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Izadi M, Sadri N, Abdi A, Serajian S, Jalalei D, Tahmasebi S. Epigenetic biomarkers in aging and longevity: Current and future application. Life Sci 2024; 351:122842. [PMID: 38879158 DOI: 10.1016/j.lfs.2024.122842] [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: 12/29/2023] [Revised: 06/06/2024] [Accepted: 06/12/2024] [Indexed: 06/20/2024]
Abstract
The aging process has been one of the most necessary research fields in the current century, and knowing different theories of aging and the role of different genetic, epigenetic, molecular, and environmental modulating factors in increasing the knowledge of aging mechanisms and developing appropriate diagnostic, therapeutic, and preventive ways would be helpful. One of the most conserved signs of aging is epigenetic changes, including DNA methylation, histone modifications, chromatin remodeling, noncoding RNAs, and extracellular RNAs. Numerous biological processes and hallmarks are vital in aging development, but epigenomic alterations are especially notable because of their importance in gene regulation and cellular identity. The mounting evidence points to a possible interaction between age-related epigenomic alterations and other aging hallmarks, like genome instability. To extend a healthy lifespan and possibly reverse some facets of aging and aging-related diseases, it will be crucial to comprehend global and locus-specific epigenomic modifications and recognize corresponding regulators of health and longevity. In the current study, we will aim to discuss the role of epigenomic mechanisms in aging and the most recent developments in epigenetic diagnostic biomarkers, which have the potential to focus efforts on reversing the destructive signs of aging and extending the lifespan.
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Affiliation(s)
- Mehran Izadi
- Department of Infectious and Tropical Diseases, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran; Synapse Laboratory Diagnostic Technologies Accelerator, Tehran, Iran; Department of Research & Technology, Zeenome Longevity Research Institute, Tehran, Iran
| | - Nariman Sadri
- Synapse Laboratory Diagnostic Technologies Accelerator, Tehran, Iran; Department of Research & Technology, Zeenome Longevity Research Institute, Tehran, Iran; School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Amirhossein Abdi
- Synapse Laboratory Diagnostic Technologies Accelerator, Tehran, Iran; Department of Research & Technology, Zeenome Longevity Research Institute, Tehran, Iran; Royan Institute for Stem Cell Biology and Technology, Tehran, Iran
| | - Sahar Serajian
- Synapse Laboratory Diagnostic Technologies Accelerator, Tehran, Iran; Department of Research & Technology, Zeenome Longevity Research Institute, Tehran, Iran; Royan Institute for Stem Cell Biology and Technology, Tehran, Iran
| | - Dorsa Jalalei
- Synapse Laboratory Diagnostic Technologies Accelerator, Tehran, Iran; Department of Research & Technology, Zeenome Longevity Research Institute, Tehran, Iran; School of Pharmacy, Zanjan University of Medical Sciences, Zanjan, Iran
| | - Safa Tahmasebi
- Synapse Laboratory Diagnostic Technologies Accelerator, Tehran, Iran; Department of Research & Technology, Zeenome Longevity Research Institute, Tehran, Iran; Department of Immunology, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
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Xiao Z, Liang J, Huang R, Chen D, Mei J, Deng J, Wang Z, Li L, Li Z, Xia H, Yang Y, Huang Y. Inhibition of miR-143-3p Restores Blood-Testis Barrier Function and Ameliorates Sertoli Cell Senescence. Cells 2024; 13:313. [PMID: 38391926 PMCID: PMC10887369 DOI: 10.3390/cells13040313] [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: 01/10/2024] [Revised: 02/04/2024] [Accepted: 02/06/2024] [Indexed: 02/24/2024] Open
Abstract
Due to the increasing trend of delayed childbirth, the age-related decline in male reproductive function has become a widely recognized issue. Sertoli cells (SCs) play a vital role in creating the necessary microenvironment for spermatogenesis in the testis. However, the mechanism underlying Sertoli cell aging is still unclear. In this study, senescent Sertoli cells showed a substantial upregulation of miR-143-3p expression. miR-143-3p was found to limit Sertoli cell proliferation, promote cellular senescence, and cause blood-testis barrier (BTB) dysfunction by targeting ubiquitin-conjugating enzyme E2 E3 (UBE2E3). Additionally, the TGF-β receptor inhibitor SB431542 showed potential in alleviating age-related BTB dysfunction, rescuing testicular atrophy, and reversing the reduction in germ cell numbers by negatively regulating miR-143-3p. These findings clarified the regulatory pathways underlying Sertoli cell senescence and suggested a promising therapeutic approach to restore BTB function, alleviate Sertoli cell senescence, and improve reproductive outcomes for individuals facing fertility challenges.
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Affiliation(s)
- Ziyan Xiao
- Department of Cell Biology, Jinan University, Guangzhou 510632, China; (Z.X.); (J.L.); (R.H.); (D.C.); (J.M.); (Z.W.); (L.L.); (Z.L.); (H.X.)
| | - Jinlian Liang
- Department of Cell Biology, Jinan University, Guangzhou 510632, China; (Z.X.); (J.L.); (R.H.); (D.C.); (J.M.); (Z.W.); (L.L.); (Z.L.); (H.X.)
| | - Rufei Huang
- Department of Cell Biology, Jinan University, Guangzhou 510632, China; (Z.X.); (J.L.); (R.H.); (D.C.); (J.M.); (Z.W.); (L.L.); (Z.L.); (H.X.)
| | - Derong Chen
- Department of Cell Biology, Jinan University, Guangzhou 510632, China; (Z.X.); (J.L.); (R.H.); (D.C.); (J.M.); (Z.W.); (L.L.); (Z.L.); (H.X.)
| | - Jiaxin Mei
- Department of Cell Biology, Jinan University, Guangzhou 510632, China; (Z.X.); (J.L.); (R.H.); (D.C.); (J.M.); (Z.W.); (L.L.); (Z.L.); (H.X.)
| | - Jingxian Deng
- Department of Pharmacology, Jinan University, Guangzhou 510632, China;
| | - Zhaoyang Wang
- Department of Cell Biology, Jinan University, Guangzhou 510632, China; (Z.X.); (J.L.); (R.H.); (D.C.); (J.M.); (Z.W.); (L.L.); (Z.L.); (H.X.)
| | - Lu Li
- Department of Cell Biology, Jinan University, Guangzhou 510632, China; (Z.X.); (J.L.); (R.H.); (D.C.); (J.M.); (Z.W.); (L.L.); (Z.L.); (H.X.)
| | - Ziyi Li
- Department of Cell Biology, Jinan University, Guangzhou 510632, China; (Z.X.); (J.L.); (R.H.); (D.C.); (J.M.); (Z.W.); (L.L.); (Z.L.); (H.X.)
| | - Huan Xia
- Department of Cell Biology, Jinan University, Guangzhou 510632, China; (Z.X.); (J.L.); (R.H.); (D.C.); (J.M.); (Z.W.); (L.L.); (Z.L.); (H.X.)
| | - Yan Yang
- Department of Cell Biology, Jinan University, Guangzhou 510632, China; (Z.X.); (J.L.); (R.H.); (D.C.); (J.M.); (Z.W.); (L.L.); (Z.L.); (H.X.)
- Guangdong Province Key Laboratory of Bioengineering Medicine, Guangzhou 510632, China
| | - Yadong Huang
- Department of Cell Biology, Jinan University, Guangzhou 510632, China; (Z.X.); (J.L.); (R.H.); (D.C.); (J.M.); (Z.W.); (L.L.); (Z.L.); (H.X.)
- Guangdong Province Key Laboratory of Bioengineering Medicine, Guangzhou 510632, China
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Zhong Q, Xiao X, Qiu Y, Xu Z, Chen C, Chong B, Zhao X, Hai S, Li S, An Z, Dai L. Protein posttranslational modifications in health and diseases: Functions, regulatory mechanisms, and therapeutic implications. MedComm (Beijing) 2023; 4:e261. [PMID: 37143582 PMCID: PMC10152985 DOI: 10.1002/mco2.261] [Citation(s) in RCA: 23] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2022] [Revised: 03/26/2023] [Accepted: 03/27/2023] [Indexed: 05/06/2023] Open
Abstract
Protein posttranslational modifications (PTMs) refer to the breaking or generation of covalent bonds on the backbones or amino acid side chains of proteins and expand the diversity of proteins, which provides the basis for the emergence of organismal complexity. To date, more than 650 types of protein modifications, such as the most well-known phosphorylation, ubiquitination, glycosylation, methylation, SUMOylation, short-chain and long-chain acylation modifications, redox modifications, and irreversible modifications, have been described, and the inventory is still increasing. By changing the protein conformation, localization, activity, stability, charges, and interactions with other biomolecules, PTMs ultimately alter the phenotypes and biological processes of cells. The homeostasis of protein modifications is important to human health. Abnormal PTMs may cause changes in protein properties and loss of protein functions, which are closely related to the occurrence and development of various diseases. In this review, we systematically introduce the characteristics, regulatory mechanisms, and functions of various PTMs in health and diseases. In addition, the therapeutic prospects in various diseases by targeting PTMs and associated regulatory enzymes are also summarized. This work will deepen the understanding of protein modifications in health and diseases and promote the discovery of diagnostic and prognostic markers and drug targets for diseases.
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Affiliation(s)
- Qian Zhong
- Department of Endocrinology and MetabolismGeneral Practice Ward/International Medical Center WardGeneral Practice Medical Center and National Clinical Research Center for GeriatricsState Key Laboratory of BiotherapyWest China Hospital, Sichuan UniversityChengduChina
| | - Xina Xiao
- Department of Endocrinology and MetabolismGeneral Practice Ward/International Medical Center WardGeneral Practice Medical Center and National Clinical Research Center for GeriatricsState Key Laboratory of BiotherapyWest China Hospital, Sichuan UniversityChengduChina
| | - Yijie Qiu
- Department of Endocrinology and MetabolismGeneral Practice Ward/International Medical Center WardGeneral Practice Medical Center and National Clinical Research Center for GeriatricsState Key Laboratory of BiotherapyWest China Hospital, Sichuan UniversityChengduChina
| | - Zhiqiang Xu
- Department of Endocrinology and MetabolismGeneral Practice Ward/International Medical Center WardGeneral Practice Medical Center and National Clinical Research Center for GeriatricsState Key Laboratory of BiotherapyWest China Hospital, Sichuan UniversityChengduChina
| | - Chunyu Chen
- Department of Endocrinology and MetabolismGeneral Practice Ward/International Medical Center WardGeneral Practice Medical Center and National Clinical Research Center for GeriatricsState Key Laboratory of BiotherapyWest China Hospital, Sichuan UniversityChengduChina
| | - Baochen Chong
- Department of Endocrinology and MetabolismGeneral Practice Ward/International Medical Center WardGeneral Practice Medical Center and National Clinical Research Center for GeriatricsState Key Laboratory of BiotherapyWest China Hospital, Sichuan UniversityChengduChina
| | - Xinjun Zhao
- Department of Endocrinology and MetabolismGeneral Practice Ward/International Medical Center WardGeneral Practice Medical Center and National Clinical Research Center for GeriatricsState Key Laboratory of BiotherapyWest China Hospital, Sichuan UniversityChengduChina
| | - Shan Hai
- Department of Endocrinology and MetabolismGeneral Practice Ward/International Medical Center WardGeneral Practice Medical Center and National Clinical Research Center for GeriatricsState Key Laboratory of BiotherapyWest China Hospital, Sichuan UniversityChengduChina
| | - Shuangqing Li
- Department of Endocrinology and MetabolismGeneral Practice Ward/International Medical Center WardGeneral Practice Medical Center and National Clinical Research Center for GeriatricsState Key Laboratory of BiotherapyWest China Hospital, Sichuan UniversityChengduChina
| | - Zhenmei An
- Department of Endocrinology and MetabolismGeneral Practice Ward/International Medical Center WardGeneral Practice Medical Center and National Clinical Research Center for GeriatricsState Key Laboratory of BiotherapyWest China Hospital, Sichuan UniversityChengduChina
| | - Lunzhi Dai
- Department of Endocrinology and MetabolismGeneral Practice Ward/International Medical Center WardGeneral Practice Medical Center and National Clinical Research Center for GeriatricsState Key Laboratory of BiotherapyWest China Hospital, Sichuan UniversityChengduChina
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Zhao T, Liu C, Liu L, Wang X, Liu C. Aging-accelerated differential production and aggregation of STAT3 protein in neuronal cells and neural stem cells in the male mouse spinal cord. Biogerontology 2023; 24:137-148. [PMID: 36550376 DOI: 10.1007/s10522-022-10004-z] [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: 11/29/2022] [Indexed: 12/24/2022]
Abstract
Aging-affected cellular compositions of the spinal cord are diverse and region specific. Age leads to the accumulation of abnormal protein aggregates and dysregulation of proteostasis. Dysregulated proteostasis and protein aggregates result from dysfunction of the ubiquitin-proteasome system (UPS) and autophagy. Understanding the molecular mechanisms of spinal cord aging is essential and important for scientists to discover new therapies for rejuvenation. We found age-related increases in STAT3 and decreases in Tuj1 in aging mouse spinal cords, which was characterized by increased expression of P16. Coaggregation of lysine-48 and lysine-63 ubiquitin with STAT3 was revealed in aging mouse spinal cords. STAT3-ubiquitin aggregates formed via lysine-48 and lysine-63 linkages were increased significantly in the aging spinal cords but not in central canal ependymal cells or neural stem cells in the spinal cord. These results highlight the increase in STAT3 and its region-specific aggregation and ubiquitin-conjugation during spinal cord aging.
