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Sánchez-Terrón G, Martínez R, Delgado J, Molina J, Estévez M. Hepatoprotective mechanisms of pomegranate bioactives on a murine models affected by NAFLD as analysed by MS-based proteomics: The mitochondria in the eye of the storm. Food Res Int 2024; 192:114769. [PMID: 39147495 DOI: 10.1016/j.foodres.2024.114769] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2024] [Revised: 07/11/2024] [Accepted: 07/14/2024] [Indexed: 08/17/2024]
Abstract
Deciphering the mechanisms underlying the direct association between fructose consumption and the onset and progression of non-alcoholic fatty liver disease (NAFLD), as well as the high prevalence of metabolic syndrome (MetS), is of great importance for adopting potential nutritional strategies. Thus, an evaluation of the impact of sustained high fructose consumption on the liver physiology of Wistar rats was made. Moreover, the effectiveness of a dietary pomegranate-derived supplement (P) at counteracting fructose-induced liver injury was also assessed. For unveiling the underlying mechanisms, an untargeted proteomic analysis of the livers from nineteen Wistar rats fed on a basal commercial feed and supplemented with either drinking water (C) (n = 6), 30 % (w/v) fructose in drinking water (F) (n = 7) or 30 % (w/v) fructose solution plus 0.2 % (w/v) P (F+P) (n = 6) was assessed. Fructose intake severely increased the abundance of several energy-production related-proteins, such as fructose-bisphosphate aldolase or fatty acid synthase, among others, as well as diminished the amount of another ones, such as carnitine O-palmitoyl transferase or different subunits of acyl-coenzyme A oxidase. These changes could facilitate mitochondrial disturbances and oxidative stress. Regarding the hepatic proteome of F, P extract restored mitochondrial homeostasis and strengthened endogenous antioxidant mechanisms diminishing the amount of proteins involved in process that could increase the oxidative status, as well as increasing both the quantity of several proteins involved in proteasome functionality, as expressing changes in the amount of certain RNA-splicing related-proteins, regarding F proteome.
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Affiliation(s)
- Guadalupe Sánchez-Terrón
- TECAL Research Group, Meat and Meat Products Research Institute (IPROCAR), Universidad de Extremadura (UEX, ROR-ID 0174shg90), Caceres 10003, Spain
| | - Remigio Martínez
- Animal Health Department, Animal Health and Zoonoses Research Group (GISAZ), UIC Zoonosis and Emergent Diseases (ENZOEM Competitive Research Unit), Universidad de Córdoba (UCO, ROR-ID 05yc77b46), Córdoba, 14014, Spain
| | - Josué Delgado
- HISEALI Research Group, Meat and Meat Products Research Institute (IPROCAR), Universidad de Extremadura (UEX), Caceres 10003, Spain
| | - Javier Molina
- Gastroenterology and Hepatology, Hospital Universitario de Cáceres (HUC), Servicio Extremeño de Salud (SES), Junta de Extremadura, Caceres 10003, Spain
| | - Mario Estévez
- TECAL Research Group, Meat and Meat Products Research Institute (IPROCAR), Universidad de Extremadura (UEX, ROR-ID 0174shg90), Caceres 10003, Spain.
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2
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Ni Y, Qiao Y, Tian X, Li H, Meng Y, Li C, Du W, Sun T, Zhu K, Huang W, Yan H, Li J, Zhou R, Ding C, Gao X. Unraveling the mechanism of thermotolerance by Set302 in Cryptococcus neoformans. Microbiol Spectr 2024; 12:e0420223. [PMID: 38874428 PMCID: PMC11302353 DOI: 10.1128/spectrum.04202-23] [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: 12/28/2023] [Accepted: 05/12/2024] [Indexed: 06/15/2024] Open
Abstract
The underlying mechanism of thermotolerance, which is a key virulence factor essential for pathogenic fungi such as Cryptococcus neoformans, is largely unexplored. In this study, our findings suggest that Set302, a homolog of Set3 and a subunit of histone deacetylase complex Set3C, contributes to thermotolerance in C. neoformans. Specifically, the deletion of the predicted Set3C core subunit, Set302, resulted in further reduction in the growth of C. neoformans at 39°C, and survival of transient incubation at 50°C. Transcriptomics analysis revealed that the expression levels of numerous heat stress-responsive genes altered at both 30°C and 39°C due to the lack of Set302. Notably, at 39°C, the absence of Set302 led to the downregulation of gene expression related to the ubiquitin-proteasome system (UPS). Based on the GFP-α-synuclein overexpression model to characterize misfolded proteins, we observed a pronounced accumulation of misfolded GFP-α-synuclein at 39°C, consequently inhibiting C. neoformans thermotolerance. Furthermore, the loss of Set302 exacerbated the accumulation of misfolded GFP-α-synuclein during heat stress. Interestingly, the set302∆ strain exhibited a similar phenotype under proteasome stress as it did at 39°C. Moreover, the absence of Set302 led to reduced production of capsule and melanin. set302∆ strain also displayed significantly reduced pathogenicity and colonization ability compared to the wild-type strain in the murine infection model. Collectively, our findings suggest that Set302 modulates thermotolerance by affecting the degradation of misfolded proteins and multiple virulence factors to mediate the pathogenicity of C. neoformans.IMPORTANCECryptococcus neoformans is a pathogenic fungus that poses a potential and significant threat to public health. Thermotolerance plays a crucial role in the wide distribution in natural environments and host colonization of this fungus. Herein, Set302, a critical core subunit for the integrity of histone deacetylase complex Set3C and widely distributed in various fungi and mammals, governs thermotolerance and affects survival at extreme temperatures as well as the formation of capsule and melanin in C. neoformans. Additionally, Set302 participates in regulating the expression of multiple genes associated with the ubiquitin-proteasome system (UPS). By eliminating misfolded proteins under heat stress, Set302 significantly contributes to the thermotolerance of C. neoformans. Moreover, Set302 regulates the pathogenicity and colonization ability of C. neoformans in a murine model. Overall, this study provides new insight into the mechanism of thermotolerance in C. neoformans.
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Affiliation(s)
- Yue Ni
- College of Life and Health Sciences, Northeastern University, Shenyang, Liaoning, China
| | - Yue Qiao
- College of Life and Health Sciences, Northeastern University, Shenyang, Liaoning, China
| | - Xing Tian
- Department of Emergency, Xinqiao Hospital, Army Medical University, Chongqing, China
| | - Hailong Li
- NHC Key Laboratory of AIDS Immunology, National Clinical Research Center for Laboratory Medicine, The First Affiliated Hospital of China Medical University, Shenyang, China
| | - Yang Meng
- College of Life and Health Sciences, Northeastern University, Shenyang, Liaoning, China
| | - Chao Li
- College of Life and Health Sciences, Northeastern University, Shenyang, Liaoning, China
| | - Wei Du
- Department of Clinical Laboratory, National Clinical Research Center for Laboratory Medicine, The First Affiliated Hospital of China Medical University, Shenyang, Liaoning, China
| | - Tianshu Sun
- Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases, Beijing, China
- Medical Research Centre, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science, Beijing, China
| | - Keting Zhu
- Department of Emergency, Xinqiao Hospital, Army Medical University, Chongqing, China
| | - Wei Huang
- Department of Emergency, Xinqiao Hospital, Army Medical University, Chongqing, China
| | - He Yan
- Department of Emergency, Xinqiao Hospital, Army Medical University, Chongqing, China
| | - Jia Li
- Department of Emergency, Xinqiao Hospital, Army Medical University, Chongqing, China
| | - Renjie Zhou
- Department of Emergency, Xinqiao Hospital, Army Medical University, Chongqing, China
| | - Chen Ding
- College of Life and Health Sciences, Northeastern University, Shenyang, Liaoning, China
| | - Xindi Gao
- Department of Emergency, Xinqiao Hospital, Army Medical University, Chongqing, China
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3
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INANAGA S, SHIMODA H, IGASE M, KONDO H, KOIZUMI I, MIZUNO T. Establishment of a histiocytic sarcoma cell line and anti-tumor effect of bortezomib in the African pygmy hedgehog (Atelerix albiventris). J Vet Med Sci 2024; 86:833-840. [PMID: 38880614 PMCID: PMC11300126 DOI: 10.1292/jvms.23-0426] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Accepted: 06/02/2024] [Indexed: 06/18/2024] Open
Abstract
The African pygmy hedgehog (Atelerix albiventris) is known to have a high incidence of tumor. However, investigating the tumors of this species has been constrained by the limited availability of research materials such as cell lines and genome information. In this study, we successfully established a novel cell line from a histiocytic sarcoma (HS) of an African pygmy hedgehog, allowing us to conduct a drug screening. We investigated using FDA-approved drug library screening to determine which anticancer drug this tumor cell line is sensitive to, and as a result of apoptosis experiments, bortezomib among the three proteasome inhibitors was found to induce cell death of cancer cells by significantly increasing caspase-3 cleavage (P<0.01). Thus, we elucidated that the proteasome inhibitors, particularly bortezomib, exhibit anti-tumor effects on a cell line derived from an HS in an African pygmy hedgehog through a mechanism comparable to that described in human tumors. This study reports the first characterized cell line from the African pygmy hedgehog and also highlights the potential utility of bortezomib as an anti-tumor treatment for HS in this species.
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Affiliation(s)
- Sakuya INANAGA
- Laboratory of Molecular Diagnostics and Therapeutics, The
United Graduate School of Veterinary Medicine, Yamaguchi University, Yamaguchi,
Japan
| | - Hiroshi SHIMODA
- Laboratory of Veterinary Microbiology, The United Graduate
School of Veterinary Medicine, Yamaguchi University, Yamaguchi, Japan
| | - Masaya IGASE
- Laboratory of Molecular Diagnostics and Therapeutics, The
United Graduate School of Veterinary Medicine, Yamaguchi University, Yamaguchi,
Japan
| | - Hirotaka KONDO
- Laboratory of Veterinary Pathology, Department of Veterinary
Medicine, Nihon University, Kanagawa, Japan
| | - Iori KOIZUMI
- Laboratory of Veterinary Microbiology, The United Graduate
School of Veterinary Medicine, Yamaguchi University, Yamaguchi, Japan
- Koizumi Nest Animal Hospital, Fukuoka, Japan
| | - Takuya MIZUNO
- Laboratory of Molecular Diagnostics and Therapeutics, The
United Graduate School of Veterinary Medicine, Yamaguchi University, Yamaguchi,
Japan
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Samuel VP, Moglad E, Afzal M, Kazmi I, Alzarea SI, Ali H, Almujri SS, Abida, Imran M, Gupta G, Chinni SV, Tiwari A. Exploring Ubiquitin-specific proteases as therapeutic targets in Glioblastoma. Pathol Res Pract 2024; 260:155443. [PMID: 38981348 DOI: 10.1016/j.prp.2024.155443] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/01/2024] [Revised: 06/24/2024] [Accepted: 06/28/2024] [Indexed: 07/11/2024]
Abstract
Glioblastoma (GB) remains a formidable challenge and requires new treatment strategies. The vital part of the Ubiquitin-proteasome system (UPS) in cellular regulation has positioned it as a potentially crucial target in GB treatment, given its dysregulation oncolines. The Ubiquitin-specific proteases (USPs) in the UPS system were considered due to the garden role in the cellular processes associated with oncolines and their vital function in the apoptotic process, cell cycle regulation, and autophagy. The article provides a comprehensive summary of the evidence base for targeting USPs as potential factors for neoplasm treatment. The review considers the participation of the UPS system in the development, resulting in the importance of p53, Rb, and NF-κB, and evaluates specific goals for therapeutic administration using midnight proteasomal inhibitors and small molecule antagonists of E1 and E2 enzymes. Despite the slowed rate of drug creation, recent therapeutic discoveries based on USP system dynamics hold promise for specialized therapies. The review concludes with an analysis of future wanderers and the feasible effects of targeting USPs on personalized GB therapies, which can improve patient hydration in this current and unattractive therapeutic landscape. The manuscript emphasizes the possibility of USP oncogene therapy as a promising alternative treatment line for GB. It stresses the direct creation of research on the medical effectiveness of the approach.
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Affiliation(s)
- Vijaya Paul Samuel
- Department of Anatomy, RAK College of Medicine, RAK Medical and Health Sciences University, Ras Al Khaimah, the United Arab Emirates
| | - Ehssan Moglad
- Department of Pharmaceutics, College of Pharmacy, Prince Sattam bin Abdulaziz University, Alkharj 11942, Saudi Arabia
| | - Muhammad Afzal
- Department of Pharmaceutical Sciences, Pharmacy Program, Batterjee Medical College, P.O. Box 6231, Jeddah 21442, Saudi Arabia
| | - Imran Kazmi
- Department of Biochemistry, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Sami I Alzarea
- Department of Pharmacology, College of Pharmacy, Jouf University, Sakaka 72341, Al-Jouf, Saudi Arabia
| | - Haider Ali
- Centre for Global Health Research, Saveetha Medical College, Saveetha Institute of Medical and Technical Sciences, Saveetha University, India; Department of Pharmacology, Kyrgyz State Medical College, Bishkek, Kyrgyzstan
| | - Salem Salman Almujri
- Department of Pharmacology, College of Pharmacy, King Khalid University, Abha, Aseer 61421, Saudi Arabia
| | - Abida
- Department of Pharmaceutical Chemistry, College of Pharmacy, Northern Border University, Rafha 91911, Saudi Arabia
| | - Mohd Imran
- Department of Pharmaceutical Chemistry, College of Pharmacy, Northern Border University, Rafha 91911, Saudi Arabia
| | - Gaurav Gupta
- Centre for Research Impact & Outcome-Chitkara College of Pharmacy, Chitkara University, Punjab, India
| | - Suresh V Chinni
- Department of Biochemistry, Faculty of Medicine, Bioscience, and Nursing, MAHSA University, Jenjarom, Selangor 42610, Malaysia
| | - Abhishek Tiwari
- Department of Pharmacy, Pharmacy Academy, IFTM University, Lodhipur-Rajpur, Moradabad 244102, India.
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5
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Meadow ME, Broas S, Hoare M, Alimohammadi F, Welle KA, Swovick K, Hryhorenko JR, Martinez JC, Biashad SA, Seluanov A, Gorbunova V, Buchwalter A, Ghaemmaghami S. Proteome Birthdating Reveals Age-Selectivity of Protein Ubiquitination. Mol Cell Proteomics 2024; 23:100791. [PMID: 38797438 PMCID: PMC11260378 DOI: 10.1016/j.mcpro.2024.100791] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Revised: 03/27/2024] [Accepted: 05/15/2024] [Indexed: 05/29/2024] Open
Abstract
Within a cell, proteins have distinct and highly variable half-lives. As a result, the molecular ages of proteins can range from seconds to years. How the age of a protein influences its environmental interactions is a largely unexplored area of biology. To investigate the age-selectivity of cellular pathways, we developed a methodology termed "proteome birthdating" that barcodes proteins based on their time of synthesis. We demonstrate that this approach provides accurate measurements of protein turnover kinetics from a single biological sample encoding multiple labeling time-points. As a first application of the birthdated proteome, we investigated the age distribution of the human ubiquitinome. Our results indicate that the vast majority of ubiquitinated proteins in a cell consist of newly synthesized proteins and that these young proteins constitute the bulk of the degradative flux through the proteasome. Rapidly ubiquitinated nascent proteins are enriched in cytosolic subunits of large protein complexes. Conversely, proteins destined for the secretory pathway and vesicular transport have older ubiquitinated populations. Our data also identify a smaller subset of older ubiquitinated cellular proteins that do not appear to be targeted to the proteasome for rapid degradation. Together, our data provide an age census of the human ubiquitinome and establish proteome birthdating as a robust methodology for investigating the protein age-selectivity of diverse cellular pathways.
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Affiliation(s)
- Michael E Meadow
- Department of Biology, University of Rochester, New York, USA; Medical Scientist Training Program, University of Rochester, New York, USA
| | - Sarah Broas
- Department of Biology, University of Rochester, New York, USA
| | - Margaret Hoare
- Department of Biology, University of Rochester, New York, USA
| | - Fatemeh Alimohammadi
- Department of Pharmacology and Physiology, University of Rochester Medical Center, Rochester, New York, USA
| | - Kevin A Welle
- University of Rochester Mass Spectrometry Resource Laboratory, New York, USA
| | - Kyle Swovick
- University of Rochester Mass Spectrometry Resource Laboratory, New York, USA
| | | | - John C Martinez
- Department of Biology, University of Rochester, New York, USA
| | | | - Andrei Seluanov
- Department of Biology, University of Rochester, New York, USA; Department of Medicine, University of Rochester Medical Center, Rochester, New York, USA
| | - Vera Gorbunova
- Department of Biology, University of Rochester, New York, USA; Department of Medicine, University of Rochester Medical Center, Rochester, New York, USA
| | - Abigail Buchwalter
- Cardiovascular Research Institute, University of California San Francisco, San Francisco, California, USA
| | - Sina Ghaemmaghami
- Department of Biology, University of Rochester, New York, USA; University of Rochester Mass Spectrometry Resource Laboratory, New York, USA.
