1
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Dutta T, Chakraborty B, Nigam A, Minocha S, Koner AL. A small-molecule probe to decipher stress-induced ER microenvironments and ER-Golgi communication. J Mater Chem B 2024; 12:7848-7857. [PMID: 38808376 DOI: 10.1039/d4tb00572d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/30/2024]
Abstract
Cellular stress is a crucial factor in regulating and maintaining both organismal and microenvironmental homeostasis. It induces a response that also affects the micropolarity of specific cellular compartments, which is essential for early disease diagnosis. In this contribution, we present a quantitative study of micropolarity changes inside the endoplasmic reticulum (ER) during the G1/S and G2/M phases, using a biocompatible small-molecule fluorophore called ER-Oct. This probe is selectively driven to the ER by its hydrophobicity, and it has the fastest diffusion properties among a series of analogous probes. We found that induced ER stress caused cell cycle arrests leading to an increase in ER micropolarity which is well supported by lambda scanning experiments and fluorescence lifetime imaging microscopy (FLIM) as well. ER-Oct is a versatile staining agent that could effectively stain the ER in various living/fixed mammalian cells, isolated ER, Caenorhabditis elegans, and mice tissues. Furthermore, we used this probe to visualize a well-known biological event, ER to Golgi transport, by live-cell fluorescence microscopy. Our exhaustive investigation of micropolarity using ER-staining dye provides a new way to study ER stress, which could provide a deeper understanding of proteostasis in model systems and even in fixed patient samples.
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Affiliation(s)
- Tanoy Dutta
- Bionanotechnology Lab, Department of Chemistry, Indian Institute of Science Education and Research Bhopal, Bhopal Bypass Road, Bhauri, Bhopal, Madhya Pradesh - 462066, India.
- Division of Cardiovascular Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA.
| | - Barsha Chakraborty
- Bionanotechnology Lab, Department of Chemistry, Indian Institute of Science Education and Research Bhopal, Bhopal Bypass Road, Bhauri, Bhopal, Madhya Pradesh - 462066, India.
| | - Aditya Nigam
- Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, Hauz Khas, New Delhi - 110016, India
| | - Shilpi Minocha
- Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, Hauz Khas, New Delhi - 110016, India
| | - Apurba Lal Koner
- Bionanotechnology Lab, Department of Chemistry, Indian Institute of Science Education and Research Bhopal, Bhopal Bypass Road, Bhauri, Bhopal, Madhya Pradesh - 462066, India.
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2
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Zhao H, Zhao H, Ji S. A Mesenchymal stem cell Aging Framework, from Mechanisms to Strategies. Stem Cell Rev Rep 2024; 20:1420-1440. [PMID: 38727878 DOI: 10.1007/s12015-024-10732-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/02/2024] [Indexed: 08/13/2024]
Abstract
Mesenchymal stem cells (MSCs) are extensively researched for therapeutic applications in tissue engineering and show significant potential for clinical use. Intrinsic or extrinsic factors causing senescence may lead to reduced proliferation, aberrant differentiation, weakened immunoregulation, and increased inflammation, ultimately limiting the potential of MSCs. It is crucial to comprehend the molecular pathways and internal processes responsible for the decline in MSC function due to senescence in order to devise innovative approaches for rejuvenating senescent MSCs and enhancing MSC treatment. We investigate the main molecular processes involved in senescence, aiming to provide a thorough understanding of senescence-related issues in MSCs. Additionally, we analyze the most recent advancements in cutting-edge approaches to combat MSC senescence based on current research. We are curious whether the aging process of stem cells results in a permanent "memory" and if cellular reprogramming may potentially revert the aging epigenome to a more youthful state.
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Affiliation(s)
- Hongqing Zhao
- Nanbu County People's Hospital, Nanchong City, 637300, Sichuan Province, China
- Jinzhou Medical University, No.82 Songpo Road, Guta District, Jinzhou, 121001, Liaoning Province, China
| | - Houming Zhao
- Graduate School of PLA Medical College, Chinese PLA General Hospital, Beijing, 100083, China
| | - Shuaifei Ji
- Graduate School of PLA Medical College, Chinese PLA General Hospital, Beijing, 100083, China.
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3
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Parseh S, Shakerian S, Reza Tabandeh M, Habibi A. An 8-Week study on the effects of high and Moderate-Intensity interval exercises on mitochondrial MOTS-C changes and their relation to metabolic markers in male diabetic sand rats. Diabetes Res Clin Pract 2024; 212:111656. [PMID: 38636847 DOI: 10.1016/j.diabres.2024.111656] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/16/2024] [Accepted: 04/01/2024] [Indexed: 04/20/2024]
Abstract
Mitochondrial dysfunction is a significant feature of type 2 diabetes. MOTS-C, a peptide derived from mitochondria, has positive effects on metabolism and exercise capacity. This study explored the impact of high and moderate-intensity interval exercises on mitochondrial MOTS-C alterations and their correlation with metabolic markers in male diabetic sand rats. Thirty male sand rats were divided into six groups: control, MIIT, DM + HIIT, DM + MIIT, DM, and HIIT (5 rats each). Diabetes was induced using a high-fat diet (HFD) combined with streptozotocin (STZ). The Wistar sand rats in exercise groups underwent 8 weeks of interval training of varying intensities. Post sample collection, protein expressions of PCG-1a, AMPK, and GLUT4 were assessed through Western blot analysis, while MOTS-C protein expression was determined using ELISA. Both exercise intensity and diabetes significantly affected the levels of PCG-1a, MOTS-C, GLUT4 proteins, and insulin resistance (p < 0.001). The combined effect of diabetes status and exercise intensity on these levels was also significant (p < 0.001). However, the diabetes effect varied when comparing high-intensity to moderate-intensity exercise. The moderate-intensity exercise group with diabetes showed higher levels of PCG-1a, MOTS-C, and GLUT4 proteins and reduced insulin resistance levels (p < 0.001). Exercise intensity (p = 0.022) and diabetes (p = 0.008) significantly influenced AMPK protein levels. The interplay between diabetes status and exercise intensity on AMPK protein levels was noteworthy, with the moderate-intensity diabetes group exhibiting higher AMPK levels than the high-intensity diabetes group (p < 0.001). In conclusion, exercise elevates the levels of PCG-1a, MOTS-C, GLUT4, and AMPK proteins, regulating insulin resistance in diabetic sand rats. Given the AMPK-MOTS-C mitochondrial pathway's mechanisms, interval exercises might enhance the metabolic rates and general health of diabetic rodents.
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Affiliation(s)
- Sahar Parseh
- Department of Exercise Physiology, Faculty of Sport Sciences, Shahid Chamran University of Ahvaz, Ahvaz, Iran
| | - Saeid Shakerian
- Department of Exercise Physiology, Faculty of Sport Sciences, Shahid Chamran University of Ahvaz, Ahvaz, Iran.
| | - Mohammad Reza Tabandeh
- Department of Science, Faculty of Veterinary Medicine, Shahid Chamran University of Ahvaz, Ahvaz, Iran
| | - Abdolhamid Habibi
- Department of Exercise Physiology, Faculty of Sport Sciences, Shahid Chamran University of Ahvaz, Ahvaz, Iran
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4
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Chou CC, Vest R, Prado MA, Wilson-Grady J, Paulo JA, Shibuya Y, Moran-Losada P, Lee TT, Luo J, Gygi SP, Kelly JW, Finley D, Wernig M, Wyss-Coray T, Frydman J. Human tNeurons reveal aging-linked proteostasis deficits driving Alzheimer's phenotypes. RESEARCH SQUARE 2024:rs.3.rs-4407236. [PMID: 38853828 PMCID: PMC11160905 DOI: 10.21203/rs.3.rs-4407236/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2024]
Abstract
Aging is a prominent risk factor for Alzheimer's disease (AD), but the cellular mechanisms underlying neuronal phenotypes remain elusive. Both accumulation of amyloid plaques and neurofibrillary tangles in the brain1 and age-linked organelle deficits2-7 are proposed as causes of AD phenotypes but the relationship between these events is unclear. Here, we address this question using a transdifferentiated neuron (tNeuron) model directly from human dermal fibroblasts. Patient-derived tNeurons retain aging hallmarks and exhibit AD-linked deficits. Quantitative tNeuron proteomic analyses identify aging and AD-linked deficits in proteostasis and organelle homeostasis, particularly affecting endosome-lysosomal components. The proteostasis and lysosomal homeostasis deficits in aged tNeurons are exacerbated in sporadic and familial AD tNeurons, promoting constitutive lysosomal damage and defects in ESCRT-mediated repair. We find deficits in neuronal lysosomal homeostasis lead to inflammatory cytokine secretion, cell death and spontaneous development of Aß and phospho-Tau deposits. These proteotoxic inclusions co-localize with lysosomes and damage markers and resemble inclusions in brain tissue from AD patients and APP-transgenic mice. Supporting the centrality of lysosomal deficits driving AD phenotypes, lysosome-function enhancing compounds reduce AD-associated cytokine secretion and Aβ deposits. We conclude that proteostasis and organelle deficits are upstream initiating factors leading to neuronal aging and AD phenotypes.
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Affiliation(s)
- Ching-Chieh Chou
- Department of Biology, Stanford University, Stanford, California, USA
| | - Ryan Vest
- Department of Chemical Engineering, Stanford University, Stanford, California, USA
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, California, USA
- Qinotto, Inc. San Carlos, California, USA
| | - Miguel A. Prado
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts, USA
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Spain
| | - Joshua Wilson-Grady
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts, USA
| | - Joao A. Paulo
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts, USA
| | - Yohei Shibuya
- Departments of Pathology, Stanford University School of Medicine, Stanford, California, USA
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, California, USA
| | - Patricia Moran-Losada
- Wu Tsai Neurosciences Institute, Stanford University School of Medicine, Stanford, California, USA
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, California, USA
| | - Ting-Ting Lee
- Department of Biology, Stanford University, Stanford, California, USA
| | - Jian Luo
- Palo Alto Veterans Institute for Research, Inc. (PAVIR), Palo Alto, California, USA
| | - Steven P. Gygi
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts, USA
| | - Jeffery W. Kelly
- Department of Chemistry, The Scripps Research Institute, La Jolla, California, USA
- The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, California, USA
| | - Daniel Finley
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts, USA
| | - Marius Wernig
- Departments of Pathology, Stanford University School of Medicine, Stanford, California, USA
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, California, USA
| | - Tony Wyss-Coray
- Wu Tsai Neurosciences Institute, Stanford University School of Medicine, Stanford, California, USA
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, California, USA
| | - Judith Frydman
- Department of Biology, Stanford University, Stanford, California, USA
- Department of Genetics, Stanford University, Stanford, California, USA
- Wu Tsai Neurosciences Institute, Stanford University School of Medicine, Stanford, California, USA
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD, USA
- Lead contact
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5
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Pan X, Ren L, Yang Y, Xu Y, Ning L, Zhang Y, Luo H, Zou Q, Zhang Y. MCSdb, a database of proteins residing in membrane contact sites. Sci Data 2024; 11:281. [PMID: 38459036 PMCID: PMC10923927 DOI: 10.1038/s41597-024-03104-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Accepted: 02/29/2024] [Indexed: 03/10/2024] Open
Abstract
Organelles do not act as autonomous discrete units but rather as interconnected hubs that engage in extensive communication by forming close contacts called "membrane contact sites (MCSs)". And many proteins have been identified as residing in MCS and playing important roles in maintaining and fulfilling specific functions within these microdomains. However, a comprehensive compilation of these MCS proteins is still lacking. Therefore, we developed MCSdb, a manually curated resource of MCS proteins and complexes from publications. MCSdb documents 7010 MCS protein entries and 263 complexes, involving 24 organelles and 44 MCSs across 11 species. Additionally, MCSdb orchestrates all data into different categories with multitudinous information for presenting MCS proteins. In summary, MCSdb provides a valuable resource for accelerating MCS functional interpretation and interorganelle communication deciphering.