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Affiliation(s)
- Tianyi Zhao
- Department of Histology and Embryology, School of Basic Medical Sciences, Institute of Stem Cell and Tissue Engineering, Anhui Medical University, 81 Meishan Road, Hefei, 230032, Anhui, China
| | - Chang Liu
- Department of Orthopedics and Spine Surgery, The First Affiliated Hospital, Anhui Medical University, Hefei, 230032, Anhui, China
| | - Lihua Liu
- Institute of Clinical Pharmacology, Anhui Medical University, Hefei, 230032, Anhui, China
| | - Xinmeng Wang
- Department of Histology and Embryology, School of Basic Medical Sciences, Institute of Stem Cell and Tissue Engineering, Anhui Medical University, 81 Meishan Road, Hefei, 230032, Anhui, China
| | - Chao Liu
- Department of Histology and Embryology, School of Basic Medical Sciences, Institute of Stem Cell and Tissue Engineering, Anhui Medical University, 81 Meishan Road, Hefei, 230032, Anhui, China.
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Ghafouri-Fard S, Hussen BM, Jamali E, Branicki W, Taheri M, Akbari Dilmaghani N. Role of lncRNAs and circRNAs in epilepsy. Ageing Res Rev 2022; 82:101749. [PMID: 36216292 DOI: 10.1016/j.arr.2022.101749] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 08/02/2022] [Accepted: 10/05/2022] [Indexed: 02/09/2023]
Abstract
Epilepsy is a chronic disorder of with a high prevalence and extensive health burden in almost all age groups of the population. This condition is resulted from disturbance in the balance between excitatory and inhibitory factors in the brain. Genetic elements that affect synaptic connectivity, receptors functions or ion channels have been shown to predispose individuals to the epilepsy. More recently, a body of evidence points to the role of non-coding part of the transcriptome in the pathology of epilepsy. Expression levels of NEAT1, H19, PVT1, ILF3-AS1, GAS5, ZFAS1, UCA1, MALAT1 and SNHG1 have been changed in epileptic patients or animal models of epilepsy. Moreover, circ_ANKMY2, circRNA-0067835 and circHivep2 are among circRNAs which are involved in the pathogenesis of epilepsy. Although the mechanistical impact of these transcripts in the pathogenesis of epilepsy has not been fully explored, disturbances in neuron plasticity, apoptosis or differentiation might be implicated in this process. Expression levels of lncRNAs can be used for discrimination of epileptic patients from normal controls or refractory patients from non-refractory ones. JAK/STAT, Wnt, PI3K/AKT and NF-κB signaling pathways are among the regulated pathways by lncRNAs in the context of epilepsy. In the present review, we summarize the role of lncRNAs and circRNAs in the pathogenesis of epilepsy.
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Affiliation(s)
- Soudeh Ghafouri-Fard
- Department of Medical Genetics, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Bashdar Mahmud Hussen
- Department of Pharmacognosy, College of Pharmacy, Hawler Medical University, Kurdistan Region, Erbil, Iraq; Center of Research and Strategic Studies, Lebanese French University, Kurdistan Region, Erbil, Iraq
| | - Elena Jamali
- Department of Pathology, Loghman Hakim Hospital, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Wojciech Branicki
- Institute of Zoology and Biomedical Research, Faculty of Biology, Jagiellonian University, Krakow, Poland
| | - Mohammad Taheri
- Urology and Nephrology Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran; Institute of Human Genetics, Jena University Hospital, Jena, Germany.
| | - Nader Akbari Dilmaghani
- Skull Base Research Center, Loghman Hakim Hospital, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
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Mini-review: Recent advances in post-translational modification site prediction based on deep learning. Comput Struct Biotechnol J 2022; 20:3522-3532. [PMID: 35860402 PMCID: PMC9284371 DOI: 10.1016/j.csbj.2022.06.045] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Revised: 06/21/2022] [Accepted: 06/21/2022] [Indexed: 11/23/2022] Open
Abstract
Post-translational modifications (PTMs) are closely linked to numerous diseases, playing a significant role in regulating protein structures, activities, and functions. Therefore, the identification of PTMs is crucial for understanding the mechanisms of cell biology and diseases therapy. Compared to traditional machine learning methods, the deep learning approaches for PTM prediction provide accurate and rapid screening, guiding the downstream wet experiments to leverage the screened information for focused studies. In this paper, we reviewed the recent works in deep learning to identify phosphorylation, acetylation, ubiquitination, and other PTM types. In addition, we summarized PTM databases and discussed future directions with critical insights.
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Key Words
- AAindex, Amino acid index
- ATP, Adenosine triphosphate
- AUC, Area under curve
- Ac, Acetylation
- BE, Binary encoding
- BLOSUM, Blocks substitution matrix
- Bi-LSTM, Bidirectional LSTM
- CKSAAP, Composition of k-spaced amino acid Pairs
- CNN, Convolutional neural network
- CNNOH, CNN with the one-hot encoding
- CNNWE, CNN with the word-embedding encoding
- CNNrgb, CNN red green blue
- CV, Cross-validation
- DC-CNN, Densely connected convolutional neural network
- DL, Deep learning
- DNNs, Deep neural networks
- Deep learning
- E. coli, Escherichia coli
- EBGW, Encoding based on grouped weight
- EGAAC, Enhanced grouped amino acids content
- IG, Information gain
- K, Lysine
- KNN, k nearest neighbor
- LASSO, Least absolute shrinkage and selection operator
- LSTM, Long short-term memory
- LSTMWE, LSTM with the word-embedding encoding
- M.musculus, Mus musculus
- MDC, Modular densely connected convolutional networks
- MDCAN, Multilane dense convolutional attention network
- ML, Machine learning
- MLP, Multilayer perceptron
- MMI, Multivariate mutual information
- Machine learning
- Mass spectrometry
- NMBroto, Normalized Moreau-Broto autocorrelation
- P, Proline
- PSP, PhosphoSitePlus
- PSSM, Position-specific scoring matrix
- PTM, Post-translational modifications
- Ph, Phosphorylation
- Post-translational modification
- Prediction
- PseAAC, Pseudo-amino acid composition
- R, Arginine
- RF, Random forest
- RNN, Recurrent neural network
- ROC, Receiver operating characteristic
- S, Serine
- S. typhimurium, Salmonella typhimurium
- S.cerevisiae, Saccharomyces cerevisiae
- SE, Squeeze and excitation
- SEV, Split to Equal Validation
- ST, Source and target
- SUMO, Small ubiquitin-like modifier
- SVM, Support vector machines
- T, Threonine
- Ub, Ubiquitination
- Y, Tyrosine
- ZSL, Zero-shot learning
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Ubiquitin Ligases in Longevity and Aging Skeletal Muscle. Int J Mol Sci 2022; 23:ijms23147602. [PMID: 35886949 PMCID: PMC9315556 DOI: 10.3390/ijms23147602] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Revised: 07/07/2022] [Accepted: 07/08/2022] [Indexed: 12/07/2022] Open
Abstract
The development and prevalence of diseases associated with aging presents a global health burden on society. One hallmark of aging is the loss of proteostasis which is caused in part by alterations to the ubiquitin-proteasome system (UPS) and lysosome-autophagy system leading to impaired function and maintenance of mass in tissues such as skeletal muscle. In the instance of skeletal muscle, the impairment of function occurs early in the aging process and is dependent on proteostatic mechanisms. The UPS plays a pivotal role in degradation of misfolded and aggregated proteins. For the purpose of this review, we will discuss the role of the UPS system in the context of age-related loss of muscle mass and function. We highlight the significant role that E3 ubiquitin ligases play in the turnover of key components (e.g., mitochondria and neuromuscular junction) essential to skeletal muscle function and the influence of aging. In addition, we will briefly discuss the contribution of the UPS system to lifespan. By understanding the UPS system as part of the proteostasis network in age-related diseases and disorders such as sarcopenia, new discoveries can be made and new interventions can be developed which will preserve muscle function and maintain quality of life with advancing age.
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Zhang WH, Koyuncu S, Vilchez D. Insights Into the Links Between Proteostasis and Aging From C. elegans. FRONTIERS IN AGING 2022; 3:854157. [PMID: 35821832 PMCID: PMC9261386 DOI: 10.3389/fragi.2022.854157] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Accepted: 02/22/2022] [Indexed: 04/20/2023]
Abstract
Protein homeostasis (proteostasis) is maintained by a tightly regulated and interconnected network of biological pathways, preventing the accumulation and aggregation of damaged or misfolded proteins. Thus, the proteostasis network is essential to ensure organism longevity and health, while proteostasis failure contributes to the development of aging and age-related diseases that involve protein aggregation. The model organism Caenorhabditis elegans has proved invaluable for the study of proteostasis in the context of aging, longevity and disease, with a number of pivotal discoveries attributable to the use of this organism. In this review, we discuss prominent findings from C. elegans across the many key aspects of the proteostasis network, within the context of aging and disease. These studies collectively highlight numerous promising therapeutic targets, which may 1 day facilitate the development of interventions to delay aging and prevent age-associated diseases.
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Affiliation(s)
- William Hongyu Zhang
- Cologne Excellence Cluster for Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
| | - Seda Koyuncu
- Cologne Excellence Cluster for Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
| | - David Vilchez
- Cologne Excellence Cluster for Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany
- Faculty of Medicine, University Hospital Cologne, Cologne, Germany
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Shen X, Wu B, Jiang W, Li Y, Zhang Y, Zhao K, Nie N, Gong L, Liu Y, Zou X, Liu J, Jin J, Ouyang H. Scale bar of aging trajectories for screening personal rejuvenation treatments. Comput Struct Biotechnol J 2022; 20:5750-5760. [DOI: 10.1016/j.csbj.2022.10.021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Revised: 10/15/2022] [Accepted: 10/15/2022] [Indexed: 11/27/2022] Open
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Hüttenrauch M, Lopez-Noguerola JS, Castro-Obregón S. Connecting Mind-Body Therapy-Mediated Effects to Pathological Features of Alzheimer's Disease. J Alzheimers Dis 2021; 82:S65-S90. [PMID: 33044183 DOI: 10.3233/jad-200743] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Alzheimer's disease (AD) is a complex, multifactorial neurodegenerative disorder that represents a major and increasing global health challenge. In most cases, the first clinical symptoms of AD are preceded by neuropathological changes in the brain that develop years to decades before their onset. Therefore, research in the last years has focused on this preclinical stage of AD trying to discover intervention strategies that might, if implemented effectively, delay or prevent disease progression. Among those strategies, mind-body therapies such as yoga and meditation have gained increasing interest as complementary alternative interventions. Several studies have reported a positive impact of yoga and meditation on brain health in both healthy older adults and dementia patients. However, the underlying neurobiological mechanisms contributing to these effects are currently not known in detail. More specifically, it is not known whether yogic interventions, directly or indirectly, can modulate risk factors or pathological mechanisms involved in the development of dementia. In this article, we first review the literature on the effects of yogic practices on outcomes such as cognitive functioning and neuropsychiatric symptoms in patients with mild cognitive impairment and dementia. Then, we analyze how yogic interventions affect different risk factors as well as aspects of AD pathophysiology based on observations of studies in healthy individuals or subjects with other conditions than dementia. Finally, we integrate this evidence and propose possible mechanisms that might explain the positive effects of yogic interventions in cognitively impaired individuals.