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6
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Elgazzaz M, Filipeanu C, Lazartigues E. Angiotensin-Converting Enzyme 2 Posttranslational Modifications and Implications for Hypertension and SARS-CoV-2: 2023 Lewis K. Dahl Memorial Lecture. Hypertension 2024; 81:1438-1449. [PMID: 38567498 PMCID: PMC11168885 DOI: 10.1161/hypertensionaha.124.22067] [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] [Indexed: 04/04/2024]
Abstract
ACE2 (angiotensin-converting enzyme 2), a multifunctional transmembrane protein, is well recognized as an important member of the (RAS) renin-angiotensin system with important roles in the regulation of cardiovascular function by opposing the harmful effects of Ang-II (angiotensin II) and AT1R (Ang-II type 1 receptor) activation. More recently, ACE2 was found to be the entry point for the SARS-CoV-2 virus into cells, causing COVID-19. This finding has led to an exponential rise in the number of publications focused on ACE2, albeit these studies often have opposite objectives to the preservation of ACE2 in cardiovascular regulation. However, notwithstanding accumulating data of the role of ACE2 in the generation of angiotensin-(1-7) and SARS-CoV-2 internalization, numerous other putative roles of this enzyme remain less investigated and not yet characterized. Currently, no drug modulating ACE2 function or expression is available in the clinic, and the development of new pharmacological tools should attempt targeting each step of the lifespan of the protein from synthesis to degradation. The present review expands on our presentation during the 2023 Lewis K. Dahl Memorial Lecture Sponsored by the American Heart Association Council on Hypertension. We provide a critical summary of the current knowledge of the mechanisms controlling ACE2 internalization and intracellular trafficking, the mutual regulation with GPCRs (G-protein-coupled receptors) and other proteins, and posttranslational modifications. A major focus is on ubiquitination which has become a critical step in the modulation of ACE2 cellular levels.
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Affiliation(s)
- Mona Elgazzaz
- Department of Physiology, Augusta University, Medical College of Georgia, Augusta, GA 30912, USA
- Genetics Unit, Department of Histology and Cell Biology, Faculty of Medicine, Suez Canal University, Ismailia, 41522, Egypt
| | - Catalin Filipeanu
- Department of Pharmacology, Howard University, Washington, DC 20059, USA
| | - Eric Lazartigues
- Cardiovascular Center of Excellence, Louisiana State University Health Sciences Center, New Orleans, LA 70112, USA
- Southeast Louisiana Veterans Health Care System, New Orleans, LA 70119, USA
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7
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Zhou X, Xu R, Wu Y, Zhou L, Xiang T. The role of proteasomes in tumorigenesis. Genes Dis 2024; 11:101070. [PMID: 38523673 PMCID: PMC10958230 DOI: 10.1016/j.gendis.2023.06.037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Revised: 05/10/2023] [Accepted: 06/27/2023] [Indexed: 03/26/2024] Open
Abstract
Protein homeostasis is the basis of normal life activities, and the proteasome family plays an extremely important function in this process. The proteasome 20S is a concentric circle structure with two α rings and two β rings overlapped. The proteasome 20S can perform both ATP-dependent and non-ATP-dependent ubiquitination proteasome degradation by binding to various subunits (such as 19S, 11S, and 200 PA), which is performed by its active subunit β1, β2, and β5. The proteasome can degrade misfolded, excess proteins to maintain homeostasis. At the same time, it can be utilized by tumors to degrade over-proliferate and unwanted proteins to support their growth. Proteasomes can affect the development of tumors from several aspects including tumor signaling pathways such as NF-κB and p53, cell cycle, immune regulation, and drug resistance. Proteasome-encoding genes have been found to be overexpressed in a variety of tumors, providing a potential novel target for cancer therapy. In addition, proteasome inhibitors such as bortezomib, carfilzomib, and ixazomib have been put into clinical application as the first-line treatment of multiple myeloma. More and more studies have shown that it also has different therapeutic effects in other tumors such as hepatocellular carcinoma, non-small cell lung cancer, glioblastoma, and neuroblastoma. However, proteasome inhibitors are not much effective due to their tolerance and singleness in other tumors. Therefore, further studies on their mechanisms of action and drug interactions are needed to investigate their therapeutic potential.
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Affiliation(s)
- Xiangyi Zhou
- Department of Oncology, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China
- Chongqing Key Laboratory of Translational Research for Cancer Metastasis and Individualized Treatment, Chongqing University Cancer Hospital, Chongqing 400030, China
| | - Ruqing Xu
- Department of Oncology, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China
| | - Yue Wu
- Department of Oncology, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China
| | - Li Zhou
- Chongqing Key Laboratory of Translational Research for Cancer Metastasis and Individualized Treatment, Chongqing University Cancer Hospital, Chongqing 400030, China
| | - Tingxiu Xiang
- Department of Oncology, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China
- Chongqing Key Laboratory of Translational Research for Cancer Metastasis and Individualized Treatment, Chongqing University Cancer Hospital, Chongqing 400030, China
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8
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Kumar P, Kinger S, Dubey AR, Jagtap YA, Choudhary A, Prasad A, Jha HC, Dhiman R, Gutti RK, Mishra A. Trehalose Promotes Clearance of Proteotoxic Aggregation of Neurodegenerative Disease-Associated Aberrant Proteins. Mol Neurobiol 2024; 61:4055-4073. [PMID: 38057642 DOI: 10.1007/s12035-023-03824-8] [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: 05/23/2023] [Accepted: 11/21/2023] [Indexed: 12/08/2023]
Abstract
Accumulation of misfolded proteins compromises overall cellular health and fitness. The failure to remove misfolded proteins is a critical reason for their unwanted aggregation in dense cellular protein pools. The accumulation of various inclusions serves as a clinical feature for neurodegenerative diseases. Previous findings suggest that different cellular compartments can store these abnormal inclusions. Studies of transgenic mice and cellular models of neurodegenerative diseases indicate that depleted chaperone capacity contributes to the aggregation of damaged or aberrant proteins, which consequently disturb proteostasis and cell viability. However, improving these abnormal proteins' selective elimination is yet to be well understood. Still, molecular strategies that can promote the effective degradation of abnormal proteins without compromising cellular viability are unclear. Here, we reported that the trehalose treatment elevates endogenous proteasome levels and enhances the activities of the proteasome. Trehalose-mediated proteasomal activation elevates the removal of both bona fide misfolded and various neurodegenerative disease-associated proteins. Our current study suggests that trehalose may retain a proteasome activation potential, which seems helpful in the solubilization of different mutant misfolded proteins, improving cell viability. These results reveal a possible molecular approach to reduce the overload of intracellular misfolded proteins, and such cytoprotective functions may play a critical role against protein conformational diseases.
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Affiliation(s)
- Prashant Kumar
- Cellular and Molecular Neurobiology Unit, Indian Institute of Technology Jodhpur, Rajasthan, 342037, India
| | - Sumit Kinger
- Cellular and Molecular Neurobiology Unit, Indian Institute of Technology Jodhpur, Rajasthan, 342037, India
| | - Ankur Rakesh Dubey
- Cellular and Molecular Neurobiology Unit, Indian Institute of Technology Jodhpur, Rajasthan, 342037, India
| | - Yuvraj Anandrao Jagtap
- Cellular and Molecular Neurobiology Unit, Indian Institute of Technology Jodhpur, Rajasthan, 342037, India
| | - Akash Choudhary
- Cellular and Molecular Neurobiology Unit, Indian Institute of Technology Jodhpur, Rajasthan, 342037, India
| | - Amit Prasad
- School of Biosciences and Bioengineering, Indian Institute of Technology Mandi, Mandi, India
| | - Hem Chandra Jha
- Infection Bioengineering Group, Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Indore, Simrol, India
| | - Rohan Dhiman
- Laboratory of Mycobacterial Immunology, Department of Life Science, National Institute of Technology, Rourkela, Odisha, 769008, India
| | - Ravi Kumar Gutti
- Department of Biochemistry, School of Life Sciences, University of Hyderabad, Hyderabad, India
| | - Amit Mishra
- Cellular and Molecular Neurobiology Unit, Indian Institute of Technology Jodhpur, Rajasthan, 342037, India.
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9
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Manav N, Jit BP, Kataria B, Sharma A. Cellular and epigenetic perspective of protein stability and its implications in the biological system. Epigenomics 2024:1-22. [PMID: 38884355 DOI: 10.1080/17501911.2024.2351788] [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: 11/29/2023] [Accepted: 04/30/2024] [Indexed: 06/18/2024] Open
Abstract
Protein stability is a fundamental prerequisite in both experimental and therapeutic applications. Current advancements in high throughput experimental techniques and functional ontology approaches have elucidated that impairment in the structure and stability of proteins is intricately associated with the cause and cure of several diseases. Therefore, it is paramount to deeply understand the physical and molecular confounding factors governing the stability of proteins. In this review article, we comprehensively investigated the evolution of protein stability, examining its emergence over time, its relationship with organizational aspects and the experimental methods used to understand it. Furthermore, we have also emphasized the role of Epigenetics and its interplay with post-translational modifications (PTMs) in regulating the stability of proteins.
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Affiliation(s)
- Nisha Manav
- Department of Biochemistry, All India Institute of Medical Sciences New Delhi, Ansari Nagar, 110029, India
| | - Bimal Prasad Jit
- Department of Biochemistry, All India Institute of Medical Sciences New Delhi, Ansari Nagar, 110029, India
| | - Babita Kataria
- Department of Medical Oncology, National Cancer Institute, All India Institute of Medical Sciences, Jhajjar, 124105, India
| | - Ashok Sharma
- Department of Biochemistry, All India Institute of Medical Sciences New Delhi, Ansari Nagar, 110029, India
- Department of Biochemistry, National Cancer Institute, All India Institute of Medical Sciences, Jhajjar, 124105, India
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10
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Chen N, Hu H, Tang J, Zheng F, Guo Z, Lin X, Aschner M, Shao W, Yu G, Cai P, Chou WC, Wu S, Li H. LncRNA NR_030777 promotes mitophagy by targeting CDK1-related mitochondrial fission and ATG12 to attenuate paraquat-induced Parkinson's disease. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2024; 349:123875. [PMID: 38548152 DOI: 10.1016/j.envpol.2024.123875] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2023] [Revised: 03/15/2024] [Accepted: 03/25/2024] [Indexed: 04/14/2024]
Abstract
With the evidence emerging that abnormal expression of long noncoding RNAs (lncRNAs) are involved in onset of Parkinson's disease (PD), the role of NR_030777 contributing to this disease is of great interest. We recently found that a novel lncRNA "NR_030777" demonstrates protective effects on PQ-induced neurodegeneration. However, the underlying molecular mechanisms of NR_030777 in the regulation of mitochondrial fission and mitophagy involved in PQ-induced neuronal damage remain to be explored. NR_030777 brain conditional overexpressing mice as well as in vitro primary neuronal cells from cerebral cortex and Neuro2a cells were adopted. Immunofluorescence, Immunohistochemistry, qRT-PCR and Western blotting were used to evaluate the expression levels of RNA and proteins. RNA immunoprecipitation and RNA pulldown experiment were used to evaluate the interaction of NR_030777 with its target proteins. NR_030777 and mitophagy were increased, and tyrosine hydroxylase (TH) levels recovered after NR_030777 overexpression upon PQ treatment. The overexpression and knockdown of NR_030777 unveiled that NR_030777 positively regulated mitophagy such as the upregulation of LC3B-II:I, ATG12-ATG5, p62 and NBR1. Moreover, the application of mdivi-1, a DRP-1 inhibitor, in combination with NR_030777 genetic modified cells unveiled that NR_030777 promoted DRP1-mediated mitochondrial fission and mitophagy. Furthermore, NR_030777 were directly bound to CDK1 to increase p-DRP1 levels at the Ser616 site, leading to mitochondrial fission and mitophagy. On the other hand, NR_030777 acted directly on ATG12 within the ATG12-ATG5 complex in the 800-1400 nt region to modulate the membrane formation. Accordingly, NR_030777 deficiency in neuron cells compromised cell mitophagy. Finally, the above findings were confirmed using NR_030777-overexpressing mice. NR_030777 exerted a protective effect on PQ-exposed mice by enhancing mitophagy. Our data provide the first scientific evidence for the precise invention of PQ-induced PD. Our findings further propose a breakthrough for understanding the regulatory relationship between NR_030777, CDK1, ATG12 and mitophagy in PQ-induced PD.
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Affiliation(s)
- Nengzhou Chen
- Department of Preventive Medicine, School of Public Health, Fujian Medical University, Fuzhou, 350122, China; Department of Labor Hygiene and Environmental Hygiene, School of Public Health, Guangdong Pharmaceutical University, Guangzhou, 510006, China.
| | - Hong Hu
- Department of Preventive Medicine, School of Public Health, Fujian Medical University, Fuzhou, 350122, China; The Key Laboratory of Environment and Health, School of Public Health, Fujian Medical University, Fuzhou, 350122, China; Fujian Provincial Key Laboratory of Environment Factors and Cancer, School of Public Health, Fujian Medical University, Fuzhou, 350122, China
| | - Jianping Tang
- Department of Preventive Medicine, School of Public Health, Fujian Medical University, Fuzhou, 350122, China
| | - Fuli Zheng
- Department of Preventive Medicine, School of Public Health, Fujian Medical University, Fuzhou, 350122, China; The Key Laboratory of Environment and Health, School of Public Health, Fujian Medical University, Fuzhou, 350122, China; Fujian Provincial Key Laboratory of Environment Factors and Cancer, School of Public Health, Fujian Medical University, Fuzhou, 350122, China
| | - Zhenkun Guo
- The Key Laboratory of Environment and Health, School of Public Health, Fujian Medical University, Fuzhou, 350122, China; Fujian Provincial Key Laboratory of Environment Factors and Cancer, School of Public Health, Fujian Medical University, Fuzhou, 350122, China
| | - Xinpei Lin
- Department of Preventive Medicine, School of Public Health, Fujian Medical University, Fuzhou, 350122, China
| | - Michael Aschner
- Department of Molecular Pharmacology, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
| | - Wenya Shao
- Department of Preventive Medicine, School of Public Health, Fujian Medical University, Fuzhou, 350122, China; The Key Laboratory of Environment and Health, School of Public Health, Fujian Medical University, Fuzhou, 350122, China; Fujian Provincial Key Laboratory of Environment Factors and Cancer, School of Public Health, Fujian Medical University, Fuzhou, 350122, China
| | - Guangxia Yu
- Department of Preventive Medicine, School of Public Health, Fujian Medical University, Fuzhou, 350122, China; The Key Laboratory of Environment and Health, School of Public Health, Fujian Medical University, Fuzhou, 350122, China; Fujian Provincial Key Laboratory of Environment Factors and Cancer, School of Public Health, Fujian Medical University, Fuzhou, 350122, China
| | - Ping Cai
- Department of Health Inspection and Quarantine, School of Public Health, Fujian Medical University, Fuzhou, 350122, China
| | - Wei-Chun Chou
- Department of Environmental and Global Health and Center for Environmental and Human Toxicology, College of Public Health and Health Professions, University of Florida, Gainesville, FL, USA
| | - Siying Wu
- The Key Laboratory of Environment and Health, School of Public Health, Fujian Medical University, Fuzhou, 350122, China; Fujian Provincial Key Laboratory of Environment Factors and Cancer, School of Public Health, Fujian Medical University, Fuzhou, 350122, China; Department of Epidemiology and Health Statistics, School of Public Health, Fujian Medical University, Fuzhou, 350122, China
| | - Huangyuan Li
- Department of Preventive Medicine, School of Public Health, Fujian Medical University, Fuzhou, 350122, China; The Key Laboratory of Environment and Health, School of Public Health, Fujian Medical University, Fuzhou, 350122, China; Fujian Provincial Key Laboratory of Environment Factors and Cancer, School of Public Health, Fujian Medical University, Fuzhou, 350122, China.
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11
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Wang WY, Wang BP, Su HS, Wei MM, Wei YT, Niu FX. Key role of K + and Ca 2+ in high-yield ethanol production by S. Cerevisiae from concentrated sugarcane molasses. Microb Cell Fact 2024; 23:123. [PMID: 38724968 PMCID: PMC11080136 DOI: 10.1186/s12934-024-02401-5] [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: 03/09/2024] [Accepted: 04/23/2024] [Indexed: 05/13/2024] Open
Abstract
BACKGROUND Saccharomyces cerevisiae is an important microorganism in ethanol synthesis, and with sugarcane molasses as the feedstock, ethanol is being synthesized sustainably to meet growing demands. However, high-concentration ethanol fermentation based on high-concentration sugarcane molasses-which is needed for reduced energy consumption of ethanol distillation at industrial scale-is yet to be achieved. RESULTS In the present study, to identify the main limiting factors of this process, adaptive laboratory evolution and high-throughput screening (Py-Fe3+) based on ARTP (atmospheric and room-temperature plasma) mutagenesis were applied. We identified high osmotic pressure, high temperature, high alcohol levels, and high concentrations of K+, Ca2+, K+ and Ca2+ (K+&Ca2+), and sugarcane molasses as the main limiting factors. The robust S. cerevisiae strains of NGT-F1, NGW-F1, NGC-F1, NGK+, NGCa2+ NGK+&Ca2+-F1, and NGTM-F1 exhibited high tolerance to the respective limiting factor and exhibited increased yield. Subsequently, ethanol synthesis, cell morphology, comparative genomics, and gene ontology (GO) enrichment analysis were performed in a molasses broth containing 250 g/L total fermentable sugars (TFS). Additionally, S. cerevisiae NGTM-F1 was used with 250 g/L (TFS) sugarcane molasses to synthesize ethanol in a 5-L fermenter, giving a yield of 111.65 g/L, the conversion of sugar to alcohol reached 95.53%. It is the highest level of physical mutagenesis yield at present. CONCLUSION Our results showed that K+ and Ca2+ ions primarily limited the efficient production of ethanol. Then, subsequent comparative transcriptomic GO and pathway analyses showed that the co-presence of K+ and Ca2+ exerted the most prominent limitation on efficient ethanol production. The results of this study might prove useful by promoting the development and utilization of green fuel bio-manufactured from molasses.
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Affiliation(s)
- Wei-Yang Wang
- Guangxi Key Laboratory of Green Processing of Sugar Resources, Guangxi University of Science and Technology, Liuzhou, 545006, China
- Guangxi Microorganism and Enzyme Research Center of Engineering Technology, College of Life Science and Technology, Guangxi University, Nanning, 530004, Guangxi, China
| | - Bei-Ping Wang
- Guangxi Key Laboratory of Green Processing of Sugar Resources, Guangxi University of Science and Technology, Liuzhou, 545006, China
| | - Hai-Song Su
- Guangxi Key Laboratory of Green Processing of Sugar Resources, Guangxi University of Science and Technology, Liuzhou, 545006, China
| | - Mei-Ming Wei
- Guangxi Key Laboratory of Green Processing of Sugar Resources, Guangxi University of Science and Technology, Liuzhou, 545006, China
| | - Yu-Tuo Wei
- Guangxi Microorganism and Enzyme Research Center of Engineering Technology, College of Life Science and Technology, Guangxi University, Nanning, 530004, Guangxi, China
| | - Fu-Xing Niu
- Guangxi Key Laboratory of Green Processing of Sugar Resources, Guangxi University of Science and Technology, Liuzhou, 545006, China.
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12
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Krishnamurthy K, Stillman IE, Hecht JL, Vyas M. Defining the Nature and Clinicopathologic Significance of Mallory-Denk-like Inclusions in Ovarian Fibromas: A Potential Degenerative Phenomenon Associated With Torsion. Int J Gynecol Pathol 2024; 43:290-295. [PMID: 37562060 DOI: 10.1097/pgp.0000000000000974] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/12/2023]
Abstract
Mallory-Denk bodies (MBD), described in alcoholic hepatitis, are composed of intermediate filaments admixed with other proteins. These cytoplasmic inclusions are irregularly shaped and eosinophilic as seen under the light microscope. MBD-like inclusions have rarely been described outside the hepatobiliary tree. Though rare, intracytoplasmic inclusions have been reported in ovarian fibromas. This study evaluates a series of torsed ovarian fibromas with intracytoplasmic inclusions resembling MDBs. Forty-three ovarian fibromas were retrieved from the pathology archives. The H&E slides were evaluated for the presence of MBD-like inclusions and histologic evidence of torsion. The cases with histologic features of torsion were included in the study group while the nontorsed fibromas formed the control group. Among the 15 cases of fibromas with torsion, MBD-like intracytoplasmic inclusions were seen in 5 cases, predominantly in the interface between necrotic areas and viable stroma. None of the cases from the control group showed any inclusions. There was no significant difference in the size of the fibroma or patient demographics between cases with and without inclusions. The inclusions were positive for cytokeratin and ubiquitin while being negative for per acidic Schiff and periodic acid-Schiff with diastase reaction, in the 3 cases selected for immunohistochemistry and special stains. Electron microscopy of the index case revealed a predominance of type 3 Mallory hyaline. This is the first report describing MDB-like inclusions in ovarian fibromas. These MDB-like inclusions appear to be limited to a fraction of ovarian fibromas that underwent torsion, suggesting that these inclusions likely result from subacute hypoxic damage to the cells.
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Fernandez‐Luna JL, Hernández JL, Curiel‐Olmo S, Martínez‐Amador NA, Vega AI, Quirce R, Montes‐Moreno S, Gutierrez O, del Real A, Sañudo C, Riancho JA. Osteomesopyknosis associated with a novel ALOX5 variant that impacts the RANKL pathway. Mol Genet Genomic Med 2024; 12:e2471. [PMID: 38803233 PMCID: PMC11130582 DOI: 10.1002/mgg3.2471] [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: 02/24/2024] [Revised: 05/03/2024] [Accepted: 05/14/2024] [Indexed: 05/29/2024] Open
Abstract
BACKGROUND Bone tissue homeostasis relies on the coordinated activity of the bone-forming osteoblasts and bone-resorbing osteoclasts. Osteomesopyknosis is considered a distinctive rare sclerosing skeletal disorder of unelucidated pathophysiology and presumably autosomal dominant transmission. However, the causal genes are unknown. METHODS We present a case report encompassing clinical assessments, imaging studies, and whole-exome sequencing analysis, complemented by functional in vitro experiments. RESULTS This new case of osteomesopyknosis was associated with a missense ALOX5 variant predicted to induce protein misfolding and proteasomal degradation. Transfection experiments demonstrated that the variant was associated with reduced protein levels restored by proteasomal inhibition with bortezomib. Likewise, gene expression analysis showed that the mutated gene was associated with a decreased RANKL/OPG ratio, which is a critical driver of osteoclast precursor differentiation. CONCLUSION Our data indicate impaired bone resorption as the underlying mechanism of this rare osteosclerosis, implicating ALOX5 pathogenic variants as potential etiological factors.
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Affiliation(s)
- Jose L. Fernandez‐Luna
- Unidad de Genética, Hospital UM ValdecillaSantanderSpain
- Instituto de Investigación Valdecilla (IDIVAL)SantanderSpain
- Centro de investigación biomédica en red de Enfermedades Raras (CIBERER)SantanderSpain
| | - José L. Hernández
- Instituto de Investigación Valdecilla (IDIVAL)SantanderSpain
- Servicio de Medicina Interna, Hospital UM ValdecillaSantanderSpain
- Departamento de Medicina y PsiquiatríaUniversidad de CantabriaSantanderSpain
| | - Soraya Curiel‐Olmo
- Unidad de Genética, Hospital UM ValdecillaSantanderSpain
- Instituto de Investigación Valdecilla (IDIVAL)SantanderSpain
| | | | - Ana I. Vega
- Unidad de Genética, Hospital UM ValdecillaSantanderSpain
- Instituto de Investigación Valdecilla (IDIVAL)SantanderSpain
| | - Remedios Quirce
- Instituto de Investigación Valdecilla (IDIVAL)SantanderSpain
- Servicio de Medicina NuclearHospital UM ValdecillaSantanderSpain
| | - Santiago Montes‐Moreno
- Instituto de Investigación Valdecilla (IDIVAL)SantanderSpain
- Servicio de Anatomía PatológicaHospital UM ValdecillaSantanderSpain
| | - Olga Gutierrez
- Unidad de Genética, Hospital UM ValdecillaSantanderSpain
- Instituto de Investigación Valdecilla (IDIVAL)SantanderSpain
| | - Alvaro del Real
- Instituto de Investigación Valdecilla (IDIVAL)SantanderSpain
- Departamento de Medicina y PsiquiatríaUniversidad de CantabriaSantanderSpain
| | - Carolina Sañudo
- Instituto de Investigación Valdecilla (IDIVAL)SantanderSpain
- Departamento de Medicina y PsiquiatríaUniversidad de CantabriaSantanderSpain
| | - Jose A. Riancho
- Instituto de Investigación Valdecilla (IDIVAL)SantanderSpain
- Centro de investigación biomédica en red de Enfermedades Raras (CIBERER)SantanderSpain
- Servicio de Medicina Interna, Hospital UM ValdecillaSantanderSpain
- Departamento de Medicina y PsiquiatríaUniversidad de CantabriaSantanderSpain
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14
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Dear AJ, Garcia GA, Meisl G, Collins GA, Knowles TPJ, Goldberg AL. Maximum entropy determination of mammalian proteome dynamics. Proc Natl Acad Sci U S A 2024; 121:e2313107121. [PMID: 38652742 PMCID: PMC11067036 DOI: 10.1073/pnas.2313107121] [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: 08/02/2023] [Accepted: 03/04/2024] [Indexed: 04/25/2024] Open
Abstract
Full understanding of proteostasis and energy utilization in cells will require knowledge of the fraction of cell proteins being degraded with different half-lives and their rates of synthesis. We therefore developed a method to determine such information that combines mathematical analysis of protein degradation kinetics obtained in pulse-chase experiments with Bayesian data fitting using the maximum entropy principle. This approach will enable rapid analyses of whole-cell protein dynamics in different cell types, physiological states, and neurodegenerative disease. Using it, we obtained surprising insights about protein stabilities in cultured cells normally and upon activation of proteolysis by mTOR inhibition and increasing cAMP or cGMP. It revealed that >90% of protein content in dividing mammalian cell lines is long-lived, with half-lives of 24 to 200 h, and therefore comprises much of the proteins in daughter cells. The well-studied short-lived proteins (half-lives < 10 h) together comprise <2% of cell protein mass, but surprisingly account for 10 to 20% of measurable newly synthesized protein mass. Evolution thus appears to have minimized intracellular proteolysis except to rapidly eliminate misfolded and regulatory proteins.
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Affiliation(s)
- Alexander J. Dear
- Department of Cell Biology, Blavatnik Institute, Harvard Medical School, Boston, MA02115
- Department of Chemistry, University of Cambridge, CambridgeCB2 1EW, United Kingdom
| | - Gonzalo A. Garcia
- Department of Chemistry, University of Cambridge, CambridgeCB2 1EW, United Kingdom
| | - Georg Meisl
- Department of Chemistry, University of Cambridge, CambridgeCB2 1EW, United Kingdom
| | - Galen A. Collins
- Department of Cell Biology, Blavatnik Institute, Harvard Medical School, Boston, MA02115
- Department of Biochemistry, Molecular Biology, Entomology & Plant Pathology, Mississippi State University, Starkville, MS39762
| | - Tuomas P. J. Knowles
- Department of Chemistry, University of Cambridge, CambridgeCB2 1EW, United Kingdom
- Cavendish Laboratory, Department of Physics, University of Cambridge, CambridgeCB3 0HE, United Kingdom
| | - Alfred L. Goldberg
- Department of Cell Biology, Blavatnik Institute, Harvard Medical School, Boston, MA02115
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15
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Pepelnjak M, Rogawski R, Arkind G, Leushkin Y, Fainer I, Ben-Nissan G, Picotti P, Sharon M. Systematic identification of 20S proteasome substrates. Mol Syst Biol 2024; 20:403-427. [PMID: 38287148 PMCID: PMC10987551 DOI: 10.1038/s44320-024-00015-y] [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: 09/13/2023] [Revised: 12/13/2023] [Accepted: 01/05/2024] [Indexed: 01/31/2024] Open
Abstract
For years, proteasomal degradation was predominantly attributed to the ubiquitin-26S proteasome pathway. However, it is now evident that the core 20S proteasome can independently target proteins for degradation. With approximately half of the cellular proteasomes comprising free 20S complexes, this degradation mechanism is not rare. Identifying 20S-specific substrates is challenging due to the dual-targeting of some proteins to either 20S or 26S proteasomes and the non-specificity of proteasome inhibitors. Consequently, knowledge of 20S proteasome substrates relies on limited hypothesis-driven studies. To comprehensively explore 20S proteasome substrates, we employed advanced mass spectrometry, along with biochemical and cellular analyses. This systematic approach revealed hundreds of 20S proteasome substrates, including proteins undergoing specific N- or C-terminal cleavage, possibly for regulation. Notably, these substrates were enriched in RNA- and DNA-binding proteins with intrinsically disordered regions, often found in the nucleus and stress granules. Under cellular stress, we observed reduced proteolytic activity in oxidized proteasomes, with oxidized protein substrates exhibiting higher structural disorder compared to unmodified proteins. Overall, our study illuminates the nature of 20S substrates, offering crucial insights into 20S proteasome biology.
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Affiliation(s)
- Monika Pepelnjak
- Institute of Molecular Systems Biology, Department of Biology, ETH Zurich, Zurich, Switzerland
| | - Rivkah Rogawski
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Galina Arkind
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Yegor Leushkin
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Irit Fainer
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Gili Ben-Nissan
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Paola Picotti
- Institute of Molecular Systems Biology, Department of Biology, ETH Zurich, Zurich, Switzerland.
| | - Michal Sharon
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, 7610001, Israel.
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16
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Uceda AB, Mariño L, Casasnovas R, Adrover M. An overview on glycation: molecular mechanisms, impact on proteins, pathogenesis, and inhibition. Biophys Rev 2024; 16:189-218. [PMID: 38737201 PMCID: PMC11078917 DOI: 10.1007/s12551-024-01188-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/21/2024] [Indexed: 05/14/2024] Open
Abstract
The formation of a heterogeneous set of advanced glycation end products (AGEs) is the final outcome of a non-enzymatic process that occurs in vivo on long-life biomolecules. This process, known as glycation, starts with the reaction between reducing sugars, or their autoxidation products, with the amino groups of proteins, DNA, or lipids, thus gaining relevance under hyperglycemic conditions. Once AGEs are formed, they might affect the biological function of the biomacromolecule and, therefore, induce the development of pathophysiological events. In fact, the accumulation of AGEs has been pointed as a triggering factor of obesity, diabetes-related diseases, coronary artery disease, neurological disorders, or chronic renal failure, among others. Given the deleterious consequences of glycation, evolution has designed endogenous mechanisms to undo glycation or to prevent it. In addition, many exogenous molecules have also emerged as powerful glycation inhibitors. This review aims to provide an overview on what glycation is. It starts by explaining the similarities and differences between glycation and glycosylation. Then, it describes in detail the molecular mechanism underlying glycation reactions, and the bio-molecular targets with higher propensity to be glycated. Next, it discusses the precise effects of glycation on protein structure, function, and aggregation, and how computational chemistry has provided insights on these aspects. Finally, it reports the most prevalent diseases induced by glycation, and the endogenous mechanisms and the current therapeutic interventions against it.
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Affiliation(s)
- Ana Belén Uceda
- Departament de Química, Universitat de Les Illes Balears, Health Research Institute of the Balearic Islands (IdISBa), Ctra. Valldemossa Km 7.5, 07122 Palma, Spain
| | - Laura Mariño
- Departament de Química, Universitat de Les Illes Balears, Health Research Institute of the Balearic Islands (IdISBa), Ctra. Valldemossa Km 7.5, 07122 Palma, Spain
| | - Rodrigo Casasnovas
- Departament de Química, Universitat de Les Illes Balears, Health Research Institute of the Balearic Islands (IdISBa), Ctra. Valldemossa Km 7.5, 07122 Palma, Spain
| | - Miquel Adrover
- Departament de Química, Universitat de Les Illes Balears, Health Research Institute of the Balearic Islands (IdISBa), Ctra. Valldemossa Km 7.5, 07122 Palma, Spain
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17
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Mitsiades CS. Proteasome Inhibitors in Multiple Myeloma: Biological Insights on Mechanisms of Action or Resistance Informed by Functional Genomics. Hematol Oncol Clin North Am 2024; 38:321-336. [PMID: 38278626 DOI: 10.1016/j.hoc.2023.12.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2024]
Abstract
During the last 20 years, proteasome inhibitors have been a cornerstone for the therapeutic management of multiple myeloma (MM). This review highlights how MM research has evolved over time in terms of our understanding of the mechanistic basis for the pronounced clinical activity of proteasome inhibitors in MM, compared with the limited clinical applications of this drug class outside the setting of plasma cell dyscrasias.
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Affiliation(s)
- Constantine S Mitsiades
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA; Harvard Medical School, Boston, MA, USA; Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA; Ludwig Center at Harvard, Boston, MA, USA.
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18
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Sun G, DeFelice MM, Gillies TE, Ahn-Horst TA, Andrews CJ, Krummenacker M, Karp PD, Morrison JH, Covert MW. Cross-evaluation of E. coli's operon structures via a whole-cell model suggests alternative cellular benefits for low- versus high-expressing operons. Cell Syst 2024; 15:227-245.e7. [PMID: 38417437 PMCID: PMC10957310 DOI: 10.1016/j.cels.2024.02.002] [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: 08/30/2023] [Revised: 09/12/2023] [Accepted: 02/08/2024] [Indexed: 03/01/2024]
Abstract
Many bacteria use operons to coregulate genes, but it remains unclear how operons benefit bacteria. We integrated E. coli's 788 polycistronic operons and 1,231 transcription units into an existing whole-cell model and found inconsistencies between the proposed operon structures and the RNA-seq read counts that the model was parameterized from. We resolved these inconsistencies through iterative, model-guided corrections to both datasets, including the correction of RNA-seq counts of short genes that were misreported as zero by existing alignment algorithms. The resulting model suggested two main modes by which operons benefit bacteria. For 86% of low-expression operons, adding operons increased the co-expression probabilities of their constituent proteins, whereas for 92% of high-expression operons, adding operons resulted in more stable expression ratios between the proteins. These simulations underscored the need for further experimental work on how operons reduce noise and synchronize both the expression timing and the quantity of constituent genes. A record of this paper's transparent peer review process is included in the supplemental information.
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Affiliation(s)
- Gwanggyu Sun
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Mialy M DeFelice
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Taryn E Gillies
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Travis A Ahn-Horst
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Cecelia J Andrews
- Department of Developmental Biology, Stanford University, Stanford, CA 94305, USA
| | | | | | - Jerry H Morrison
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Markus W Covert
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA.
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19
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Dhawka L, Palfini V, Hambright E, Blanco I, Poon C, Kahl A, Resch U, Bhawal R, Benakis C, Balachandran V, Holder A, Zhang S, Iadecola C, Hochrainer K. Post-ischemic ubiquitination at the postsynaptic density reversibly influences the activity of ischemia-relevant kinases. Commun Biol 2024; 7:321. [PMID: 38480905 PMCID: PMC10937959 DOI: 10.1038/s42003-024-06009-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Accepted: 03/04/2024] [Indexed: 03/17/2024] Open
Abstract
Ubiquitin modifications alter protein function and stability, thereby regulating cell homeostasis and viability, particularly under stress. Ischemic stroke induces protein ubiquitination at the ischemic periphery, wherein cells remain viable, however the identity of ubiquitinated proteins is unknown. Here, we employed a proteomics approach to identify these proteins in mice undergoing ischemic stroke. The data are available in a searchable web interface ( https://hochrainerlab.shinyapps.io/StrokeUbiOmics/ ). We detected increased ubiquitination of 198 proteins, many of which localize to the postsynaptic density (PSD) of glutamatergic neurons. Among these were proteins essential for maintaining PSD architecture, such as PSD95, as well as NMDA and AMPA receptor subunits. The largest enzymatic group at the PSD with elevated post-ischemic ubiquitination were kinases, such as CaMKII, PKC, Cdk5, and Pyk2, whose aberrant activities are well-known to contribute to post-ischemic neuronal death. Concurrent phospho-proteomics revealed altered PSD-associated phosphorylation patterns, indicative of modified kinase activities following stroke. PSD-located CaMKII, PKC, and Cdk5 activities were decreased while Pyk2 activity was increased after stroke. Removal of ubiquitin restored kinase activities to pre-stroke levels, identifying ubiquitination as the responsible molecular mechanism for post-ischemic kinase regulation. These findings unveil a previously unrecognized role of ubiquitination in the regulation of essential kinases involved in ischemic injury.
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Affiliation(s)
- Luvna Dhawka
- Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, USA
| | - Victoria Palfini
- Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, USA
| | - Emma Hambright
- Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, USA
| | - Ismary Blanco
- Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, USA
| | - Carrie Poon
- Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, USA
| | - Anja Kahl
- Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, USA
| | - Ulrike Resch
- Center for Physiology and Pharmacology, Medical University of Vienna, Vienna, Austria
| | - Ruchika Bhawal
- Institute of Biotechnology, Cornell University, Ithaca, NY, USA
| | - Corinne Benakis
- Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, USA
- Institute for Stroke and Dementia Research, Ludwig-Maximilians-University Munich, Munich, Germany
| | - Vaishali Balachandran
- Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, USA
| | - Alana Holder
- Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, USA
| | - Sheng Zhang
- Institute of Biotechnology, Cornell University, Ithaca, NY, USA
| | - Costantino Iadecola
- Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, USA
| | - Karin Hochrainer
- Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, USA.
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20
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Pardyak L, Liszewska E, Judycka S, Machcińska-Zielińska S, Karol H, Dietrich MA, Gojło E, Arent Z, Bilińska B, Rusco G, Iaffaldano N, Ciereszko A, Słowińska M. Liquid semen storage-induced alteration in the protein composition of turkey (Meleagris gallopavo) spermatozoa. Theriogenology 2024; 216:69-81. [PMID: 38159387 DOI: 10.1016/j.theriogenology.2023.12.026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Revised: 12/01/2023] [Accepted: 12/20/2023] [Indexed: 01/03/2024]
Abstract
Liquid storage of turkey semen without the loss of fertilizing ability is of practical interest to the poultry industry. However, fertility rates from liquid-stored turkey semen decline within a few hours. A clear cause of the decline in spermatozoa quality remains unidentified. Therefore, the purpose of the present study was to monitor the dynamics of proteomic changes in spermatozoa during 48 h of liquid storage by 2-dimensional difference in-gel electrophoresis coupled with matrix-assisted laser desorption/ionization mass spectrometry. A total of 57 protein spots were differentially expressed between fresh and stored spermatozoa; 42 spots were more and 15 were less abundant after 48 h of semen storage. Raw proteomic data are available via ProteomeXchange with identifier PXD043050. The selected differentially expressed proteins (DEPs) were validated by western blotting and localized in specific spermatozoa structures by immunofluorescence, such as the head (acrosin and tubulin α), midpiece (acrosin, aconitate hydratase 2, and glycerol-3-phosphate dehydrogenase) and tail (tubulin α). Most of the DEPs that changed in response to liquid storage were related to flagellum-dependent cell motility, energy derivation through oxidation of organic compounds and induction of fertilization, suggesting the complexity of the processes leading to the decrease in stored semen quality. The damaging effect of liquid storage on spermatozoa flagellum manifested as more microtubule proteins, such as tubulins and tektins, most likely formed by posttranslational modifications, tubulin α relocation from the tail to the sperm head, which appeared after 48 h of semen storage, and decreases in fibrous shelf proteins at the same time. Motility could be affected by dysregulation of Ca2+-binding proteins and disturbances in energy metabolism in spermatozoa flagellum. Regarding sperm mitochondria, DEPs involved in energy derivation through the oxidation of organic compounds indicated disturbances in fatty acid beta oxidation and the tricarboxylic acid cycle as possible reasons for energy deficiency during liquid storage. Disturbances in acrosin and 1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase zeta may be involved in rapid declines in the fertility potential of stored turkey spermatozoa. These results showed the complexity of the processes leading to a decrease in stored semen quality and broadened knowledge of the detrimental effects of liquid storage on turkey spermatozoa physiology.
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Affiliation(s)
- Laura Pardyak
- Center of Experimental and Innovative Medicine, University of Agriculture in Krakow, 30-248, Kraków, Poland
| | - Ewa Liszewska
- Department of Gamete and Embryo Biology, Institute of Animal Reproduction and Food Research, Polish Academy of Sciences in Olsztyn, Tuwima 10, 10-748, Olsztyn, Poland
| | - Sylwia Judycka
- Department of Gamete and Embryo Biology, Institute of Animal Reproduction and Food Research, Polish Academy of Sciences in Olsztyn, Tuwima 10, 10-748, Olsztyn, Poland
| | - Sylwia Machcińska-Zielińska
- Department of Biological Function of Food, Institute of Animal Reproduction and Food Research, Polish Academy of Sciences in Olsztyn, 10-748, Olsztyn, Poland
| | - Halina Karol
- Department of Gamete and Embryo Biology, Institute of Animal Reproduction and Food Research, Polish Academy of Sciences in Olsztyn, Tuwima 10, 10-748, Olsztyn, Poland
| | - Mariola A Dietrich
- Department of Gamete and Embryo Biology, Institute of Animal Reproduction and Food Research, Polish Academy of Sciences in Olsztyn, Tuwima 10, 10-748, Olsztyn, Poland
| | - Ewa Gojło
- Department of Plant Physiology, Genetics and Biotechnology, Faculty of Biology and Biotechnology, University of Warmia and Mazury in Olsztyn, 10-719, Olsztyn, Poland
| | - Zbigniew Arent
- Center of Experimental and Innovative Medicine, University of Agriculture in Krakow, 30-248, Kraków, Poland
| | - Barbara Bilińska
- Department of Endocrinology, Institute of Zoology and Biomedical Research, Jagiellonian University, 30-387, Kraków, Poland
| | - Giusy Rusco
- Department of Agricultural, Environmental and Food Sciences, University of Molise, 86100, Campobasso, CB, Italy
| | - Nicolaia Iaffaldano
- Department of Agricultural, Environmental and Food Sciences, University of Molise, 86100, Campobasso, CB, Italy
| | - Andrzej Ciereszko
- Department of Gamete and Embryo Biology, Institute of Animal Reproduction and Food Research, Polish Academy of Sciences in Olsztyn, Tuwima 10, 10-748, Olsztyn, Poland
| | - Mariola Słowińska
- Department of Gamete and Embryo Biology, Institute of Animal Reproduction and Food Research, Polish Academy of Sciences in Olsztyn, Tuwima 10, 10-748, Olsztyn, Poland.
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21
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Gurubaran IS. Mitochondrial damage and clearance in retinal pigment epithelial cells. Acta Ophthalmol 2024; 102 Suppl 282:3-53. [PMID: 38467968 DOI: 10.1111/aos.16661] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Accepted: 01/31/2024] [Indexed: 03/13/2024]
Abstract
Age-related macular degeneration (AMD) is a devastating eye disease that causes permanent vision loss in the central part of the retina, known as the macula. Patients with such severe visual loss face a reduced quality of life and are at a 1.5 times greater risk of death compared to the general population. Currently, there is no cure for or effective treatment for dry AMD. There are several mechanisms thought to underlie the disease, for example, ageing-associated chronic oxidative stress, mitochondrial damage, harmful protein aggregation and inflammation. As a way of gaining a better understanding of the molecular mechanisms behind AMD and thus developing new therapies, we have created a peroxisome proliferator-activated receptor gamma coactivator 1-alpha and nuclear factor erythroid 2-related factor 2 (PGC1α/NFE2L2) double-knockout (dKO) mouse model that mimics many of the clinical features of dry AMD, including elevated levels of oxidative stress markers, damaged mitochondria, accumulating lysosomal lipofuscin and extracellular drusen-like structures in retinal pigment epithelial cells (RPE). In addition, a human RPE cell-based model was established to examine the impact of non-functional intracellular clearance systems on inflammasome activation. In this study, we found that there was a disturbance in the autolysosomal machinery responsible for clearing mitochondria in the RPE cells of one-year-old PGC1α/NFE2L2-deficient mice. The confocal immunohistochemical analysis revealed an increase in autophagosome marker microtubule-associated proteins 1A/1B light chain 3B (LC3B) as well as multiple mitophagy markers such as PTE-induced putative kinase 1 (PINK1) and E3 ubiquitin ligase (PARKIN), along with signs of damaged mitochondria. However, no increase in autolysosome formation was detected, nor was there a colocalization of the lysosomal marker LAMP2 or the mitochondrial marker, ATP synthase β. There was an upregulation of late autolysosomal fusion Ras-related protein (Rab7) in the perinuclear space of RPE cells, together with autofluorescent aggregates. Additionally, we observed an increase in the numbers of Toll-like receptors 3 and 9, while those of NOD-like receptor 3 were decreased in PGC1α/NFE2L2 dKO retinal specimens compared to wild-type animals. There was a trend towards increased complement component C5a and increased involvement of the serine protease enzyme, thrombin, in enhancing the terminal pathway producing C5a, independent of C3. The levels of primary acute phase C-reactive protein and receptor for advanced glycation end products were also increased in the PGC1α/NFE2L2 dKO retina. Furthermore, selective proteasome inhibition with epoxomicin promoted both nicotinamide adenine dinucleotide phosphate (NADPH) oxidase and mitochondrial-mediated oxidative stress, leading to the release of mitochondrial DNA to the cytosol, resulting in potassium efflux-dependent activation of the absent in melanoma 2 (AIM2) inflammasome and the subsequent secretion of interleukin-1β in ARPE-19 cells. In conclusion, the data suggest that there is at least a relative decrease in mitophagy, increases in the amounts of C5 and thrombin and decreased C3 levels in this dry AMD-like model. Moreover, selective proteasome inhibition evoked mitochondrial damage and AIM2 inflammasome activation in ARPE-19 cells.
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Affiliation(s)
- Iswariyaraja Sridevi Gurubaran
- Department of Medicine, Clinical Medicine Unit, University of Eastern Finland Institute of Clinical Medicine, Kuopio, Northern Savonia, Finland
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22
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Zhang L, Du Y, Qu Q, Zheng Q. Structure basis for recognition of plant Rpn10 by phytoplasma SAP05 in ubiquitin-independent protein degradation. iScience 2024; 27:108892. [PMID: 38322988 PMCID: PMC10844826 DOI: 10.1016/j.isci.2024.108892] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Revised: 11/26/2023] [Accepted: 01/09/2024] [Indexed: 02/08/2024] Open
Abstract
Besides traditional ubiquitin-dependent proteasome degradation, thousands of eukaryotic proteins more than previously appreciated could undergo ubiquitin-independent proteasomal degradation (UbInPD). A pathogen-encoded effector protein SAP05 secreted by phytoplasma, could hijack hostage Rpn10 subunit of proteasome derived from Arabidopsis thaliana and target the degradation of GATA BINDING FACTOR (GATA) or SQUAMOSA-PROMOTER BINDING PROTEIN-LIKE (SPL) transcription factors (TFs) without ubiquitin or additional proteasome shuttle factors. To explain how could SAP05 target the degradation bypassing the ubiquitin-dependent pathway, we have determined the crystal structure of the complex between Arabidopsis thaliana Rpn10 and Aster Yellows witches'-broom phytoplasma SAP05 or onion yellow phytoplasma SAP05, which showed a previously unknown recognition interface. Sequence alignment and structural biological evidence showed that this interaction is highly conserved in various SAP05 homologs, suggesting a general mode in plant infection. After docking the complex structure to the plant proteasome, SAP05 was near to the adenosine triphosphatase (ATPase) central pore and enough to submit substrate to degradation process, which suggested a molecular glue-like role to bridge TFs close to the ATPase central pore of proteasomes for the direct degradation.
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Affiliation(s)
- Liying Zhang
- Institute of Translational Medicine, National Center for Translational Medicine (Shanghai), School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
- Tsinghua-Peking Center for Life Sciences, Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Department of Chemistry, Tsinghua University, Beijing 100084, China
| | - Yunxiang Du
- Institute of Translational Medicine, National Center for Translational Medicine (Shanghai), School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
- Tsinghua-Peking Center for Life Sciences, Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Department of Chemistry, Tsinghua University, Beijing 100084, China
| | - Qian Qu
- Institute of Translational Medicine, National Center for Translational Medicine (Shanghai), School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Qingyun Zheng
- Institute of Translational Medicine, National Center for Translational Medicine (Shanghai), School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
- Tsinghua-Peking Center for Life Sciences, Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Department of Chemistry, Tsinghua University, Beijing 100084, China
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23
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Chen Y, Qiang Y, Fan J, Zheng Q, Yan L, Fan G, Song X, Zhang N, Lv Q, Xiong J, Wang J, Cao J, Liu Y, Xiong J, Zhang W, Li F. Aggresome formation promotes ASK1/JNK signaling activation and stemness maintenance in ovarian cancer. Nat Commun 2024; 15:1321. [PMID: 38351029 PMCID: PMC10864366 DOI: 10.1038/s41467-024-45698-x] [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: 05/09/2023] [Accepted: 02/01/2024] [Indexed: 02/16/2024] Open
Abstract
Aggresomes are the product of misfolded protein aggregation, and the presence of aggresomes has been correlated with poor prognosis in cancer patients. However, the exact role of aggresomes in tumorigenesis and cancer progression remains largely unknown. Herein, the multiomics screening reveal that OTUD1 protein plays an important role in retaining ovarian cancer stem cell (OCSC) properties. Mechanistically, the elevated OTUD1 protein levels lead to the formation of OTUD1-based cytoplasmic aggresomes, which is mediated by a short peptide located in the intrinsically disordered OTUD1 N-terminal region. Furthermore, OTUD1-based aggresomes recruit ASK1 via protein-protein interactions, which in turn stabilize ASK1 in a deubiquitinase-independent manner and activate the downstream JNK signaling pathway for OCSC maintenance. Notably, the disruption of OTUD1-based aggresomes or treatment with ASK1/JNK inhibitors, including ibrutinib, an FDA-approved drug that was recently identified as an MKK7 inhibitor, effectively reduced OCSC stemness (OSCS) of OTUD1high ovarian cancer cells. In summary, our work suggests that aggresome formation in tumor cells could function as a signaling hub and that aggresome-based therapy has translational potential for patients with OTUD1high ovarian cancer.
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Affiliation(s)
- Yurou Chen
- Department of Gynecology, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China
| | - Yulong Qiang
- Department of Medical Genetics, TaiKang Medical School (School of Basic Medical Science), Wuhan University, Wuhan, 430071, China
| | - Jiachen Fan
- Department of Medical Genetics, TaiKang Medical School (School of Basic Medical Science), Wuhan University, Wuhan, 430071, China
| | - Qian Zheng
- Department of Medical Genetics, TaiKang Medical School (School of Basic Medical Science), Wuhan University, Wuhan, 430071, China
| | - Leilei Yan
- Department of Medical Genetics, TaiKang Medical School (School of Basic Medical Science), Wuhan University, Wuhan, 430071, China
| | - Guanlan Fan
- Department of Gynecology, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China
| | - Xiaofei Song
- Department of Medical Genetics, TaiKang Medical School (School of Basic Medical Science), Wuhan University, Wuhan, 430071, China
| | - Nan Zhang
- Department of Medical Genetics, TaiKang Medical School (School of Basic Medical Science), Wuhan University, Wuhan, 430071, China
| | - Qiongying Lv
- Department of Gynecology, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China
| | - Jiaqiang Xiong
- Department of Gynecology, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China
| | - Jingtao Wang
- Department of Gynecology, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China
| | - Jing Cao
- Department of Gynecology, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China
| | - Yanyan Liu
- Department of Gynecology, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China
| | - Jie Xiong
- Department of Immunology, TaiKang Medical School (School of Basic Medical Science), Wuhan University, Wuhan, 430071, China.
| | - Wei Zhang
- Department of Gynecology, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China.
| | - Feng Li
- Department of Gynecology, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China.
- Department of Medical Genetics, TaiKang Medical School (School of Basic Medical Science), Wuhan University, Wuhan, 430071, China.
- Hubei Provincial Key Laboratory of Allergy and Immunology, Wuhan University, Wuhan, 430071, China.
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24
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Zhang Y, Wei Y, Wu M, Liu M, Liang S, Zhu X, Liu X, Lin F. Cand2 inhibits CRL-mediated ubiquitination and suppresses autophagy to facilitate pathogenicity of phytopathogenic fungi. PLANT COMMUNICATIONS 2024; 5:100720. [PMID: 37718510 PMCID: PMC10873881 DOI: 10.1016/j.xplc.2023.100720] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Revised: 09/11/2023] [Accepted: 09/14/2023] [Indexed: 09/19/2023]
Abstract
The ubiquitin-proteasome system and the autophagy system are the two primary mechanisms used by eukaryotes to maintain protein homeostasis, and both are closely related to the pathogenicity of the rice blast fungus. In this research, we identified MoCand2 as an inhibitor of ubiquitination in Magnaporthe oryzae. Through this role, MoCand2 participates in the regulation of autophagy and pathogenicity. Specifically, we found that deletion of MoCand2 increased the ubiquitination level in M. oryzae, whereas overexpression of MoCand2 inhibited the accumulation of ubiquitinated proteins. Interaction analyses showed that MoCand2 is a subunit of Cullin-RING ligases (CRLs). It suppresses ubiquitination by blocking the assembly of CRLs and downregulating the expression of key CRL subunits. Further research indicated that MoCand2 regulates autophagy through ubiquitination. MoCand2 knockout led to over-ubiquitination and over-degradation of MoTor, and we confirmed that MoTor content was negatively correlated with autophagy level. In addition, MoCand2 knockout accelerated the K63 ubiquitination of MoAtg6 and strengthened the assembly and activity of the phosphatidylinositol-3-kinase class 3 complex, thus enhancing autophagy. Abnormal ubiquitination and autophagy in ΔMocand2 resulted in defects in growth, conidiation, stress resistance, and pathogenicity. Finally, sequence alignment and functional analyses in other phytopathogenic fungi confirmed the high conservation of fungal Cand2s. Our research thus reveals a novel mechanism by which ubiquitination regulates autophagy and pathogenicity in phytopathogenic fungi.
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Affiliation(s)
- Yunran Zhang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China; Hainan Institute, Zhejiang University, Sanya 572025, China
| | - Yunyun Wei
- College of Biology and Environmental Engineering, Zhejiang Shuren University, Hangzhou 310015, China
| | - Minghua Wu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Mengyu Liu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Shuang Liang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Plant Protection and Microbiology, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Xueming Zhu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Plant Protection and Microbiology, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Xiaohong Liu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Fucheng Lin
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China; State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Plant Protection and Microbiology, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China.
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25
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Asti AL, Crespi S, Rampino T, Zelini P, Gregorini M, Pascale A, Marchesi N, Saccucci S, Colombani C, Vitalini S, Iriti M. Yet another in vitro evidence that natural compounds introduced by diet have anti-amyloidogenic activities and can counteract neurodegenerative disease depending on aging. Nat Prod Res 2024; 38:861-866. [PMID: 36964661 DOI: 10.1080/14786419.2023.2192493] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Accepted: 03/11/2023] [Indexed: 03/26/2023]
Abstract
A major issue in Alzheimer's disease (AD) research is to find some new therapeutic drug which decrease Amyloid-beta (Aβ) aggregation. From a therapeutic point of view the major question is whether pharmacological inhibition of inflammation pathways will be able to safely reverse or slow the course of disease. Natural compounds are capable of binding to different targets implicated in AD and exert neuroprotective effects. Aim of this study was to evaluate the in vitro inhibition of Aβ1-42 fibrillogenesis in presence of Gallic acid, Rutin, Melatonin and ProvinolsTM . We performed the analysis with Transmission and Scanning Electron Microscopy, and with X-ray microanalysis. Samples treated with Rutin, that arises from phenylalanine via the phenylpropanoid pathway, show the best effective result obtained because a significantly fibril inhibition activity is detectable compared to the other compounds. Melatonin shows a better inhibitory activity than ProvinolsTM and Gallic acid at the considered concentrations.
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Affiliation(s)
- Anna Lia Asti
- Unit of Nephrology, Dialysis and Transplantation, Fondazione I.R.C.C.S. Policlinico San Matteo, Pavia, Italy
| | - Stefania Crespi
- Department of Earth Sciences Ardito Desio, University of Milan, Milan, Italy
| | - Teresa Rampino
- Unit of Nephrology, Dialysis and Transplantation, Fondazione I.R.C.C.S. Policlinico San Matteo, Pavia, Italy
| | - Paola Zelini
- Unit of Obstetrics and Gynecology, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
| | - Marilena Gregorini
- Unit of Nephrology, Dialysis and Transplantation, Fondazione I.R.C.C.S. Policlinico San Matteo, Pavia, Italy
- Department of Internal Medicine and Therapeutics, University of Pavia, Pavia, Italy
| | - Alessia Pascale
- Department of Drug Sciences, Pharmacology Section, University of Pavia, Pavia, Italy
| | - Nicoletta Marchesi
- Department of Drug Sciences, Pharmacology Section, University of Pavia, Pavia, Italy
| | | | - Carla Colombani
- Department of Agricultural and Environmental Sciences Territorial Production and Agroenergy, University of Milan, Milan, Italy
| | - Sara Vitalini
- Department of Biomedical, Surgical and Dental Sciences, University of Milan, Milan, Italy
| | - Marcello Iriti
- Department of Biomedical, Surgical and Dental Sciences, University of Milan, Milan, Italy
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26
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Kotian NP, Prabhu A, Tender T, Raghu Chandrashekar H. Methylglyoxal Induced Modifications to Stabilize Therapeutic Proteins: A Review. Protein J 2024; 43:39-47. [PMID: 38017314 DOI: 10.1007/s10930-023-10166-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/10/2023] [Indexed: 11/30/2023]
Abstract
Therapeutic proteins are potent, fast-acting drugs that are highly effective in treating various conditions. Medicinal protein usage has increased in the past 10 years, and it will evolve further as we better understand disease molecular pathways. However, it is associated with high processing costs, limited stability, difficulty in being administered as an oral medication, and the inability of large proteins to penetrate tissue and reach their target locations. Many methods have been developed to overcome the problems with the stability and chaperone activity of therapeutic proteins, viz., the addition of external agents (changing the properties of the surrounding solvent by using stabilizing excipients, e.g., amino acids, sugars, polyols) and internal agents (chemical modifications that influence its structural properties, e.g., mutations, glycosylation). However, these methods must completely clear protein instability and chaperone issues. There is still much work to be done on finetuning chaperone proteins to increase their biological efficacy and stability. Methylglyoxal (MGO), a potent dicarbonyl compound, reacts with proteins and forms covalent cross-links. Much research on MGO scavengers has been conducted since they are known to alter protein structure, which may result in alterations in biological activity and stability. MGO is naturally produced within our body, however, its impact on chaperones and protein stability needs to be better understood and seems to vary based on concentration. This review highlights the efforts of several research groups on the effect of MGO on various proteins. It also addresses the impact of MGO on a client protein, α-crystallin, to understand the potential solutions to the protein's chaperone and stability problems.
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Affiliation(s)
- Nainika Prashant Kotian
- Department of Pharmaceutical Biotechnology, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal, 576104, India
| | - Anusha Prabhu
- Department of Pharmaceutical Biotechnology, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal, 576104, India
| | - Tenzin Tender
- Department of Pharmaceutical Biotechnology, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal, 576104, India
| | - Hariharapura Raghu Chandrashekar
- Department of Pharmaceutical Biotechnology, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal, 576104, India.
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27
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Wang H, Bai C, Dang X, Wang H. MiR-383 sensitizes osteosarcoma cells to bortezomib treatment via down-regulating PSMB5. Mol Biol Rep 2024; 51:170. [PMID: 38252234 DOI: 10.1007/s11033-023-08964-7] [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: 08/05/2023] [Accepted: 11/17/2023] [Indexed: 01/23/2024]
Abstract
BACKGROUND Proteasome inhibition is a promising strategy for cancer therapy. Bortezomib, which primarily targets the chymotrypsin-like activity of PSMB5, has demonstrated efficacy in various tumors. However, there is variable sensitivity to bortezomib, which could be attributed, in part, to variations in the expression of proteasome subunits. METHODS AND RESULTS In this study, we investigated whether miR-383 affects the expression of proteasome subunits in osteosarcoma (OS) cells, and if so, whether OS cells display differential sensitivity to bortezomib concerning miR-383 expression. We detected a decreased miR-383 expression in OS cells and tissues. Then we found a negative correlation between the cytotoxicity of bortezomib and the expression level of the proteasome 20S core particle subunit β5 (PSMB5). Intriguingly, we identified PSMB5 as a direct target of miR-383. Increased expression of miR-383 resulted in decreased PSMB5 expression and increased sensitivity to bortezomib in OS cells. CONCLUSIONS In summary, our findings present the initial comprehensive analysis of the function of miR-383 in OS. The outcomes indicate that miR-383 may augment the anticancer effect of bortezomib through PSMB5 repression, offering a novel therapeutic approach in OS and a fresh pathway for proteasome regulation.
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Affiliation(s)
- Haifan Wang
- Department of Orthopaedics, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, 710004, Shaanxi, China
| | - Chuanyi Bai
- Department of Orthopaedics, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, 710004, Shaanxi, China
| | - Xiaoqian Dang
- Department of Orthopaedics, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, 710004, Shaanxi, China
| | - Haoyu Wang
- Department of Orthopaedics, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, 710004, Shaanxi, China.
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28
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Guo Y, Wang S, Li L, Zhang H, Chen X, Huang Z, Liu Y. Immunoproteasome Subunit Low Molecular Mass Peptide 2 (LMP2) Deficiency Ameliorates LPS/Aβ 1-42-Induced Neuroinflammation. Mol Neurobiol 2024; 61:28-41. [PMID: 37568045 DOI: 10.1007/s12035-023-03564-9] [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: 05/16/2023] [Accepted: 08/07/2023] [Indexed: 08/13/2023]
Abstract
Low molecular mass peptide 2 (LMP2) is the β1i subunit of immunoproteasome (iP) which plays a key role in neuroinflammatory responses, and inhibition of iP exhibits a high neuroprotective action against neurodegenerative diseases. Since neuroinflammation has been shown to be involved in the development and progression of Alzheimer's disease (AD), the aim of this study was to evaluate the anti-inflammatory role of LMP2 deficiency in AD in vivo and in vitro. Here, we found that LMP2 was upregulated in the brains of 5 × FAD and APP/PS1 mice and increased with age in C57/BL6 mice. We showed that the lack of LMP2 significantly decreased NLRP3 expression and downstream cytokine release in microglia, resulting in partially blocking Aβ1-42- or LPS-induced inflammation in vivo and in vitro, which ameliorated cognitive deficits in aged rats and D-galactose + Aβ1-42-treated rats. These results suggest that LMP2 contributes to the regulation of LPS-or Aβ-driven innate immune responses by diminishing NLRP3 expression and clarify that inhibition of iP function may mediate the inflammatory-related cognitive phenotype.
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Affiliation(s)
- Yueting Guo
- Key Laboratory of Stem Cell Engineering and Regenerative Medicine, Fujian Province University/School of Basic Medical Science, Fujian Medical University, Fuzhou City, 350122, Fujian Province, China
| | - Shiyi Wang
- Key Laboratory of Stem Cell Engineering and Regenerative Medicine, Fujian Province University/School of Basic Medical Science, Fujian Medical University, Fuzhou City, 350122, Fujian Province, China
| | - Li Li
- Key Laboratory of Gastrointestinal Cancer (Fujian Medical University), Ministry of Education, Fuzhou City, 350122, Fujian Province, China
- Department of Cell Biology and Genetics of Basic Medical Sciences, Fujian Medical University, Fuzhou City, 350122, Fujian Province, China
| | - Hengce Zhang
- Key Laboratory of Stem Cell Engineering and Regenerative Medicine, Fujian Province University/School of Basic Medical Science, Fujian Medical University, Fuzhou City, 350122, Fujian Province, China
| | - Xiaoyang Chen
- Key Laboratory of Stem Cell Engineering and Regenerative Medicine, Fujian Province University/School of Basic Medical Science, Fujian Medical University, Fuzhou City, 350122, Fujian Province, China
| | - Zihan Huang
- Key Laboratory of Stem Cell Engineering and Regenerative Medicine, Fujian Province University/School of Basic Medical Science, Fujian Medical University, Fuzhou City, 350122, Fujian Province, China
| | - Yingchun Liu
- Key Laboratory of Stem Cell Engineering and Regenerative Medicine, Fujian Province University/School of Basic Medical Science, Fujian Medical University, Fuzhou City, 350122, Fujian Province, China.
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Sundram S, Dhiman N, Malviya R, Awasthi R. Non-coding RNAs in Regulation of Protein Aggregation and Clearance Pathways: Current Perspectives Towards Alzheimer's Research and Therapy. Curr Gene Ther 2024; 24:8-16. [PMID: 37519207 DOI: 10.2174/1566523223666230731093030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Revised: 05/07/2023] [Accepted: 07/04/2023] [Indexed: 08/01/2023]
Abstract
Alzheimer's disease (AD) is the leading cause of dementia, affecting approximately 45.0 million people worldwide and ranking as the fifth leading cause of mortality. AD is identified by neurofibrillary tangles (NFTs), which include abnormally phosphorylated tau-protein and amyloid protein (amyloid plaques). Peptide dysregulation is caused by an imbalance between the production and clearance of the amyloid-beta (Aβ) and NFT. AD begins to develop when these peptides are not cleared from the body. As a result, understanding the processes that control both normal and pathological protein recycling in neuronal cells is critical. Insufficient Aβ and NFT clearance are important factors in the development of AD. Autophagy, lysosomal dysfunction, and ubiquitin-proteasome dysfunction have potential roles in the pathogenesis of many neurodegenerative disorders, particularly in AD. Modulation of these pathways may provide a novel treatment strategy for AD. Non-coding RNAs (ncRNAs) have recently emerged as important biological regulators, with particular relevance to the emergence and development of neurodegenerative disorders such as AD. ncRNAs can be used as potential therapeutic targets and diagnostic biomarkers due to their critical regulatory functions in several biological processes involved in disease development, such as the aggregation and accumulation of Aβ and NFT. It is evident that ncRNAs play a role in the pathophysiology of AD. In this communication, we explored the link between ncRNAs and AD and their regulatory mechanisms that may help in finding new therapeutic targets and AD medications.
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Affiliation(s)
- Sonali Sundram
- Department of Pharmacy, School of Medical and Allied Sciences, Galgotias University, Greater Noida, India
- Amity Institute of Pharmacy, Amity University Uttar Pradesh, Noida, India
| | - Neerupma Dhiman
- Amity Institute of Pharmacy, Amity University Uttar Pradesh, Noida, India
| | - Rishabha Malviya
- Department of Pharmacy, School of Medical and Allied Sciences, Galgotias University, Greater Noida, India
| | - Rajendra Awasthi
- Department of Pharmaceutical Sciences, School of Health Sciences & Technology, UPES University, Dehradun, Uttarakhand, India
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Afolabi LO, Bi J, Chen L, Yang X, Wan X. Suppression of protein quality control system by TRIM30a sensitises tumour cells to NK cell-mediated immune surveillance. Immunology 2024; 171:60-76. [PMID: 37753964 DOI: 10.1111/imm.13694] [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: 02/05/2023] [Accepted: 08/30/2023] [Indexed: 09/28/2023] Open
Abstract
Tumorigenesis entails circumventing cell-intrinsic regulatory mechanisms while avoiding extrinsic immune surveillance and other host defence systems. Nevertheless, how tumour cells' ability to eliminate misfolded proteins affects immune surveillance remains poorly understood. In this study, we find that overexpression of murine tripartite motif-containing protein 30a (TRIM30a) sensitises tumour cells to natural killer (NK) cells-mediated cytolysis. TRIM30a has no effect on tumour cell proliferation or apoptosis in vitro. However, TRIM30a-overexpressing tumour cells grow substantially slower than control tumour cells in immune-competent mice but not in NK cell-depleted mice. [Correction added on 04 October 2023, after first online publication: 'NK-depleted' has been changed to 'NK cell-depleted' in the preceding sentence.] Mechanistically, TRIM30a overexpression impedes the clearance of misfolded proteins and increases the production of reactive oxygen species induced by proteotoxic stress, implying that TRIM30a impairs protein quality control (PQC) systems in tumour cells. Furthermore, TRIM30a reduces expression of genes encoding proteasome subunits and antioxidant proteins. Our study demonstrates that TRIM30a is a potential tumour suppressor and immune modulator that promotes tumour cytolysis by NK cells, and suggests that an enhanced PQC and antioxidant capacity is an integral part of the immune escape mechanism during tumorigenesis.
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Affiliation(s)
- Lukman O Afolabi
- Guangdong Immune Cell Therapy Engineering and Technology Research Center, Center for Protein and Cell-based Drugs, Institute of Biomedicine and Biotechnology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Jiacheng Bi
- Guangdong Immune Cell Therapy Engineering and Technology Research Center, Center for Protein and Cell-based Drugs, Institute of Biomedicine and Biotechnology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
- University of Chinese Academy of Sciences, Beijing, China
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Liang Chen
- University of Chinese Academy of Sciences, Beijing, China
- Shenzhen Laboratory of Tumor Cell Biology, Institute of Biomedicine and Biotechnology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Xiaolu Yang
- Department of Cancer Biology and Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Xiaochun Wan
- Guangdong Immune Cell Therapy Engineering and Technology Research Center, Center for Protein and Cell-based Drugs, Institute of Biomedicine and Biotechnology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
- University of Chinese Academy of Sciences, Beijing, China
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31
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Tilahun HG, Mullagura HN, Humphrey JD, Baek S. A biochemomechanical model of collagen turnover in arterial adaptations to hemodynamic loading. Biomech Model Mechanobiol 2023; 22:2063-2082. [PMID: 37505299 DOI: 10.1007/s10237-023-01750-1] [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: 01/31/2023] [Accepted: 07/06/2023] [Indexed: 07/29/2023]
Abstract
The production, removal, and remodeling of fibrillar collagen is fundamental to mechanical homeostasis in arteries, including dynamic morphological and microstructural changes that occur in response to sustained changes in blood flow and pressure under physiological conditions. These dynamic processes involve complex, coupled biological, chemical, and mechanical mechanisms that are not completely understood. Nevertheless, recent simulations using constrained mixture models with phenomenologically motivated constitutive relations have proven able to predict salient features of the progression of certain vascular adaptations as well as disease processes. Collagen turnover is modeled, in part, via stress-dependent changes in collagen half-life, typically within the range of 10-70 days. By contrast, in this work we introduce a biochemomechanical approach to model the cellular synthesis of procollagen as well as its transition from an intermediate state of assembled microfibrils to mature cross-linked fibers, with mechano-regulated removal. The resulting model can simulate temporal changes in geometry, composition, and stress during early vascular adaptation (weeks to months) for modest changes in blood flow or pressure. It is shown that these simulations capture salient features from data presented in the literature from different animal models.
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Affiliation(s)
- Hailu G Tilahun
- Department of Mechanical Engineering, Michigan State University, 3259 Engineering Building, East Lansing, MI, 48824, USA
| | - Haritha N Mullagura
- Department of Mechanical Engineering, Michigan State University, 3259 Engineering Building, East Lansing, MI, 48824, USA
| | - Jay D Humphrey
- Department of Biomedical Engineering, Yale University, New Haven, CT, 06520, USA
| | - Seungik Baek
- Department of Mechanical Engineering, Michigan State University, 3259 Engineering Building, East Lansing, MI, 48824, USA.
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32
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Omari S, Lee H, Wang J, Zeng SX, Lu H. Extracellular and intracellular functions of coiled-coil domain containing 3. J Mol Cell Biol 2023; 15:mjad037. [PMID: 37263799 PMCID: PMC10849165 DOI: 10.1093/jmcb/mjad037] [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: 04/03/2023] [Revised: 05/25/2023] [Accepted: 05/31/2023] [Indexed: 06/03/2023] Open
Abstract
Coiled-coil domain containing 3 (CCDC3, also called Favine) is a highly conserved protein initially identified as a protein secreted from adipocytes and endothelial cells in the vascular system with endocrine-like functions. Recently, CCDC3 was also found to function as a nuclear tumor suppressor in breast cancers. Although it is still understudied, CCDC3, since its discovery, has been shown to play multiple roles in lipid metabolism, fatty liver, abdominal obesity, anti-inflammation, atherosclerosis, and cancer. This essay is thus composed to offer an overview of these extracellular endocrine-like and intracellular (nuclear) functions of CCDC3. We also discuss the possible underlying cellular and molecular mechanisms of CCDC3, the implications for clinical translation, and the remaining puzzles about this special molecule.
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Affiliation(s)
- Sara Omari
- Department of Biochemistry & Molecular Biology, Tulane University School of Medicine, New Orleans, LA 70112, USA
- Tulane Cancer Center, Tulane University School of Medicine, New Orleans, LA 70112, USA
| | - Hyemin Lee
- Department of Biochemistry & Molecular Biology, Tulane University School of Medicine, New Orleans, LA 70112, USA
- Tulane Cancer Center, Tulane University School of Medicine, New Orleans, LA 70112, USA
| | - Jieqiong Wang
- Department of Biochemistry & Molecular Biology, Tulane University School of Medicine, New Orleans, LA 70112, USA
- Tulane Cancer Center, Tulane University School of Medicine, New Orleans, LA 70112, USA
| | - Shelya X Zeng
- Department of Biochemistry & Molecular Biology, Tulane University School of Medicine, New Orleans, LA 70112, USA
- Tulane Cancer Center, Tulane University School of Medicine, New Orleans, LA 70112, USA
| | - Hua Lu
- Department of Biochemistry & Molecular Biology, Tulane University School of Medicine, New Orleans, LA 70112, USA
- Tulane Cancer Center, Tulane University School of Medicine, New Orleans, LA 70112, USA
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33
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Jiang Y, MacNeil LT. Simple model systems reveal conserved mechanisms of Alzheimer's disease and related tauopathies. Mol Neurodegener 2023; 18:82. [PMID: 37950311 PMCID: PMC10638731 DOI: 10.1186/s13024-023-00664-x] [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: 04/02/2023] [Accepted: 10/04/2023] [Indexed: 11/12/2023] Open
Abstract
The lack of effective therapies that slow the progression of Alzheimer's disease (AD) and related tauopathies highlights the need for a more comprehensive understanding of the fundamental cellular mechanisms underlying these diseases. Model organisms, including yeast, worms, and flies, provide simple systems with which to investigate the mechanisms of disease. The evolutionary conservation of cellular pathways regulating proteostasis and stress response in these organisms facilitates the study of genetic factors that contribute to, or protect against, neurodegeneration. Here, we review genetic modifiers of neurodegeneration and related cellular pathways identified in the budding yeast Saccharomyces cerevisiae, the nematode Caenorhabditis elegans, and the fruit fly Drosophila melanogaster, focusing on models of AD and related tauopathies. We further address the potential of simple model systems to better understand the fundamental mechanisms that lead to AD and other neurodegenerative disorders.
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Affiliation(s)
- Yuwei Jiang
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Canada
| | - Lesley T MacNeil
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Canada.
- Farncombe Family Digestive Health Research Institute, McMaster University, Hamilton, Canada.
- Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, 1280 Main St W, Hamilton, ON, L8S 4K1, Canada.
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34
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Guarnido-Lopez P, Ortigues-Marty I, David J, Polakof S, Cantalapiedra-Hijar G. Comparative analysis of signalling pathways in tissue protein metabolism in efficient and non-efficient beef cattle: acute response to an identical single meal size. Animal 2023; 17:101017. [PMID: 37948891 DOI: 10.1016/j.animal.2023.101017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 10/09/2023] [Accepted: 10/10/2023] [Indexed: 11/12/2023] Open
Abstract
Protein turnover has been associated to residual feed intake (RFI) in beef cattle. However, this relationship may be confounded by feeding level and affected by the composition of the diet being fed. Our aim was to assess postmortem the protein metabolism signalling pathways in skeletal muscle and liver of 32 Charolais young bulls with extreme RFI phenotypes. Bulls were fed two contrasting diets during the whole fattening period but were subjected to a similar and single nutritional stimulus, induced by their respective concentrate, just prior to slaughter. The key targets were protein degradation (autophagy and ubiquitin) and synthesis signalling pathways through western-blot analysis, as well as hepatic transaminase activity. To ensure a precise assessment of all animals at the same postprandial time, they were provided with a test meal (2.5 kg of either a high-starch and high-protein concentrate or high-fibre and low-protein concentrate) 3 hours prior to slaughter, irrespective of their RFI grouping. Blood and tissues were sampled at the slaughterhouse (3 h and 3 h30 postprandially, respectively). In response to an identical single meal size, efficient RFI animals showed higher (P < 0.05) postprandial plasma β-hydroxybutyrate concentrations and insulinemia (only with the high-starch concentrate) than non-efficient animals. Moreover, efficient RFI bulls had lower muscle (P = 0.04) and liver (P = 0.08) ubiquitin protein abundance (degradation pathway) and tended to have lower alanine transaminase activity in the liver (P = 0.06) compared to non-efficient bulls, regardless of diet. A positive correlation between protein degradation potential and amino acid catabolism was identified in this study (r = 0.52, P = 0.004), which was interpreted as being biologically linked to the RFI phenotype. Efficient RFI bulls also had a faster potential for protein synthesis in the muscle, as indicated by their greater ratio of phosphorylated to total form of ribosomal protein S6 kinase (P = 0.05), regardless of diet. Results on protein synthesis pathway in muscle and plasma metabolite concentrations suggested that efficient RFI cattle may have a faster nutrient absorption and insulin responsiveness after feeding than inefficient cattle. We did not find significant differences in hepatic protein synthesis pathways between the two RFI groups (P > 0.05). Our findings suggest that, in response to an identical single meal size, efficient RFI animals exhibited lower activation of tissue protein degradation pathways and faster muscle protein synthesis activation compared to their inefficient counterparts. This pattern was observed regardless of the composition of the tested meals.
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Affiliation(s)
- P Guarnido-Lopez
- INRAE, VetAgro Sup, UMR Herbivores, Université Clermont Auvergne, F-63122 Saint-Genès-Champanelle, France
| | - I Ortigues-Marty
- INRAE, VetAgro Sup, UMR Herbivores, Université Clermont Auvergne, F-63122 Saint-Genès-Champanelle, France
| | - J David
- Université Clermont-Auvergne, INRAE, UMR1019, Unité Nutrition Humaine, Clermont-Ferrand, France
| | - S Polakof
- Université Clermont-Auvergne, INRAE, UMR1019, Unité Nutrition Humaine, Clermont-Ferrand, France
| | - G Cantalapiedra-Hijar
- INRAE, VetAgro Sup, UMR Herbivores, Université Clermont Auvergne, F-63122 Saint-Genès-Champanelle, France.
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35
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Wysocki R, Rodrigues JI, Litwin I, Tamás MJ. Mechanisms of genotoxicity and proteotoxicity induced by the metalloids arsenic and antimony. Cell Mol Life Sci 2023; 80:342. [PMID: 37904059 PMCID: PMC10616229 DOI: 10.1007/s00018-023-04992-5] [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: 06/23/2023] [Revised: 09/12/2023] [Accepted: 09/29/2023] [Indexed: 11/01/2023]
Abstract
Arsenic and antimony are metalloids with profound effects on biological systems and human health. Both elements are toxic to cells and organisms, and exposure is associated with several pathological conditions including cancer and neurodegenerative disorders. At the same time, arsenic- and antimony-containing compounds are used in the treatment of multiple diseases. Although these metalloids can both cause and cure disease, their modes of molecular action are incompletely understood. The past decades have seen major advances in our understanding of arsenic and antimony toxicity, emphasizing genotoxicity and proteotoxicity as key contributors to pathogenesis. In this review, we highlight mechanisms by which arsenic and antimony cause toxicity, focusing on their genotoxic and proteotoxic effects. The mechanisms used by cells to maintain proteostasis during metalloid exposure are also described. Furthermore, we address how metalloid-induced proteotoxicity may promote neurodegenerative disease and how genotoxicity and proteotoxicity may be interrelated and together contribute to proteinopathies. A deeper understanding of cellular toxicity and response mechanisms and their links to pathogenesis may promote the development of strategies for both disease prevention and treatment.
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Affiliation(s)
- Robert Wysocki
- Department of Genetics and Cell Physiology, Faculty of Biological Sciences, University of Wroclaw, 50-328, Wroclaw, Poland.
| | - Joana I Rodrigues
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, 405 30, Göteborg, Sweden
| | - Ireneusz Litwin
- Academic Excellence Hub - Research Centre for DNA Repair and Replication, Faculty of Biological Sciences, University of Wroclaw, 50-328, Wroclaw, Poland
| | - Markus J Tamás
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, 405 30, Göteborg, Sweden.
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36
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Zhang C, Duan Y, Huang C, Li L. Inhibition of SQSTM1 S403 phosphorylation facilitates the aggresome formation of ubiquitinated proteins during proteasome dysfunction. Cell Mol Biol Lett 2023; 28:85. [PMID: 37872526 PMCID: PMC10594750 DOI: 10.1186/s11658-023-00500-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Accepted: 10/11/2023] [Indexed: 10/25/2023] Open
Abstract
BACKGROUND Ubiquitin-proteasome-system-mediated clearance of misfolded proteins is essential for cells to maintain proteostasis and reduce the proteotoxicity caused by these aberrant proteins. When proteasome activity is inadequate, ubiquitinated proteins are sorted into perinuclear aggresomes, which is a significant defense mechanism employed by cells to combat insufficient proteasome activity, hence mitigating the proteotoxic crisis. It has been demonstrated that phosphorylation of SQSTM1 is crucial in regulating misfolded protein aggregation and autophagic degradation. Although SQSTM1 S403 phosphorylation is essential for the autophagic degradation of ubiquitinated proteins, its significance in proteasome inhibition-induced aggresome formation is yet unknown. Herein, we investigated the influence of SQSTM1 S403 phosphorylation on the aggresome production of ubiquitinated proteins during proteasome suppression. METHODS We examined the phosphorylation levels of SQSTM1 S403 or T269/S272 in cells after treated with proteasome inhibitors or/and autophagy inhibitors, by western blot and immunofluorescence. We detected the accumulation and aggresome formation of ubiquitinated misfolded proteins in cells treated with proteasome inhibition by western blot and immunofluorescence. Furthermore, we used SQSTM1 phosphorylation-associated kinase inhibitors and mutant constructs to confirm the regulation of different SQSTM1 phosphorylation in aggresome formation. We examined the cell viability using CCK-8 assay. RESULTS Herein, we ascertained that phosphorylation of SQSTM1 S403 did not enhance the autophagic degradation of ubiquitinated proteins during proteasome inhibition. Proteasome inhibition suppresses the phosphorylation of SQSTM1 S403, which facilitated the aggresome production of polyubiquitinated proteins. Interestingly, we found proteasome inhibition-induced SQSTM1 T269/S272 phosphorylation inhibits the S403 phosphorylation. Suppressing S403 phosphorylation rescues the defective aggresome formation and protects cells from cell death caused by unphosphorylated SQSTM1 (T269/S272). CONCLUSIONS This study shows that inhibition of SQSTM1 S403 phosphorylation facilitates the aggresome formation of ubiquitinated proteins during proteasome dysfunction. SQSTM1 T269/S272 phosphorylation inhibits the S403 phosphorylation, boosting the aggresome formation of ubiquitinated protein and shielding cells from proteotoxic crisis.
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Affiliation(s)
- Chenliang Zhang
- Division of Abdominal Tumor Multimodality Treatment, Cancer Center and Laboratory of Molecular Targeted Therapy in Oncology, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan Province, China.
| | - YiChun Duan
- Division of Abdominal Tumor Multimodality Treatment, Cancer Center, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan Province, China
| | - Chen Huang
- Division of Abdominal Tumor Multimodality Treatment, Cancer Center, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan Province, China
| | - Liping Li
- Department of Pharmacy, Chengdu Fifth People's Hospital, Chengdu University of Traditional Chinese Medicine, Chengdu, 611130, Sichuan Province, China
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37
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Khamwachirapithak P, Sae-Tang K, Mhuantong W, Tanapongpipat S, Zhao XQ, Liu CG, Wei DQ, Champreda V, Runguphan W. Optimizing Ethanol Production in Saccharomyces cerevisiae at Ambient and Elevated Temperatures through Machine Learning-Guided Combinatorial Promoter Modifications. ACS Synth Biol 2023; 12:2897-2908. [PMID: 37681736 PMCID: PMC10594650 DOI: 10.1021/acssynbio.3c00199] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Indexed: 09/09/2023]
Abstract
Bioethanol has gained popularity in recent decades as an ecofriendly alternative to fossil fuels due to increasing concerns about global climate change. However, economically viable ethanol fermentation remains a challenge. High-temperature fermentation can reduce production costs, but Saccharomyces cerevisiae yeast strains normally ferment poorly under high temperatures. In this study, we present a machine learning (ML) approach to optimize bioethanol production in S. cerevisiae by fine-tuning the promoter activities of three endogenous genes. We created 216 combinatorial strains of S. cerevisiae by replacing native promoters with five promoters of varying strengths to regulate ethanol production. Promoter replacement resulted in a 63% improvement in ethanol production at 30 °C. We created an ML-guided workflow by utilizing XGBoost to train high-performance models based on promoter strengths and cellular metabolite concentrations obtained from ethanol production of 216 combinatorial strains at 30 °C. This strategy was then applied to optimize ethanol production at 40 °C, where we selected 31 strains for experimental fermentation. This reduced experimental load led to a 7.4% increase in ethanol production in the second round of the ML-guided workflow. Our study offers a comprehensive library of promoter strength modifications for key ethanol production enzymes, showcasing how machine learning can guide yeast strain optimization and make bioethanol production more cost-effective and efficient. Furthermore, we demonstrate that metabolic engineering processes can be accelerated and optimized through this approach.
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Affiliation(s)
- Peerapat Khamwachirapithak
- National
Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency
(NSTDA) 111 Thailand Science Park, Phahonyothin Road, Khlong
Nueng, Khlong Luang, Pathum Thani 12120, Thailand
| | - Kittapong Sae-Tang
- National
Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency
(NSTDA) 111 Thailand Science Park, Phahonyothin Road, Khlong
Nueng, Khlong Luang, Pathum Thani 12120, Thailand
| | - Wuttichai Mhuantong
- National
Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency
(NSTDA) 111 Thailand Science Park, Phahonyothin Road, Khlong
Nueng, Khlong Luang, Pathum Thani 12120, Thailand
| | - Sutipa Tanapongpipat
- National
Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency
(NSTDA) 111 Thailand Science Park, Phahonyothin Road, Khlong
Nueng, Khlong Luang, Pathum Thani 12120, Thailand
| | - Xin-Qing Zhao
- State
Key Laboratory of Microbial Metabolism, Joint International Research
Laboratory of Metabolic & Developmental Sciences, School of Life
Sciences and Biotechnology, Shanghai Jiao
Tong University, Shanghai 200240, People’s
Republic of China
| | - Chen-Guang Liu
- State
Key Laboratory of Microbial Metabolism, Joint International Research
Laboratory of Metabolic & Developmental Sciences, School of Life
Sciences and Biotechnology, Shanghai Jiao
Tong University, Shanghai 200240, People’s
Republic of China
| | - Dong-Qing Wei
- Department
of Bioinformatics and Biological Statistics, School of Life Sciences
and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, People’s Republic of China
| | - Verawat Champreda
- National
Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency
(NSTDA) 111 Thailand Science Park, Phahonyothin Road, Khlong
Nueng, Khlong Luang, Pathum Thani 12120, Thailand
| | - Weerawat Runguphan
- National
Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency
(NSTDA) 111 Thailand Science Park, Phahonyothin Road, Khlong
Nueng, Khlong Luang, Pathum Thani 12120, Thailand
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38
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Kwon Y, Kim J, Cho SY, Kang YJ, Lee J, Kwon J, Rhee H, Bauer S, Kim HS, Lee E, Kim HS, Jung JH, Kim H, Kim WK. Identification of novel pathogenic roles of BLZF1/ATF6 in tumorigenesis of gastrointestinal stromal tumor showing Golgi-localized mutant KIT. Cell Death Differ 2023; 30:2309-2321. [PMID: 37704840 PMCID: PMC10589262 DOI: 10.1038/s41418-023-01220-2] [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: 03/15/2023] [Revised: 08/29/2023] [Accepted: 08/30/2023] [Indexed: 09/15/2023] Open
Abstract
Gastrointestinal stromal tumors (GISTs) frequently show KIT mutations, accompanied by overexpression and aberrant localization of mutant KIT (MT-KIT). As previously established by multiple studies, including ours, we confirmed that MT-KIT initiates downstream signaling in the Golgi complex. Basic leucine zipper nuclear factor 1 (BLZF1) was identified as a novel MT-KIT-binding partner that tethers MT-KIT to the Golgi complex. Sustained activation of activated transcription factor 6 (ATF6), which belongs to the unfolded protein response (UPR) family, alleviates endoplasmic reticulum (ER) stress by upregulating chaperone expression, including heat shock protein 90 (HSP90), which assists in MT-KIT folding. BLZF1 knockdown and ATF6 inhibition suppressed both imatinib-sensitive and -resistant GIST in vitro. ATF6 inhibitors further showed potent antitumor effects in GIST xenografts, and the effect was enhanced with ER stress-inducing drugs. ATF6 activation was frequently observed in 67% of patients with GIST (n = 42), and was significantly associated with poorer relapse-free survival (P = 0.033). Overall, GIST bypasses ER quality control (QC) and ER stress-mediated cell death via UPR activation and uses the QC-free Golgi to initiate signaling.
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Affiliation(s)
- Yujin Kwon
- Natural Product Research Center, Korea Institute of Science and Technology (KIST), Gangneung, 25451, South Korea
- Division of Bio-Medical Science & Technology, University of Science and Technology (UST), Daejeon, 34113, South Korea
| | - Jiyoon Kim
- Department of Pharmacology, Department of Biomedicine & Health Sciences, College of Medicine, The Catholic University of Korea, Seoul, 06591, South Korea
| | - Su-Yeon Cho
- Natural Product Research Center, Korea Institute of Science and Technology (KIST), Gangneung, 25451, South Korea
- Division of Bio-Medical Science & Technology, University of Science and Technology (UST), Daejeon, 34113, South Korea
| | - Yoon Jin Kang
- Natural Product Research Center, Korea Institute of Science and Technology (KIST), Gangneung, 25451, South Korea
- Department of Marine Life Sciences, College of Life Science, Gangneung-Wonju National University, Gangneung, 25457, South Korea
| | - Jongsoo Lee
- Department of Urology, Urologic Science Institute, Yonsei University College of Medicine, Seoul, 03722, South Korea
| | - Jaeyoung Kwon
- Division of Bio-Medical Science & Technology, University of Science and Technology (UST), Daejeon, 34113, South Korea
- Natural Product Informatics Research Center, Korea Institute of Science and Technology (KIST), Gangneung, 25451, South Korea
| | - Hyungjin Rhee
- Department of Radiology, Research Institute of Radiological Science, Center for Clinical Imaging Data Science, Severance Hospital, Yonsei University College of Medicine, Seoul, 03722, South Korea
| | - Sebastian Bauer
- Sarcoma Center, West German Cancer Center, University Hospital Essen, University Duisburg-Essen, Germany and German Cancer Consortium (DKTK), Essen, 45141, Germany
| | - Hyung-Sik Kim
- Department of Oral Biochemistry; Dental and Life Science Institute, School of Dentistry, Pusan National University, Yangsan, 50612, South Korea
| | - Esak Lee
- Nancy E. and Peter C. Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY, 14853, USA
| | - Han Sang Kim
- Division of Medical Oncology, Department of Internal Medicine, Yonsei Cancer Center, Yonsei University College of Medicine, Seoul, 03722, South Korea
| | - Jae Hung Jung
- Department of Urology, Yonsei University Wonju College of Medicine/Center of Evidence Based Medicine Institute of Convergence Science, Wonju, 26426, South Korea
| | - Hoguen Kim
- Department of Pathology, Yonsei University College of Medicine, Seoul, 03722, South Korea
| | - Won Kyu Kim
- Natural Product Research Center, Korea Institute of Science and Technology (KIST), Gangneung, 25451, South Korea.
- Department of Convergence Medicine, Yonsei University Wonju College of Medicine, Wonju, 26426, South Korea.
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Fiore APZP, Vogel C. Fractionation of Native Protein Complexes from Mammalian Cells to Determine the Differential Proteasome Activity and Abundance. Bio Protoc 2023; 13:e4822. [PMID: 37753477 PMCID: PMC10518779 DOI: 10.21769/bioprotoc.4822] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Revised: 07/02/2023] [Accepted: 07/13/2023] [Indexed: 09/28/2023] Open
Abstract
Eukaryotic cells have different types of proteasomes that differ in size. The smallest proteolytically active particle is the 20S proteasome, which degrades damaged and oxidized proteins; the most common larger particle is the 26S proteasome, which degrades ubiquitylated proteins. The 26S proteasome is formed by a 20S particle capped with one or two regulatory particles, named 19S. While proteasome particles function in the cytoplasm, endoplasmic reticulum, and nucleus, our understanding of their abundance and activity in different cellular compartments is still limited. We provide a three-step protocol that first involves detergent-based fractionation of the cytoplasmic and nuclear compartments, maintaining the integrity and activity of proteasome complexes. Second, the protocol employs native gel separation of large multiprotein complexes in the fractions and a fluorescence-based in-gel quantitation of the activity and different proteasome particles. Finally, the protocol involves protein in-gel denaturation and transfer to a PVDF membrane. Western blotting then detects and quantifies the different proteasome particles. Therefore, the protocol allows for sensitive measurements of activity and abundance of individual proteasome particles from different cellular compartments. It has been optimized for motor neurons induced from mouse embryonic stem cells but can be applied to a variety of mammalian cell lines. Key features • Protocol for fractionation of active nuclear and cytoplasmic proteasome complexes. • Native electrophoresis and fluorescence-based in-gel activity assay, which allows the visualization and quantification of active complexes within the acrylamide gel matrix. • In-gel protein denaturation followed by transfer of complexes to PVDF membrane, which allows the analysis of complexes' abundance using antibodies.
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Affiliation(s)
| | - Christine Vogel
- Center of Genomic and System Biology, Department of Biology, New York University, New York, NY, USA
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Doroudgar S. Resolving Proteotoxicity: Genetic Examination of Proteasome Activation by PKA In Vivo. Circ Res 2023; 133:588-591. [PMID: 37708246 DOI: 10.1161/circresaha.123.323502] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 09/16/2023]
Affiliation(s)
- Shirin Doroudgar
- Department of Internal Medicine and the Translational Cardiovascular Research Center, University of Arizona College of Medicine - Phoenix, Phoenix, AZ
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41
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Willot Q, du Toit A, de Wet S, Huisamen EJ, Loos B, Terblanche JS. Exploring the connection between autophagy and heat-stress tolerance in Drosophila melanogaster. Proc Biol Sci 2023; 290:20231305. [PMID: 37700658 PMCID: PMC10498041 DOI: 10.1098/rspb.2023.1305] [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: 06/16/2023] [Accepted: 08/16/2023] [Indexed: 09/14/2023] Open
Abstract
Mechanisms aimed at recovering from heat-induced damages are closely associated with the ability of ectotherms to survive exposure to stressful temperatures. Autophagy, a ubiquitous stress-responsive catabolic process, has recently gained renewed attention as one of these mechanisms. By increasing the turnover of cellular structures as well as the clearance of long-lived protein and protein aggregates, the induction of autophagy has been linked to increased tolerance to a range of abiotic stressors in diverse ectothermic organisms. However, whether a link between autophagy and heat-tolerance exists in insect models remains unclear despite broad ecophysiological implications thereof. Here, we explored the putative association between autophagy and heat-tolerance using Drosophila melanogaster as a model. We hypothesized that (i) heat-stress would cause an increase of autophagy in flies' tissues, and (ii) rapamycin exposure would trigger a detectable autophagic response in adults and increase their heat-tolerance. In line with our hypothesis, we report that flies exposed to heat-stress present signs of protein aggregation and appear to trigger an autophagy-related homoeostatic response as a result. We further show that rapamycin feeding causes the systemic effect associated with target of rapamycin (TOR) inhibition, induces autophagy locally in the fly gut, and increases the heat-stress tolerance of individuals. These results argue in favour of a substantial contribution of autophagy to the heat-stress tolerance mechanisms of insects.
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Affiliation(s)
- Quentin Willot
- Centre for Invasion Biology, Department of Conservation Ecology & Entomology, Stellenbosch University, Stellenbosch 7600, South Africa
| | - Andre du Toit
- Department of Physiological Sciences, Stellenbosch University, Stellenbosch 7600, South Africa
| | - Sholto de Wet
- Department of Physiological Sciences, Stellenbosch University, Stellenbosch 7600, South Africa
| | - Elizabeth J. Huisamen
- Centre for Invasion Biology, Department of Conservation Ecology & Entomology, Stellenbosch University, Stellenbosch 7600, South Africa
| | - Ben Loos
- Department of Physiological Sciences, Stellenbosch University, Stellenbosch 7600, South Africa
| | - John S. Terblanche
- Centre for Invasion Biology, Department of Conservation Ecology & Entomology, Stellenbosch University, Stellenbosch 7600, South Africa
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Osana S, Kitajima Y, Naoki S, Murayama K, Takada H, Tabuchi A, Kano Y, Nagatomi R. The aminopeptidase LAP3 suppression accelerates myogenic differentiation via the AKT-TFE3 pathway in C2C12 myoblasts. J Cell Physiol 2023; 238:2103-2119. [PMID: 37435895 DOI: 10.1002/jcp.31070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Revised: 06/08/2023] [Accepted: 06/15/2023] [Indexed: 07/13/2023]
Abstract
Skeletal muscle maintenance depends largely on muscle stem cells (satellite cells) that supply myoblasts required for muscle regeneration and growth. The ubiquitin-proteasome system is the major intracellular protein degradation pathway. We previously reported that proteasome dysfunction in skeletal muscle significantly impairs muscle growth and development. Furthermore, the inhibition of aminopeptidase, a proteolytic enzyme that removes amino acids from the termini of peptides derived from proteasomal proteolysis, impairs the proliferation and differentiation ability of C2C12 myoblasts. However, no evidence has been reported on the role of aminopeptidases with different substrate specificities on myogenesis. In this study, therefore, we investigated whether the knockdown of aminopeptidases in differentiating C2C12 myoblasts affects myogenesis. The knockdown of the X-prolyl aminopeptidase 1, aspartyl aminopeptidase, leucyl-cystinyl aminopeptidase, methionyl aminopeptidase 1, methionyl aminopeptidase 2, puromycine-sensitive aminopeptidase, and arginyl aminopeptidase like 1 gene in C2C12 myoblasts resulted in defective myogenic differentiation. Surprisingly, the knockdown of leucine aminopeptidase 3 (LAP3) in C2C12 myoblasts promoted myogenic differentiation. We also found that suppression of LAP3 expression in C2C12 myoblasts resulted in the inhibition of proteasomal proteolysis, decreased intracellular branched-chain amino acid levels, and enhanced mTORC2-mediated AKT phosphorylation (S473). Furthermore, phosphorylated AKT induced the translocation of TFE3 from the nucleus to the cytoplasm, promoting myogenic differentiation through increased expression of myogenin. Overall, our study highlights the association of aminopeptidases with myogenic differentiation.
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Affiliation(s)
- Shion Osana
- Department of Sports and Medical Science, Kokushikan University, Tokyo, Japan
- Graduate School of Informatics and Engineering, University of Electro-Communications, Chofu, Japan
- Department of Medicine and Science in Sports and Exercise, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Yasuo Kitajima
- Department of Immunology, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Suzuki Naoki
- Department of Neurology, Tohoku University School of Medicine, Sendai, Japan
| | - Kazutaka Murayama
- Division of Biomedical Measurements and Diagnostics, Tohoku University Graduate School of Biomedical Engineering, Sendai, Japan
| | - Hiroaki Takada
- Division of Biomedical Engineering for Health and Welfare, Tohoku University Graduate School of Biomedical Engineering, Sendai, Japan
| | - Ayaka Tabuchi
- Graduate School of Informatics and Engineering, University of Electro-Communications, Chofu, Japan
| | - Yutaka Kano
- Graduate School of Informatics and Engineering, University of Electro-Communications, Chofu, Japan
| | - Ryoichi Nagatomi
- Department of Medicine and Science in Sports and Exercise, Tohoku University Graduate School of Medicine, Sendai, Japan
- Division of Biomedical Engineering for Health and Welfare, Tohoku University Graduate School of Biomedical Engineering, Sendai, Japan
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Dhawka L, Palfini V, Hambright E, Blanco I, Poon C, Kahl A, Resch U, Bhawal R, Benakis C, Balachandran V, Zhang S, Iadecola C, Hochrainer K. Post-ischemic ubiquitination at the postsynaptic density reversibly influences the activity of ischemia-relevant kinases. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.21.552860. [PMID: 37662420 PMCID: PMC10473581 DOI: 10.1101/2023.08.21.552860] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/05/2023]
Abstract
Ubiquitin modifications alter protein function and stability, thereby regulating cell homeostasis and viability, particularly under stress. Ischemic stroke induces protein ubiquitination at the ischemic periphery, wherein cells remain viable, however the identity of ubiquitinated proteins is unknown. Here, we employed a proteomics approach to identify these proteins in mice undergoing ischemic stroke. The data are available in a searchable web interface ( https://hochrainerlab.shinyapps.io/StrokeUbiOmics/ ). We detected increased ubiquitination of 198 proteins, many of which localize to the postsynaptic density (PSD) of glutamatergic neurons. Among these were proteins essential for maintaining PSD architecture, such as PSD95, as well as NMDA and AMPA receptor subunits. The largest enzymatic group at the PSD with elevated post-ischemic ubiquitination were kinases, such as CaMKII, PKC, Cdk5, and Pyk2, whose aberrant activities are well-known to contribute to post-ischemic neuronal death. Concurrent phospho-proteomics revealed altered PSD-associated phosphorylation patterns, indicative of modified kinase activities following stroke. PSD-located CaMKII, PKC, and Cdk5 activities were decreased while Pyk2 activity was increased after stroke. Removal of ubiquitin restored kinase activities to pre-stroke levels, identifying ubiquitination as the responsible molecular mechanism for post-ischemic kinase regulation. These findings unveil a previously unrecognized role of ubiquitination in the regulation of essential kinases involved in ischemic injury.
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Gupta A, Venkatesh AR, Arora K, Guptasarma P. Avoidance of the use of tryptophan in buried chromosomal proteins as a mechanism for reducing photo/oxidative damage to genomes. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY. B, BIOLOGY 2023; 245:112733. [PMID: 37311303 DOI: 10.1016/j.jphotobiol.2023.112733] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Revised: 05/13/2023] [Accepted: 05/29/2023] [Indexed: 06/15/2023]
Abstract
In cells that are exposed to terrestrial sunlight, the indole moiety in the side chain of tryptophan (Trp) can suffer photo/oxidative damage (POD) by reactive oxygen species (ROS) and/or ultraviolet light (UV-B). Trp is oxidized to produce N-formylkynurenine (NFK), a UV-A-responsive photosensitizer that further degenerates into photosensitizers capable of generating ROS through exposure to visible light. Thus, Trp-containing proteins function as both victims, and perpetrators, of POD if they are not rapidly replaced through protein turnover. The literature indicates that protein turnover and DNA repair occur poorly in chromosomal interiors. We contend, therefore, that basic chromosomal proteins (BCPs) that are enveloped by DNA should have evolved to lack Trp residues in their amino acid sequences, since these could otherwise function as 'Trojan horse-type' DNA-damaging agents. Our global analyses of protein sequences demonstrates that BCPs consistently lack Trp residues, although DNA-binding proteins in general do not display such a lack. We employ HU-B (a wild-type, Trp-lacking bacterial BCP) and HU-B F47W (a mutant, Trp-containing form of the same bacterial BCP) to demonstrate that the possession of Trp is deleterious to BCPs and associated chromosomal DNA. Basically, we show that UV-B and UV-A (a) cause no POD in HU-B, but cause extensive POD in HU-B F47W (in vitro), as well as (b) only nominal DNA damage in bacteria expressing HU-B, but extensive DNA damage in bacteria expressing F47W HU-B (in vivo). Our results suggest that Trp-lacking BCPs could have evolved to reduce scope for protein-facilitated, sunlight-mediated damage of DNA by UV-A and visible light, within chromosomal interiors that are poorly serviced by protein turnover and DNA repair machinery.
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Affiliation(s)
- Archit Gupta
- Centre for Protein Science, Design and Engineering (CPSDE), Department of Biological Sciences, Indian Institute of Science Education and Research (IISER) Mohali, Knowledge City, Sector-81, SAS Nagar, Punjab 140306, India
| | - Achuthan Raja Venkatesh
- Centre for Protein Science, Design and Engineering (CPSDE), Department of Biological Sciences, Indian Institute of Science Education and Research (IISER) Mohali, Knowledge City, Sector-81, SAS Nagar, Punjab 140306, India
| | - Kanika Arora
- Centre for Protein Science, Design and Engineering (CPSDE), Department of Biological Sciences, Indian Institute of Science Education and Research (IISER) Mohali, Knowledge City, Sector-81, SAS Nagar, Punjab 140306, India
| | - Purnananda Guptasarma
- Centre for Protein Science, Design and Engineering (CPSDE), Department of Biological Sciences, Indian Institute of Science Education and Research (IISER) Mohali, Knowledge City, Sector-81, SAS Nagar, Punjab 140306, India.
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Wu DG, Wang YN, Zhou Y, Gao H, Zhao B. Inhibition of the Proteasome Regulator PA28 Aggravates Oxidized Protein Overload in the Diabetic Rat Brain. Cell Mol Neurobiol 2023; 43:2857-2869. [PMID: 36715894 DOI: 10.1007/s10571-023-01322-y] [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: 06/05/2022] [Accepted: 01/19/2023] [Indexed: 01/31/2023]
Abstract
Oxidized protein overloading caused by diabetes is one accelerating pathological pathway in diabetic encephalopathy development. To determine whether the PA28-regulated function of the proteasome plays a role in diabetes-induced oxidative damaged protein degradation, brain PA28α and PA28β interference experiments were performed in a high-fat diet (HFD) and streptozotocin (STZ)-induced rat model. The present results showed that proteasome activity was changed in the brains of diabetic rats, but the constitutive subunits were not. In vivo PA28α and PA28β inhibition via adeno-associated virus (AAV) shRNA infection successfully decreased PA28 protein levels and further exacerbated oxidized proteins load by regulating proteasome catalytic activity. These findings suggest that the proteasome plays a role in the elimination of oxidized proteins and that PA28 is functionally involved in the regulation of proteasome activity in vivo. This study suggests that abnormal protein turbulence occurring in the diabetic brain could be explained by the proteasome-mediated degradation pathway. Changes in proteasome activity regulator PA28 could be a reason to induce oxidative aggregation in diabetic brain. Proteasome regulator PA28 inhibition in vivo by AAV vector injection could aggravate oxidized proteins abundance in brain of HFD-STZ diabetic rat model.
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Affiliation(s)
- Dong-Gui Wu
- School of Basic Medicine Sciences, Dali University, 6th Snowman Road, Dali, 671000, Yunnan, People's Republic of China
- Zhuhai People's Hospital, 79th Kangning Road, Zhuhai, 519000, Guangdong, People's Republic of China
| | - Yu-Na Wang
- School of Basic Medicine Sciences, Dali University, 6th Snowman Road, Dali, 671000, Yunnan, People's Republic of China
| | - Ye Zhou
- School of Basic Medicine Sciences, Dali University, 6th Snowman Road, Dali, 671000, Yunnan, People's Republic of China
| | - Han Gao
- School of Basic Medicine Sciences, Dali University, 6th Snowman Road, Dali, 671000, Yunnan, People's Republic of China
| | - Bei Zhao
- School of Basic Medicine Sciences, Dali University, 6th Snowman Road, Dali, 671000, Yunnan, People's Republic of China.
- Li Yun-Qing Expert Workstation of Yunnan Province (No. 202005AF150014) based in Dali University, 6th Snowman Road, Dali, 671000, Yunnan, People's Republic of China.
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Mashahreh B, Armony S, Ravid T. yGPS-P: A Yeast-Based Peptidome Screen for Studying Quality Control-Associated Proteolysis. Biomolecules 2023; 13:987. [PMID: 37371568 DOI: 10.3390/biom13060987] [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: 05/15/2023] [Revised: 06/11/2023] [Accepted: 06/12/2023] [Indexed: 06/29/2023] Open
Abstract
Quality control-associated proteolysis (QCAP) is a fundamental mechanism that maintains cellular homeostasis by eliminating improperly folded proteins. In QCAP, the exposure of normally hidden cis-acting protein sequences, termed degrons, triggers misfolded protein ubiquitination, resulting in their elimination by the proteasome. To identify the landscape of QCAP degrons and learn about their unique features we have developed an unbiased screening method in yeast, termed yGPS-P, which facilitates the determination of thousands of proteome-derived sequences that enhance proteolysis. Here we describe the fundamental features of the yGPS-P method and provide a detailed protocol for its use as a tool for degron search. This includes the cloning of a synthetic peptidome library in a fluorescence-based reporter system, and data acquisition, which entails the combination of Fluorescence-Activated Cell Sorting (FACS) and Next-Generation Sequencing (NGS). We also provide guidelines for data extraction and analysis and for the application of a machine-learning algorithm that established the evolutionarily conserved amino acid preferences and secondary structure propensities of QCAP degrons.
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Affiliation(s)
- Bayan Mashahreh
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Shir Armony
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Tommer Ravid
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
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Bianchi C, Alvarez-Castelao B, Sebastián-Serrano Á, Di Lauro C, Soria-Tobar L, Nicke A, Engel T, Díaz-Hernández M. P2X7 receptor inhibition ameliorates ubiquitin-proteasome system dysfunction associated with Alzheimer's disease. Alzheimers Res Ther 2023; 15:105. [PMID: 37287063 DOI: 10.1186/s13195-023-01258-x] [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: 10/10/2022] [Accepted: 06/01/2023] [Indexed: 06/09/2023]
Abstract
BACKGROUND Over recent years, increasing evidence suggests a causal relationship between neurofibrillary tangles (NFTs) formation, the main histopathological hallmark of tauopathies, including Alzheimer's disease (AD), and the ubiquitin-proteasome system (UPS) dysfunction detected in these patients. Nevertheless, the mechanisms underlying UPS failure and the factors involved remain poorly understood. Given that AD and tauopathies are associated with chronic neuroinflammation, here, we explore if ATP, one of the danger-associated molecules patterns (DAMPs) associated with neuroinflammation, impacts on AD-associated UPS dysfunction. METHODS To evaluate if ATP may modulate the UPS via its selective P2X7 receptor, we combined in vitro and in vivo approaches using both pharmacological and genetic tools. We analyze postmortem samples from human AD patients and P301S mice, a mouse model that mimics pathology observed in AD patients, and those from the new transgenic mouse lines generated, such as P301S mice expressing the UPS reporter UbG76V-YFP or P301S deficient of P2X7R. RESULTS We describe for the first time that extracellular ATP-induced activation of the purinergic P2X7 receptor (P2X7R) downregulates the transcription of β5 and β1 proteasomal catalytic subunits via the PI3K/Akt/GSK3/Nfr2 pathway, leading to their deficient assembly into the 20S core proteasomal complex, resulting in a reduced proteasomal chymotrypsin-like and postglutamyl-like activities. Using UPS-reported mice (UbGFP mice), we identified neurons and microglial cells as the most sensitive cell linages to a P2X7R-mediated UPS regulation. In vivo pharmacological or genetic P2X7R blockade reverted the proteasomal impairment developed by P301S mice, which mimics that were detected in AD patients. Finally, the generation of P301S;UbGFP mice allowed us to identify those hippocampal cells more sensitive to UPS impairment and demonstrate that the pharmacological or genetic blockade of P2X7R promotes their survival. CONCLUSIONS Our work demonstrates the sustained and aberrant activation of P2X7R caused by Tau-induced neuroinflammation contributes to the UPS dysfunction and subsequent neuronal death associated with AD, especially in the hippocampus.
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Affiliation(s)
- Carolina Bianchi
- Department of Biochemistry and Molecular Biology, Veterinary School, Complutense University of Madrid, Avda. Puerta de Hierro S/N, 28040, Madrid, Spain
- Instituto de Investigación Sanitaria del Hospital Clínico San Carlos, IdISSC, Madrid, Spain
| | - Beatriz Alvarez-Castelao
- Department of Biochemistry and Molecular Biology, Veterinary School, Complutense University of Madrid, Avda. Puerta de Hierro S/N, 28040, Madrid, Spain
- Instituto de Investigación Sanitaria del Hospital Clínico San Carlos, IdISSC, Madrid, Spain
| | - Álvaro Sebastián-Serrano
- Department of Biochemistry and Molecular Biology, Veterinary School, Complutense University of Madrid, Avda. Puerta de Hierro S/N, 28040, Madrid, Spain
- Instituto de Investigación Sanitaria del Hospital Clínico San Carlos, IdISSC, Madrid, Spain
| | - Caterina Di Lauro
- Department of Biochemistry and Molecular Biology, Veterinary School, Complutense University of Madrid, Avda. Puerta de Hierro S/N, 28040, Madrid, Spain
- Instituto de Investigación Sanitaria del Hospital Clínico San Carlos, IdISSC, Madrid, Spain
| | - Lucia Soria-Tobar
- Department of Biochemistry and Molecular Biology, Veterinary School, Complutense University of Madrid, Avda. Puerta de Hierro S/N, 28040, Madrid, Spain
- Instituto de Investigación Sanitaria del Hospital Clínico San Carlos, IdISSC, Madrid, Spain
| | - Annette Nicke
- Walther Straub Institute of Pharmacology and Toxicology, Faculty of Medicine, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Tobias Engel
- Department of Physiology and Medical Physics, RCSI, University of Medicine and Health Sciences, Dublin, D02 YN77, Ireland
- FutureNeuro, SFI Research Centre for Chronic and Rare Neurological Diseases, RCSI, University of Medicine and Health Sciences, Dublin, D02 YN77, Ireland
| | - Miguel Díaz-Hernández
- Department of Biochemistry and Molecular Biology, Veterinary School, Complutense University of Madrid, Avda. Puerta de Hierro S/N, 28040, Madrid, Spain.
- Instituto de Investigación Sanitaria del Hospital Clínico San Carlos, IdISSC, Madrid, Spain.
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48
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Oliveri F, Keller SJ, Goebel H, Alvarez Salinas GO, Basler M. The ubiquitin-like modifier FAT10 is degraded by the 20S proteasome in vitro but not in cellulo. Life Sci Alliance 2023; 6:e202201760. [PMID: 37012049 PMCID: PMC10070814 DOI: 10.26508/lsa.202201760] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Revised: 03/23/2023] [Accepted: 03/23/2023] [Indexed: 04/05/2023] Open
Abstract
Ubiquitin-independent protein degradation via the 20S proteasome without the 19S regulatory particle has gained increasing attention over the last years. The degradation of the ubiquitin-like modifier FAT10 by the 20S proteasome was investigated in this study. We found that FAT10 was rapidly degraded by purified 20S proteasomes in vitro, which was attributed to the weak folding of FAT10 and the N-terminally disordered tail. To confirm our results in cellulo, we established an inducible RNA interference system in which the AAA-ATPase Rpt2 of the 19S regulatory particle is knocked down to impair the function of the 26S proteasome. Using this system, degradation of FAT10 in cellulo was strongly dependent on functional 26S proteasome. Our data indicate that in vitro degradation studies with purified proteins do not necessarily reflect biological degradation mechanisms occurring in cells and, therefore, cautious data interpretation is required when 20S proteasome function is studied in vitro.
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Affiliation(s)
- Franziska Oliveri
- Division of Immunology, Department of Biology, University of Konstanz, Konstanz, Germany
| | | | - Heike Goebel
- Division of Immunology, Department of Biology, University of Konstanz, Konstanz, Germany
| | | | - Michael Basler
- Division of Immunology, Department of Biology, University of Konstanz, Konstanz, Germany;
- Biotechnology Institute Thurgau https://ror.org/0546hnb39 at the University of Konstanz, Kreuzlingen, Switzerland
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49
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Singh H. Role of Molecular Targeted Therapeutic Drugs in Treatment of Glioblastoma: A Review Article. Glob Med Genet 2023; 10:42-47. [PMID: 37077370 PMCID: PMC10110362 DOI: 10.1055/s-0043-57028] [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: 04/21/2023] Open
Abstract
Glioblastoma is remarkably periodic primary brain tumor, characterizing an eminently heterogeneous pattern of neoplasms that are utmost destructive and threatening cancers. An enhanced and upgraded knowledge of the various molecular pathways that cause malignant changes in glioblastoma has resulted in advancement of numerous biomarkers and the interpretation of various agents that pointedly target tumor cells and microenvironment. In this review, literature or information on various targeted therapy for glioblastoma is discussed. English language articles were scrutinized in plentiful directory or databases like PubMed, ScienceDirect, Web of Sciences, Google Scholar, and Scopus. The important keywords used for searching databases are "Glioblastoma," "Targeted therapy in glioblastoma," "Therapeutic drugs in glioblastoma," and "Molecular targets in glioblastoma."
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Affiliation(s)
- Himanshu Singh
- Department of Oral and Maxillofacial Pathology and Oral Microbiology, Index Institute of Dental Sciences, Indore, Madhya Pradesh, India
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50
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Dey P, Biswas P. Exploring the aggregation of amyloid-β 42 through Monte Carlo simulations. Biophys Chem 2023; 297:107011. [PMID: 37037120 DOI: 10.1016/j.bpc.2023.107011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Revised: 03/25/2023] [Accepted: 03/26/2023] [Indexed: 04/09/2023]
Abstract
Coarse-grained Monte Carlo simulations are performed for a disordered protein, amyloid-β 42 to identify the interactions and understand the mechanism of its aggregation. A statistical potential is developed from a selected dataset of intrinsically disordered proteins, which accounts for the respective contributions of the bonded and non-bonded potentials. While, the bonded potential comprises the bond, bend, and dihedral constraints, the nonbonded interactions include van der Waals interactions, hydrogen bonds, and the two-body potential. The two-body potential captures the features of both hydrophobic and electrostatic interactions that brings the chains at a contact distance, while the repulsive van der Waals interactions prevent them from a collapse. Increased two-body hydrophobic interactions facilitate the formation of amorphous aggregates rather than the fibrillar ones. The formation of aggregates is validated from the interchain distances, and the total energy of the system. The aggregate is structurally characterized by the root-mean-square deviation, root-mean-square fluctuation and the radius of gyration. The aggregates are characterized by a decrease in SASA, an increase in the non-local interactions and a distinct free energy minimum relative to that of the monomeric state of amyloid-β 42. The hydrophobic residues help in nucleation, while the charged residues help in oligomerization and aggregation.
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