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Affiliation(s)
- Xianrun Pan
- College of Medical Technology, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Liping Ren
- School of Healthcare Technology, Chengdu Neusoft University, Chengdu, China
| | - Yu Yang
- School of Healthcare Technology, Chengdu Neusoft University, Chengdu, China
| | - Yi Xu
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, China
| | - Lin Ning
- School of Healthcare Technology, Chengdu Neusoft University, Chengdu, China
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, China
| | - Yibing Zhang
- Glasgow College, University of Electronic Science and Technology of China, Chengdu, China
| | - Huaichao Luo
- Department of Clinical Laboratory, Sichuan Clinical Research Center for Cancer, Sichuan Cancer Hospital & Institute, Sichuan Cancer Center, Affiliated Cancer Hospital of University of Electronic Science and Technology of China, Chengdu, China.
| | - Quan Zou
- Institute of Fundamental and Frontier Sciences, University of Electronic Science and Technology of China, Chengdu, China.
| | - Yang Zhang
- Innovative Institute of Chinese Medicine and Pharmacy, Academy for Interdiscipline, Chengdu University of Traditional Chinese Medicine, Chengdu, China.
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6
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Chen SY, Chang CK, Lan CY. Antimicrobial peptide LL-37 disrupts plasma membrane and calcium homeostasis in Candida albicans via the Rim101 pathway. Microbiol Spectr 2023; 11:e0255123. [PMID: 37888991 PMCID: PMC10715129 DOI: 10.1128/spectrum.02551-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2023] [Accepted: 09/19/2023] [Indexed: 10/28/2023] Open
Abstract
IMPORTANCE Candida albicans is a major human fungal pathogen, and antimicrobial peptides are key components of innate immunity. Studying the interplay between C. albicans and human antimicrobial peptides would enhance a better understanding of pathogen-host interactions. Moreover, potential applications of antimicrobial peptides in antifungal therapy have aroused great interest. This work explores new mechanisms of LL-37 against C. albicans and reveals the complex connection among calcium homeostasis, oxidative stress, signaling, and possibly organelle interaction. Notably, these findings support the possible use of antimicrobial peptides to prevent and treat fungal infections.
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Affiliation(s)
- Sheng-Yuan Chen
- Institute of Molecular and Cellular Biology, National Tsing Hua University, Hsinchu, Taiwan
| | - Che-Kang Chang
- Institute of Molecular and Cellular Biology, National Tsing Hua University, Hsinchu, Taiwan
| | - Chung-Yu Lan
- Institute of Molecular and Cellular Biology, National Tsing Hua University, Hsinchu, Taiwan
- Department of Life Science, National Tsing Hua University, Hsinchu, Taiwan
- School of Medicine, National Tsing Hua University, Hsinchu, Taiwan
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7
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Barabino S, Lombardi S, Zilocchi M. Keep in touch: a perspective on the mitochondrial social network and its implication in health and disease. Cell Death Discov 2023; 9:417. [PMID: 37973903 PMCID: PMC10654391 DOI: 10.1038/s41420-023-01710-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Revised: 10/31/2023] [Accepted: 11/06/2023] [Indexed: 11/19/2023] Open
Abstract
Mitochondria have been the focus of extensive research for decades since their dysfunction is linked to more than 150 distinct human disorders. Despite considerable efforts, researchers have only been able to skim the surface of the mitochondrial social complexity and the impact of inter-organelle and inter-organ communication alterations on human health. While some progress has been made in deciphering connections among mitochondria and other cytoplasmic organelles through direct (i.e., contact sites) or indirect (i.e., inter-organelle trafficking) crosstalk, most of these efforts have been restricted to a limited number of proteins involved in specific physiological pathways or disease states. This research bottleneck is further narrowed by our incomplete understanding of the cellular alteration timeline in a specific pathology, which prevents the distinction between a primary organelle dysfunction and the defects occurring due to the disruption of the organelle's interconnectivity. In this perspective, we will (i) summarize the current knowledge on the mitochondrial crosstalk within cell(s) or tissue(s) in health and disease, with a particular focus on neurodegenerative disorders, (ii) discuss how different large-scale and targeted approaches could be used to characterize the different levels of mitochondrial social complexity, and (iii) consider how investigating the different expression patterns of mitochondrial proteins in different cell types/tissues could represent an important step forward in depicting the distinctive architecture of inter-organelle communication.
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Affiliation(s)
- Silvia Barabino
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, 20126, Milan, Italy.
| | - Silvia Lombardi
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, 20126, Milan, Italy
| | - Mara Zilocchi
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, 20126, Milan, Italy.
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8
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Mouton SN, Boersma AJ, Veenhoff LM. A physicochemical perspective on cellular ageing. Trends Biochem Sci 2023; 48:949-962. [PMID: 37716870 DOI: 10.1016/j.tibs.2023.08.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 08/17/2023] [Accepted: 08/18/2023] [Indexed: 09/18/2023]
Abstract
Cellular ageing described at the molecular level is a multifactorial process that leads to a spectrum of ageing trajectories. There has been recent discussion about whether a decline in physicochemical homeostasis causes aberrant phase transitions, which are a driver of ageing. Indeed, the function of all biological macromolecules, regardless of their participation in biomolecular condensates, depends on parameters such as pH, crowding, and redox state. We expand on the physicochemical homeostasis hypothesis and summarise recent evidence that the intracellular milieu influences molecular processes involved in ageing.
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Affiliation(s)
- Sara N Mouton
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands.
| | - Arnold J Boersma
- Cellular Protein Chemistry, Bijvoet Centre for Biomolecular Research, Faculty of Science, Utrecht University, Utrecht, The Netherlands
| | - Liesbeth M Veenhoff
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands.
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9
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Rouya C, Yambire KF, Derbyshire ML, Alwaseem H, Tavazoie SF. Inter-organellar nucleic acid communication by a mitochondrial tRNA regulates nuclear metabolic transcription. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.21.558912. [PMID: 37790361 PMCID: PMC10542527 DOI: 10.1101/2023.09.21.558912] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/05/2023]
Abstract
Efficient communication between mitochondria and the nucleus underlies homoeostatic metabolic control, though the involved mitochondrial factors and their mechanisms are poorly defined. Here, we report the surprising detection of multiple mitochondrial-derived transfer RNAs (mito-tRNAs) within the nuclei of human cells. Focused studies of nuclear-transported mito-tRNA-asparagine (mtAsn) revealed that its cognate charging enzyme (NARS2) is also present in the nucleus. MtAsn promoted interaction of NARS2 with histone deacetylase 2 (HDAC2), and repressed HDAC2 association with specific chromatin loci. Perturbation of this axis using antisense oligonucleotides promoted nucleotide biogenesis and enhanced breast cancer growth, and RNA and nascent transcript sequencing demonstrated specific alterations in the transcription of nuclear genes. These findings uncover nucleic-acid mediated communication between two organelles and the existence of a machinery for nuclear gene regulation by a mito-tRNA that restricts tumor growth through metabolic control. Highlights Multiple mitochondrial-derived tRNAs are detected in human cell nucleiMtAsn promotes binding between NARS2 and HDAC2Metabolic alterations driven by mtAsn impact cell proliferationMtAsn inhibition releases HDAC2 to bind and transcriptionally regulate multiple nuclear genes.
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10
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Chelius X, Bartosch V, Rausch N, Haubner M, Schramm J, Braun RJ, Klecker T, Westermann B. Selective retention of dysfunctional mitochondria during asymmetric cell division in yeast. PLoS Biol 2023; 21:e3002310. [PMID: 37721958 PMCID: PMC10538663 DOI: 10.1371/journal.pbio.3002310] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 09/28/2023] [Accepted: 08/23/2023] [Indexed: 09/20/2023] Open
Abstract
Decline of mitochondrial function is a hallmark of cellular aging. To counteract this process, some cells inherit mitochondria asymmetrically to rejuvenate daughter cells. The molecular mechanisms that control this process are poorly understood. Here, we made use of matrix-targeted D-amino acid oxidase (Su9-DAO) to selectively trigger oxidative damage in yeast mitochondria. We observed that dysfunctional mitochondria become fusion-incompetent and immotile. Lack of bud-directed movements is caused by defective recruitment of the myosin motor, Myo2. Intriguingly, intact mitochondria that are present in the same cell continue to move into the bud, establishing that quality control occurs directly at the level of the organelle in the mother. The selection of healthy organelles for inheritance no longer works in the absence of the mitochondrial Myo2 adapter protein Mmr1. Together, our data suggest a mechanism in which the combination of blocked fusion and loss of motor protein ensures that damaged mitochondria are retained in the mother cell to ensure rejuvenation of the bud.
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Affiliation(s)
- Xenia Chelius
- Zellbiologie, Universität Bayreuth, Bayreuth, Germany
| | | | | | | | - Jana Schramm
- Zellbiologie, Universität Bayreuth, Bayreuth, Germany
| | - Ralf J. Braun
- Department Medizin, Fakultät Medizin/Zahnmedizin, Danube Private University, Krems, Austria
| | - Till Klecker
- Zellbiologie, Universität Bayreuth, Bayreuth, Germany
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11
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Wang L, Goldwag J, Bouyea M, Barra J, Matteson K, Maharjan N, Eladdadi A, Embrechts MJ, Intes X, Kruger U, Barroso M. Spatial topology of organelle is a new breast cancer cell classifier. iScience 2023; 26:107229. [PMID: 37519903 PMCID: PMC10384275 DOI: 10.1016/j.isci.2023.107229] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Revised: 05/10/2023] [Accepted: 06/23/2023] [Indexed: 08/01/2023] Open
Abstract
Genomics and proteomics have been central to identify tumor cell populations, but more accurate approaches to classify cell subtypes are still lacking. We propose a new methodology to accurately classify cancer cells based on their organelle spatial topology. Herein, we developed an organelle topology-based cell classification pipeline (OTCCP), which integrates artificial intelligence (AI) and imaging quantification to analyze organelle spatial distribution and inter-organelle topology. OTCCP was used to classify a panel of human breast cancer cells, grown as 2D monolayer or 3D tumor spheroids using early endosomes, mitochondria, and their inter-organelle contacts. Organelle topology allows for a highly precise differentiation between cell lines of different subtypes and aggressiveness. These findings lay the groundwork for using organelle topological profiling as a fast and efficient method for phenotyping breast cancer function as well as a discovery tool to advance our understanding of cancer cell biology at the subcellular level.
