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Negi S, Khurana N, Duggal N. The misfolding mystery: α-synuclein and the pathogenesis of Parkinson's disease. Neurochem Int 2024; 177:105760. [PMID: 38723900 DOI: 10.1016/j.neuint.2024.105760] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Revised: 05/02/2024] [Accepted: 05/06/2024] [Indexed: 05/12/2024]
Abstract
Neurodegenerative diseases such as Parkinson's disease (PD) are characterized by the death of neurons in specific areas of the brain. One of the proteins that is involved in the pathogenesis of PD is α-synuclein (α-syn). α-Syn is a normal protein that is found in all neurons, but in PD, it misfolds and aggregates into toxic fibrils. These fibrils can then coalesce into pathological inclusions, such as Lewy bodies and Lewy neurites. The pathogenic pathway of PD is thought to involve a number of steps, including misfolding and aggregation of α-syn, mitochondrial dysfunction, protein clearance impairment, neuroinflammation and oxidative stress. A deeper insight into the structure of α-syn and its fibrils could aid in understanding the disease's etiology. The prion-like nature of α-syn is also an important area of research. Prions are misfolded proteins that can spread from cell to cell, causing other proteins to misfold as well. It is possible that α-syn may behave in a similar way, spreading from cell to cell and causing a cascade of misfolding and aggregation. Various post-translational alterations have also been observed to play a role in the pathogenesis of PD. These alterations can involve a variety of nuclear and extranuclear activities, and they can lead to the misfolding and aggregation of α-syn. A better understanding of the pathogenic pathway of PD could lead to the development of new therapies for the treatment of this disease.
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Affiliation(s)
- Samir Negi
- School of Pharmaceutical Sciences, Lovely Professional University, Jalandhar-Delhi, G.T. Road, Phagwara, Punjab, 144411, India
| | - Navneet Khurana
- School of Pharmaceutical Sciences, Lovely Professional University, Jalandhar-Delhi, G.T. Road, Phagwara, Punjab, 144411, India
| | - Navneet Duggal
- School of Pharmaceutical Sciences, Lovely Professional University, Jalandhar-Delhi, G.T. Road, Phagwara, Punjab, 144411, India.
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2
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Rodzik A, Railean V, Pomastowski P, Buszewski B, Szumski M. Immobilized enzyme microreactors for analysis of tryptic peptides in β-casein and β-lactoglobulin. Sci Rep 2023; 13:16551. [PMID: 37783762 PMCID: PMC10545664 DOI: 10.1038/s41598-023-43521-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Accepted: 09/25/2023] [Indexed: 10/04/2023] Open
Abstract
In this study, our primary objective was to develop an effective analytical method for studying trypsin-digested peptides of two proteins commonly found in cow's milk: β-casein (βCN) and β-lactoglobulin (βLG). To achieve this, we employed two distinct approaches: traditional in-gel protein digestion and protein digestion using immobilized enzyme microreactors (μ-IMER). Both methods utilized ZipTip pipette tips filled with C18 reverse phase media for sample concentration. The μ-IMER was fabricated through a multi-step process that included preconditioning the capillary, modifying its surface, synthesizing a monolithic support, and further surface modification. Its performance was evaluated under HPLC chromatography conditions using a small-molecule trypsin substrate (BAEE). Hydrolysates from both digestion methods were analyzed using MALDI-TOF MS. Our findings indicate that the μ-IMER method demonstrated superior sequence coverage for oxidized molecules in βCN (33 ± 1.5%) and βLG (65 ± 3%) compared to classical in-gel digestion (20 ± 2% for βCN; 49 ± 2% for βLG). The use of ZipTips further improved sequence coverage in both classical in-gel digestion (26 ± 1% for βCN; 60 ± 4% for βLG) and μ-IMER (41 ± 3% for βCN; 80 ± 5% for βLG). Additionally, phosphorylations were identified. For βCN, no phosphorylation was detected using classical digestion, but the use of ZipTips showed a value of 27 ± 4%. With μ-IMER and μ-IMER-ZipTip, the values increased to 30 ± 2% and 33 ± 1%, respectively. For βLG, the use of ZipTip enabled the detection of a higher percentage of modified peptides in both classical (79 ± 2%) and μ-IMER (79 ± 4%) digestions. By providing a comprehensive comparison of traditional in-gel digestion and μ-IMER methods, this study offers valuable insights into the advantages and limitations of each approach, particularly in the context of complex biological samples. The findings set a new benchmark in protein digestion and analysis, highlighting the potential of μ-IMER systems for enhanced sequence coverage and post-translational modification detection.
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Affiliation(s)
- Agnieszka Rodzik
- Centre for Modern Interdisciplinary Technologies, Nicolaus Copernicus University in Toruń, Wileńska 4, 87-100, Toruń, Poland.
- Department of Environmental Chemistry and Bioanalysis, Faculty of Chemistry, Nicolaus Copernicus University in Toruń, Gagarina 7, 87-100, Toruń, Poland.
| | - Viorica Railean
- Centre for Modern Interdisciplinary Technologies, Nicolaus Copernicus University in Toruń, Wileńska 4, 87-100, Toruń, Poland
- Department of Infectious, Invasive Diseases and Veterinary Administration, Institute of Veterinary Medicine, Nicolaus Copernicus University in Torun, Gagarina 7, 87-100, Toruń, Poland
| | - Paweł Pomastowski
- Centre for Modern Interdisciplinary Technologies, Nicolaus Copernicus University in Toruń, Wileńska 4, 87-100, Toruń, Poland
| | - Bogusław Buszewski
- Centre for Modern Interdisciplinary Technologies, Nicolaus Copernicus University in Toruń, Wileńska 4, 87-100, Toruń, Poland
- Department of Environmental Chemistry and Bioanalysis, Faculty of Chemistry, Nicolaus Copernicus University in Toruń, Gagarina 7, 87-100, Toruń, Poland
| | - Michał Szumski
- Centre for Modern Interdisciplinary Technologies, Nicolaus Copernicus University in Toruń, Wileńska 4, 87-100, Toruń, Poland.
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Chen C, McDonald D, Blain A, Mossman E, Atkin K, Marusich MF, Capaldi R, Bone L, Smith A, Filby A, Erskine D, Russell O, Hudson G, Vincent AE, Reeve AK. Parkinson's disease neurons exhibit alterations in mitochondrial quality control proteins. NPJ Parkinsons Dis 2023; 9:120. [PMID: 37553379 PMCID: PMC10409763 DOI: 10.1038/s41531-023-00564-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Accepted: 07/21/2023] [Indexed: 08/10/2023] Open
Abstract
Mitochondrial dysfunction has been suggested to contribute to Parkinson's disease pathogenesis, though an understanding of the extent or exact mechanism of this contribution remains elusive. This has been complicated by challenging nature of pathway-based analysis and an inability simultaneously study multiple related proteins within human brain tissue. We used imaging mass cytometry (IMC) to overcome these challenges, measuring multiple protein targets, whilst retaining the spatial relationship between targets in post-mortem midbrain sections. We used IMC to simultaneously interrogate subunits of the mitochondrial oxidative phosphorylation complexes, and several key signalling pathways important for mitochondrial homoeostasis, in a large cohort of PD patient and control cases. We revealed a generalised and synergistic reduction in mitochondrial quality control proteins in dopaminergic neurons from Parkinson's patients. Further, protein-protein abundance relationships appeared significantly different between PD and disease control tissue. Our data showed a significant reduction in the abundance of PINK1, Parkin and phosphorylated ubiquitinSer65, integral to the mitophagy machinery; two mitochondrial chaperones, HSP60 and PHB1; and regulators of mitochondrial protein synthesis and the unfolded protein response, SIRT3 and TFAM. Further, SIRT3 and PINK1 did not show an adaptive response to an ATP synthase defect in the Parkinson's neurons. We also observed intraneuronal aggregates of phosphorylated ubiquitinSer65, alongside increased abundance of mitochondrial proteases, LONP1 and HTRA2, within the Parkinson's neurons with Lewy body pathology, compared to those without. Taken together, these findings suggest an inability to turnover mitochondria and maintain mitochondrial proteostasis in Parkinson's neurons. This may exacerbate the impact of oxidative phosphorylation defects and ageing related oxidative stress, leading to neuronal degeneration. Our data also suggest that that Lewy pathology may affect mitochondrial quality control regulation through the disturbance of mitophagy and intramitochondrial proteostasis.
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Affiliation(s)
- Chun Chen
- Wellcome Centre for Mitochondrial Research, Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, UK.
| | - David McDonald
- Innovation, Methodology and Application Research Theme, Biosciences Institute, Newcastle University, Newcastle upon Tyne, UK
- Flow Cytometry Core Facility, Newcastle University, Newcastle upon Tyne, UK
| | - Alasdair Blain
- Wellcome Centre for Mitochondrial Research, Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Emily Mossman
- Wellcome Centre for Mitochondrial Research, Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Kiera Atkin
- Wellcome Centre for Mitochondrial Research, Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, UK
| | | | | | - Laura Bone
- Wellcome Centre for Mitochondrial Research, Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Anna Smith
- Wellcome Centre for Mitochondrial Research, Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Andrew Filby
- Innovation, Methodology and Application Research Theme, Biosciences Institute, Newcastle University, Newcastle upon Tyne, UK
- Flow Cytometry Core Facility, Newcastle University, Newcastle upon Tyne, UK
| | - Daniel Erskine
- Wellcome Centre for Mitochondrial Research, Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Oliver Russell
- Wellcome Centre for Mitochondrial Research, Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Gavin Hudson
- Wellcome Centre for Mitochondrial Research, Biosciences Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Amy E Vincent
- Wellcome Centre for Mitochondrial Research, Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Amy K Reeve
- Wellcome Centre for Mitochondrial Research, Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, UK.
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Xiong W, Xiong Z, Song A, Lei C, Ye C, Su H, Zhang C. UCP1 alleviates renal interstitial fibrosis progression through oxidative stress pathway mediated by SIRT3 protein stability. J Transl Med 2023; 21:521. [PMID: 37533052 PMCID: PMC10399010 DOI: 10.1186/s12967-023-04376-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Accepted: 07/21/2023] [Indexed: 08/04/2023] Open
Abstract
BACKGROUND Renal interstitial fibrosis is a common pathway for the progressive development of chronic renal diseases (CKD) with different etiology, and is the main pathological basis leading to end-stage renal disease. Although the current research on renal interstitial fibrosis is gradually deepening, the diagnosis and treatment methods are still very lacking. Uncoupling protein 1 (UCP1) is a nuclear encoded protein in mitochondria inner membrane and plays an important role in regulating energy metabolism and mitochondrial homeostasis. However, the biological significance of UCP1 and potential regulatory mechanisms in the development of CKD remain unclear. METHODS Unilateral ureteral obstruction (UUO) model was used to construct the animal model of renal fibrosis, and TGF-β1 stimulation of HK2 cells was used to construct the vitro model of renal fibrosis. UCP1 expression was detected by Western blot, immunoblot analysis and immunohistochemistry. UCP1 was upregulated by UCP1 overexpressing lentivirus and UCP1 agonist CL316243. Western blot and immunofluorescence were used to detect epithelial mesenchymal transition (EMT)-related markers, such as collagen I, fibronectin, antioxidant enzyme SOD2 and CAT. Reactive oxygen species (ROS) production was detected by ROS detection kit. SIRT3 knockdown was performed by siRNA. RESULTS This study presents that UCP1 is significantly downregulated in patients with renal fibrosis and UUO model. Further studies discover that UCP1 overexpression and CL316243 treatments (UCP1 agonists) reversed EMT and extracellular matrix (ECM) accumulation in renal fibrosis models in vivo and in vitro. Simultaneously, UCP1 reduced the ROS production by increasing the stability of SIRT3. When SIRT3 was knocked down, the production of ROS decreased. CONCLUSIONS Elevating the expression of UCP1 can inhibit the occurrence of oxidative stress by stabilizing SIRT3, thereby reducing EMT and ECM accumulation, and ultimately alleviating renal interstitial fibrosis. It will provide new instructions and targets for the treatment of CKD.
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Affiliation(s)
- Wei Xiong
- Department of Nephrology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
| | - Zhiyong Xiong
- Department of Urology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
| | - Anni Song
- Department of Nephrology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
| | - Chuntao Lei
- Department of Nephrology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
| | - Chen Ye
- Department of Nephrology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
| | - Hua Su
- Department of Nephrology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
| | - Chun Zhang
- Department of Nephrology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China.
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5
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Castillo-Rangel C, Marin G, Hernández-Contreras KA, Vichi-Ramírez MM, Zarate-Calderon C, Torres-Pineda O, Diaz-Chiguer DL, De la Mora González D, Gómez Apo E, Teco-Cortes JA, Santos-Paez FDM, Coello-Torres MDLÁ, Baldoncini M, Reyes Soto G, Aranda-Abreu GE, García LI. Neuroinflammation in Parkinson’s Disease: From Gene to Clinic: A Systematic Review. Int J Mol Sci 2023; 24:ijms24065792. [PMID: 36982866 PMCID: PMC10051221 DOI: 10.3390/ijms24065792] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 03/13/2023] [Accepted: 03/14/2023] [Indexed: 03/22/2023] Open
Abstract
Parkinson’s disease is a neurodegenerative disease whose progression and clinical characteristics have a close bidirectional and multilevel relationship with the process of neuroinflammation. In this context, it is necessary to understand the mechanisms involved in this neuroinflammation–PD link. This systematic search was, hereby, conducted with a focus on the four levels where alterations associated with neuroinflammation in PD have been described (genetic, cellular, histopathological and clinical-behavioral) by consulting the PubMed, Google Scholar, Scielo and Redalyc search engines, including clinical studies, review articles, book chapters and case studies. Initially, 585,772 articles were included, and, after applying the inclusion and exclusion criteria, 84 articles were obtained that contained information about the multilevel association of neuroinflammation with alterations in gene, molecular, cellular, tissue and neuroanatomical expression as well as clinical-behavioral manifestations in PD.
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Affiliation(s)
- Carlos Castillo-Rangel
- Neurosurgery Department, “Hospital Regional 1° de Octubre”, Institute of Social Security and Services for State Workers (ISSSTE), México City 07300, Mexico
| | - Gerardo Marin
- Neural Dynamics and Modulation Lab, Cleveland Clinic, Cleveland, OH 44195, USA
- Correspondence: ; Tel.: +52-296-102-5707
| | | | | | | | | | - Dylan L. Diaz-Chiguer
- Neurosurgery Department, “Hospital Regional 1° de Octubre”, Institute of Social Security and Services for State Workers (ISSSTE), México City 07300, Mexico
| | | | - Erick Gómez Apo
- Pathology Department, “Hospital General de México”, Dr. Eduardo Liceaga, México City 06720, Mexico
| | | | | | | | - Matías Baldoncini
- Laboratory of Microsurgical Neuroanatomy, Second Chair of Gross Anatomy, University of Buenos Aires, Buenos Aires C1052AAA, Argentina
| | | | | | - Luis I. García
- Brain Research Institute, Universidad Veracruzana, Xalapa 91192, Mexico
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6
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Xing X, Xu F, Wang Y, Liu H. Role of the OTUB1/IRF7/NOX4 axis in oxidative stress injury and inflammatory responses in mice with Parkinson's disease. Psychogeriatrics 2023; 23:32-44. [PMID: 36332656 DOI: 10.1111/psyg.12900] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 09/21/2022] [Accepted: 10/10/2022] [Indexed: 11/06/2022]
Abstract
BACKGROUND Parkinson's disease (PD) is one of the most devastating neurodegenerative disorders and is associated with oxidative stress injury (OSI) and inflammatory responses. This study sought to investigate the mechanism of ovarian tumour domain-containing ubiquitin aldehyde binding 1 (OTUB1) in OSI and inflammatory responses in PD, providing a theoretical foundation for PD treatment. METHODS The PD mouse model was established by an intraperitoneal injection of 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine, followed by behavioural tests, observation of brain pathological changes, and quantification of inflammatory (TNF-α, IL-1β, and IL-10) and OS (ROS, SOD, and MDA) factors. Next, the expression levels of OTUB1, interferon regulatory factor 7 (IRF7), and NADPH oxidase 4 (NOX4) levels were determined by real-time quantitative polymerase chain reaction and western blot assay, the binding of OTUB1 to IRF7 was analysed by co-immunoprecipitation, and the ubiquitination level of IRF7 and the enrichment and binding of IRF7 and the NOX4 promoter were measured by chromatin immunoprecipitation and dual-luciferase assays. Afterwards, rescue experiments were performed with IRF7 or NOX4 overexpression in OTUB1 knockout PD mice. RESULTS OTUB1 was upregulated in brain tissues of PD mice. Inhibition of OTUB1 alleviated PD progression, OSI, and inflammatory responses. OTUB1 stabilized IRF7 through deubiquitination, and IRF7 bound to the NOX4 promoter to promote NOX4 expression. IRF7 or NOX4 overexpression reversed the effects of silencing OTUB1 on OSI and inflammatory responses in PD mice. CONCLUSION OTUB1-mediated deubiquitination stabilized IRF7 and upregulated NOX4 expression, thereby promoting OSI and inflammatory responses in PD mice.
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Affiliation(s)
- Xiaolian Xing
- Department of Neurology, Taiyuan Central Hospital, Shanxi Medical University, Taiyuan, China
| | - Fei Xu
- Department of Neurology, Taiyuan Central Hospital, Shanxi Medical University, Taiyuan, China
| | - Yu Wang
- Departments of Emergency Internal Medicine, Shanxi Bethune Hospital, Shanxi Academy of Medical Sciences, Tong ji Shanxi Hospital, Third Hospital of Shanxi Medical University, Taiyuan, China
| | - Hongwei Liu
- Department of Neurology, Taiyuan Central Hospital, Shanxi Medical University, Taiyuan, China
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How phosphorylation impacts intrinsically disordered proteins and their function. Essays Biochem 2022; 66:901-913. [PMID: 36350035 PMCID: PMC9760426 DOI: 10.1042/ebc20220060] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Revised: 10/14/2022] [Accepted: 10/17/2022] [Indexed: 11/10/2022]
Abstract
Phosphorylation is the most common post-translational modification (PTM) in eukaryotes, occurring particularly frequently in intrinsically disordered proteins (IDPs). These proteins are highly flexible and dynamic by nature. Thus, it is intriguing that the addition of a single phosphoryl group to a disordered chain can impact its function so dramatically. Furthermore, as many IDPs carry multiple phosphorylation sites, the number of possible states increases, enabling larger complexities and novel mechanisms. Although a chemically simple and well-understood process, the impact of phosphorylation on the conformational ensemble and molecular function of IDPs, not to mention biological output, is highly complex and diverse. Since the discovery of the first phosphorylation site in proteins 75 years ago, we have come to a much better understanding of how this PTM works, but with the diversity of IDPs and their capacity for carrying multiple phosphoryl groups, the complexity grows. In this Essay, we highlight some of the basic effects of IDP phosphorylation, allowing it to serve as starting point when embarking on studies into this topic. We further describe how recent complex cases of multisite phosphorylation of IDPs have been instrumental in widening our view on the effect of protein phosphorylation. Finally, we put forward perspectives on the phosphorylation of IDPs, both in relation to disease and in context of other PTMs; areas where deep insight remains to be uncovered.
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8
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Ma X, Sun Y, Pan D, Cao J, Dang Y. Structural characterization and stability analysis of phosphorylated nitrosohemoglobin. Food Chem 2022; 373:131475. [PMID: 34763930 DOI: 10.1016/j.foodchem.2021.131475] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Revised: 10/18/2021] [Accepted: 10/24/2021] [Indexed: 11/04/2022]
Abstract
Phosphorylation modification by sodium tripolyphosphate (STP) on nitrosohemoglobin (NO-Hb) and its effect on the protein structure and stability were studied. Phosphate groups were found to bridge to NO-Hb via C-O-P bonds through serine and tyrosine residues. Hydrothermal treatment with STP maintained the α-helix stability of NO-Hb, and this change in secondary structure improved the proteins stability. Compared to NO-Hb, phosphorylated NO-Hb (P-NO-Hb) was more stable with respect to light (outdoor light, indoor light, and dark conditions), oxidant (hydrogen peroxide), high temperature, and non-neutral pH. The absorbance of P-NO-Hb was nearly twice those of Hb and NO-Hb (P < 0.05), and the absorbance of P-NO-Hb decreased more slowly over time than those of Hb and NO-Hb. The results confirm that the presence of phosphate groups can increase the stability of Hb through structural changes.
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Affiliation(s)
- Xiaoqing Ma
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo 315211, PR China; Key Laboratory of Animal Protein Food Deep Processing Technology of Zhejiang Province, College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo 315800, PR China
| | - Yangying Sun
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo 315211, PR China; Key Laboratory of Animal Protein Food Deep Processing Technology of Zhejiang Province, College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo 315800, PR China.
| | - Daodong Pan
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo 315211, PR China; Key Laboratory of Animal Protein Food Deep Processing Technology of Zhejiang Province, College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo 315800, PR China.
| | - Jinxuan Cao
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo 315211, PR China; Key Laboratory of Animal Protein Food Deep Processing Technology of Zhejiang Province, College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo 315800, PR China
| | - Yali Dang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo 315211, PR China; Key Laboratory of Animal Protein Food Deep Processing Technology of Zhejiang Province, College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo 315800, PR China
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9
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p38-MAPK recruits the proteolytic pathways in Caenorhabditis elegans during bacterial infection. Int J Biol Macromol 2022; 204:116-135. [PMID: 35124023 DOI: 10.1016/j.ijbiomac.2022.01.191] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Revised: 01/28/2022] [Accepted: 01/29/2022] [Indexed: 11/21/2022]
Abstract
In eukaryotic organisms, cell-signalling completely relies on Post Translational Modifications (PTMs) that can function as regulatory switches. Phosphorylation is a fundamental and frequently occurring PTM in almost all eukaryotes. Herein, we have studied the importance of protein phosphorylation using classical proteomic techniques in C. elegans upon bacterial infection. The differentially regulated proteins during bacterial infection were excised from SDS-PAGE (One-Dimensional) gel (TiO2 column elutes) and subjected to MALDI-TOF-MS which ended up in identifying 220 proteins kinetically. KEGG pathway analysis of those proteins suggested that MAPK pathway was part of the innate immunity. Thus, we have characterized p38-MAPK (one of the crucial downstream MAPKs) using immunoblotting, subcellular fractionation, coimmunoprecipitation, LC-MS/MS, bioinformatics studies and qPCR. Meanwhile, KU25 strain (pmk-1 mutant) exhibited an earlier mortality during infection suggesting the crucial role of p38-MAPK during host-pathogen interaction. Interestingly, Reactome pathway analysis of p38 interactors (CoIP coupled to LC-MS/MS) revealed the involvement of various proteolytic pathway players (ubiquitination, SUMOylation and Neddylation) during bacterial infection. Further, the regulation of SUMOylation and Neddylation was identified and validated using immunoblotting and qPCR analyses, respectively. Concisely, our study indicated that bacterial infection triggers the MAPK cascade to elicit innate immunity which in turn recruits proteolytic pathways to counteract the invading pathogen.
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10
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Zhao YW, Pan HX, Liu Z, Wang Y, Zeng Q, Fang ZH, Luo TF, Xu K, Wang Z, Zhou X, He R, Li B, Zhao G, Xu Q, Sun QY, Yan XX, Tan JQ, Li JC, Guo JF, Tang BS. The Association Between Lysosomal Storage Disorder Genes and Parkinson's Disease: A Large Cohort Study in Chinese Mainland Population. Front Aging Neurosci 2021; 13:749109. [PMID: 34867278 PMCID: PMC8634711 DOI: 10.3389/fnagi.2021.749109] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Accepted: 09/29/2021] [Indexed: 12/20/2022] Open
Abstract
Background: Recent years have witnessed an increasing number of studies indicating an essential role of the lysosomal dysfunction in Parkinson’s disease (PD) at the genetic, biochemical, and cellular pathway levels. In this study, we investigated the association between rare variants in lysosomal storage disorder (LSD) genes and Chinese mainland PD. Methods: We explored the association between rare variants of 69 LSD genes and PD in 3,879 patients and 2,931 controls from Parkinson’s Disease & Movement Disorders Multicenter Database and Collaborative Network in China (PD-MDCNC) using next-generation sequencing, which were analyzed by using the optimized sequence kernel association test. Results: We identified the significant burden of rare putative LSD gene variants in Chinese mainland patients with PD. This association was robust in familial or sporadic early-onset patients after excluding the GBA variants but not in sporadic late-onset patients. The burden analysis of variant sets in genes of LSD subgroups revealed a suggestive significant association between variant sets in genes of sphingolipidosis deficiency disorders and familial or sporadic early-onset patients. In contrast, variant sets in genes of sphingolipidoses, mucopolysaccharidoses, and post-translational modification defect disorders were suggestively associated with sporadic late-onset patients. Then, SMPD1 and other four novel genes (i.e., GUSB, CLN6, PPT1, and SCARB2) were suggestively associated with sporadic early-onset or familial patients, whereas GALNS and NAGA were suggestively associated with late-onset patients. Conclusion: Our findings supported the association between LSD genes and PD and revealed several novel risk genes in Chinese mainland patients with PD, which confirmed the importance of lysosomal mechanisms in PD pathogenesis. Moreover, we identified the genetic heterogeneity in early-onset and late-onset of patients with PD, which may provide valuable suggestions for the treatment.
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Affiliation(s)
- Yu-Wen Zhao
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
| | - Hong-Xu Pan
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
| | - Zhenhua Liu
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
| | - Yige Wang
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
| | - Qian Zeng
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
| | - Zheng-Huan Fang
- Centre for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, China
| | - Teng-Fei Luo
- Centre for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, China
| | - Kun Xu
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
| | - Zheng Wang
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
| | - Xun Zhou
- Department of Geriatrics, Xiangya Hospital, Central South University, Changsha, China
| | - Runcheng He
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
| | - Bin Li
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
| | - Guihu Zhao
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
| | - Qian Xu
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
| | - Qi-Ying Sun
- Department of Geriatrics, Xiangya Hospital, Central South University, Changsha, China
| | - Xin-Xiang Yan
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
| | - Jie-Qiong Tan
- Centre for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, China
| | - Jin-Chen Li
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China.,Centre for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, China.,Department of Geriatrics, Xiangya Hospital, Central South University, Changsha, China
| | - Ji-Feng Guo
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China.,Centre for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, China.,Key Laboratory of Hunan Province in Neurodegenerative Disorders, Central South University, Changsha, China
| | - Bei-Sha Tang
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China.,Centre for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, China.,Key Laboratory of Hunan Province in Neurodegenerative Disorders, Central South University, Changsha, China
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11
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Gupta R, Sahu M, Srivastava D, Tiwari S, Ambasta RK, Kumar P. Post-translational modifications: Regulators of neurodegenerative proteinopathies. Ageing Res Rev 2021; 68:101336. [PMID: 33775891 DOI: 10.1016/j.arr.2021.101336] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Revised: 03/10/2021] [Accepted: 03/22/2021] [Indexed: 12/14/2022]
Abstract
One of the hallmark features in the neurodegenerative disorders (NDDs) is the accumulation of aggregated and/or non-functional protein in the cellular milieu. Post-translational modifications (PTMs) are an essential regulator of non-functional protein aggregation in the pathogenesis of NDDs. Any alteration in the post-translational mechanism and the protein quality control system, for instance, molecular chaperone, ubiquitin-proteasome system, autophagy-lysosomal degradation pathway, enhances the accumulation of misfolded protein, which causes neuronal dysfunction. Post-translational modification plays many roles in protein turnover rate, accumulation of aggregate and can also help in the degradation of disease-causing toxic metabolites. PTMs such as acetylation, glycosylation, phosphorylation, ubiquitination, palmitoylation, SUMOylation, nitration, oxidation, and many others regulate protein homeostasis, which includes protein structure, functions and aggregation propensity. Different studies demonstrated the involvement of PTMs in the regulation of signaling cascades such as PI3K/Akt/GSK3β, MAPK cascade, AMPK pathway, and Wnt signaling pathway in the pathogenesis of NDDs. Further, mounting evidence suggests that targeting different PTMs with small chemical molecules, which acts as an inhibitor or activator, reverse misfolded protein accumulation and thus enhances the neuroprotection. Herein, we briefly discuss the protein aggregation and various domain structures of different proteins involved in the NDDs, indicating critical amino acid residues where PTMs occur. We also describe the implementation and involvement of various PTMs on signaling cascade and cellular processes in NDDs. Lastly, we implement our current understanding of the therapeutic importance of PTMs in neurodegeneration, along with emerging techniques targeting various PTMs.
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12
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Li A, Deng Y, Tan Y, Chen M. A Transfer Learning-Based Approach for Lysine Propionylation Prediction. Front Physiol 2021; 12:658633. [PMID: 33967828 PMCID: PMC8096918 DOI: 10.3389/fphys.2021.658633] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Accepted: 03/15/2021] [Indexed: 12/12/2022] Open
Abstract
Lysine propionylation is a newly discovered posttranslational modification (PTM) and plays a key role in the cellular process. Although proteomics techniques was capable of detecting propionylation, large-scale detection was still challenging. To bridge this gap, we presented a transfer learning-based method for computationally predicting propionylation sites. The recurrent neural network-based deep learning model was trained firstly by the malonylation and then fine-tuned by the propionylation. The trained model served as feature extractor where protein sequences as input were translated into numerical vectors. The support vector machine was used as the final classifier. The proposed method reached a matthews correlation coefficient (MCC) of 0.6615 on the 10-fold crossvalidation and 0.3174 on the independent test, outperforming state-of-the-art methods. The enrichment analysis indicated that the propionylation was associated with these GO terms (GO:0016620, GO:0051287, GO:0003735, GO:0006096, and GO:0005737) and with metabolism. We developed a user-friendly online tool for predicting propoinylation sites which is available at http://47.113.117.61/.
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Affiliation(s)
- Ang Li
- School of Computer Science and Technology, Hunan Institute of Technology, Hengyang, China
| | - Yingwei Deng
- School of Computer Science and Technology, Hunan Institute of Technology, Hengyang, China
| | - Yan Tan
- School of Computer Science and Technology, Hunan Institute of Technology, Hengyang, China
| | - Min Chen
- School of Computer Science and Technology, Hunan Institute of Technology, Hengyang, China
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13
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Yang D, Ying J, Wang X, Zhao T, Yoon S, Fang Y, Zheng Q, Liu X, Yu W, Hua F. Mitochondrial Dynamics: A Key Role in Neurodegeneration and a Potential Target for Neurodegenerative Disease. Front Neurosci 2021; 15:654785. [PMID: 33912006 PMCID: PMC8072049 DOI: 10.3389/fnins.2021.654785] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2021] [Accepted: 03/11/2021] [Indexed: 12/14/2022] Open
Abstract
In neurodegenerative diseases, neurodegeneration has been related to several mitochondrial dynamics imbalances such as excessive fragmentation of mitochondria, impaired mitophagy, and blocked mitochondria mitochondrial transport in axons. Mitochondria are dynamic organelles, and essential for energy conversion, neuron survival, and cell death. As mitochondrial dynamics have a significant influence on homeostasis, in this review, we mainly discuss the role of mitochondrial dynamics in several neurodegenerative diseases. There is evidence that several mitochondrial dynamics-associated proteins, as well as related pathways, have roles in the pathological process of neurodegenerative diseases with an impact on mitochondrial functions and metabolism. However, specific pathological mechanisms need to be better understood in order to propose new therapeutic strategies targeting mitochondrial dynamics that have shown promise in recent studies.
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Affiliation(s)
- Danying Yang
- Department of Anesthesiology, The Second Affiliated Hospital of Nanchang University, Nanchang, China.,Key Laboratory of Anesthesiology of Jiangxi Province, Nanchang, China
| | - Jun Ying
- Department of Anesthesiology, The Second Affiliated Hospital of Nanchang University, Nanchang, China.,Key Laboratory of Anesthesiology of Jiangxi Province, Nanchang, China
| | - Xifeng Wang
- Department of Anesthesiology, The First Affiliated Hospital of Nanchang University, Nanchang, China
| | - Tiancheng Zhao
- Mailman School of Public Health, Columbia University, New York, NY, United States
| | - Sungtae Yoon
- Helping Minds International Charitable Foundation, New York, NY, United States
| | - Yang Fang
- Department of Anesthesiology, The Second Affiliated Hospital of Nanchang University, Nanchang, China.,Key Laboratory of Anesthesiology of Jiangxi Province, Nanchang, China
| | - Qingcui Zheng
- Department of Anesthesiology, The Second Affiliated Hospital of Nanchang University, Nanchang, China.,Key Laboratory of Anesthesiology of Jiangxi Province, Nanchang, China
| | - Xing Liu
- Department of Anesthesiology, The Second Affiliated Hospital of Nanchang University, Nanchang, China.,Key Laboratory of Anesthesiology of Jiangxi Province, Nanchang, China
| | - Wen Yu
- Department of Anesthesiology, The Second Affiliated Hospital of Nanchang University, Nanchang, China.,Key Laboratory of Anesthesiology of Jiangxi Province, Nanchang, China
| | - Fuzhou Hua
- Department of Anesthesiology, The Second Affiliated Hospital of Nanchang University, Nanchang, China.,Key Laboratory of Anesthesiology of Jiangxi Province, Nanchang, China
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14
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Structure, functional properties and iron bioavailability of Pneumatophorus japonicus myoglobin and its glycosylation products. Int J Biol Macromol 2021; 173:524-531. [PMID: 33493563 DOI: 10.1016/j.ijbiomac.2021.01.138] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Revised: 12/27/2020] [Accepted: 01/19/2021] [Indexed: 01/19/2023]
Abstract
Developing safe and efficient iron supplements is significant for the alleviation of iron-deficient anemia (IDA). Myoglobin (Mb) is a heme-protein rich in bioavailable iron. Pneumatophorus japonicus (P. japonicus), one important economic fish in China, contain a high Mb level in its dark meat normally discarded during processing. The present study aimed to determine the structure, physicochemical properties, and iron bioavailability of Mb extracted from P. japonicus. Meanwhile, the effects of glycosylation, a commonly applied chemical modification of proteins, on these parameters were evaluated. Using Box-Behnken design, the optimal conditions for Mb-chitosan glycosylation were obtained: 45.07 °C, pH 6.10 and Mb/chitosan mass ratio of 6.29. The structure and functional properties of the glycosylated Mb (Mb-gly) were investigated. Compared with the original Mb, Mb-gly obtained a more ordered secondary structure. The surface hydrophobicity of Mb-gly was found to be decreased together with the observations of elevated water solubility. Moreover, glycosylation enhanced the Mb antioxidant capacity, and improved its stability in enzymatic digestion system. Regarding to the iron bioavailability, the cellular uptake of Mb‑iron was significantly higher than FeSO4, and further elevated by glycosylation. These results provided a basis for the development of Mb-based iron supplements, promoting the utilization of fish-processing industries wastes.
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15
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Ravanidis S, Bougea A, Karampatsi D, Papagiannakis N, Maniati M, Stefanis L, Doxakis E. Differentially Expressed Circular RNAs in Peripheral Blood Mononuclear Cells of Patients with Parkinson's Disease. Mov Disord 2021; 36:1170-1179. [PMID: 33433033 PMCID: PMC8248110 DOI: 10.1002/mds.28467] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2020] [Revised: 11/18/2020] [Accepted: 12/08/2020] [Indexed: 12/12/2022] Open
Abstract
Background New noninvasive and affordable molecular approaches that will complement current practices and increase the accuracy of Parkinson's disease (PD) diagnosis are urgently needed. Circular RNAs (circRNAs) are stable noncoding RNAs that accumulate with aging in neurons and are increasingly shown to regulate all aspects of neuronal development and function. Objectives Τhe aims of this study were to identify differentially expressed circRNAs in blood mononuclear cells of patients with idiopathic PD and explore the competing endogenous RNA networks affected. Methods Eighty‐seven circRNAs were initially selected based on relatively high gene expression in the human brain. More than half of these were readily detectable in blood mononuclear cells using real‐time reverse transcription‐polymerase chain reaction. Comparative expression analysis was then performed in blood mononuclear cells from 60 control subjects and 60 idiopathic subjects with PD. Results Six circRNAs were significantly down‐regulated in patients with PD. The classifier that best distinguished PD consisted of four circRNAs with an area under the curve of 0.84. Cross‐linking immunoprecipitation‐sequencing data revealed that the RNA‐binding proteins bound by most of the deregulated circRNAs include the neurodegeneration‐associated FUS, TDP43, FMR1, and ATXN2. MicroRNAs predicted to be sequestered by most deregulated circRNAs have the Gene Ontology categories “protein modification” and “transcription factor activity” mostly enriched. Conclusions This is the first study that identifies specific circRNAs that may serve as diagnostic biomarkers for PD. Because they are highly expressed in the brain and are derived from genes with essential brain functions, they may also hint on the PD pathways affected. © 2021 Biomedical Research Foundation, Academy of Athens. Movement Disorders published by Wiley Periodicals LLC on behalf of International Parkinson and Movement Disorder Society.
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Affiliation(s)
- Stylianos Ravanidis
- Center of Basic Research, Biomedical Research Foundation, Academy of Athens, Athens, Greece
| | - Anastasia Bougea
- Center of Basic Research, Biomedical Research Foundation, Academy of Athens, Athens, Greece.,Center of Clinical Research, Biomedical Research Foundation, Academy of Athens, Athens, Greece.,First Department of Neurology, National and Kapodistrian University of Athens Medical School, Athens, Greece
| | - Dimitra Karampatsi
- Center of Basic Research, Biomedical Research Foundation, Academy of Athens, Athens, Greece
| | - Nikolaos Papagiannakis
- Center of Clinical Research, Biomedical Research Foundation, Academy of Athens, Athens, Greece.,First Department of Neurology, National and Kapodistrian University of Athens Medical School, Athens, Greece
| | - Matina Maniati
- Center of Clinical Research, Biomedical Research Foundation, Academy of Athens, Athens, Greece
| | - Leonidas Stefanis
- Center of Clinical Research, Biomedical Research Foundation, Academy of Athens, Athens, Greece.,First Department of Neurology, National and Kapodistrian University of Athens Medical School, Athens, Greece
| | - Epaminondas Doxakis
- Center of Basic Research, Biomedical Research Foundation, Academy of Athens, Athens, Greece
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16
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Ceruloplasmin Deamidation in Neurodegeneration: From Loss to Gain of Function. Int J Mol Sci 2021; 22:ijms22020663. [PMID: 33440850 PMCID: PMC7827708 DOI: 10.3390/ijms22020663] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Revised: 01/08/2021] [Accepted: 01/08/2021] [Indexed: 02/07/2023] Open
Abstract
Neurodegenerative disorders can induce modifications of several proteins; one of which is ceruloplasmin (Cp), a ferroxidase enzyme found modified in the cerebrospinal fluid (CSF) of neurodegenerative diseases patients. Cp modifications are caused by the oxidation induced by the pathological environment and are usually associated with activity loss. Together with oxidation, deamidation of Cp was found in the CSF from Alzheimer’s and Parkinson’s disease patients. Protein deamidation is a process characterized by asparagine residues conversion in either aspartate or isoaspartate, depending on protein sequence/structure and cellular environment. Cp deamidation occurs at two Asparagine-Glycine-Arginine (NGR)-motifs which, once deamidated to isoAspartate-Glycine-Arginine (isoDGR), bind integrins, a family of receptors mediating cell adhesion. Therefore, on the one hand, Cp modifications lead to loss of enzymatic activity, while on the other hand, these alterations confer gain of function to Cp. In fact, deamidated Cp binds to integrins and triggers intracellular signaling on choroid plexus epithelial cells, changing cell functioning. Working in concert with the oxidative environment, Cp deamidation could reach different target cells in the brain, altering their physiology and causing detrimental effects, which might contribute to the pathological mechanism.
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17
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GasPhos: Protein Phosphorylation Site Prediction Using a New Feature Selection Approach with a GA-Aided Ant Colony System. Int J Mol Sci 2020; 21:ijms21217891. [PMID: 33114312 PMCID: PMC7660635 DOI: 10.3390/ijms21217891] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2020] [Revised: 10/20/2020] [Accepted: 10/20/2020] [Indexed: 02/06/2023] Open
Abstract
Protein phosphorylation is one of the most important post-translational modifications, and many biological processes are related to phosphorylation, such as DNA repair, transcriptional regulation and signal transduction and, therefore, abnormal regulation of phosphorylation usually causes diseases. If we can accurately predict human phosphorylation sites, this could help to solve human diseases. Therefore, we developed a kinase-specific phosphorylation prediction system, GasPhos, and proposed a new feature selection approach, called Gas, based on the ant colony system and a genetic algorithm and used performance evaluation strategies focused on different kinases to choose the best learning model. Gas uses the mean decrease Gini index (MDGI) as a heuristic value for path selection and adopts binary transformation strategies and new state transition rules. GasPhos can predict phosphorylation sites for six kinases and showed better performance than other phosphorylation prediction tools. The disease-related phosphorylated proteins that were predicted with GasPhos are also discussed. Finally, Gas can be applied to other issues that require feature selection, which could help to improve prediction performance.
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18
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Thawornpan P, Jumpathong W, Thanapongpichat S, Tansila N, Win Tun A, de Jong L, Buncherd H. Magnetic Fraction of Fly Ash as a Low-Cost Magnetic Adsorbent for Selective Capture of Phosphoproteins. ANAL LETT 2020. [DOI: 10.1080/00032719.2020.1825467] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Pongsakorn Thawornpan
- Department of Molecular Biotechnology and Bioinformatics, Faculty of Science, Prince of Songkla University, Songkhla, Thailand
| | - Watthanachai Jumpathong
- Program on Chemical Biology, Center of Excellence on Environmental Health and Toxicology (EHT), Ministry of Education, Chulabhorn Graduate Institute, Bangkok, Thailand
| | | | - Natta Tansila
- Faculty of Medical Technology, Prince of Songkla University, Songkhla, Thailand
| | - Aung Win Tun
- Faculty of Graduate Studies, Mahidol University, Salaya, Thailand
| | - Luitzen de Jong
- Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, The Netherlands
| | - Hansuk Buncherd
- Faculty of Medical Technology, Prince of Songkla University, Songkhla, Thailand
- Medical Science Research and Innovation Institute, Prince of Songkla University, Songkhla, Thailand
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19
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Guanosine modulates SUMO2/3-ylation in neurons and astrocytes via adenosine receptors. Purinergic Signal 2020; 16:439-450. [PMID: 32892251 PMCID: PMC7524998 DOI: 10.1007/s11302-020-09723-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Accepted: 08/17/2020] [Indexed: 12/13/2022] Open
Abstract
SUMOylation is a post-translational modification (PTM) whereby members of the Small Ubiquitin-like MOdifier (SUMO) family of proteins are conjugated to lysine residues in target proteins. SUMOylation has been implicated in a wide range of physiological and pathological processes, and much attention has been given to its role in neurodegenerative conditions. Due to its reported role in neuroprotection, pharmacological modulation of SUMOylation represents an attractive potential therapeutic strategy in a number of different brain disorders. However, very few compounds that target the SUMOylation pathway have been identified. Guanosine is an endogenous nucleoside with important neuromodulatory and neuroprotective effects. Experimental evidence has shown that guanosine can modulate different intracellular pathways, including PTMs. In the present study we examined whether guanosine alters global protein SUMOylation. Primary cortical neurons and astrocytes were treated with guanosine at 1, 10, 100, 300, or 500 μM at four time points, 1, 6, 24, or 48 h. We show that guanosine increases global SUMO2/3-ylation in neurons and astrocytes at 1 h at concentrations above 10 μM. The molecular mechanisms involved in this effect were evaluated in neurons. The guanosine-induced increase in global SUMO2/3-ylation was still observed in the presence of dipyridamole, which prevents guanosine internalization, demonstrating an extracellular guanosine-induced effect. Furthermore, the A1 adenosine receptor antagonist DPCPX abolished the guanosine-induced increase in SUMO2/3-ylation. The A2A adenosine receptor antagonist ZM241385 increased SUMOylation per se, but did not alter guanosine-induced SUMOylation, suggesting that guanosine may modulate SUMO2/3-ylation through an A1-A2A receptor interaction. Taken together, this is the first report to show guanosine as a SUMO2/3-ylation enhancer in astrocytes and neurons.
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20
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Ravanidis S, Bougea A, Papagiannakis N, Koros C, Simitsi AM, Pachi I, Breza M, Stefanis L, Doxakis E. Validation of differentially expressed brain-enriched microRNAs in the plasma of PD patients. Ann Clin Transl Neurol 2020; 7:1594-1607. [PMID: 32860338 PMCID: PMC7480914 DOI: 10.1002/acn3.51146] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Accepted: 07/06/2020] [Indexed: 12/16/2022] Open
Abstract
Objective There is a pressing need to identify and validate, minimally invasive, molecular biomarkers that will complement current practices and increase the diagnostic accuracy in Parkinson’s disease (PD). Brain‐enriched miRNAs regulate all aspects of neuron development and function; importantly, they are secreted by neurons in amounts that can be readily detected in the plasma. Τhe aim of the present study was to validate a set of previously identified brain‐enriched miRNAs with diagnostic potential for idiopathic PD and recognize the molecular pathways affected by these deregulated miRNAs. Methods RT‐qPCR was performed in the plasma of 92 healthy controls and 108 idiopathic PD subjects. Statistical and in silico analyses were used to validate deregulated miRNAs and pathways in PD, respectively. Results miR‐22‐3p, miR‐124‐3p, miR‐136‐3p, miR‐154‐5p, and miR‐323a‐3p levels were found to be differentially expressed between healthy controls and PD patients. miR‐330‐5p, miR‐433‐3p, and miR‐495‐3p levels were overall higher in male subjects. Most of these miRNAs are clustered at Chr14q32 displaying CREB1, CEBPB, and MAZ transcription factor binding sites. Gene Ontology annotation analysis of deregulated miRNA targets revealed that “Protein modification,” “Transcription factor activity,” and “Cell death” terms were over‐represented. Kyoto Encyclopedia of Genes and Genome analysis revealed that “Long‐term depression,” “TGF‐beta signaling,” and “FoxO signaling” pathways were significantly affected. Interpretation We validated a panel of brain‐enriched miRNAs that can be used along with other measures for the detection of PD, revealed molecular pathways targeted by these deregulated miRNAs, and identified upstream transcription factors that may be directly implicated in PD pathogenesis.
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Affiliation(s)
- Stylianos Ravanidis
- Center of Basic Research, Biomedical Research Foundation, Academy of Athens, Athens, 11527, Greece
| | - Anastasia Bougea
- Center of Basic Research, Biomedical Research Foundation, Academy of Athens, Athens, 11527, Greece.,Center of Clinical Research, Biomedical Research Foundation, Academy of Athens, Athens, 11527, Greece.,First Department of Neurology, National and Kapodistrian University of Athens Medical School, Athens, 11528, Greece
| | - Nikolaos Papagiannakis
- Center of Clinical Research, Biomedical Research Foundation, Academy of Athens, Athens, 11527, Greece.,First Department of Neurology, National and Kapodistrian University of Athens Medical School, Athens, 11528, Greece
| | - Christos Koros
- First Department of Neurology, National and Kapodistrian University of Athens Medical School, Athens, 11528, Greece
| | - Athina Maria Simitsi
- First Department of Neurology, National and Kapodistrian University of Athens Medical School, Athens, 11528, Greece
| | - Ioanna Pachi
- First Department of Neurology, National and Kapodistrian University of Athens Medical School, Athens, 11528, Greece
| | - Marianthi Breza
- First Department of Neurology, National and Kapodistrian University of Athens Medical School, Athens, 11528, Greece
| | - Leonidas Stefanis
- Center of Clinical Research, Biomedical Research Foundation, Academy of Athens, Athens, 11527, Greece.,First Department of Neurology, National and Kapodistrian University of Athens Medical School, Athens, 11528, Greece
| | - Epaminondas Doxakis
- Center of Basic Research, Biomedical Research Foundation, Academy of Athens, Athens, 11527, Greece
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21
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Prieto M, Folci A, Martin S. Post-translational modifications of the Fragile X Mental Retardation Protein in neuronal function and dysfunction. Mol Psychiatry 2020; 25:1688-1703. [PMID: 31822816 DOI: 10.1038/s41380-019-0629-4] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Revised: 11/22/2019] [Accepted: 11/27/2019] [Indexed: 12/17/2022]
Abstract
The Fragile X Mental Retardation Protein (FMRP) is an RNA-binding protein essential to the regulation of local translation at synapses. In the mammalian brain, synapses are constantly formed and eliminated throughout development to achieve functional neuronal networks. At the molecular level, thousands of proteins cooperate to accomplish efficient neuronal communication. Therefore, synaptic protein levels and their functional interactions need to be tightly regulated. FMRP generally acts as a translational repressor of its mRNA targets. FMRP is the target of several post-translational modifications (PTMs) that dynamically regulate its function. Here we provide an overview of the PTMs controlling the FMRP function and discuss how their spatiotemporal interplay contributes to the physiological regulation of FMRP. Importantly, FMRP loss-of-function leads to Fragile X syndrome (FXS), a rare genetic developmental condition causing a range of neurological alterations including intellectual disability (ID), learning and memory impairments, autistic-like features and seizures. Here, we also explore the possibility that recently reported missense mutations in the FMR1 gene disrupt the PTM homoeostasis of FMRP, thus participating in the aetiology of FXS. This suggests that the pharmacological targeting of PTMs may be a promising strategy to develop innovative therapies for patients carrying such missense mutations.
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Affiliation(s)
- Marta Prieto
- Université Côte d'Azur, CNRS, IPMC, Valbonne, France
| | | | - Stéphane Martin
- Université Côte d'Azur, INSERM, CNRS, IPMC, Valbonne, France.
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22
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Chakraborty J, Ziviani E. Deubiquitinating Enzymes in Parkinson's Disease. Front Physiol 2020; 11:535. [PMID: 32581833 PMCID: PMC7283616 DOI: 10.3389/fphys.2020.00535] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Accepted: 04/30/2020] [Indexed: 01/19/2023] Open
Abstract
Mitochondrial dysfunction and neurodegeneration have been directly correlated in many neurodegenerative disorders. Parkinson’s disease (PD) in particular has been extensively studied in this context because of its well-characterized association with mitophagy, a selective type of autophagy that degrades mitochondria. Mitophagy is triggered by ubiquitin modification of proteins residing on the surface of mitochondria. Therefore, mitophagy is subject to suppression by deubiquitination. In recent years, many deubiquitinase enzymes (DUBs) emerged as therapeutic targets to compensate hindered mitophagy in PD. It is reasonable that inhibition of specific DUBs should induce mitophagy by blocking deubiquitination of mitochondrial proteins, although the signaling pathway is not always that linear. The broad aspect suggests that there could be cross talks among DUBs, which may in turn have synergistic effect to rescue the disease progression. In this short review we have highlighted DUBs that hold therapeutic value in the field of neurodegenerative diseases, PD in particular.
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Affiliation(s)
- Joy Chakraborty
- Department of Cell Biology and Physiology, CSIR-Indian Institute of Chemical Biology-TRUE Campus, Kolkata, India
| | - Elena Ziviani
- Department of Biology, University of Padova, Padua, Italy
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23
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Unequivocal Biomarker for Parkinson’s Disease: A Hunt that Remains a Pester. Neurotox Res 2019; 36:627-644. [DOI: 10.1007/s12640-019-00080-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Revised: 06/17/2019] [Accepted: 06/19/2019] [Indexed: 12/14/2022]
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24
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Correia SC, Carvalho C, Cardoso S, Moreira PI. Post-translational modifications in brain health and disease. Biochim Biophys Acta Mol Basis Dis 2019; 1865:1947-1948. [PMID: 31102788 DOI: 10.1016/j.bbadis.2019.05.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Sónia C Correia
- CNC - Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal; IIIUC - Institute for Interdisciplinary Research, University of Coimbra, Coimbra, Portugal.
| | - Cristina Carvalho
- CNC - Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal; IIIUC - Institute for Interdisciplinary Research, University of Coimbra, Coimbra, Portugal
| | - Susana Cardoso
- CNC - Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal; IIIUC - Institute for Interdisciplinary Research, University of Coimbra, Coimbra, Portugal
| | - Paula I Moreira
- CNC - Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal; Institute of Physiology, Faculty of Medicine, University of Coimbra, Coimbra, Portugal
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