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Affiliation(s)
- Melanie Hüttenrauch
- División de Neurosciencias, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México (UNAM), Ciudad Universitaria, Ciudad de México, México
| | - José Sócrates Lopez-Noguerola
- Área Académica de Gerontología, Instituto de Ciencias de la Salud, Universidad Autónoma del Estado de Hidalgo, Pachuca de Soto, México
| | - Susana Castro-Obregón
- División de Neurosciencias, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México (UNAM), Ciudad Universitaria, Ciudad de México, México
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Lee T, Chen P, Su MP, Li J, Chang Y, Liu R, Juan H, Yang J, Chan S, Tsai Y, Stockum S, Ziviani E, Kamikouchi A, Wang H, Chen C. Loss of Fis1 impairs proteostasis during skeletal muscle aging in Drosophila. Aging Cell 2021; 20:e13379. [PMID: 34061429 PMCID: PMC8208795 DOI: 10.1111/acel.13379] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Revised: 03/25/2021] [Accepted: 04/26/2021] [Indexed: 02/06/2023] Open
Abstract
Increased levels of dysfunctional mitochondria within skeletal muscle are correlated with numerous age‐related physiopathological conditions. Improving our understanding of the links between mitochondrial function and muscle proteostasis, and the role played by individual genes and regulatory networks, is essential to develop treatments for these conditions. One potential player is the mitochondrial outer membrane protein Fis1, a crucial fission factor heavily involved in mitochondrial dynamics in yeast but with an unknown role in higher‐order organisms. By using Drosophila melanogaster as a model, we explored the effect of Fis1 mutations generated by transposon Minos‐mediated integration. Mutants exhibited a higher ratio of damaged mitochondria with age as well as elevated reactive oxygen species levels compared with controls. This caused an increase in oxidative stress, resulting in large accumulations of ubiquitinated proteins, accelerated muscle function decline, and mitochondrial myopathies in young mutant flies. Ectopic expression of Fis1 isoforms was sufficient to suppress this phenotype. Loss of Fis1 led to unbalanced mitochondrial proteostasis within fly muscle, decreasing both flight capabilities and lifespan. Fis1 thus clearly plays a role in fly mitochondrial dynamics. Further investigations into the detailed function of Fis1 are necessary for exploring how mitochondrial function correlates with muscle health during aging.
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Affiliation(s)
- Tai‐Ting Lee
- National Institute of Infectious Diseases and Vaccinology National Health Research Institutes Zhunan Taiwan
- Division of Biological Science Graduate School of Science Nagoya University Nagoya Japan
- Institute of Biotechnology National Tsing Hua University Hsinchu Taiwan
| | - Po‐Lin Chen
- National Institute of Infectious Diseases and Vaccinology National Health Research Institutes Zhunan Taiwan
- National Mosquito‐Borne Diseases Control Research Center National Health Research Institutes Zhunan Taiwan
| | - Matthew P. Su
- Division of Biological Science Graduate School of Science Nagoya University Nagoya Japan
| | - Jian‐Chiuan Li
- National Institute of Infectious Diseases and Vaccinology National Health Research Institutes Zhunan Taiwan
| | - Yi‐Wen Chang
- Department of Life Science National Taiwan University Taipei Taiwan
| | - Rei‐Wen Liu
- National Institute of Infectious Diseases and Vaccinology National Health Research Institutes Zhunan Taiwan
- Department of Life Science and Life Science Center Tunghai University Taichung Taiwan
| | - Hsueh‐Fen Juan
- Department of Life Science National Taiwan University Taipei Taiwan
| | - Jinn‐Moon Yang
- Institute of Bioinformatics and Systems Biology National Chiao Tung University Hsinchu Taiwan
| | - Shih‐Peng Chan
- Graduate Institute of Microbiology College of Medicine National Taiwan University Taipei Taiwan
- Genome and Systems Biology Degree Program College of Life Science National Taiwan University Taipei Taiwan
| | - Yu‐Chen Tsai
- Department of Life Science and Life Science Center Tunghai University Taichung Taiwan
| | - Sophia Stockum
- Department of Biology University of Padova Padova Italy
- Fondazione Ospedale San Camillo IRCCS, Lido di Venezia Venezia Italy
| | - Elena Ziviani
- Department of Biology University of Padova Padova Italy
- Fondazione Ospedale San Camillo IRCCS, Lido di Venezia Venezia Italy
| | - Azusa Kamikouchi
- Division of Biological Science Graduate School of Science Nagoya University Nagoya Japan
| | - Horng‐Dar Wang
- Institute of Biotechnology National Tsing Hua University Hsinchu Taiwan
| | - Chun‐Hong Chen
- National Institute of Infectious Diseases and Vaccinology National Health Research Institutes Zhunan Taiwan
- National Mosquito‐Borne Diseases Control Research Center National Health Research Institutes Zhunan Taiwan
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12
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Vasilopoulou MΑ, Ioannou E, Roussis V, Chondrogianni N. Modulation of the ubiquitin-proteasome system by marine natural products. Redox Biol 2021; 41:101897. [PMID: 33640701 PMCID: PMC7921624 DOI: 10.1016/j.redox.2021.101897] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Revised: 02/05/2021] [Accepted: 02/10/2021] [Indexed: 02/07/2023] Open
Abstract
The ubiquitin-proteasome system (UPS) is a key player in the maintenance of cellular protein homeostasis (proteostasis). Since proteasome function declines upon aging leading to the acceleration of its progression and the manifestation of age-related pathologies, many attempts have been performed towards proteasome activation as a strategy to promote healthspan and longevity. The marine environment hosts a plethora of organisms that produce a vast array of primary and secondary metabolites, the majority of which are unique, exhibiting a wide spectrum of biological activities. The fact that these biologically important compounds are also present in edible marine organisms has sparked the interest for elucidating their potential health-related applications. In this review, we focus on the antioxidant, anti-aging, anti-aggregation and anti-photoaging properties of various marine constituents. We further discuss representatives of marine compounds classes with regard to their potential (direct or indirect) action on UPS components that could serve as UPS modulators and exert beneficial effects on conditions such as oxidative stress, aging and age-related diseases.
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Affiliation(s)
- Mary Α Vasilopoulou
- Institute of Chemical Biology, National Hellenic Research Foundation, 48 Vassileos Constantinou Ave., Athens, 11635, Greece; Department of Biochemistry and Biotechnology, University of Thessaly, Biopolis, 41500, Larisa, Greece.
| | - Efstathia Ioannou
- Section of Pharmacognosy and Chemistry of Natural Products, Department of Pharmacy, School of Health Sciences, National and Kapodistrian University of Athens, Panepistimiopolis Zografou, Athens, 15771, Greece.
| | - Vassilios Roussis
- Section of Pharmacognosy and Chemistry of Natural Products, Department of Pharmacy, School of Health Sciences, National and Kapodistrian University of Athens, Panepistimiopolis Zografou, Athens, 15771, Greece.
| | - Niki Chondrogianni
- Institute of Chemical Biology, National Hellenic Research Foundation, 48 Vassileos Constantinou Ave., Athens, 11635, Greece.
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13
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Baldensperger T, Glomb MA. Pathways of Non-enzymatic Lysine Acylation. Front Cell Dev Biol 2021; 9:664553. [PMID: 33996820 PMCID: PMC8116961 DOI: 10.3389/fcell.2021.664553] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Accepted: 04/07/2021] [Indexed: 12/18/2022] Open
Abstract
Posttranslational protein modification by lysine acylation is an emerging mechanism of cellular regulation and fine-tunes metabolic processes to environmental changes. In this review we focus on recently discovered pathways of non-enzymatic lysine acylation by reactive acyl-CoA species, acyl phosphates, and α-dicarbonyls. We summarize the metabolic sources of these highly reactive intermediates, demonstrate their reaction mechanisms, give an overview of the resulting acyl lysine modifications, and evaluate the consequences for cellular regulatory processes. Finally, we discuss interferences between lysine acylation and lysine ubiquitylation as a potential molecular mechanism of dysregulated protein homeostasis in aging and related diseases.
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Affiliation(s)
- Tim Baldensperger
- Department of Molecular Toxicology, German Institute of Human Nutrition Potsdam-Rehbruecke (DIfE), Nuthetal, Germany
| | - Marcus A Glomb
- Institute of Chemistry, Food Chemistry, Martin-Luther-University Halle-Wittenberg, Halle, Germany
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14
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Erez N, Israitel L, Bitman-Lotan E, Wong WH, Raz G, Cornelio-Parra DV, Danial S, Flint Brodsly N, Belova E, Maksimenko O, Georgiev P, Druley T, Mohan RD, Orian A. A Non-stop identity complex (NIC) supervises enterocyte identity and protects from premature aging. eLife 2021; 10:62312. [PMID: 33629655 PMCID: PMC7936876 DOI: 10.7554/elife.62312] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Accepted: 02/17/2021] [Indexed: 02/06/2023] Open
Abstract
A hallmark of aging is loss of differentiated cell identity. Aged Drosophila midgut differentiated enterocytes (ECs) lose their identity, impairing tissue homeostasis. To discover identity regulators, we performed an RNAi screen targeting ubiquitin-related genes in ECs. Seventeen genes were identified, including the deubiquitinase Non-stop (CG4166). Lineage tracing established that acute loss of Non-stop in young ECs phenocopies aged ECs at cellular and tissue levels. Proteomic analysis unveiled that Non-stop maintains identity as part of a Non-stop identity complex (NIC) containing E(y)2, Sgf11, Cp190, (Mod) mdg4, and Nup98. Non-stop ensured chromatin accessibility, maintaining the EC-gene signature, and protected NIC subunit stability. Upon aging, the levels of Non-stop and NIC subunits declined, distorting the unique organization of the EC nucleus. Maintaining youthful levels of Non-stop in wildtype aged ECs safeguards NIC subunits, nuclear organization, and suppressed aging phenotypes. Thus, Non-stop and NIC, supervise EC identity and protects from premature aging.
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Affiliation(s)
- Neta Erez
- Rappaport Research Institute and Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, Israel
| | - Lena Israitel
- Rappaport Research Institute and Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, Israel
| | - Eliya Bitman-Lotan
- Rappaport Research Institute and Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, Israel
| | - Wing H Wong
- Division of Pediatric Hematology and Oncology, Washington University, Saint-Louis, United States
| | - Gal Raz
- Rappaport Research Institute and Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, Israel
| | - Dayanne V Cornelio-Parra
- Department of Genetics, Developmental & Evolutionary Biology, School of Biological and Chemical Sciences University of Missouri, Kansas City, United States
| | - Salwa Danial
- Rappaport Research Institute and Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, Israel
| | - Na'ama Flint Brodsly
- Rappaport Research Institute and Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, Israel
| | - Elena Belova
- Department of the Control of Genetic Processes, Institute of Gene Biology Russian Academy of Sciences, Moscow, Russian Federation
| | - Oksana Maksimenko
- Department of the Control of Genetic Processes, Institute of Gene Biology Russian Academy of Sciences, Moscow, Russian Federation
| | - Pavel Georgiev
- Department of the Control of Genetic Processes, Institute of Gene Biology Russian Academy of Sciences, Moscow, Russian Federation
| | - Todd Druley
- Division of Pediatric Hematology and Oncology, Washington University, Saint-Louis, United States
| | - Ryan D Mohan
- Department of Genetics, Developmental & Evolutionary Biology, School of Biological and Chemical Sciences University of Missouri, Kansas City, United States
| | - Amir Orian
- Rappaport Research Institute and Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, Israel
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15
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Siametis A, Niotis G, Garinis GA. DNA Damage and the Aging Epigenome. J Invest Dermatol 2021; 141:961-967. [PMID: 33494932 DOI: 10.1016/j.jid.2020.10.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Revised: 09/28/2020] [Accepted: 10/01/2020] [Indexed: 12/29/2022]
Abstract
In mammals, genome instability and aging are intimately linked as illustrated by the growing list of patients with progeroid and animal models with inborn DNA repair defects. Until recently, DNA damage was thought to drive aging by compromising transcription or DNA replication, thereby leading to age-related cellular malfunction and somatic mutations triggering cancer. However, recent evidence suggests that DNA lesions also elicit widespread epigenetic alterations that threaten cell homeostasis as a function of age. In this review, we discuss the functional links of persistent DNA damage with the epigenome in the context of aging and age-related diseases.
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Affiliation(s)
- Athanasios Siametis
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology, Heraklion, Greece; Department of Biology, University of Crete, Heraklion, Greece
| | - George Niotis
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology, Heraklion, Greece; Department of Biology, University of Crete, Heraklion, Greece
| | - George A Garinis
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology, Heraklion, Greece; Department of Biology, University of Crete, Heraklion, Greece.
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16
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The dialogue between the ubiquitin-proteasome system and autophagy: Implications in ageing. Ageing Res Rev 2020; 64:101203. [PMID: 33130248 DOI: 10.1016/j.arr.2020.101203] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Revised: 10/09/2020] [Accepted: 10/25/2020] [Indexed: 02/06/2023]
Abstract
Dysregulated proteostasis is one of the hallmarks of ageing. Damaged proteins may impair cellular function and their accumulation may lead to tissue dysfunction and disease. This is why protective mechanisms to safeguard the cell proteome have evolved. These mechanisms consist of cellular machineries involved in protein quality control, including regulators of protein translation, folding, trafficking and degradation. In eukaryotic cells, protein degradation occurs via two main pathways: the ubiquitin-proteasome system (UPS) and the autophagy-lysosome pathway. Although distinct pathways, they are not isolated systems and have a complementary nature, as evidenced by recent studies. These findings raise the question of how autophagy and the proteasome crosstalk. In this review we address how the two degradation pathways impact each other, thereby adding a new layer of regulation to protein degradation. We also analyze the implications of the UPS and autophagy in ageing.