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Affiliation(s)
- Ling Wang
- Department of Molecular and Cellular Physiology, Albany Medical College, Albany, NY 12208, USA
| | - Joshua Goldwag
- Department of Molecular and Cellular Physiology, Albany Medical College, Albany, NY 12208, USA
| | - Megan Bouyea
- Department of Molecular and Cellular Physiology, Albany Medical College, Albany, NY 12208, USA
| | - Jonathan Barra
- Department of Molecular and Cellular Physiology, Albany Medical College, Albany, NY 12208, USA
| | - Kailie Matteson
- Department of Molecular and Cellular Physiology, Albany Medical College, Albany, NY 12208, USA
| | - Niva Maharjan
- Department of Mathematics, The College of Saint Rose, Albany, NY 12203, USA
| | - Amina Eladdadi
- Department of Mathematics, The College of Saint Rose, Albany, NY 12203, USA
| | - Mark J. Embrechts
- Department of Industrial and Systems Engineering, Rensselaer Polytechnic Institute, Troy, NY 12180, USA
| | - Xavier Intes
- Department of Biomedical Engineering, Rensselaer Polytechnic Institute, Troy, NY 12180, USA
| | - Uwe Kruger
- Department of Biomedical Engineering, Rensselaer Polytechnic Institute, Troy, NY 12180, USA
| | - Margarida Barroso
- Department of Molecular and Cellular Physiology, Albany Medical College, Albany, NY 12208, USA
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12
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Vazquez‐Calvo C, Kohler V, Höög JL, Büttner S, Ott M. Newly imported proteins in mitochondria are particularly sensitive to aggregation. Acta Physiol (Oxf) 2023; 238:e13985. [PMID: 37171464 PMCID: PMC10909475 DOI: 10.1111/apha.13985] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 04/20/2023] [Accepted: 05/09/2023] [Indexed: 05/13/2023]
Abstract
AIM A functional proteome is essential for life and maintained by protein quality control (PQC) systems in the cytosol and organelles. Protein aggregation is an indicator of a decline of PQC linked to aging and disease. Mitochondrial PQC is critical to maintain mitochondrial function and thus cellular fitness. How mitochondria handle aggregated proteins is not well understood. Here we tested how the metabolic status impacts on formation and clearance of aggregates within yeast mitochondria and assessed which proteins are particularly sensitive to denaturation. METHODS Confocal microscopy, electron microscopy, immunoblotting and genetics were applied to assess mitochondrial aggregate handling in response to heat shock and ethanol using the mitochondrial disaggregase Hsp78 as a marker for protein aggregates. RESULTS We show that aggregates formed upon heat or ethanol stress with different dynamics depending on the metabolic state. While fermenting cells displayed numerous small aggregates that coalesced into one large foci that was resistant to clearance, respiring cells showed less aggregates and cleared these aggregates more efficiently. Acute inhibition of mitochondrial translation had no effect, while preventing protein import into mitochondria by inhibition of cytosolic translation prevented aggregate formation. CONCLUSION Collectively, our data show that the metabolic state of the cells impacts the dynamics of aggregate formation and clearance, and that mainly newly imported and not yet assembled proteins are prone to form aggregates. Because mitochondrial functionality is crucial for cellular metabolism, these results highlight the importance of efficient protein biogenesis to maintain the mitochondrial proteome operational during metabolic adaptations and cellular stress.
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Affiliation(s)
- Carmela Vazquez‐Calvo
- Department of Biochemistry and BiophysicsStockholm UniversityStockholmSweden
- Department of Molecular Biosciences, The Wenner‐Gren InstituteStockholm UniversityStockholmSweden
| | - Verena Kohler
- Department of Molecular Biosciences, The Wenner‐Gren InstituteStockholm UniversityStockholmSweden
- Institute of Molecular BiosciencesUniversity of GrazGrazAustria
| | - Johanna L. Höög
- Department of Chemistry and Molecular BiologyUniversity of GothenburgGothenburgSweden
| | - Sabrina Büttner
- Department of Molecular Biosciences, The Wenner‐Gren InstituteStockholm UniversityStockholmSweden
| | - Martin Ott
- Department of Biochemistry and BiophysicsStockholm UniversityStockholmSweden
- Department of Medical Biochemistry and Cell BiologyUniversity of GothenburgGothenburgSweden
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13
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Tanwar J, Ahuja K, Sharma A, Sehgal P, Ranjan G, Sultan F, Priya A, Venkatesan M, Yenamandra VK, Singh A, Madesh M, Sivasubbu S, Motiani RK. Mitochondrial calcium signaling mediated transcriptional regulation of keratin filaments is a critical determinant of melanogenesis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.26.542250. [PMID: 37292659 PMCID: PMC10245956 DOI: 10.1101/2023.05.26.542250] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Mitochondria are versatile organelles that regulate several physiological functions. Many mitochondria-controlled processes are driven by mitochondrial Ca2+ signaling. However, role of mitochondrial Ca2+ signaling in melanosome biology remains unknown. Here, we show that pigmentation requires mitochondrial Ca2+ uptake. In vitro gain and loss of function studies demonstrated that Mitochondrial Ca2+ Uniporter (MCU) is crucial for melanogenesis while the MCU rheostats, MCUb and MICU1 negatively control melanogenesis. Zebrafish and mouse models showed that MCU plays a vital role in pigmentation in vivo. Mechanistically, MCU controls activation of transcription factor NFAT2 to induce expression of three keratins (keratin 5, 7 and 8), which we report as positive regulators of melanogenesis. Interestingly, keratin 5 in turn modulates mitochondrial Ca2+ uptake thereby this signaling module acts as a negative feedback loop that fine-tunes both mitochondrial Ca2+ signaling and melanogenesis. Mitoxantrone, an FDA approved drug that inhibits MCU, decreases physiological melanogenesis. Collectively, our data demonstrates a critical role for mitochondrial Ca2+ signaling in vertebrate pigmentation and reveal the therapeutic potential of targeting MCU for clinical management of pigmentary disorders. Given the centrality of mitochondrial Ca2+ signaling and keratin filaments in cellular physiology, this feedback loop may be functional in a variety of other pathophysiological conditions.
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Affiliation(s)
- Jyoti Tanwar
- Laboratory of Calciomics and Systemic Pathophysiology (LCSP), Regional Centre for Biotechnology (RCB), Faridabad-121001, Delhi-NCR, India
| | - Kriti Ahuja
- Laboratory of Calciomics and Systemic Pathophysiology (LCSP), Regional Centre for Biotechnology (RCB), Faridabad-121001, Delhi-NCR, India
| | - Akshay Sharma
- Laboratory of Calciomics and Systemic Pathophysiology (LCSP), Regional Centre for Biotechnology (RCB), Faridabad-121001, Delhi-NCR, India
| | - Paras Sehgal
- CSIR-Institute of Genomics and Integrative Biology (IGIB), New Delhi, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002 India
| | - Gyan Ranjan
- CSIR-Institute of Genomics and Integrative Biology (IGIB), New Delhi, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002 India
| | - Farina Sultan
- Laboratory of Calciomics and Systemic Pathophysiology (LCSP), Regional Centre for Biotechnology (RCB), Faridabad-121001, Delhi-NCR, India
| | - Anshu Priya
- CSIR-Institute of Genomics and Integrative Biology (IGIB), New Delhi, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002 India
| | - Manigandan Venkatesan
- Department of Medicine, Center for Mitochondrial Medicine, Cardiology Division, University of Texas Health San Antonio, San Antonio, TX 78229, USA
| | - Vamsi K Yenamandra
- CSIR-Institute of Genomics and Integrative Biology (IGIB), New Delhi, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002 India
| | - Archana Singh
- CSIR-Institute of Genomics and Integrative Biology (IGIB), New Delhi, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002 India
| | - Muniswamy Madesh
- Department of Medicine, Center for Mitochondrial Medicine, Cardiology Division, University of Texas Health San Antonio, San Antonio, TX 78229, USA
| | - Sridhar Sivasubbu
- CSIR-Institute of Genomics and Integrative Biology (IGIB), New Delhi, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002 India
| | - Rajender K Motiani
- Laboratory of Calciomics and Systemic Pathophysiology (LCSP), Regional Centre for Biotechnology (RCB), Faridabad-121001, Delhi-NCR, India
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14
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Sontag EM, Morales-Polanco F, Chen JH, McDermott G, Dolan PT, Gestaut D, Le Gros MA, Larabell C, Frydman J. Nuclear and cytoplasmic spatial protein quality control is coordinated by nuclear-vacuolar junctions and perinuclear ESCRT. Nat Cell Biol 2023; 25:699-713. [PMID: 37081164 DOI: 10.1038/s41556-023-01128-6] [Citation(s) in RCA: 19] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Accepted: 03/14/2023] [Indexed: 04/22/2023]
Abstract
Effective protein quality control (PQC), essential for cellular health, relies on spatial sequestration of misfolded proteins into defined inclusions. Here we reveal the coordination of nuclear and cytoplasmic spatial PQC. Cytoplasmic misfolded proteins concentrate in a cytoplasmic juxtanuclear quality control compartment, while nuclear misfolded proteins sequester into an intranuclear quality control compartment (INQ). Particle tracking reveals that INQ and the juxtanuclear quality control compartment converge to face each other across the nuclear envelope at a site proximal to the nuclear-vacuolar junction marked by perinuclear ESCRT-II/III protein Chm7. Strikingly, convergence at nuclear-vacuolar junction contacts facilitates VPS4-dependent vacuolar clearance of misfolded cytoplasmic and nuclear proteins, the latter entailing extrusion of nuclear INQ into the vacuole. Finding that nuclear-vacuolar contact sites are cellular hubs of spatial PQC to facilitate vacuolar clearance of nuclear and cytoplasmic inclusions highlights the role of cellular architecture in proteostasis maintenance.
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Affiliation(s)
- Emily M Sontag
- Department of Biology, Stanford University, Stanford, CA, USA.
- Department of Biological Sciences, Marquette University, Milwaukee, WI, USA.
| | | | - Jian-Hua Chen
- Department of Anatomy, School of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Gerry McDermott
- Department of Anatomy, School of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Patrick T Dolan
- Department of Biology, Stanford University, Stanford, CA, USA
- Quantitative Virology and Evolution Unit, National Institute of Allergy and Infectious Diseases, Bethesda, MD, USA
| | - Daniel Gestaut
- Department of Biology, Stanford University, Stanford, CA, USA
| | - Mark A Le Gros
- Department of Anatomy, School of Medicine, University of California San Francisco, San Francisco, CA, USA
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Carolyn Larabell
- Department of Anatomy, School of Medicine, University of California San Francisco, San Francisco, CA, USA
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Judith Frydman
- Department of Biology, Stanford University, Stanford, CA, USA.
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15
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Li H, Zhang H, He X, Zhao P, Wu T, Xiahou J, Wu Y, Liu Y, Chen Y, Jiang X, Lv G, Yao Z, Wu J, Bu W. Blocking Spatiotemporal Crosstalk between Subcellular Organelles for Enhancing Anticancer Therapy with Nanointercepters. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2023; 35:e2211597. [PMID: 36746119 DOI: 10.1002/adma.202211597] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Revised: 01/16/2023] [Indexed: 05/05/2023]
Abstract
The spatiotemporal characterization of signaling crosstalk between subcellular organelles is crucial for the therapeutic effect of malignant tumors. Blocking interactive crosstalk in this fashion is significant but challenging. Herein, a communication interception strategy is reported, which blocks spatiotemporal crosstalk between subcellular organelles for cancer therapy with underlying molecular mechanisms. Briefly, amorphous-core@crystalline-shell Fe@Fe3 O4 nanoparticles (ACFeNPs) are fabricated to specifically block the crosstalk between lysosomes and endoplasmic reticulum (ER) by hydroxyl radicals generated along with their trajectory through heterogeneous Fenton reaction. ACFeNPs initially enter lysosomes and trigger autophagy, then continuous lysosomal damage blocks the generation of functional autolysosomes, which mediates ER-lysosome crosstalk, thus the autophagy is paralyzed. Thereafter, released ACFeNPs from lysosomes induce ER stress. Without the alleviation by autophagy, the ER-stress-associated apoptotic pathway is fully activated, resulting in a remarkable therapeutic effect. This strategy provides a wide venue for nanomedicine to exert biological advantages and confers new perspective for the design of novel anticancer drugs.
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Affiliation(s)
- Huiyan Li
- Department of Materials Science and State Key Laboratory of Molecular Engineering of Polymers, Fudan University, Shanghai, 200433, P. R. China
- Department of Medical Microbiology and Parasitology, MOE/NHC/CAMS Key Laboratory of Medical Molecular Virology, School of Basic Medical Sciences, Fudan University, Shanghai, 200032, P. R. China
| | - Huilin Zhang
- Department of Materials Science and State Key Laboratory of Molecular Engineering of Polymers, Fudan University, Shanghai, 200433, P. R. China
- Departments of Radiology and Neurosurgery, Huashan Hospital, Fudan University, Shanghai, 200040, P. R. China
| | - Xiaofang He
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, 210023, P. R. China
| | - Peiran Zhao
- Department of Materials Science and State Key Laboratory of Molecular Engineering of Polymers, Fudan University, Shanghai, 200433, P. R. China
| | - Tong Wu
- Department of Materials Science and State Key Laboratory of Molecular Engineering of Polymers, Fudan University, Shanghai, 200433, P. R. China
| | - Jinxuan Xiahou
- Department of Medical Microbiology and Parasitology, MOE/NHC/CAMS Key Laboratory of Medical Molecular Virology, School of Basic Medical Sciences, Fudan University, Shanghai, 200032, P. R. China
| | - Yelin Wu
- Tongji University Cancer Center, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, 200072, P. R. China
| | - Yanyan Liu
- Department of Materials Science and State Key Laboratory of Molecular Engineering of Polymers, Fudan University, Shanghai, 200433, P. R. China
| | - Yang Chen
- Tongji University Cancer Center, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, 200072, P. R. China
| | - Xingwu Jiang
- Department of Materials Science and State Key Laboratory of Molecular Engineering of Polymers, Fudan University, Shanghai, 200433, P. R. China
| | - Guanglei Lv
- Department of Materials Science and State Key Laboratory of Molecular Engineering of Polymers, Fudan University, Shanghai, 200433, P. R. China
| | - Zhenwei Yao
- Departments of Radiology and Neurosurgery, Huashan Hospital, Fudan University, Shanghai, 200040, P. R. China
| | - Jian Wu
- Department of Medical Microbiology and Parasitology, MOE/NHC/CAMS Key Laboratory of Medical Molecular Virology, School of Basic Medical Sciences, Fudan University, Shanghai, 200032, P. R. China
| | - Wenbo Bu
- Department of Materials Science and State Key Laboratory of Molecular Engineering of Polymers, Fudan University, Shanghai, 200433, P. R. China
- Departments of Radiology and Neurosurgery, Huashan Hospital, Fudan University, Shanghai, 200040, P. R. China
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16
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Chou CC, Vest R, Prado MA, Wilson-Grady J, Paulo JA, Shibuya Y, Moran-Losada P, Lee TT, Luo J, Gygi SP, Kelly JW, Finley D, Wernig M, Wyss-Coray T, Frydman J. Proteostasis and lysosomal quality control deficits in Alzheimer's disease neurons. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.27.534444. [PMID: 37034684 PMCID: PMC10081252 DOI: 10.1101/2023.03.27.534444] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
The role of proteostasis and organelle homeostasis dysfunction in human aging and Alzheimer's disease (AD) remains unclear. Analyzing proteome-wide changes in human donor fibroblasts and their corresponding transdifferentiated neurons (tNeurons), we find aging and AD synergistically impair multiple proteostasis pathways, most notably lysosomal quality control (LQC). In particular, we show that ESCRT-mediated lysosomal repair defects are associated with both sporadic and PSEN1 familial AD. Aging- and AD-linked defects are detected in fibroblasts but highly exacerbated in tNeurons, leading to enhanced neuronal vulnerability, unrepaired lysosomal damage, inflammatory factor secretion and cytotoxicity. Surprisingly, tNeurons from aged and AD donors spontaneously develop amyloid-β inclusions co-localizing with LQC markers, LAMP1/2-positive lysosomes and proteostasis factors; we observe similar inclusions in brain tissue from AD patients and APP-transgenic mice. Importantly, compounds enhancing lysosomal function broadly ameliorate these AD-associated pathologies. Our findings establish cell-autonomous LQC dysfunction in neurons as a central vulnerability in aging and AD pathogenesis.
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17
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Wei W, Lu H, Dai W, Zheng X, Dong H. Multiplexed Organelles Portrait Barcodes for Subcellular MicroRNA Array Detection in Living Cells. ACS NANO 2022; 16:20329-20339. [PMID: 36410732 DOI: 10.1021/acsnano.2c06252] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Multiplexed profiling of microRNAs' subcellular expression and distribution is essential to understand their spatiotemporal function information, but it remains a crucial challenge. Herein, we report an encoding approach that leverages combinational fluorescent dye barcodes, organelle targeting elements, and an independent quantification signal, termed Multiplexed Organelles Portrait Barcodes (MOPB), for high-throughput profiling of miRNAs from organelles. The MOPB barcodes consist of heterochromatic fluorescent dye-loaded shell-core mesoporous silica nanoparticles modified with organelle targeting peptides and molecular beacon detection probes. Using mitochondria and endoplasmic reticulum as models, we encoded four Cy3/AMCA ER-MOPB and four Cy5/AMCA Mito-MOPB by varying the Cy3 and Cy5 intensity for distinguishing eight organelles' miRNAs. Significantly, the MOPB strategy successfully and accurately profiled eight subcellular organelle miRNAs' alterations in the drug-induced Ca2+ homeostasis breakdown. The approach should allow more widespread application of subcellular miRNAs and multiplexed subcellular protein biomarkers' monitoring for drug discovery, cellular metabolism, signaling transduction, and gene expression regulation readout.
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Affiliation(s)
- Wei Wei
- Marshall Laboratory of Biomedical Engineering, Research Center for Biosensor and Nanotheranostic, School of Biomedical Engineering, Shenzhen University, 3688 Nanhai Road, Shenzhen, Guangdong518060, China
- Beijing Key Laboratory for Bioengineering and Sensing Technology, School of Chemistry and Bioengineering, University of Science and Technology Beijing30 Xueyuan Road, 100083, Beijing, China
| | - Huiting Lu
- Department of Chemistry, School of Chemistry and Bioengineering, University of Science and Technology Beijing, 30 Xueyuan Road, Beijing100083, China
| | - Wenhao Dai
- Beijing Key Laboratory for Bioengineering and Sensing Technology, School of Chemistry and Bioengineering, University of Science and Technology Beijing30 Xueyuan Road, 100083, Beijing, China
| | - Xiaonan Zheng
- Beijing Key Laboratory for Bioengineering and Sensing Technology, School of Chemistry and Bioengineering, University of Science and Technology Beijing30 Xueyuan Road, 100083, Beijing, China
| | - Haifeng Dong
- Marshall Laboratory of Biomedical Engineering, Research Center for Biosensor and Nanotheranostic, School of Biomedical Engineering, Shenzhen University, 3688 Nanhai Road, Shenzhen, Guangdong518060, China
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18
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Abstract
The analogy of mitochondria as powerhouses has expired. Mitochondria are living, dynamic, maternally inherited, energy-transforming, biosynthetic, and signaling organelles that actively transduce biological information. We argue that mitochondria are the processor of the cell, and together with the nucleus and other organelles they constitute the mitochondrial information processing system (MIPS). In a three-step process, mitochondria (1) sense and respond to both endogenous and environmental inputs through morphological and functional remodeling; (2) integrate information through dynamic, network-based physical interactions and diffusion mechanisms; and (3) produce output signals that tune the functions of other organelles and systemically regulate physiology. This input-to-output transformation allows mitochondria to transduce metabolic, biochemical, neuroendocrine, and other local or systemic signals that enhance organismal adaptation. An explicit focus on mitochondrial signal transduction emphasizes the role of communication in mitochondrial biology. This framework also opens new avenues to understand how mitochondria mediate inter-organ processes underlying human health.
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Affiliation(s)
- Martin Picard
- Department of Psychiatry, Division of Behavioral Medicine, Columbia University Irving Medical Center, New York, NY 10032, USA; Department of Neurology, H. Houston Merritt Center, Columbia Translational Neuroscience Initiative, Columbia University Irving Medical Center, New York, NY 10032, USA; New York State Psychiatric Institute, New York, NY 10032, USA.
| | - Orian S Shirihai
- Department of Medicine, Endocrinology, and Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA; Metabolism Theme, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
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19
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Fundamental roles for inter-organelle communication in aging. Biochem Soc Trans 2022; 50:1389-1402. [PMID: 36305642 PMCID: PMC9704535 DOI: 10.1042/bst20220519] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Revised: 09/27/2022] [Accepted: 10/17/2022] [Indexed: 11/17/2022]
Abstract
Advances in public health have nearly doubled life expectancy over the last century, but this demographic shift has also changed the landscape of human illness. Today, chronic and age-dependent diseases dominate the leading causes of morbidity and mortality worldwide. Targeting the underlying molecular, genetic and cell biological drivers of the aging process itself appears to be an increasingly viable strategy for developing therapeutics against these diseases of aging. Towards this end, one of the most exciting developments in cell biology over the last decade is the explosion of research into organelle contact sites and related mechanisms of inter-organelle communication. Identification of the molecular mediators of inter-organelle tethering and signaling is now allowing the field to investigate the consequences of aberrant organelle interactions, which frequently seem to correlate with age-onset pathophysiology. This review introduces the major cellular roles for inter-organelle interactions, including the regulation of organelle morphology, the transfer of ions, lipids and other metabolites, and the formation of hubs for nutrient and stress signaling. We explore how these interactions are disrupted in aging and present findings that modulation of inter-organelle communication is a promising avenue for promoting longevity. Through this review, we propose that the maintenance of inter-organelle interactions is a pillar of healthy aging. Learning how to target the cellular mechanisms for sensing and controlling inter-organelle communication is a key next hurdle for geroscience.
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20
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Sun M, Yuan F, Tang Y, Zou P, Lei X. Subcellular Interactomes Revealed by Merging APEX with Cross-Linking Mass Spectrometry. Anal Chem 2022; 94:14878-14888. [PMID: 36265550 DOI: 10.1021/acs.analchem.2c02116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Subcellular protein-protein interactions (PPIs) are essential to understanding the mechanism of diverse cellular signaling events and the pathogenesis of diseases. Herein, we report an integrated APEX proximity labeling and chemical cross-linking coupled with mass spectrometry (CXMS) platform named APEX-CXMS for spatially resolved subcellular interactome profiling in a high-throughput manner. APEX proximity labeling rapidly captures subcellular proteomes, and the highly reactive chemical cross-linkers can capture weak and dynamic interactions globally without extra genetic manipulation. APEX-CXMS was first applied to mitochondria and identified 653 pairs of interprotein cross-links. Six pairs of new interactions were selected and verified by coimmunoprecipitation, the mammalian two-hybrid system, and surface plasmon resonance method. Besides, our approach was further applied to the nucleus, capturing 336 pairs of interprotein cross-links with approximately 94% nuclear specificity. APEX-CXMS thus provides a simple, fast, and general alternative to map diverse subcellular PPIs.
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Affiliation(s)
- Mengze Sun
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Department of Chemical Biology, College of Chemistry and Molecular Engineering, Synthetic and Functional Biomolecules Center, and Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Feng Yuan
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Department of Chemical Biology, College of Chemistry and Molecular Engineering, Synthetic and Functional Biomolecules Center, and Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Yuliang Tang
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Department of Chemical Biology, College of Chemistry and Molecular Engineering, Synthetic and Functional Biomolecules Center, and Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Peng Zou
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Department of Chemical Biology, College of Chemistry and Molecular Engineering, Synthetic and Functional Biomolecules Center, and Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China.,PKU-IDG/McGovern Institute for Brain Research, Peking University, Beijing 100871, China.,Chinese Institute for Brain Research (CIBR), Beijing 102206, China
| | - Xiaoguang Lei
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Department of Chemical Biology, College of Chemistry and Molecular Engineering, Synthetic and Functional Biomolecules Center, and Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China.,Institute for Cancer Research, Shenzhen Bay Laboratory, Shenzhen 518107, China
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21
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Jeon H, Kim YJ, Hwang SK, Seo J, Mun JY. Restoration of Cathepsin D Level via L-Serine Attenuates PPA-Induced Lysosomal Dysfunction in Neuronal Cells. Int J Mol Sci 2022; 23:ijms231810613. [PMID: 36142514 PMCID: PMC9504002 DOI: 10.3390/ijms231810613] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 09/05/2022] [Accepted: 09/08/2022] [Indexed: 11/21/2022] Open
Abstract
L-serine is a non-essential amino acid endogenously produced by astrocytes and is abundant in human diets. Beneficial roles of the metabolic products from L-serine in various conditions in the brain including neuronal development have been reported. Through several preclinical studies, L-serine treatment was also shown to offer beneficial therapeutic effects for brain damage such as ischemic stroke, amyotrophic lateral sclerosis, and Parkinson’s disease. Despite evidence for the value of L-serine in the clinic, however, its beneficial effects on the propionic acid (PPA)-induced neuronal toxicity and underlying mechanisms of L-serine-mediated neuroprotection are unknown. In this study, we observed that PPA-induced acidic stress induces abnormal lipid accumulation and functional defects in lysosomes of hippocampal neurons. L-serine treatment was able to rescue the structure and function of lysosomes in PPA-treated hippocampal neuronal cells. We further identified that L-serine suppressed the formation of lipid droplets and abnormal lipid membrane accumulations inside the lysosomes in PPA-treated hippocampal neuronal cells. Taken together, these findings indicate that L-serine can be utilized as a neuroprotective agent for the functionality of lysosomes through restoration of cathepsin D in disease conditions.
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Affiliation(s)
- Hyunbum Jeon
- Neural Circuit Research Group, Korea Brain Research Institute, Daegu 41062, Korea
- Department of Brain Sciences, Daegu Gyeongbuk Institute of Science and Technology (DGIST), Daegu 42988, Korea
| | - Yeo Jin Kim
- Neural Circuit Research Group, Korea Brain Research Institute, Daegu 41062, Korea
| | - Su-Kyeong Hwang
- Department of Pediatrics, School of Medicine, Kyungpook National University, Daegu 41944, Korea
- Astrogen Inc., 440, Hyeoksin-daero, Dong-gu, Daegu 41072, Korea
| | - Jinsoo Seo
- Department of Brain Sciences, Daegu Gyeongbuk Institute of Science and Technology (DGIST), Daegu 42988, Korea
| | - Ji Young Mun
- Neural Circuit Research Group, Korea Brain Research Institute, Daegu 41062, Korea
- Correspondence:
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22
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Lippi A, Krisko A. CORE at the boundary of stress resistance and longevity. Int J Biochem Cell Biol 2022; 151:106277. [PMID: 35995386 DOI: 10.1016/j.biocel.2022.106277] [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: 06/09/2022] [Revised: 08/11/2022] [Accepted: 08/12/2022] [Indexed: 10/15/2022]
Abstract
As chronological age of an organism increases, a number of errors accumulate at different levels of biological organization. The tendency of errors to accumulate and cause downstream problems in maintenance of cellular homeostasis is met by numerous protection and repair mechanisms. Maintenance of proteins is vital for cell viability and longevity, thus cellular proteostasis is supported by chaperone networks in every cellular compartment, as well as other pathways ensuring timely chaperone expression and activity. In this minireview, we summarize the progress related to the cross-organelle stress response (CORE), in charge of orchestrating a cell-wide response to compartmentalized proteotoxicity. The proposed CORE pathway encompasses activation of protein conformational maintenance machineries, antioxidant enzymes and metabolic changes simultaneously in the cytosol, mitochondria and the ER. We discuss its importance in cell survival and longevity as well as its potential to serve as a pharmaceutical target in age-related diseases.
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Affiliation(s)
- Alice Lippi
- Department of Experimental Neurodegeneration, University Medical Center Goettingen, Waldweg 33, 37075 Goettingen, Germany
| | - Anita Krisko
- Department of Experimental Neurodegeneration, University Medical Center Goettingen, Waldweg 33, 37075 Goettingen, Germany.
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23
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Metabolite trafficking enables membrane-impermeable-terpene secretion by yeast. Nat Commun 2022; 13:2605. [PMID: 35546160 PMCID: PMC9095633 DOI: 10.1038/s41467-022-30312-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Accepted: 04/26/2022] [Indexed: 11/08/2022] Open
Abstract
Metabolites are often unable to permeate cell membranes and are thus accumulated inside cells. We investigate whether engineered microbes can exclusively secrete intracellular metabolites because sustainable metabolite secretion holds a great potential for mass-production of high-value chemicals in an efficient and continuous manner. In this study, we demonstrate a synthetic pathway for a metabolite trafficking system that enables lipophilic terpene secretion by yeast cells. When metabolite-binding proteins are tagged with signal peptides, metabolite trafficking is highly achievable; loaded metabolites can be precisely delivered to a desired location within or outside the cell. As a proof of concept, we systematically couple a terpene-binding protein with an export signal peptide and subsequently demonstrate efficient, yet selective terpene secretion by yeast (~225 mg/L for squalene and ~1.6 mg/L for β-carotene). Other carrier proteins can also be readily fused with desired signal peptides, thereby tailoring different metabolite trafficking pathways in different microbes. To the best of our knowledge, this is the most efficient cognate pathway for metabolite secretion by microorganisms. The engineering of metabolite secretion from microorganisms can lead to many applications in synthetic biology. In this article, the authors engineer a metabolite trafficking system for the secretion of medicinal terpenes.
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24
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Li Z, Liu Z, Luo M, Li X, Chen H, Gong S, Zhang M, Zhang Y, Liu H, Li X. The pathological role of damaged organelles in renal tubular epithelial cells in the progression of acute kidney injury. Cell Death Dis 2022; 8:239. [PMID: 35501332 PMCID: PMC9061711 DOI: 10.1038/s41420-022-01034-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Revised: 04/13/2022] [Accepted: 04/14/2022] [Indexed: 12/14/2022]
Abstract
Acute kidney injury (AKI) is a common clinical condition associated with high morbidity and mortality. The pathogenesis of AKI has not been fully elucidated, with a lack of effective treatment. Renal tubular epithelial cells (TECs) play an important role in AKI, and their damage and repair largely determine the progression and prognosis of AKI. In recent decades, it has been found that the mitochondria, endoplasmic reticulum (ER), lysosomes, and other organelles in TECs are damaged to varying degrees in AKI, and that they can influence each other through various signaling mechanisms that affect the recovery of TECs. However, the association between these multifaceted signaling platforms, particularly between mitochondria and lysosomes during AKI remains unclear. This review summarizes the specific pathophysiological mechanisms of the main TECs organelles in the context of AKI, particularly the potential interactions among them, in order to provide insights into possible novel treatment strategies.
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Affiliation(s)
- Zixian Li
- Institute of Nephrology, and Guangdong Provincial Key Laboratory of Autophagy and Major Chronic Non-communicable Diseases, Affiliated Hospital of Guangdong Medical University, Zhanjiang, 524001, China
| | - Zejian Liu
- Institute of Nephrology, and Guangdong Provincial Key Laboratory of Autophagy and Major Chronic Non-communicable Diseases, Affiliated Hospital of Guangdong Medical University, Zhanjiang, 524001, China
| | - Mianna Luo
- Institute of Nephrology, and Guangdong Provincial Key Laboratory of Autophagy and Major Chronic Non-communicable Diseases, Affiliated Hospital of Guangdong Medical University, Zhanjiang, 524001, China
| | - Xingyu Li
- Institute of Nephrology, and Guangdong Provincial Key Laboratory of Autophagy and Major Chronic Non-communicable Diseases, Affiliated Hospital of Guangdong Medical University, Zhanjiang, 524001, China
| | - Huixia Chen
- Institute of Nephrology, and Guangdong Provincial Key Laboratory of Autophagy and Major Chronic Non-communicable Diseases, Affiliated Hospital of Guangdong Medical University, Zhanjiang, 524001, China
| | - Siqiao Gong
- Institute of Nephrology, and Guangdong Provincial Key Laboratory of Autophagy and Major Chronic Non-communicable Diseases, Affiliated Hospital of Guangdong Medical University, Zhanjiang, 524001, China
| | - Minjie Zhang
- Institute of Nephrology, and Guangdong Provincial Key Laboratory of Autophagy and Major Chronic Non-communicable Diseases, Affiliated Hospital of Guangdong Medical University, Zhanjiang, 524001, China
| | - Yaozhi Zhang
- Institute of Nephrology, and Guangdong Provincial Key Laboratory of Autophagy and Major Chronic Non-communicable Diseases, Affiliated Hospital of Guangdong Medical University, Zhanjiang, 524001, China
| | - Huafeng Liu
- Institute of Nephrology, and Guangdong Provincial Key Laboratory of Autophagy and Major Chronic Non-communicable Diseases, Affiliated Hospital of Guangdong Medical University, Zhanjiang, 524001, China.
| | - Xiaoyu Li
- Institute of Nephrology, and Guangdong Provincial Key Laboratory of Autophagy and Major Chronic Non-communicable Diseases, Affiliated Hospital of Guangdong Medical University, Zhanjiang, 524001, China.
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25
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Infectious Spleen and Kidney Necrosis Virus (ISKNV) Triggers Mitochondria-Mediated Dynamic Interaction Signals via an Imbalance of Bax/Bak over Bcl-2/Bcl-xL in Fish Cells. Viruses 2022; 14:v14050922. [PMID: 35632664 PMCID: PMC9144193 DOI: 10.3390/v14050922] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 04/26/2022] [Accepted: 04/26/2022] [Indexed: 12/30/2022] Open
Abstract
The molecular pathogenesis of infectious spleen and kidney necrosis virus (ISKNV) infections is important but has rarely been studied in connection to host organelle behavior. In the present study, we demonstrated that ISKNV can induce host cell death via a pro-apoptotic Bcl-2 and anti-apoptotic Bcl-2 family member imbalance in mitochondrial membrane potential (MMP or ΔΨm) regulation in GF-1 cells. The results of our study on ISKNV infection showed that it can induce host cell death by up to 80% at day 5 post-infection. Subsequently, in an apoptotic assay, ISKNV infection was seen to induce an increase in Annexin-V-positive signals by 20% and in propidium iodide (PI) staining-positive signals by up to 30% at day 5 (D5) in GF-1 cells. Then, through our studies on the mechanism of cell death in mitochondria function, we found that ISKNV can induce MMP loss by up to 58% and 78% at days 4 and 5 with a JC1 dye staining assay. Furthermore, we found that pro-apoptotic members Bax and Bak were upregulated from the early replication stage (day one) to the late stage (day 5), but the expression profiles were very dynamically different. On the other hand, by Western blotted analysis, the anti-apoptotic members Bcl-2 and Bcl-xL were upregulated very quickly at the same time from day one (two-fold) and continued to maintain this level at day five. Finally, we found that pro-apoptotic death signals strongly activated the downstream signals of caspase-9 and -3. Taken together, these results suggest that ISKNV infection can induce Bax/Bak-mediated cell death signaling downstream of caspase-9 and -3 activation. During the viral replication cycle with the cell death induction process, the anti-apoptotic members Bcl-2/Bcl-xL interacted with the pro-apoptotic members Bax/Bak to maintain the mitochondrial function in the dynamic interaction so as to maintain the MMP in GF-1 cells. These findings may provide insights into DNA-virus control and treatment.
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26
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Hotz M, Thayer NH, Hendrickson DG, Schinski EL, Xu J, Gottschling DE. rDNA array length is a major determinant of replicative lifespan in budding yeast. Proc Natl Acad Sci U S A 2022; 119:e2119593119. [PMID: 35394872 PMCID: PMC9169770 DOI: 10.1073/pnas.2119593119] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Accepted: 03/01/2022] [Indexed: 12/29/2022] Open
Abstract
The complex processes and interactions that regulate aging and determine lifespan are not fully defined for any organism. Here, taking advantage of recent technological advances in studying aging in budding yeast, we discovered a previously unappreciated relationship between the number of copies of the ribosomal RNA gene present in its chromosomal array and replicative lifespan (RLS). Specifically, the chromosomal ribosomal DNA (rDNA) copy number (rDNA CN) positively correlated with RLS and this interaction explained over 70% of variability in RLS among a series of wild-type strains. In strains with low rDNA CN, SIR2 expression was attenuated and extrachromosomal rDNA circle (ERC) accumulation was increased, leading to shorter lifespan. Suppressing ERC formation by deletion of FOB1 eliminated the relationship between rDNA CN and RLS. These data suggest that previously identified rDNA CN regulatory mechanisms limit lifespan. Importantly, the RLSs of reported lifespan-enhancing mutations were significantly impacted by rDNA CN, suggesting that changes in rDNA CN might explain the magnitude of some of those reported effects. We propose that because rDNA CN is modulated by environmental, genetic, and stochastic factors, considering rDNA CN is a prerequisite for accurate interpretation of lifespan data.
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Affiliation(s)
- Manuel Hotz
- Calico Life Sciences LLC, South San Francisco, CA 94080
| | | | | | | | - Jun Xu
- Calico Life Sciences LLC, South San Francisco, CA 94080
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27
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Döhla J, Kuuluvainen E, Gebert N, Amaral A, Englund JI, Gopalakrishnan S, Konovalova S, Nieminen AI, Salminen ES, Torregrosa Muñumer R, Ahlqvist K, Yang Y, Bui H, Otonkoski T, Käkelä R, Hietakangas V, Tyynismaa H, Ori A, Katajisto P. Metabolic determination of cell fate through selective inheritance of mitochondria. Nat Cell Biol 2022; 24:148-154. [PMID: 35165416 PMCID: PMC7612378 DOI: 10.1038/s41556-021-00837-0] [Citation(s) in RCA: 42] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Accepted: 12/20/2021] [Indexed: 12/13/2022]
Abstract
Metabolic characteristics of adult stem cells are distinct from their differentiated progeny, and cellular metabolism is emerging as a potential driver of cell fate conversions1-4. How these metabolic features are established remains unclear. Here we identified inherited metabolism imposed by functionally distinct mitochondrial age-classes as a fate determinant in asymmetric division of epithelial stem-like cells. While chronologically old mitochondria support oxidative respiration, the electron transport chain of new organelles is proteomically immature and they respire less. After cell division, selectively segregated mitochondrial age-classes elicit a metabolic bias in progeny cells, with oxidative energy metabolism promoting differentiation in cells that inherit old mitochondria. Cells that inherit newly synthesized mitochondria with low levels of Rieske iron-sulfur polypeptide 1 have a higher pentose phosphate pathway activity, which promotes de novo purine biosynthesis and redox balance, and is required to maintain stemness during early fate determination after division. Our results demonstrate that fate decisions are susceptible to intrinsic metabolic bias imposed by selectively inherited mitochondria.
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Affiliation(s)
- Julia Döhla
- Institute of Biotechnology, HiLIFE, University of Helsinki, Helsinki, Finland
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | - Emilia Kuuluvainen
- Institute of Biotechnology, HiLIFE, University of Helsinki, Helsinki, Finland
| | - Nadja Gebert
- Leibniz Institute on Aging-Fritz Lipmann Institute (FLI), Jena, Germany
| | - Ana Amaral
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | - Johanna I Englund
- Institute of Biotechnology, HiLIFE, University of Helsinki, Helsinki, Finland
| | | | - Svetlana Konovalova
- Stem Cells and Metabolism Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Anni I Nieminen
- Institute of Biotechnology, HiLIFE, University of Helsinki, Helsinki, Finland
- Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - Ella S Salminen
- Institute of Biotechnology, HiLIFE, University of Helsinki, Helsinki, Finland
| | - Rubén Torregrosa Muñumer
- Stem Cells and Metabolism Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Kati Ahlqvist
- Institute of Biotechnology, HiLIFE, University of Helsinki, Helsinki, Finland
| | - Yang Yang
- Stem Cells and Metabolism Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Hien Bui
- Institute of Biotechnology, HiLIFE, University of Helsinki, Helsinki, Finland
| | - Timo Otonkoski
- Stem Cells and Metabolism Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Reijo Käkelä
- Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - Ville Hietakangas
- Institute of Biotechnology, HiLIFE, University of Helsinki, Helsinki, Finland
- Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - Henna Tyynismaa
- Stem Cells and Metabolism Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Neuroscience Center, HiLIFE, University of Helsinki, Helsinki, Finland
| | - Alessandro Ori
- Leibniz Institute on Aging-Fritz Lipmann Institute (FLI), Jena, Germany
| | - Pekka Katajisto
- Institute of Biotechnology, HiLIFE, University of Helsinki, Helsinki, Finland.
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden.
- Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland.
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28
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Keuenhof KS, Larsson Berglund L, Malmgren Hill S, Schneider KL, Widlund PO, Nyström T, Höög JL. Large organellar changes occur during mild heat shock in yeast. J Cell Sci 2021; 135:271806. [PMID: 34378783 PMCID: PMC8403982 DOI: 10.1242/jcs.258325] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Accepted: 06/25/2021] [Indexed: 12/14/2022] Open
Abstract
When the temperature is increased, the heat-shock response is activated to protect the cellular environment. The transcriptomics and proteomics of this process are intensively studied, while information about how the cell responds structurally to heat stress is mostly lacking. Here, Saccharomyces cerevisiae were subjected to a mild continuous heat shock (38°C) and intermittently cryo-immobilised for electron microscopy. Through measuring changes in all distinguishable organelle numbers, sizes and morphologies in over 2100 electron micrographs, a major restructuring of the internal architecture of the cell during the progressive heat shock was revealed. The cell grew larger but most organelles within it expanded even more, shrinking the volume of the cytoplasm. Organelles responded to heat shock at different times, both in terms of size and number, and adaptations of the morphology of some organelles (such as the vacuole) were observed. Multivesicular bodies grew by almost 70%, indicating a previously unknown involvement in the heat-shock response. A previously undescribed electron-translucent structure accumulated close to the plasma membrane. This all-encompassing approach provides a detailed chronological progression of organelle adaptation throughout the cellular heat-stress response.
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Affiliation(s)
- Katharina S Keuenhof
- Department for Chemistry and Molecular Biology, University of Gothenburg, Gothenburg 41390, Sweden
| | - Lisa Larsson Berglund
- Department for Chemistry and Molecular Biology, University of Gothenburg, Gothenburg 41390, Sweden.,Department of Microbiology and Immunology, The Sahlgrenska Academy at the University of Gothenburg, Gothenburg 41390, Sweden
| | - Sandra Malmgren Hill
- Department of Psychiatry and Neurochemistry, Institute of Neuroscience and Physiology, The Sahlgrenska Academy at the University of Gothenburg, Gothenburg 41390, Sweden.,Department of Medical Genetics, Cambridge Institute for Medical Research, Cambridge CB2 0XY, UK
| | - Kara L Schneider
- Department of Microbiology and Immunology, The Sahlgrenska Academy at the University of Gothenburg, Gothenburg 41390, Sweden
| | - Per O Widlund
- Department of Microbiology and Immunology, The Sahlgrenska Academy at the University of Gothenburg, Gothenburg 41390, Sweden
| | - Thomas Nyström
- Department of Microbiology and Immunology, The Sahlgrenska Academy at the University of Gothenburg, Gothenburg 41390, Sweden
| | - Johanna L Höög
- Department for Chemistry and Molecular Biology, University of Gothenburg, Gothenburg 41390, Sweden
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29
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Lopez-Crisosto C, Díaz-Vegas A, Castro PF, Rothermel BA, Bravo-Sagua R, Lavandero S. Endoplasmic reticulum-mitochondria coupling increases during doxycycline-induced mitochondrial stress in HeLa cells. Cell Death Dis 2021; 12:657. [PMID: 34183648 PMCID: PMC8238934 DOI: 10.1038/s41419-021-03945-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Revised: 06/16/2021] [Accepted: 06/16/2021] [Indexed: 02/06/2023]
Abstract
Subcellular organelles communicate with each other to regulate function and coordinate responses to changing cellular conditions. The physical-functional coupling of the endoplasmic reticulum (ER) with mitochondria allows for the direct transfer of Ca2+ between organelles and is an important avenue for rapidly increasing mitochondrial metabolic activity. As such, increasing ER-mitochondrial coupling can boost the generation of ATP that is needed to restore homeostasis in the face of cellular stress. The mitochondrial unfolded protein response (mtUPR) is activated by the accumulation of unfolded proteins in mitochondria. Retrograde signaling from mitochondria to the nucleus promotes mtUPR transcriptional responses aimed at restoring protein homeostasis. It is currently unknown whether the changes in mitochondrial-ER coupling also play a role during mtUPR stress. We hypothesized that mitochondrial stress favors an expansion of functional contacts between mitochondria and ER, thereby increasing mitochondrial metabolism as part of a protective response. Hela cells were treated with doxycycline, an antibiotic that inhibits the translation of mitochondrial-encoded proteins to create protein disequilibrium. Treatment with doxycycline decreased the abundance of mitochondrial encoded proteins while increasing expression of CHOP, C/EBPβ, ClpP, and mtHsp60, markers of the mtUPR. There was no change in either mitophagic activity or cell viability. Furthermore, ER UPR was not activated, suggesting focused activation of the mtUPR. Within 2 h of doxycycline treatment, there was a significant increase in physical contacts between mitochondria and ER that was distributed throughout the cell, along with an increase in the kinetics of mitochondrial Ca2+ uptake. This was followed by the rise in the rate of oxygen consumption at 4 h, indicating a boost in mitochondrial metabolic activity. In conclusion, an early phase of the response to doxycycline-induced mitochondrial stress is an increase in mitochondrial-ER coupling that potentiates mitochondrial metabolic activity as a means to support subsequent steps in the mtUPR pathway and sustain cellular adaptation.
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Affiliation(s)
- Camila Lopez-Crisosto
- Advanced Center for Chronic Diseases (ACCDiS), Facultad de Ciencias Químicas y Farmaceuticas & Facultad de Medicina, Universidad de Chile, Santiago, Chile
- Advanced Center for Chronic Diseases (ACCDiS), Facultad de Medicina, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Alexis Díaz-Vegas
- Charles Perkins Centre, School of Life and Environmental Sciences, The University of Sydney, Camperdown, 2050, Sydney, NSW, Australia
| | - Pablo F Castro
- Advanced Center for Chronic Diseases (ACCDiS), Facultad de Medicina, Pontificia Universidad Católica de Chile, Santiago, Chile
- Corporacion Centro de Estudios Científicos de las Enfermedades Cronicas (CECEC), Santiago, 7680201, Chile
| | - Beverly A Rothermel
- Department of Internal Medicine (Cardiology Division), University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Roberto Bravo-Sagua
- Advanced Center for Chronic Diseases (ACCDiS), Facultad de Ciencias Químicas y Farmaceuticas & Facultad de Medicina, Universidad de Chile, Santiago, Chile
- Instituto de Nutrición y Tecnología de los Alimentos (INTA), Universidad de Chile, Santiago, 7830490, Chile
- Chilean State Universities Network on Aging, Universidad de Chile, Santiago, Chile
| | - Sergio Lavandero
- Advanced Center for Chronic Diseases (ACCDiS), Facultad de Ciencias Químicas y Farmaceuticas & Facultad de Medicina, Universidad de Chile, Santiago, Chile.
- Corporacion Centro de Estudios Científicos de las Enfermedades Cronicas (CECEC), Santiago, 7680201, Chile.
- Department of Internal Medicine (Cardiology Division), University of Texas Southwestern Medical Center, Dallas, TX, USA.
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30
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Chang J, Ge Y, Wu Z, Du Y, Pan K, Yang G, Ren Y, Heino MP, Mao F, Cheong KH, Qu Z, Fan X, Min Y, Peng C, Meyerson LA. Modern cities modelled as "super-cells" rather than multicellular organisms: Implications for industry, goods and services. Bioessays 2021; 43:e2100041. [PMID: 34085302 DOI: 10.1002/bies.202100041] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Revised: 04/10/2021] [Accepted: 04/16/2021] [Indexed: 11/06/2022]
Abstract
The structure and "metabolism" (movement and conversion of goods and energy) of urban areas has caused cities to be identified as "super-organisms", placed between ecosystems and the biosphere, in the hierarchy of living systems. Yet most such analogies are weak, and render the super-organism model ineffective for sustainable development of cities. Via a cluster analysis of 15 shared traits of the hierarchical living system, we found that industrialized cities are more similar to eukaryotic cells than to multicellular organisms; enclosed systems, such as factories and greenhouses, paralleling organelles in eukaryotic cells. We further developed a "super-cell" industrialized city model: a "eukarcity" with citynucleus (urban area) as a regulating centre, and organaras (enclosed systems, which provide the majority of goods and services) as the functional components, and cityplasm (natural ecosystems and farmlands) as the matrix. This model may improve the vitality and sustainability of cities through planning and management.
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Affiliation(s)
- Jie Chang
- College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Ying Ge
- College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Zhaoping Wu
- College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Yuanyuan Du
- College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Kaixuan Pan
- College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Guofu Yang
- College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Yuan Ren
- College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Mikko P Heino
- Department of Biological Sciences, University of Bergen, Bergen, Norway
| | - Feng Mao
- School of Earth and Environmental Sciences, Cardiff University, Cardiff, UK
| | - Kang Hao Cheong
- Science, Mathematics and Technology Cluster, Singapore University of Technology and Design (SUTD), Singapore.,SUTD-Massachusetts Institute of Technology International Design Centre, Singapore
| | - Zelong Qu
- College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Xing Fan
- College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Yong Min
- College of Computer Science and Technology, Zhejiang University of Technology, Hangzhou, China
| | - Changhui Peng
- Center of CEF/ESCER, Department of Biological Sciences, University of Quebec at Montreal, Quebec, Montreal, Canada
| | - Laura A Meyerson
- Natural Resources Science, University of Rhode Island, Kingston, Rhode Island, USA
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31
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Lakpa KL, Khan N, Afghah Z, Chen X, Geiger JD. Lysosomal Stress Response (LSR): Physiological Importance and Pathological Relevance. J Neuroimmune Pharmacol 2021; 16:219-237. [PMID: 33751445 PMCID: PMC8099033 DOI: 10.1007/s11481-021-09990-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Accepted: 03/08/2021] [Indexed: 02/08/2023]
Abstract
Extensive work has characterized endoplasmic reticulum (ER) and mitochondrial stress responses. In contrast, very little has been published about stress responses in lysosomes; subcellular acidic organelles that are physiologically important and are of pathological relevance. The greater lysosomal system is dynamic and is comprised of endosomes, lysosomes, multivesicular bodies, autophagosomes, and autophagolysosomes. They are important regulators of cellular physiology, they represent about 5% of the total cellular volume, they are heterogeneous in their sizes and distribution patterns, they are electron dense, and their subcellular positioning within cells varies in response to stimuli, insults and pH. These organelles are also integral to the pathogenesis of lysosomal storage diseases and it is increasingly recognized that lysosomes play important roles in the pathogenesis of such diverse conditions as neurodegenerative disorders and cancer. The purpose of this review is to focus attention on lysosomal stress responses (LSR), compare LSR with better characterized stress responses in ER and mitochondria, and form a framework for future characterizations of LSR. We synthesized data into the concept of LSR and present it here such that the definition of LSR can be modified as new knowledge is added and specific therapeutics are developed.
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Affiliation(s)
- Koffi L Lakpa
- Department of Biomedical Sciences, Dakota School of Medicine and Health Sciences, University of North, Grand Forks, ND, 58203, USA
| | - Nabab Khan
- Department of Biomedical Sciences, Dakota School of Medicine and Health Sciences, University of North, Grand Forks, ND, 58203, USA
| | - Zahra Afghah
- Department of Biomedical Sciences, Dakota School of Medicine and Health Sciences, University of North, Grand Forks, ND, 58203, USA
| | - Xuesong Chen
- Department of Biomedical Sciences, Dakota School of Medicine and Health Sciences, University of North, Grand Forks, ND, 58203, USA
| | - Jonathan D Geiger
- Department of Biomedical Sciences, Dakota School of Medicine and Health Sciences, University of North, Grand Forks, ND, 58203, USA.
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32
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Patergnani S, Marchi S, Delprat B, Wieckowski MR. Editorial: Organelles Relationships and Interactions: A Cancer Perspective. Front Cell Dev Biol 2021; 9:678307. [PMID: 33898471 PMCID: PMC8060626 DOI: 10.3389/fcell.2021.678307] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Accepted: 03/15/2021] [Indexed: 11/22/2022] Open
Affiliation(s)
- Simone Patergnani
- Section of Experimental Medicine, Laboratory for Technologies of Advanced Therapies (LTTA), Department of Medical Sciences, University of Ferrara, Ferrara, Italy
| | - Saverio Marchi
- Department of Clinical and Molecular Sciences, Marche Polytechnic University, Ancona, Italy
| | | | - Mariusz R Wieckowski
- Laboratory of Mitochondrial Biology and Metabolism, Nencki Institute of Experimental Biology of the Polish Academy of Sciences, Warsaw, Poland
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33
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Abstract
Our cells are comprised of billions of proteins, lipids, and other small molecules packed into their respective subcellular organelles, with the daunting task of maintaining cellular homeostasis over a lifetime. However, it is becoming increasingly evident that organelles do not act as autonomous discrete units but rather as interconnected hubs that engage in extensive communication through membrane contacts. In the last few years, our understanding of how these contacts coordinate organelle function has redefined our view of the cell. This review aims to present novel findings on the cellular interorganelle communication network and how its dysfunction may contribute to aging and neurodegeneration. The consequences of disturbed interorganellar communication are intimately linked with age-related pathologies. Given that both aging and neurodegenerative diseases are characterized by the concomitant failure of multiple cellular pathways, coordination of organelle communication and function could represent an emerging regulatory mechanism critical for long-term cellular homeostasis. We anticipate that defining the relationships between interorganelle communication, aging, and neurodegeneration will open new avenues for therapeutics.
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Affiliation(s)
- Maja Petkovic
- Department of Physiology, University of California at San Francisco, San Francisco, California 94158, USA
| | - Caitlin E O'Brien
- Howard Hughes Medical Institute, University of California at San Francisco, San Francisco, California 94158, USA
| | - Yuh Nung Jan
- Department of Physiology, University of California at San Francisco, San Francisco, California 94158, USA
- Howard Hughes Medical Institute, University of California at San Francisco, San Francisco, California 94158, USA
- Department of Biochemistry and Biophysics, University of California at San Francisco, San Francisco, California 94158, USA
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34
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Wang Z, Wang X, Zhang Y, Xu W, Han X. Principles and Applications of Single Particle Tracking in Cell Research. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2021; 17:e2005133. [PMID: 33533163 DOI: 10.1002/smll.202005133] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Revised: 11/24/2020] [Indexed: 06/12/2023]
Abstract
It is a tough challenge for many decades to decipher the complex relationships between cell behaviors and cellular physical properties. Single particle tracking (SPT) with high spatial and temporal resolution has been applied extensively in cell research to understand physicochemical properties of cells and their bio-functions by tracking endogenous or exogenous probes. This review describes the fundamental principles of SPT as well as its applications in intracellular mechanics, membrane dynamics, organelles distribution, and processes of internalization and transport. Finally, challenges and future directions of SPT are also discussed.
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Affiliation(s)
- Zhao Wang
- State Key Laboratory of Urban Water Resource and Environment, School of Chemistry and Chemical Engineering, Harbin Institute of Technology, Harbin, 150001, China
| | - Xuejing Wang
- College of Biomedical Engineering and Instrument Science, Zhejiang University, Hangzhou, 310058, China
| | - Ying Zhang
- School of Materials and Chemical Engineering, Heilongjiang Institute of Technology, Harbin, 150027, China
| | - Weili Xu
- State Key Laboratory of Urban Water Resource and Environment, School of Chemistry and Chemical Engineering, Harbin Institute of Technology, Harbin, 150001, China
| | - Xiaojun Han
- State Key Laboratory of Urban Water Resource and Environment, School of Chemistry and Chemical Engineering, Harbin Institute of Technology, Harbin, 150001, China
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35
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MOTS-c is an exercise-induced mitochondrial-encoded regulator of age-dependent physical decline and muscle homeostasis. Nat Commun 2021; 12:470. [PMID: 33473109 PMCID: PMC7817689 DOI: 10.1038/s41467-020-20790-0] [Citation(s) in RCA: 92] [Impact Index Per Article: 30.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2019] [Accepted: 12/18/2020] [Indexed: 12/20/2022] Open
Abstract
Healthy aging can be promoted by enhanced metabolic fitness and physical capacity. Mitochondria are chief metabolic organelles with strong implications in aging that also coordinate broad physiological functions, in part, using peptides that are encoded within their independent genome. However, mitochondrial-encoded factors that actively regulate aging are unknown. Here, we report that mitochondrial-encoded MOTS-c can significantly enhance physical performance in young (2 mo.), middle-age (12 mo.), and old (22 mo.) mice. MOTS-c can regulate (i) nuclear genes, including those related to metabolism and proteostasis, (ii) skeletal muscle metabolism, and (iii) myoblast adaptation to metabolic stress. We provide evidence that late-life (23.5 mo.) initiated intermittent MOTS-c treatment (3x/week) can increase physical capacity and healthspan in mice. In humans, exercise induces endogenous MOTS-c expression in skeletal muscle and in circulation. Our data indicate that aging is regulated by genes encoded in both of our co-evolved mitochondrial and nuclear genomes. Exercise has beneficial effects on metabolism and overall physiologic fitness in aged organisms. Here the authors show that MOTS-c is a mitochondrial-encoded exercise-induced peptide that regulates skeletal muscle metabolism and improves healthspan of older mice.
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36
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Yao Y, Lawrence DA. Susceptibility to COVID-19 in populations with health disparities: Posited involvement of mitochondrial disorder, socioeconomic stress, and pollutants. J Biochem Mol Toxicol 2021; 35:e22626. [PMID: 32905655 PMCID: PMC9340490 DOI: 10.1002/jbt.22626] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Revised: 07/30/2020] [Accepted: 08/25/2020] [Indexed: 12/18/2022]
Abstract
SARS-CoV-2 is a novel betacoronavirus that has caused the global health crisis known as COVID-19. The implications of mitochondrial dysfunction with COVID-19 are discussed as well as deregulated mitochondria and inter-organelle functions as a posited comorbidity enhancing detrimental outcomes. Many environmental chemicals (ECs) and endocrine-disrupting chemicals can do damage to mitochondria and cause mitochondrial dysfunction. During infection, SARS-CoV-2 via its binding target ACE2 and TMPRSS2 can disrupt mitochondrial function. Viral genomic RNA and structural proteins may also affect the normal function of the mitochondria-endoplasmic reticulum-Golgi apparatus. Drugs considered for treatment of COVID-19 should consider effects on organelles including mitochondria functions. Mitochondrial self-balance and clearance via mitophagy are important in SARS-CoV-2 infection, which indicate monitoring and protection of mitochondria against SARS-CoV-2 are important. Mitochondrial metabolomic analysis may provide new indicators of COVID-19 prognosis. A better understanding of the role of mitochondria during SARS-CoV-2 infection may help to improve intervention therapies and better protect mitochondrial disease patients from pathogens as well as people living with poor nutrition and elevated levels of socioeconomic stress and ECs.
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Affiliation(s)
- Yunyi Yao
- Wadsworth Center, New York State Department of Health, Center for Medical Science, Albany, New York
| | - David A Lawrence
- Wadsworth Center, New York State Department of Health, Center for Medical Science, Albany, New York
- Department of Environmental Health Sciences, University at Albany School of Public Health, Rensselaer, New York
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37
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Li W, Zhang S, Yang G. Dynamic organization of intracellular organelle networks. WIREs Mech Dis 2020; 13:e1505. [PMID: 32865347 DOI: 10.1002/wsbm.1505] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Revised: 06/06/2020] [Accepted: 07/09/2020] [Indexed: 01/07/2023]
Abstract
Intracellular organelles are membrane-bound and biochemically distinct compartments constructed to serve specialized functions in eukaryotic cells. Through extensive interactions, they form networks to coordinate and integrate their specialized functions for cell physiology. A fundamental property of these organelle networks is that they constantly undergo dynamic organization via membrane fusion and fission to remodel their internal connections and to mediate direct material exchange between compartments. The dynamic organization not only enables them to serve critical physiological functions adaptively but also differentiates them from many other biological networks such as gene regulatory networks and cell signaling networks. This review examines this fundamental property of the organelle networks from a systems point of view. The focus is exclusively on homotypic networks formed by mitochondria, lysosomes, endosomes, and the endoplasmic reticulum, respectively. First, key mechanisms that drive the dynamic organization of these networks are summarized. Then, several distinct organizational properties of these networks are highlighted. Next, spatial properties of the dynamic organization of these networks are emphasized, and their functional implications are examined. Finally, some representative molecular machineries that mediate the dynamic organization of these networks are surveyed. Overall, the dynamic organization of intracellular organelle networks is emerging as a fundamental and unifying paradigm in the internal organization of eukaryotic cells. This article is categorized under: Metabolic Diseases > Molecular and Cellular Physiology.
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Affiliation(s)
- Wenjing Li
- Laboratory of Computational Biology and Machine Intelligence, School of Artificial Intelligence, University of Chinese Academy of Sciences, Beijing, China.,National Laboratory of Pattern Recognition, Institute of Automation, Chinese Academy of Sciences, Beijing, China
| | - Shuhao Zhang
- Laboratory of Computational Biology and Machine Intelligence, School of Artificial Intelligence, University of Chinese Academy of Sciences, Beijing, China.,National Laboratory of Pattern Recognition, Institute of Automation, Chinese Academy of Sciences, Beijing, China.,College of Life Sciences, Nankai University, Tianjin, China
| | - Ge Yang
- Laboratory of Computational Biology and Machine Intelligence, School of Artificial Intelligence, University of Chinese Academy of Sciences, Beijing, China.,National Laboratory of Pattern Recognition, Institute of Automation, Chinese Academy of Sciences, Beijing, China.,Department of Biomedical Engineering, Carnegie Mellon University, Pittsburgh, Pennsylvania, USA.,Department of Computational Biology, Carnegie Mellon University, Pittsburgh, Pennsylvania, USA
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38
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Ruan L, McNamara JT, Zhang X, Chang ACC, Zhu J, Dong Y, Sun G, Peterson A, Na CH, Li R. Solid-phase inclusion as a mechanism for regulating unfolded proteins in the mitochondrial matrix. SCIENCE ADVANCES 2020; 6:eabc7288. [PMID: 32821848 PMCID: PMC7406381 DOI: 10.1126/sciadv.abc7288] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2020] [Accepted: 06/22/2020] [Indexed: 05/05/2023]
Abstract
Proteostasis declines with age, characterized by the accumulation of unfolded or damaged proteins. Recent studies suggest that proteins constituting pathological inclusions in neurodegenerative diseases also enter and accumulate in mitochondria. How unfolded proteins are managed within mitochondria remains unclear. Here, we found that excessive unfolded proteins in the mitochondrial matrix of yeast cells are consolidated into solid-phase inclusions, which we term deposits of unfolded mitochondrial proteins (DUMP). Formation of DUMP occurs in mitochondria near endoplasmic reticulum-mitochondria contact sites and is regulated by mitochondrial proteins controlling the production of cytidine 5'-diphosphate-diacylglycerol. DUMP formation is age dependent but accelerated by exogenous unfolded proteins. Many enzymes of the tricarboxylic acid cycle were enriched in DUMP. During yeast cell division, DUMP formation is necessary for asymmetric inheritance of damaged mitochondrial proteins between mother and daughter cells. We provide evidence that DUMP-like structures may be induced by excessive unfolded proteins in human cells.
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Affiliation(s)
- Linhao Ruan
- Center for Cell Dynamics and Department of Cell Biology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Biochemistry, Cellular and Molecular Biology (BCMB) Graduate Program, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Joshua T. McNamara
- Center for Cell Dynamics and Department of Cell Biology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Biochemistry, Cellular and Molecular Biology (BCMB) Graduate Program, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Xi Zhang
- Center for Cell Dynamics and Department of Cell Biology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Alexander Chih-Chieh Chang
- Center for Cell Dynamics and Department of Cell Biology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Department of Chemical and Biomolecular Engineering, Whiting School of Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Jin Zhu
- Center for Cell Dynamics and Department of Cell Biology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Yi Dong
- Center for Cell Dynamics and Department of Cell Biology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Immunology Graduate Program, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Gordon Sun
- Center for Cell Dynamics and Department of Cell Biology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Amy Peterson
- Biochemistry, Cellular and Molecular Biology (BCMB) Graduate Program, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Chan Hyun Na
- Department of Neurology, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Rong Li
- