth of Plasmodium berghei in vivo but showed signs of toxicity in mice. Considering their modular structure and broad spectrum of activity against different stages of the plasmodial life cycle, proteasome inhibitors based on PSF have a great potential for further development as preclinical candidate compounds with improved species-specific activity and less toxicity.
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Volkov A, Hagner S, Löser S, Alnahas S, Raifer H, Hellhund A, Garn H, Steinhoff U. β5i subunit deficiency of the immunoproteasome leads to reduced Th2 response in OVA induced acute asthma. PLoS One 2013; 8:e60565. [PMID: 23593249 PMCID: PMC3617144 DOI: 10.1371/journal.pone.0060565] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2012] [Accepted: 02/27/2013] [Indexed: 11/22/2022] Open
Abstract
The immunoproteasome subunit β5i has been shown to play an important role in Th1/Th17 driven models of colitis and arthritis. However, the function of β5i in Th2 dependent diseases remains enigmatic. To study the role of β5i in Th2-driven pathology, β5i knockout (KO) and control mice were tested in different models of experimental allergic asthma. β5i-deficient mice showed reduced OVA/Alum- and subcutaneous/OVA-induced acute asthma with decreased eosinophilia in the bronchoalveolar lavage (BAL), low OVA-specific IgG1 and reduced local and systemic Th2 cytokines. While Th2 cells in the lungs were reduced, Tregs and Th1 cells were not affected. Attenuated asthma in β5i KO mice could not be attributed to defects in OVA uptake or maturation of dendritic cells in the lung. Surprisingly, β5i deficient mice developed HDM asthma which was comparable to control mice. Here, we present novel evidence for the requirement of the β5i immunosubunit to generate a strong Th2 response during OVA- but not HDM-induced acute asthma. The unexpected role of β5i in OVA asthma remains to be clarified.
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Affiliation(s)
- Anton Volkov
- Institute for Medical Microbiology and Hygiene, Philipps University of Marburg, Marburg, Germany
| | - Stefanie Hagner
- Institute for Laboratory Medicine and Pathobiochemistry, Philipps University of Marburg, Marburg, Germany
| | - Stephan Löser
- Institute for Medical Microbiology and Hygiene, Philipps University of Marburg, Marburg, Germany
| | - Safa Alnahas
- Institute for Medical Microbiology and Hygiene, Philipps University of Marburg, Marburg, Germany
| | - Hartmann Raifer
- Institute for Medical Microbiology and Hygiene, Philipps University of Marburg, Marburg, Germany
| | - Anne Hellhund
- Institute for Medical Microbiology and Hygiene, Philipps University of Marburg, Marburg, Germany
| | - Holger Garn
- Institute for Laboratory Medicine and Pathobiochemistry, Philipps University of Marburg, Marburg, Germany
| | - Ulrich Steinhoff
- Institute for Medical Microbiology and Hygiene, Philipps University of Marburg, Marburg, Germany
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Höhn A, König J, Grune T. Protein oxidation in aging and the removal of oxidized proteins. J Proteomics 2013; 92:132-59. [PMID: 23333925 DOI: 10.1016/j.jprot.2013.01.004] [Citation(s) in RCA: 154] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2012] [Accepted: 01/08/2013] [Indexed: 12/12/2022]
Abstract
Reactive oxygen species (ROS) are generated constantly within cells at low concentrations even under physiological conditions. During aging the levels of ROS can increase due to a limited capacity of antioxidant systems and repair mechanisms. Proteins are among the main targets for oxidants due to their high rate constants for several reactions with ROS and their abundance in biological systems. Protein damage has an important influence on cellular viability since most protein damage is non-repairable, and has deleterious consequences on protein structure and function. In addition, damaged and modified proteins can form cross-links and provide a basis for many senescence-associated alterations and may contribute to a range of human pathologies. Two proteolytic systems are responsible to ensure the maintenance of cellular functions: the proteasomal (UPS) and the lysosomal system. Those degrading systems provide a last line of antioxidative protection, removing irreversible damaged proteins and recycling amino acids for the continuous protein synthesis. But during aging, both systems are affected and their proteolytic activity declines significantly. Here we highlight the recent advantages in the understanding of protein oxidation and the fate of these damaged proteins during aging. This article is part of a Special Issue entitled: Posttranslational Protein modifications in biology and Medicine.
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Affiliation(s)
- Annika Höhn
- Department of Nutritional Toxicology, Institute of Nutrition, Friedrich Schiller University Jena, 07743 Jena, Germany
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Huber R. “Wie ich zur Proteaseforschung kam oder, richtiger gesagt, wie die Proteaseforschung zu mir kam”. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201205629] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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49
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Gambogic Acid Is a Tissue-Specific Proteasome Inhibitor In Vitro and In Vivo. Cell Rep 2013; 3:211-22. [DOI: 10.1016/j.celrep.2012.11.023] [Citation(s) in RCA: 71] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2012] [Revised: 06/13/2012] [Accepted: 11/27/2012] [Indexed: 01/09/2023] Open
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Abstract
Proteasomes are ATP-dependent protein degradation machines present in all archaea and eukaryotes, and found in several bacterial species of the order Actinomycetales. Mycobacterium tuberculosis (Mtb), an Actinomycete pathogenic to humans, requires proteasome function to cause disease. In this chapter, we describe what is currently understood about the biochemistry of the Mtb proteasome and its role in virulence. The characterization of the Mtb proteasome has led to the discovery that proteins can be targeted for degradation by a small protein modifier in bacteria as they are in eukaryotes. Furthermore, the understanding of proteasome function in Mtb has helped reveal new insight into how the host battles infections.
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Affiliation(s)
- Marie I Samanovic
- Department of Microbiology, New York University School of Medicine, 550 First Avenue, MSB 236, New York, NY, 10016, USA
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