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17
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Toren D, Kulaga A, Jethva M, Rubin E, Snezhkina AV, Kudryavtseva AV, Nowicki D, Tacutu R, Moskalev AA, Fraifeld VE. Gray whale transcriptome reveals longevity adaptations associated with DNA repair and ubiquitination. Aging Cell 2020; 19:e13158. [PMID: 32515539 PMCID: PMC7433004 DOI: 10.1111/acel.13158] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Revised: 03/16/2020] [Accepted: 04/09/2020] [Indexed: 12/29/2022] Open
Abstract
One important question in aging research is how differences in genomics and transcriptomics determine the maximum lifespan in various species. Despite recent progress, much is still unclear on the topic, partly due to the lack of samples in nonmodel organisms and due to challenges in direct comparisons of transcriptomes from different species. The novel ranking‐based method that we employ here is used to analyze gene expression in the gray whale and compare its de novo assembled transcriptome with that of other long‐ and short‐lived mammals. Gray whales are among the top 1% longest‐lived mammals. Despite the extreme environment, or maybe due to a remarkable adaptation to its habitat (intermittent hypoxia, Arctic water, and high pressure), gray whales reach at least the age of 77 years. In this work, we show that long‐lived mammals share common gene expression patterns between themselves, including high expression of DNA maintenance and repair, ubiquitination, apoptosis, and immune responses. Additionally, the level of expression for gray whale orthologs of pro‐ and anti‐longevity genes found in model organisms is in support of their alleged role and direction in lifespan determination. Remarkably, among highly expressed pro‐longevity genes many are stress‐related, reflecting an adaptation to extreme environmental conditions. The conducted analysis suggests that the gray whale potentially possesses high resistance to cancer and stress, at least in part ensuring its longevity. This new transcriptome assembly also provides important resources to support the efforts of maintaining the endangered population of gray whales.
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Affiliation(s)
- Dmitri Toren
- The Shraga Segal Department of Microbiology, Immunology and Genetics Center for Multidisciplinary Research on Aging Ben‐Gurion University of the Negev Beer Sheva Israel
- Systems Biology of Aging Group Institute of Biochemistry of the Romanian Academy Bucharest Romania
| | - Anton Kulaga
- Systems Biology of Aging Group Institute of Biochemistry of the Romanian Academy Bucharest Romania
- Humenhance OÜ Tallinn Estonia
| | - Mineshbhai Jethva
- The Shraga Segal Department of Microbiology, Immunology and Genetics Center for Multidisciplinary Research on Aging Ben‐Gurion University of the Negev Beer Sheva Israel
| | - Eitan Rubin
- The Shraga Segal Department of Microbiology, Immunology and Genetics Center for Multidisciplinary Research on Aging Ben‐Gurion University of the Negev Beer Sheva Israel
| | | | - Anna V. Kudryavtseva
- Engelhardt Institute of Molecular Biology Russian Academy of Sciences Moscow Russia
| | - Dmitry Nowicki
- Center for Cybernetics Institute of MMS of NASU Kiev Ukraine
| | - Robi Tacutu
- Systems Biology of Aging Group Institute of Biochemistry of the Romanian Academy Bucharest Romania
- Chronos Biosystems SRL Bucharest Romania
| | - Alexey A. Moskalev
- Engelhardt Institute of Molecular Biology Russian Academy of Sciences Moscow Russia
- Institute of Biology of Komi Science Center of Ural Branch of RAS Syktyvkar Russia
| | - Vadim E. Fraifeld
- The Shraga Segal Department of Microbiology, Immunology and Genetics Center for Multidisciplinary Research on Aging Ben‐Gurion University of the Negev Beer Sheva Israel
- 8IVAO LLC Saint Petersburg Russia
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18
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Teissier T, Boulanger E, Deramecourt V. Normal ageing of the brain: Histological and biological aspects. Rev Neurol (Paris) 2020; 176:649-660. [PMID: 32418702 DOI: 10.1016/j.neurol.2020.03.017] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2020] [Revised: 03/20/2020] [Accepted: 03/23/2020] [Indexed: 02/02/2023]
Abstract
All the hallmarks of ageing are observed in the brain, and its cells, especially neurons, are characterized by their remarkably long lifetime. Like any organ or system, the brain is exposed to ageing processes which affect molecules, cells, blood vessels, gross morphology and, uniquely for this organ, cognition. The preponderant cerebral structures are characterized by the cellular processes of neurons and glial cells and while the quantity of cerebral interstitial fluid is limited, it is now recognized as playing a crucial role in maintaining cerebral homeostasis. Most of our current knowledge of the ageing brain derives from studies of neurodegenerative disorders. It is interesting to note that common features of these disorders, like Tau, phosphoTau and amyloid peptide accumulation, can begin relatively early in life as a result of physiological ageing and are present in subclinical cases while also being used as early-stage markers of neurodegenerative diseases in progression. In this article, we review tissue and cellular modifications in the ageing brain. Commonly described macroscopic, microscopic and vascular changes that in the ageing brain are contrasted with those seen in neurodegenerative contexts. We also review the molecular changes that occur with age in the brain, such as modifications in gene expression, insulin/insulin-like growth factor 1 signalling dysfunction, post-translational protein modifications, mitochondrial dysfunction, autophagy and calcium conductance changes.
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Affiliation(s)
- T Teissier
- Inserm, université de Lille, CHU de Lille, Institut Pasteur de Lille, U1167 - RID-AGE - facteurs de risque et déterminants moléculaires des maladies liées au vieillissement, équipe « de l'inflammation au vieillissement, 59000 Lille, France.
| | - E Boulanger
- Inserm, université de Lille, CHU de Lille, Institut Pasteur de Lille, U1167 - RID-AGE - facteurs de risque et déterminants moléculaires des maladies liées au vieillissement, équipe « de l'inflammation au vieillissement, 59000 Lille, France; Pôle de gérontologie, CHU de Lille, 59000 Lille, France
| | - V Deramecourt
- Inserm, UMR-S 1172 « Alzheimer et Tauopathies », centre mémoire de ressources et de recherche, Labex DISTALZ, université de Lille, CHU de Lille, 59000 Lille, France; Pôle de neurologie, CHU de Lille, 59000 Lille, France
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19
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Tian W, Trader DJ. Discovery of a Small Molecule Probe of Rpn-6, an Essential Subunit of the 26S Proteasome. ACS Chem Biol 2020; 15:554-561. [PMID: 31877015 DOI: 10.1021/acschembio.9b01019] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
A considerable number of essential cellular proteins have no catalytic activity and serve instead as structural components to aid in assembling protein complexes. For example, the assembly and function of the 26S proteasome, the major enzymatic complex necessary for ubiquitin-dependent protein degradation, require a number of essential protein contacts to associate the 19S regulatory particle with the 20S core particle. Previously, small molecule inhibitors of the active sites of the 20S core particle have been developed, but the activity of the 26S proteasome could also be altered via the disruption of its assembly. We were interested in discovering a small molecule binder of Rpn-6, as it is among several essential proteins that facilitate 26S assembly, which could be used to further our understanding of the association of the 19S regulatory particle with the 20S core particle. Additionally, we were interested in whether a small molecule-Rpn-6 interaction could potentially be cytotoxic to cancer cells that rely heavily on proteasome activity for survival. A workflow for utilizing a one-bead, one-compound library and a thermal shift assay was developed to discover such a molecule. TXS-8, our lead hit, was discovered to have a low micromolar binding affinity for Rpn-6 as well as very limited binding to other proteins. The cytotoxicity of TXS-8 was evaluated in several cell lines, revealing increased cytotoxicity to hematological cancers. Discovery of this peptoid binder of Rpn-6 provides the initial evidence that Rpn-6 could be a druggable target to affect protein degradation and serves as a primary scaffold from which to design more potent binders. We suspect that Rpn-6 could have additional essential roles beyond that of a molecular clamp of the proteasome to help hematological cancer cells survive and that TXS-8 can serve as a useful tool for further elucidating its roles.
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Affiliation(s)
- Wenzhi Tian
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, 575 West Stadium Avenue, West Lafayette, Indiana 47907, United States
| | - Darci J. Trader
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, 575 West Stadium Avenue, West Lafayette, Indiana 47907, United States
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20
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Lopez‐Castejon G. Control of the inflammasome by the ubiquitin system. FEBS J 2020; 287:11-26. [PMID: 31679183 PMCID: PMC7138099 DOI: 10.1111/febs.15118] [Citation(s) in RCA: 90] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Revised: 09/27/2019] [Accepted: 10/31/2019] [Indexed: 12/25/2022]
Abstract
Inflammation is the body's response to danger. One of the first immune cell types to encounter danger is the macrophage. Macrophages sense danger signals such as extracellular ATP or bacterial toxins, derived from tissue damage or infection, and initiate the activation of an intracellular molecular complex called the inflammasome. The inflammasome consists of a cytosolic pattern recognition receptor, an adaptor molecule ASC (apoptosis-associated speck-like protein containing a CARD) and the protease caspase-1. Assembly of the complex leads to the cleavage and activation of caspase-1 that triggers processing and release of the cytokines interleukin (IL)-1β and IL-18, and ultimately cell death via the process of pyroptosis. The ability to sense and respond to danger appropriately is critical for maintaining immune homeostasis. Dysregulation of inflammasomes contributes to the progression of chronic diseases prevalent in the ageing population, such as Alzheimer's disease, COPD and metabolic disease; hence, it is critical that activation of the inflammatory response and inflammasome activation are tightly regulated. Post-translational modifications (PTMs) such as ubiquitination have recently emerged as important regulators of inflammasome assembly. However, the mechanisms by which PTMs regulate the inflammasome are still not understood. This review aims to summarize our knowledge to date on how the ubiquitin system controls inflammasome activation and where this area of research is heading.
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Affiliation(s)
- Gloria Lopez‐Castejon
- Division of Infection, Immunity and Respiratory MedicineFaculty of Biology, Medicine and HealthLydia Becker Institute of Immunology and InflammationManchester Collaborative Centre for Inflammation ResearchManchester Academic Health Science CentreUniversity of ManchesterUK
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21
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Wang Z, Yang W. Impaired capacity to restore proteostasis in the aged brain after ischemia: Implications for translational brain ischemia research. Neurochem Int 2018; 127:87-93. [PMID: 30599146 DOI: 10.1016/j.neuint.2018.12.018] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Revised: 12/28/2018] [Accepted: 12/28/2018] [Indexed: 12/15/2022]
Abstract
Brain ischemia induced by cardiac arrest or ischemic stroke is a severe form of metabolic stress that substantially disrupts cellular homeostasis, especially protein homeostasis (proteostasis). As proteostasis is fundamental for cellular and organismal health, cells have developed a complex network to restore proteostasis impaired by stress. Many components of this network - including ubiquitination, small ubiquitin-like modifier (SUMO) conjugation, autophagy, and the unfolded protein response (UPR) - are activated in the post-ischemic brain, and play a crucial role in cell survival and recovery of neurologic function. Importantly, recent studies have shown that ischemia-induced activation of these proteostasis-related pathways in the aged brain is impaired, indicating an aging-related decline in the self-healing capacity of the brain. This impaired capacity is a significant factor for consideration in the field of brain ischemia because the vast majority of cardiac arrest and stroke patients are elderly. In this review, we focus on the effects of aging on these critical proteostasis-related pathways in the brain, and discuss their implications in translational brain ischemia research.
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Affiliation(s)
- Zhuoran Wang
- Center for Perioperative Organ Protection, Department of Anesthesiology, Duke University Medical Center, Durham, NC, USA
| | - Wei Yang
- Center for Perioperative Organ Protection, Department of Anesthesiology, Duke University Medical Center, Durham, NC, USA.
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22
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Serrano RL, Chen LY, Lotz MK, Liu-Bryan R, Terkeltaub R. Impaired Proteasomal Function in Human Osteoarthritic Chondrocytes Can Contribute to Decreased Levels of SOX9 and Aggrecan. Arthritis Rheumatol 2018; 70:1030-1041. [PMID: 29457374 DOI: 10.1002/art.40456] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2017] [Accepted: 02/13/2018] [Indexed: 12/17/2022]
Abstract
OBJECTIVE Osteoarthritis (OA) chondrocytes exhibit impairment of autophagy, one arm of the proteostasis network that coordinates proteome and organelle quality control and degradation. Deficient proteostasis impacts differentiation and viability, and inflammatory processes in aging and disease. The present study was undertaken to assess ubiquitin proteasome system proteasomal function in OA chondrocytes. METHODS We evaluated human knee cartilage by immunohistochemistry, and assessed proteasomal function, levels of proteasomal core subunits and chaperones, and autophagy in cultured chondrocytes. Assays included Western blotting, quantitative reverse transcription-polymerase chain reaction, proteasomal protease activity assessment, and cell immunofluorescence analysis. RESULTS Human knee OA cartilage exhibited polyubiquitin accumulation, with increased ubiquitin K48-linked polyubiquitinated proteins in situ, suggesting proteasomal impairment. Cultured OA chondrocytes demonstrated accumulation of K48 polyubiquitinated proteins, significantly reduced 20S proteasome core protease activity, and decreased levels of phosphorylated FOXO4 and proteasome 26S subunit, non-ATPase 11 (PSMD11), a FOXO4-inducible promoter of proteasomal activation. Levels of proteasome subunit β type 3 (PSMB3), PSMB5, PSMB6, and proteasome assembly chaperone 1 were not decreased in OA chondrocytes. In normal chondrocytes, PSMD11 small interfering RNA knockdown stimulated certain autophagy machinery elements, increased extracellular nitric oxide (NO) levels, and reduced chondrocytic master transcription factor SOX9 protein and messenger RNA (mRNA) and aggrecan (AGC1) mRNA. PSMD11 gain-of- function by transfection increased proteasomal function, increased levels of SOX9-induced AGC1 mRNA, stimulated elements of the autophagic machinery, and inhibited extracellular levels of interleukin-1-induced NO and matrix metalloproteinase 13 in OA chondrocytes. CONCLUSION Deficient PSMD11, associated with reduced phosphorylated FOXO4, promotes impaired proteasomal function in OA chondrocytes, dysregulation of chondrocytic homeostasis, and decreased levels of SOX9 mRNA, SOX9 protein, and AGC1 mRNA. Chondrocyte proteasomal impairment may be a therapeutic target for OA.
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Affiliation(s)
- Ramon L Serrano
- VA San Diego Healthcare System, University of California San Diego, La Jolla, California
| | - Liang-Yu Chen
- VA San Diego Healthcare System, University of California San Diego, La Jolla, California
| | - Martin K Lotz
- The Scripps Research Institute, La Jolla, California
| | - Ru Liu-Bryan
- VA San Diego Healthcare System, University of California San Diego, La Jolla, California
| | - Robert Terkeltaub
- VA San Diego Healthcare System, University of California San Diego, La Jolla, California
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23
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Sahm A, Bens M, Szafranski K, Holtze S, Groth M, Görlach M, Calkhoven C, Müller C, Schwab M, Kraus J, Kestler HA, Cellerino A, Burda H, Hildebrandt T, Dammann P, Platzer M. Long-lived rodents reveal signatures of positive selection in genes associated with lifespan. PLoS Genet 2018; 14:e1007272. [PMID: 29570707 PMCID: PMC5884551 DOI: 10.1371/journal.pgen.1007272] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Revised: 04/04/2018] [Accepted: 02/22/2018] [Indexed: 12/11/2022] Open
Abstract
The genetics of lifespan determination is poorly understood. Most research has been done on short-lived animals and it is unclear if these insights can be transferred to long-lived mammals like humans. Some African mole-rats (Bathyergidae) have life expectancies that are multiple times higher than similar sized and phylogenetically closely related rodents. To gain new insights into genetic mechanisms determining mammalian lifespans, we obtained genomic and transcriptomic data from 17 rodent species and scanned eleven evolutionary branches associated with the evolution of enhanced longevity for positively selected genes (PSGs). Indicating relevance for aging, the set of 250 identified PSGs showed in liver of long-lived naked mole-rats and short-lived rats an expression pattern that fits the antagonistic pleiotropy theory of aging. Moreover, we found the PSGs to be enriched for genes known to be related to aging. Among these enrichments were “cellular respiration” and “metal ion homeostasis”, as well as functional terms associated with processes regulated by the mTOR pathway: translation, autophagy and inflammation. Remarkably, among PSGs are RHEB, a regulator of mTOR, and IGF1, both central components of aging-relevant pathways, as well as genes yet unknown to be aging-associated but representing convincing functional candidates, e.g. RHEBL1, AMHR2, PSMG1 and AGER. Exemplary protein homology modeling suggests functional consequences for amino acid changes under positive selection. Therefore, we conclude that our results provide a meaningful resource for follow-up studies to mechanistically link identified genes and amino acids under positive selection to aging and lifespan determination. As an adaption to different environments rodents have evolved a wide range of lifespans. While most rodents are short-lived, along several phylogenetic branches long-lived species evolved. This provided us a unique opportunity to search for genes that are associated with enhanced longevity in mammals. Towards this, we computationally compared gene sequences of exceptional long-lived rodent species (like the naked mole-rat and chinchilla) and short-lived rodents (like rat and mouse) and identified those which evolved exceptional fast. As natural selection acts in parallel on a multitude of phenotypes, only a subset of the identified genes is probably associated with enhanced longevity. Applying several tests, we ensured that the dataset is related to aging. We conclude that lifespan extension in rodents can be attributed to changes in their defense against free radicals, iron homeostasis as well as cellular respiration and translation as central parts of the growth program. This confirms aging theories assuming a tradeoff between fast growth and long lifespan. Moreover, our study offers a meaningful resource of targets, i.e. genes and specific positions therein, for functional follow-up studies on their potential roles in the determination of lifespan–regardless whether they are currently known to be aging-related or not.
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Affiliation(s)
- Arne Sahm
- Leibniz Institute on Aging–Fritz Lipmann Institute, Jena, Germany
- * E-mail:
| | - Martin Bens
- Leibniz Institute on Aging–Fritz Lipmann Institute, Jena, Germany
| | - Karol Szafranski
- Leibniz Institute on Aging–Fritz Lipmann Institute, Jena, Germany
| | - Susanne Holtze
- Department of Reproduction Management, Leibniz Institute for Zoo and Wildlife Research, Berlin, Germany
| | - Marco Groth
- Leibniz Institute on Aging–Fritz Lipmann Institute, Jena, Germany
| | - Matthias Görlach
- Leibniz Institute on Aging–Fritz Lipmann Institute, Jena, Germany
| | - Cornelis Calkhoven
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Centre Groningen, Groningen, The Netherlands
| | - Christine Müller
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Centre Groningen, Groningen, The Netherlands
| | - Matthias Schwab
- Department of Neurology; Jena University Hospital-Friedrich Schiller University, Jena, Germany
| | - Johann Kraus
- Institute of Medical Systems Biology, Ulm University, Ulm, Germany
| | - Hans A. Kestler
- Leibniz Institute on Aging–Fritz Lipmann Institute, Jena, Germany
- Institute of Medical Systems Biology, Ulm University, Ulm, Germany
| | - Alessandro Cellerino
- Leibniz Institute on Aging–Fritz Lipmann Institute, Jena, Germany
- Laboratory of Biology Bio@SNS, Scuola Normale Superiore, Pisa, Italy
| | - Hynek Burda
- Department of General Zoology, Faculty of Biology, University of Duisburg-Essen, Essen, Germany
| | - Thomas Hildebrandt
- Department of Reproduction Management, Leibniz Institute for Zoo and Wildlife Research, Berlin, Germany
| | - Philip Dammann
- Department of General Zoology, Faculty of Biology, University of Duisburg-Essen, Essen, Germany
- University Hospital, University of Duisburg-Essen, Essen, Germany
| | - Matthias Platzer
- Leibniz Institute on Aging–Fritz Lipmann Institute, Jena, Germany
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The Good, the Bad, and the Ugly of ROS: New Insights on Aging and Aging-Related Diseases from Eukaryotic and Prokaryotic Model Organisms. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2018; 2018:1941285. [PMID: 29743972 PMCID: PMC5878877 DOI: 10.1155/2018/1941285] [Citation(s) in RCA: 89] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/04/2017] [Revised: 12/18/2017] [Accepted: 01/02/2018] [Indexed: 12/13/2022]
Abstract
Aging is associated with the accumulation of cellular damage over the course of a lifetime. This process is promoted in large part by reactive oxygen species (ROS) generated via cellular metabolic and respiratory pathways. Pharmacological, nonpharmacological, and genetic interventions have been used to target cellular and mitochondrial networks in an effort to decipher aging and age-related disorders. While ROS historically have been viewed as a detrimental byproduct of normal metabolism and associated with several pathologies, recent research has revealed a more complex and beneficial role of ROS in regulating metabolism, development, and lifespan. In this review, we summarize the recent advances in ROS research, focusing on both the beneficial and harmful roles of ROS, many of which are conserved across species from bacteria to humans, in various aspects of cellular physiology. These studies provide a new context for our understanding of the parts ROS play in health and disease. Moreover, we highlight the utility of bacterial models to elucidate the molecular pathways by which ROS mediate aging and aging-related diseases.
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25
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Cheng X, Zheng J, Li G, Göbel V, Zhang H. Degradation for better survival? Role of ubiquitination in epithelial morphogenesis. Biol Rev Camb Philos Soc 2018; 93:1438-1460. [PMID: 29493067 DOI: 10.1111/brv.12404] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2017] [Revised: 01/31/2018] [Accepted: 02/05/2018] [Indexed: 02/06/2023]
Abstract
As a prevalent post-translational modification, ubiquitination is essential for many developmental processes. Once covalently attached to the small and conserved polypeptide ubiquitin (Ub), a substrate protein can be directed to perform specific biological functions via its Ub-modified form. Three sequential catalytic reactions contribute to this process, among which E3 ligases serve to identify target substrates and promote the activated Ub to conjugate to substrate proteins. Ubiquitination has great plasticity, with diverse numbers, topologies and modifications of Ub chains conjugated at different substrate residues adding a layer of complexity that facilitates a huge range of cellular functions. Herein, we highlight key advances in the understanding of ubiquitination in epithelial morphogenesis, with an emphasis on the latest insights into its roles in cellular events involved in polarized epithelial tissue, including cell adhesion, asymmetric localization of polarity determinants and cytoskeletal organization. In addition, the physiological roles of ubiquitination are discussed for typical examples of epithelial morphogenesis, such as lung branching, vascular development and synaptic formation and plasticity. Our increased understanding of ubiquitination in epithelial morphogenesis may provide novel insights into the molecular mechanisms underlying epithelial regeneration and maintenance.
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Affiliation(s)
- Xiaoxiang Cheng
- Faculty of Health Sciences, University of Macau, Avenida da Universidade, Taipa, Macau 999078, China
| | - Jun Zheng
- Faculty of Health Sciences, University of Macau, Avenida da Universidade, Taipa, Macau 999078, China
| | - Gang Li
- Faculty of Health Sciences, University of Macau, Avenida da Universidade, Taipa, Macau 999078, China
| | - Verena Göbel
- Department of Pediatrics, Mucosal Immunology and Biology Research Center, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114,, U.S.A
| | - Hongjie Zhang
- Faculty of Health Sciences, University of Macau, Avenida da Universidade, Taipa, Macau 999078, China
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26
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YOD1 attenuates neurogenic proteotoxicity through its deubiquitinating activity. Neurobiol Dis 2018; 112:14-23. [PMID: 29330040 DOI: 10.1016/j.nbd.2018.01.006] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Revised: 12/04/2017] [Accepted: 01/08/2018] [Indexed: 11/21/2022] Open
Abstract
Ubiquitination, a fundamental post-translational modification of intracellular proteins, is enzymatically reversed by deubiquitinase enzymes (deubiquitinases). >90 deubiquitinases have been identified. One of these enzymes, YOD1, possesses deubiquitinase activity and is similar to ovarian tumor domain-containing protein 1, which is associated with regulation of the endoplasmic reticulum (ER)-associated degradation pathway. Indeed, YOD1 is reported to be involved in the ER stress response induced by mislocalization of unfolded proteins in mammalian cells. However, it has remained unclear whether YOD1 is associated with pathophysiological conditions such as mitochondrial damage, impaired proteostasis, and neurodegeneration. We demonstrated that YOD1 possesses deubiquitinating activity and exhibits preference for K48- and K63-linked ubiquitin. Furthermore, YOD1 expression levels increased as a result of various stress conditions. We demonstrated that the neurogenic proteins that cause Huntington disease and Parkinson's disease induced upregulation of YOD1 level. We observed that YOD1 reduced disease cytotoxicity through efficient degradation of mutant proteins, whereas this activity was abolished by catalytically inactive YOD1. Additionally, YOD1 localized to Lewy bodies in Parkinson's disease patients. Collectively, these data suggest that the deubiquitinase YOD1 contributes to pathogenesis of neurodegenerative disease by decreasing ubiquitination of abnormal proteins and their subsequent degradation.
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27
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Cho SJ, Moon JS, Lee CM, Choi AMK, Stout-Delgado HW. Glucose Transporter 1-Dependent Glycolysis Is Increased during Aging-Related Lung Fibrosis, and Phloretin Inhibits Lung Fibrosis. Am J Respir Cell Mol Biol 2017; 56:521-531. [PMID: 27997810 DOI: 10.1165/rcmb.2016-0225oc] [Citation(s) in RCA: 86] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Aging is associated with metabolic diseases such as type 2 diabetes mellitus, cardiovascular disease, cancer, and neurodegeneration. Aging contributes to common processes including metabolic dysfunction, DNA damage, and reactive oxygen species generation. Although glycolysis has been linked to cell growth and proliferation, the mechanisms by which the activation of glycolysis by aging regulates fibrogenesis in the lung remain unclear. The objective of this study was to determine if glucose transporter 1 (GLUT1)-induced glycolysis regulates age-dependent fibrogenesis of the lung. Mouse and human lung tissues were analyzed for GLUT1 and glycolytic markers using immunoblotting. Glycolytic function was measured using a Seahorse apparatus. To study the effect of GLUT1, genetic inhibition of GLUT1 was performed by short hairpin RNA transduction, and phloretin was used for pharmacologic inhibition of GLUT1. GLUT1-dependent glycolysis is activated in aged lung. Genetic and pharmacologic inhibition of GLUT1 suppressed the protein expression of α-smooth muscle actin, a key cytoskeletal component of activated fibroblasts, in mouse primary lung fibroblast cells. Moreover, we demonstrated that the activation of AMP-activated protein kinase, which is regulated by GLUT1-dependent glycolysis, represents a critical metabolic pathway for fibroblast activation. Furthermore, we demonstrated that phloretin, a potent inhibitor of GLUT1, significantly inhibited bleomycin-induced lung fibrosis in vivo. These results suggest that GLUT1-dependent glycolysis regulates fibrogenesis in aged lung and that inhibition of GLUT1 provides a potential target of therapy of age-related lung fibrosis.
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Affiliation(s)
- Soo Jung Cho
- 1 Joan and Sanford I. Weill Department of Medicine, Weill Cornell Medical College and New York-Presbyterian Hospital, New York, New York.,2 Division of Pulmonary and Critical Care Medicine, Weill Cornell Medical College, New York, New York; and
| | - Jong-Seok Moon
- 1 Joan and Sanford I. Weill Department of Medicine, Weill Cornell Medical College and New York-Presbyterian Hospital, New York, New York.,2 Division of Pulmonary and Critical Care Medicine, Weill Cornell Medical College, New York, New York; and
| | - Chang-Min Lee
- 3 Department of Molecular Microbiology and Immunology, Brown University, Providence, Rhode Island
| | - Augustine M K Choi
- 1 Joan and Sanford I. Weill Department of Medicine, Weill Cornell Medical College and New York-Presbyterian Hospital, New York, New York.,2 Division of Pulmonary and Critical Care Medicine, Weill Cornell Medical College, New York, New York; and
| | - Heather W Stout-Delgado
- 1 Joan and Sanford I. Weill Department of Medicine, Weill Cornell Medical College and New York-Presbyterian Hospital, New York, New York.,2 Division of Pulmonary and Critical Care Medicine, Weill Cornell Medical College, New York, New York; and
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The Ubiquitin Ligase CHIP Integrates Proteostasis and Aging by Regulation of Insulin Receptor Turnover. Cell 2017; 169:470-482.e13. [PMID: 28431247 PMCID: PMC5406386 DOI: 10.1016/j.cell.2017.04.003] [Citation(s) in RCA: 86] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2016] [Revised: 02/21/2017] [Accepted: 04/03/2017] [Indexed: 12/13/2022]
Abstract
Aging is attended by a progressive decline in protein homeostasis (proteostasis), aggravating the risk for protein aggregation diseases. To understand the coordination between proteome imbalance and longevity, we addressed the mechanistic role of the quality-control ubiquitin ligase CHIP, which is a key regulator of proteostasis. We observed that CHIP deficiency leads to increased levels of the insulin receptor (INSR) and reduced lifespan of worms and flies. The membrane-bound INSR regulates the insulin and IGF1 signaling (IIS) pathway and thereby defines metabolism and aging. INSR is a direct target of CHIP, which triggers receptor monoubiquitylation and endocytic-lysosomal turnover to promote longevity. However, upon proteotoxic stress conditions and during aging, CHIP is recruited toward disposal of misfolded proteins, reducing its capacity to degrade the INSR. Our study indicates a competitive relationship between proteostasis and longevity regulation through CHIP-assisted proteolysis, providing a mechanistic concept for understanding the impact of proteome imbalance on aging. The ubiquitin ligase CHIP triggers insulin receptor turnover Insulin receptor level is linked to insulin and IGF1 signaling and longevity Engagement of CHIP in protein quality control limits insulin receptor degradation Proteotoxic stress aggravates insulin receptor stability, drives aging, and shortens lifespan
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29
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Tramutola A, Di Domenico F, Barone E, Arena A, Giorgi A, di Francesco L, Schininà ME, Coccia R, Head E, Butterfield DA, Perluigi M. Polyubiquitinylation Profile in Down Syndrome Brain Before and After the Development of Alzheimer Neuropathology. Antioxid Redox Signal 2017; 26:280-298. [PMID: 27627691 PMCID: PMC5327052 DOI: 10.1089/ars.2016.6686] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
AIMS Among the putative mechanisms proposed to be common factors in Down syndrome (DS) and Alzheimer's disease (AD) neuropathology, deficits in protein quality control (PQC) have emerged as a unifying mechanism of neurodegeneration. Considering that disturbance of protein degradation systems is present in DS and that oxidized/misfolded proteins require polyubiquitinylation for degradation via the ubiquitin proteasome system, this study investigated if dysregulation of protein polyubiquitinylation is associated with AD neurodegeneration in DS. RESULTS Postmortem brains from DS cases before and after development of AD neuropathology and age-matched controls were analyzed. By selectively isolating polyubiquitinated proteins, we were able to identify specific proteins with an altered pattern of polyubiquitinylation as a function of age. Interestingly, we found that oxidation is coupled with polyubiquitinylation for most proteins mainly involved in PQC and energy metabolism. INNOVATION This is the first study showing alteration of the polyubiquitinylation profile as a function of aging in DS brain compared with healthy controls. Understanding the onset of the altered ubiquitome profile in DS brain may contribute to identification of key molecular regulators of age-associated cognitive decline. CONCLUSIONS Disturbance of the polyubiquitinylation machinery may be a key feature of aging and neurodegeneration. In DS, age-associated deficits of the proteolytic system may further exacerbate the accumulation of oxidized/misfolded/polyubiquitinated proteins, which is not efficiently degraded and may become harmful to neurons and contribute to AD neuropathology. Antioxid. Redox Signal. 26, 280-298.
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Affiliation(s)
- Antonella Tramutola
- 1 Department of Biochemical Sciences, Sapienza University of Rome , Italy, Rome
| | - Fabio Di Domenico
- 1 Department of Biochemical Sciences, Sapienza University of Rome , Italy, Rome
| | - Eugenio Barone
- 1 Department of Biochemical Sciences, Sapienza University of Rome , Italy, Rome
| | - Andrea Arena
- 1 Department of Biochemical Sciences, Sapienza University of Rome , Italy, Rome
| | - Alessandra Giorgi
- 1 Department of Biochemical Sciences, Sapienza University of Rome , Italy, Rome
| | - Laura di Francesco
- 1 Department of Biochemical Sciences, Sapienza University of Rome , Italy, Rome
| | | | - Raffaella Coccia
- 1 Department of Biochemical Sciences, Sapienza University of Rome , Italy, Rome
| | - Elizabeth Head
- 2 Sanders-Brown Center on Aging, University of Kentucky , Lexington, Kentucky.,3 Department of Pharmacology and Nutritional Sciences, University of Kentucky , Lexington, Kentucky
| | - D Allan Butterfield
- 2 Sanders-Brown Center on Aging, University of Kentucky , Lexington, Kentucky.,4 Department of Chemistry, University of Kentucky , Lexington, Kentucky
| | - Marzia Perluigi
- 1 Department of Biochemical Sciences, Sapienza University of Rome , Italy, Rome
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30
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Abstract
Uric acid is a damage-associated molecular pattern (DAMP), released from ischemic tissues and dying cells which, when crystalized, is able to activate the NLRP3 inflammasome. Soluble uric acid (sUA) is found in high concentrations in the serum of great apes, and even higher in some diseases, before the appearance of crystals. In the present study, we sought to investigate whether uric acid, in the soluble form, could also activate the NLRP3 inflammasome and induce the production of IL-1β. We monitored ROS, mitochondrial area and respiratory parameters from macrophages following sUA stimulus. We observed that sUA is released in a hypoxic environment and is able to induce IL-1β release. This process is followed by production of mitochondrial ROS, ASC speck formation and caspase-1 activation. Nlrp3-/- macrophages presented a protected redox state, increased maximum and reserve oxygen consumption ratio (OCR) and higher VDAC protein levels when compared to WT and Myd88-/- cells. Using a disease model characterized by increased sUA levels, we observed a correlation between sUA, inflammasome activation and fibrosis. These findings suggest sUA activates the NLRP3 inflammasome. We propose that future therapeutic strategies for renal fibrosis should include strategies that block sUA or inhibit its recognition by phagocytes.
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31
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Ma S, Upneja A, Galecki A, Tsai YM, Burant CF, Raskind S, Zhang Q, Zhang ZD, Seluanov A, Gorbunova V, Clish CB, Miller RA, Gladyshev VN. Cell culture-based profiling across mammals reveals DNA repair and metabolism as determinants of species longevity. eLife 2016; 5:e19130. [PMID: 27874830 PMCID: PMC5148604 DOI: 10.7554/elife.19130] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2016] [Accepted: 11/21/2016] [Indexed: 12/30/2022] Open
Abstract
Mammalian lifespan differs by >100 fold, but the mechanisms associated with such longevity differences are not understood. Here, we conducted a study on primary skin fibroblasts isolated from 16 species of mammals and maintained under identical cell culture conditions. We developed a pipeline for obtaining species-specific ortholog sequences, profiled gene expression by RNA-seq and small molecules by metabolite profiling, and identified genes and metabolites correlating with species longevity. Cells from longer lived species up-regulated genes involved in DNA repair and glucose metabolism, down-regulated proteolysis and protein transport, and showed high levels of amino acids but low levels of lysophosphatidylcholine and lysophosphatidylethanolamine. The amino acid patterns were recapitulated by further analyses of primate and bird fibroblasts. The study suggests that fibroblast profiling captures differences in longevity across mammals at the level of global gene expression and metabolite levels and reveals pathways that define these differences.
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Affiliation(s)
- Siming Ma
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, United States
| | - Akhil Upneja
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, United States
| | - Andrzej Galecki
- Department of Pathology, University of Michigan Medical School, Ann Arbor, United States
- Geriatrics Center, University of Michigan Medical School, Ann Arbor, United States
- Department of Biostatistics, School of Public Health, University of Michigan, Ann Arbor, United States
| | - Yi-Miau Tsai
- Department of Pathology, University of Michigan Medical School, Ann Arbor, United States
- Geriatrics Center, University of Michigan Medical School, Ann Arbor, United States
| | - Charles F Burant
- Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, United States
| | - Sasha Raskind
- Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, United States
| | - Quanwei Zhang
- Department of Genetics, Albert Einstein College of Medicine, Bronx, United States
| | - Zhengdong D Zhang
- Department of Genetics, Albert Einstein College of Medicine, Bronx, United States
| | - Andrei Seluanov
- Department of Biology, University of Rochester, Rochester, United States
| | - Vera Gorbunova
- Department of Biology, University of Rochester, Rochester, United States
| | | | - Richard A Miller
- Department of Pathology, University of Michigan Medical School, Ann Arbor, United States
- Geriatrics Center, University of Michigan Medical School, Ann Arbor, United States
| | - Vadim N Gladyshev
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, United States
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32
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Pistollato F, Sumalla Cano S, Elio I, Masias Vergara M, Giampieri F, Battino M. Associations between Sleep, Cortisol Regulation, and Diet: Possible Implications for the Risk of Alzheimer Disease. Adv Nutr 2016; 7:679-89. [PMID: 27422503 PMCID: PMC4942871 DOI: 10.3945/an.115.011775] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Accumulation of proteinaceous amyloid β plaques and tau oligomers may occur several years before the onset of Alzheimer disease (AD). Under normal circumstances, misfolded proteins get cleared by proteasome degradation, autophagy, and the recently discovered brain glymphatic system, an astroglial-mediated interstitial fluid bulk flow. It has been shown that the activity of the glymphatic system is higher during sleep and disengaged or low during wakefulness. As a consequence, poor sleep quality, which is associated with dementia, might negatively affect glymphatic system activity, thus contributing to amyloid accumulation. The diet is another important factor to consider in the regulation of this complex network. Diets characterized by high intakes of refined sugars, salt, animal-derived proteins and fats and by low intakes of fruit and vegetables are associated with a higher risk of AD and can perturb the circadian modulation of cortisol secretion, which is associated with poor sleep quality. For this reason, diets and nutritional interventions aimed at restoring cortisol concentrations may ease sleep disorders and may facilitate brain clearance, consequentially reducing the risk of cognitive impairment and dementia. Here, we describe the associations that exist between sleep, cortisol regulation, and diet and their possible implications for the risk of cognitive impairment and AD.
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Affiliation(s)
- Francesca Pistollato
- Center for Nutrition and Health, European University of the Atlantic (UEA), Santander, Spain
| | - Sandra Sumalla Cano
- Center for Nutrition and Health, European University of the Atlantic (UEA), Santander, Spain;,International Ibero-American University (UNINI), Campeche, Mexico;,Ibero-American University Foundation (FUNIBER), Barcelona, Spain
| | - Iñaki Elio
- Center for Nutrition and Health, European University of the Atlantic (UEA), Santander, Spain;,International Ibero-American University (UNINI), Campeche, Mexico;,Ibero-American University Foundation (FUNIBER), Barcelona, Spain
| | - Manuel Masias Vergara
- Center for Nutrition and Health, European University of the Atlantic (UEA), Santander, Spain;,International Ibero-American University (UNINI), Puerto Rico; and
| | - Francesca Giampieri
- Center for Nutrition and Health, European University of the Atlantic (UEA), Santander, Spain; Department of Specialized Clinical Sciences and Dentistry, Marche Polytechnic University, Ancona, Italy
| | - Maurizio Battino
- Center for Nutrition and Health, European University of the Atlantic (UEA), Santander, Spain; Department of Specialized Clinical Sciences and Dentistry, Marche Polytechnic University, Ancona, Italy
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Sunshine AB, Ong GT, Nickerson DP, Carr D, Murakami CJ, Wasko BM, Shemorry A, Merz AJ, Kaeberlein M, Dunham MJ. Aneuploidy shortens replicative lifespan in Saccharomyces cerevisiae. Aging Cell 2016; 15:317-24. [PMID: 26762766 PMCID: PMC4783355 DOI: 10.1111/acel.12443] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/16/2015] [Indexed: 11/28/2022] Open
Abstract
Aneuploidy and aging are correlated; however, a causal link between these two phenomena has remained elusive. Here, we show that yeast disomic for a single native yeast chromosome generally have a decreased replicative lifespan. In addition, the extent of this lifespan deficit correlates with the size of the extra chromosome. We identified a mutation in BUL1 that rescues both the lifespan deficit and a protein trafficking defect in yeast disomic for chromosome 5. Bul1 is an E4 ubiquitin ligase adaptor involved in a protein quality control pathway that targets membrane proteins for endocytosis and destruction in the lysosomal vacuole, thereby maintaining protein homeostasis. Concurrent suppression of the aging and trafficking phenotypes suggests that disrupted membrane protein homeostasis in aneuploid yeast may contribute to their accelerated aging. The data reported here demonstrate that aneuploidy can impair protein homeostasis, shorten lifespan, and may contribute to age-associated phenotypes.
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Affiliation(s)
- Anna B. Sunshine
- Department of Genome SciencesUniversity of WashingtonFoege Building, Room S403B, 3720 15th Ave NE, Box 355065SeattleWA98195‐5065USA
| | - Giang T. Ong
- Department of Genome SciencesUniversity of WashingtonFoege Building, Room S403B, 3720 15th Ave NE, Box 355065SeattleWA98195‐5065USA
| | - Daniel P. Nickerson
- Departments of Biochemistry and Physiology and BiophysicsUniversity of WashingtonRoom HSB J‐355, 1705 NE Pacific St, UW box 357350SeattleWA98195‐7350USA
| | - Daniel Carr
- Department of PathologyUniversity of WashingtonRoom HSB D‐514, 1705 NE Pacific St, Box 357470SeattleWA98195‐7470USA
| | - Christopher J. Murakami
- Department of PathologyUniversity of WashingtonRoom HSB D‐514, 1705 NE Pacific St, Box 357470SeattleWA98195‐7470USA
| | - Brian M. Wasko
- Department of PathologyUniversity of WashingtonRoom HSB D‐514, 1705 NE Pacific St, Box 357470SeattleWA98195‐7470USA
| | - Anna Shemorry
- Department of PathologyUniversity of WashingtonRoom HSB D‐514, 1705 NE Pacific St, Box 357470SeattleWA98195‐7470USA
| | - Alexey J. Merz
- Departments of Biochemistry and Physiology and BiophysicsUniversity of WashingtonRoom HSB J‐355, 1705 NE Pacific St, UW box 357350SeattleWA98195‐7350USA
| | - Matt Kaeberlein
- Department of PathologyUniversity of WashingtonRoom HSB D‐514, 1705 NE Pacific St, Box 357470SeattleWA98195‐7470USA
| | - Maitreya J. Dunham
- Department of Genome SciencesUniversity of WashingtonFoege Building, Room S403B, 3720 15th Ave NE, Box 355065SeattleWA98195‐5065USA
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Differential Proteomic Analysis of Human Placenta-Derived Mesenchymal Stem Cells Cultured on Normal Tissue Culture Surface and Hyaluronan-Coated Surface. Stem Cells Int 2015; 2016:2809192. [PMID: 27057169 PMCID: PMC4709773 DOI: 10.1155/2016/2809192] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2015] [Revised: 09/07/2015] [Accepted: 10/07/2015] [Indexed: 12/15/2022] Open
Abstract
Our previous results showed that hyaluronan (HA) preserved human placenta-derived mesenchymal stem cells (PDMSC) in a slow cell cycling mode similar to quiescence, the pristine state of stem cells in vivo, and HA was found to prevent murine adipose-derived mesenchymal stem cells from senescence. Here, stable isotope labeling by amino acid in cell culture (SILAC) proteomic profiling was used to evaluate the effects of HA on aging phenomenon in stem cells, comparing (1) old and young passage PDMSC cultured on normal tissue culture surface (TCS); (2) old passage on HA-coated surface (CHA) compared to TCS; (3) old and young passage on CHA. The results indicated that senescence-associated protein transgelin (TAGLN) was upregulated in old TCS. Protein CYR61, reportedly senescence-related, was downregulated in old CHA compared to old TCS. The SIRT1-interacting Nicotinamide phosphoribosyltransferase (NAMPT) increased by 2.23-fold in old CHA compared to old TCS, and is 0.48-fold lower in old TCS compared to young TCS. Results also indicated that components of endoplasmic reticulum associated degradation (ERAD) pathway were upregulated in old CHA compared to old TCS cells, potentially for overcoming stress to maintain cell function and suppress senescence. Our data points to pathways that may be targeted by HA to maintain stem cells youth.
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Larabee CM, Georgescu C, Wren JD, Plafker SM. Expression profiling of the ubiquitin conjugating enzyme UbcM2 in murine brain reveals modest age-dependent decreases in specific neurons. BMC Neurosci 2015; 16:76. [PMID: 26566974 PMCID: PMC4644300 DOI: 10.1186/s12868-015-0194-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2015] [Accepted: 08/24/2015] [Indexed: 01/29/2023] Open
Abstract
BACKGROUND UbcM2 is a ubiquitin-conjugating enzyme with roles in the turnover of damaged and misfolded proteins, cell cycle progression, development, and regulation of the antioxidant transcription factor, Nrf2. Recent screens have identified binding partners of the enzyme that are associated with various neurodegenerative diseases, and our previous studies have shown that UbcM2 is enriched in retina and brain. RESULTS In the current study, we characterized UbcM2 protein expression in various structures and cell types in the murine brain. Immunofluorescence analysis of paraffin-embedded brain sections revealed that UbcM2 is ubiquitously expressed throughout the brain, is enriched in hindbrain and cortex, and is robustly expressed in neurons. In contrast, the enzyme is undetectable in most astrocytes and microglia. As dysfunction of the ubiquitin proteasome system (UPS) has been linked to many age-related neurological diseases, we compared UbcM2 expression levels in young versus aged wild-type mice and found a global decrease in expression in aged brains, with reductions of 10 % or greater in five substructures (cerebellar granule cell layer, primary motor cortex, olfactory nucleus, superior colliculus, and secondary visual cortex). CONCLUSIONS These studies represent the first protein expression profiling of a ubiquitin-conjugating enzyme in the brain and support the notion that deficits in protein degradation and proteostasis associated with neurodegenerative diseases may be, in part, attributable to age-dependent reductions in the enzymatic machinery of the UPS.
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Affiliation(s)
- Chelsea M Larabee
- Aging and Metabolism Research Program, Oklahoma Medical Research Foundation, 825 Northeast 13th Street, Oklahoma City, OK, USA. .,Oklahoma Center for Neuroscience, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA.
| | - Constantin Georgescu
- Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, 825 Northeast 13th Street, Oklahoma City, OK, USA.
| | - Jonathan D Wren
- Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, 825 Northeast 13th Street, Oklahoma City, OK, USA.
| | - Scott M Plafker
- Aging and Metabolism Research Program, Oklahoma Medical Research Foundation, 825 Northeast 13th Street, Oklahoma City, OK, USA. .,Oklahoma Center for Neuroscience, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA.
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Upadhyay A, Amanullah A, Chhangani D, Mishra R, Mishra A. Selective multifaceted E3 ubiquitin ligases barricade extreme defense: Potential therapeutic targets for neurodegeneration and ageing. Ageing Res Rev 2015; 24:138-59. [PMID: 26247845 DOI: 10.1016/j.arr.2015.07.009] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2015] [Revised: 06/24/2015] [Accepted: 07/30/2015] [Indexed: 12/24/2022]
Abstract
Efficient and regular performance of Ubiquitin Proteasome System and Autophagy continuously eliminate deleterious accumulation of nonnative protiens. In cellular quality control system, E3 ubiquitin ligases are significant employees for defense mechanism against abnormal toxic proteins. Few findings indicate that lack of functions of E3 ubiquitin ligases can be a causative factor of neurodevelopmental disorders, neurodegeneration, cancer and ageing. However, the detailed molecular pathomechanism implying E3 ubiquitin ligases in cellular functions in multifactorial disease conditions are not well understood. This article systematically represents the unique characteristics, molecular nature, and recent developments in the knowledge of neurobiological functions of few crucial E3 ubiquitin ligases. Here, we review recent literature on the roles of E6-AP, HRD1 and ITCH E3 ubiquitin ligases in the neuro-pathobiological mechanisms, with precise focus on the processes of neurodegeneration, and thereby propose new lines of potential targets for therapeutic interventions.
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Expression profile of a Caenorhabditis elegans model of adult neuronal ceroid lipofuscinosis reveals down regulation of ubiquitin E3 ligase components. Sci Rep 2015; 5:14392. [PMID: 26395859 PMCID: PMC4585785 DOI: 10.1038/srep14392] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2015] [Accepted: 08/28/2015] [Indexed: 12/24/2022] Open
Abstract
Cysteine string protein (CSP) is a chaperone of the Dnaj/Hsp40 family of proteins and is essential for synaptic maintenance. Mutations in the human gene encoding CSP, DNAJC5, cause adult neuronal ceroid lipofucinosis (ANCL) which is characterised by progressive dementia, movement disorders, seizures and premature death. CSP null models in mice, flies and worms have been shown to also exhibit similar neurodegenerative phenotypes. Here we have explored the mechanisms underlying ANCL disease progression using Caenorhaditis elegans mutant strains of dnj-14, the worm orthologue of DNAJC5. Transcriptional profiling of these mutants compared to control strains revealed a broad down-regulation of ubiquitin proteasome system (UPS)-related genes, in particular, components of multimeric RING E3 ubiquitin ligases including F-Box, SKR and BTB proteins. These data were supported by the observation that dnj-14 mutant worm strains expressing a GFP-tagged ubiquitin fusion degradation substrate exhibited decreased ubiquitylated protein degradation. The results indicate that disruption of an essential synaptic chaperone leads to changes in expression levels of UPS-related proteins which has a knock-on effect on overall protein degradation in C. elegans. The specific over-representation of E3 ubiquitin ligase components revealed in our study, suggests that proteins and complexes upstream of the proteasome itself may be beneficial therapeutic targets.
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Ori A, Toyama BH, Harris MS, Bock T, Iskar M, Bork P, Ingolia NT, Hetzer MW, Beck M. Integrated Transcriptome and Proteome Analyses Reveal Organ-Specific Proteome Deterioration in Old Rats. Cell Syst 2015; 1:224-37. [PMID: 27135913 PMCID: PMC4802414 DOI: 10.1016/j.cels.2015.08.012] [Citation(s) in RCA: 126] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2015] [Revised: 07/21/2015] [Accepted: 08/26/2015] [Indexed: 12/29/2022]
Abstract
Aging is associated with the decline of protein, cell, and organ function. Here, we use an integrated approach to characterize gene expression, bulk translation, and cell biology in the brains and livers of young and old rats. We identify 468 differences in protein abundance between young and old animals. The majority are a consequence of altered translation output, that is, the combined effect of changes in transcript abundance and translation efficiency. In addition, we identify 130 proteins whose overall abundance remains unchanged but whose sub-cellular localization, phosphorylation state, or splice-form varies. While some protein-level differences appear to be a generic property of the rats’ chronological age, the majority are specific to one organ. These may be a consequence of the organ’s physiology or the chronological age of the cells within the tissue. Taken together, our study provides an initial view of the proteome at the molecular, sub-cellular, and organ level in young and old rats. An integrated approach identifies molecular alterations between young and old rats Changes in translation output explain the majority of the altered protein abundances Key protein complexes are altered in abundance and composition We provide a rich data resource to stimulate further studies of aging
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Affiliation(s)
- Alessandro Ori
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, Meyerhofstrasse 1, Heidelberg 69117, Germany
| | - Brandon H Toyama
- Molecular and Cell Biology Laboratory, Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Michael S Harris
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA; Department of Biology, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Thomas Bock
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, Meyerhofstrasse 1, Heidelberg 69117, Germany
| | - Murat Iskar
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, Meyerhofstrasse 1, Heidelberg 69117, Germany
| | - Peer Bork
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, Meyerhofstrasse 1, Heidelberg 69117, Germany; Max Delbrück Center for Molecular Medicine, Robert-Rössle-Strasse 10, Berlin 13125, Germany
| | - Nicholas T Ingolia
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA.
| | - Martin W Hetzer
- Molecular and Cell Biology Laboratory, Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA.
| | - Martin Beck
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, Meyerhofstrasse 1, Heidelberg 69117, Germany.
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Sun D, Yi SV. Impacts of Chromatin States and Long-Range Genomic Segments on Aging and DNA Methylation. PLoS One 2015; 10:e0128517. [PMID: 26091484 PMCID: PMC4475080 DOI: 10.1371/journal.pone.0128517] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2015] [Accepted: 04/28/2015] [Indexed: 01/13/2023] Open
Abstract
Understanding the fundamental dynamics of epigenome variation during normal aging is critical for elucidating key epigenetic alterations that affect development, cell differentiation and diseases. Advances in the field of aging and DNA methylation strongly support the aging epigenetic drift model. Although this model aligns with previous studies, the role of other epigenetic marks, such as histone modification, as well as the impact of sampling specific CpGs, must be evaluated. Ultimately, it is crucial to investigate how all CpGs in the human genome change their methylation with aging in their specific genomic and epigenomic contexts. Here, we analyze whole genome bisulfite sequencing DNA methylation maps of brain frontal cortex from individuals of diverse ages. Comparisons with blood data reveal tissue-specific patterns of epigenetic drift. By integrating chromatin state information, divergent degrees and directions of aging-associated methylation in different genomic regions are revealed. Whole genome bisulfite sequencing data also open a new door to investigate whether adjacent CpG sites exhibit coordinated DNA methylation changes with aging. We identified significant 'aging-segments', which are clusters of nearby CpGs that respond to aging by similar DNA methylation changes. These segments not only capture previously identified aging-CpGs but also include specific functional categories of genes with implications on epigenetic regulation of aging. For example, genes associated with development are highly enriched in positive aging segments, which are gradually hyper-methylated with aging. On the other hand, regions that are gradually hypo-methylated with aging ('negative aging segments') in the brain harbor genes involved in metabolism and protein ubiquitination. Given the importance of protein ubiquitination in proteome homeostasis of aging brains and neurodegenerative disorders, our finding suggests the significance of epigenetic regulation of this posttranslational modification pathway in the aging brain. Utilizing aging segments rather than individual CpGs will provide more comprehensive genomic and epigenomic contexts to understand the intricate associations between genomic neighborhoods and developmental and aging processes. These results complement the aging epigenetic drift model and provide new insights.
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Affiliation(s)
- Dan Sun
- School of Biology, Georgia Institute of Technology, Atlanta, GA, 30332, United States of America
| | - Soojin V. Yi
- School of Biology, Georgia Institute of Technology, Atlanta, GA, 30332, United States of America
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Jiang S, Park DW, Gao Y, Ravi S, Darley-Usmar V, Abraham E, Zmijewski JW. Participation of proteasome-ubiquitin protein degradation in autophagy and the activation of AMP-activated protein kinase. Cell Signal 2015; 27:1186-97. [PMID: 25728513 PMCID: PMC4380640 DOI: 10.1016/j.cellsig.2015.02.024] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2014] [Revised: 02/04/2015] [Accepted: 02/23/2015] [Indexed: 01/05/2023]
Abstract
Although activation of the AMP-activated protein kinase (AMPK) as well as of ubiquitin/proteasome degradative pathways play an essential role in the preservation of metabolic homeostasis, little is known concerning interactions between protein turnover and AMPK activity. In the present studies, we found that inhibition of the 26S proteasome resulted in rapid activation of AMPK in macrophages, epithelial and endothelial cells. This was associated with increased levels of non-degraded Ub-protein conjugates, in both cytosolic and mitochondrial fractions. Selective inhibitors of ubiquitination or siRNA-dependent knockdown of Ub-ligase E1 diminished AMPK activation in cells treated with MG132, a 26S proteasome inhibitor. In addition to inhibition of AMPK activation by Ub-ligase E1 inhibitors, deficiency in Park2 mitochondria-associated Ub-ligase E3 also reduced AMPK activation upon dissipation of mitochondrial membrane potential (Δψm). Accumulation of Ub-proteins was correlated with decreases in cellular bioenergetics, including mitochondria oxidative phosphorylation, and an increase in ROS formation. Antioxidants, such as N-acetyl-L-cysteine or mitochondria-targeted MitoTEMPO, effectively diminished MG132-induced AMPK activation. Glucose-dependent regulation of AMPK or AMPK-mediated autophagy was modulated by alterations in intracellular levels of Ub-protein conjugates. Our results indicate that accumulation of ubiquitinated proteins alter cellular bioenergetics and redox status, leading to AMPK activation.
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Affiliation(s)
- Shaoning Jiang
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294-0012, USA
| | - Dae Won Park
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294-0012, USA; Division of Infectious Diseases, Korea University Ansan Hospital, Ansan 425-707, Republic of Korea
| | - Yong Gao
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294-0012, USA
| | - Saranya Ravi
- Department of Pathology, University of Alabama at Birmingham, Birmingham, AL 35294-0012, USA; Center for Free Radical Biology, University of Alabama at Birmingham, Birmingham, AL 35294-0012, USA
| | - Victor Darley-Usmar
- Department of Pathology, University of Alabama at Birmingham, Birmingham, AL 35294-0012, USA; Center for Free Radical Biology, University of Alabama at Birmingham, Birmingham, AL 35294-0012, USA
| | - Edward Abraham
- Office of the Dean, Wake Forest University School of Medicine, Winston-Salem, NC, USA
| | - Jaroslaw W Zmijewski
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294-0012, USA; Center for Free Radical Biology, University of Alabama at Birmingham, Birmingham, AL 35294-0012, USA.
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Thannickal VJ, Murthy M, Balch WE, Chandel NS, Meiners S, Eickelberg O, Selman M, Pardo A, White ES, Levy BD, Busse PJ, Tuder RM, Antony VB, Sznajder JI, Budinger GRS. Blue journal conference. Aging and susceptibility to lung disease. Am J Respir Crit Care Med 2015; 191:261-9. [PMID: 25590812 DOI: 10.1164/rccm.201410-1876pp] [Citation(s) in RCA: 132] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
The aging of the population in the United States and throughout the developed world has increased morbidity and mortality attributable to lung disease, while the morbidity and mortality from other prevalent diseases has declined or remained stable. Recognizing the importance of aging in the development of lung disease, the American Thoracic Society (ATS) highlighted this topic as a core theme for the 2014 annual meeting. The relationship between aging and lung disease was discussed in several oral symposiums and poster sessions at the annual ATS meeting. In this article, we used the input gathered at the conference to develop a broad framework and perspective to stimulate basic, clinical, and translational research to understand how the aging process contributes to the onset and/or progression of lung diseases. A consistent theme that emerged from the conference was the need to apply novel, systems-based approaches to integrate a growing body of genomic, epigenomic, transcriptomic, and proteomic data and elucidate the relationship between biologic hallmarks of aging, altered lung function, and increased susceptibility to lung diseases in the older population. The challenge remains to causally link the molecular and cellular changes of aging with age-related changes in lung physiology and disease susceptibility. The purpose of this review is to stimulate further research to identify new strategies to prevent or treat age-related lung disease.
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Bidlingmaier S, Liu B. Identification of Posttranslational Modification-Dependent Protein Interactions Using Yeast Surface Displayed Human Proteome Libraries. Methods Mol Biol 2015; 1319:193-202. [PMID: 26060076 DOI: 10.1007/978-1-4939-2748-7_10] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The identification of proteins that interact specifically with posttranslational modifications such as phosphorylation is often necessary to understand cellular signaling pathways. Numerous methods for identifying proteins that interact with posttranslational modifications have been utilized, including affinity-based purification and analysis, protein microarrays, phage display, and tethered catalysis. Although these techniques have been used successfully, each has limitations. Recently, yeast surface-displayed human proteome libraries have been utilized to identify protein fragments with affinity for various target molecules, including phosphorylated peptides. When coupled with fluorescently activated cell sorting and high throughput methods for the analysis of selection outputs, yeast surface-displayed human proteome libraries can rapidly and efficiently identify protein fragments with affinity for any soluble ligand that can be fluorescently detected, including posttranslational modifications. In this review we compare the use of yeast surface display libraries to other methods for the identification of interactions between proteins and posttranslational modifications and discuss future applications of the technology.
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Affiliation(s)
- Scott Bidlingmaier
- Department of Anesthesia, UCSF Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, 1001 Potrero Avenue, 1305, San Francisco, CA, 94110, USA
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GHK and DNA: resetting the human genome to health. BIOMED RESEARCH INTERNATIONAL 2014; 2014:151479. [PMID: 25302294 PMCID: PMC4180391 DOI: 10.1155/2014/151479] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 07/08/2014] [Accepted: 08/27/2014] [Indexed: 02/07/2023]
Abstract
During human aging there is an increase in the activity of inflammatory, cancer promoting, and tissue destructive genes plus a decrease in the activity of regenerative and reparative genes. The human blood tripeptide GHK possesses many positive effects but declines with age. It improves wound healing and tissue regeneration (skin, hair follicles, stomach and intestinal linings, and boney tissue), increases collagen and glycosaminoglycans, stimulates synthesis of decorin, increases angiogenesis, and nerve outgrowth, possesses antioxidant and anti-inflammatory effects, and increases cellular stemness and the secretion of trophic factors by mesenchymal stem cells. Recently, GHK has been found to reset genes of diseased cells from patients with cancer or COPD to a more healthy state. Cancer cells reset their programmed cell death system while COPD patients' cells shut down tissue destructive genes and stimulate repair and remodeling activities. In this paper, we discuss GHK's effect on genes that suppress fibrinogen synthesis, the insulin/insulin-like system, and cancer growth plus activation of genes that increase the ubiquitin-proteasome system, DNA repair, antioxidant systems, and healing by the TGF beta superfamily. A variety of methods and dosages to effectively use GHK to reset genes to a healthier state are also discussed.
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Controlled sumoylation of the mevalonate pathway enzyme HMGS-1 regulates metabolism during aging. Proc Natl Acad Sci U S A 2014; 111:E3880-9. [PMID: 25187565 DOI: 10.1073/pnas.1414748111] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Many metabolic pathways are critically regulated during development and aging but little is known about the molecular mechanisms underlying this regulation. One key metabolic cascade in eukaryotes is the mevalonate pathway. It catalyzes the synthesis of sterol and nonsterol isoprenoids, such as cholesterol and ubiquinone, as well as other metabolites. In humans, an age-dependent decrease in ubiquinone levels and changes in cholesterol homeostasis suggest that mevalonate pathway activity changes with age. However, our knowledge of the mechanistic basis of these changes remains rudimentary. We have identified a regulatory circuit controlling the sumoylation state of Caenorhabditis elegans HMG-CoA synthase (HMGS-1). This protein is the ortholog of human HMGCS1 enzyme, which mediates the first committed step of the mevalonate pathway. In vivo, HMGS-1 undergoes an age-dependent sumoylation that is balanced by the activity of ULP-4 small ubiquitin-like modifier protease. ULP-4 exhibits an age-regulated expression pattern and a dynamic cytoplasm-to-mitochondria translocation. Thus, spatiotemporal ULP-4 activity controls the HMGS-1 sumoylation state in a mechanism that orchestrates mevalonate pathway activity with the age of the organism. To expand the HMGS-1 regulatory network, we combined proteomic analyses with knockout studies and found that the HMGS-1 level is also governed by the ubiquitin-proteasome pathway. We propose that these conserved molecular circuits have evolved to govern the level of mevalonate pathway flux during aging, a flux whose dysregulation is associated with numerous age-dependent cardiovascular and cancer pathologies.
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Hoppe T. Limited proteolysis: DisRUPting proteasomal inhibition. Curr Biol 2014; 24:R693-5. [PMID: 25093561 DOI: 10.1016/j.cub.2014.06.056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The 26S proteasome is a protease complex that completely degrades substrate proteins marked with a chain of ubiquitins, but is also able to perform endoproteolytic cleavage. A new study now demonstrates that regulated ubiquitin-proteasome-dependent processing ameliorates proteasomal inhibition.
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Affiliation(s)
- Thorsten Hoppe
- Institute for Genetics and Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Joseph Stelzmann Str. 26, 50931 Cologne, Germany.
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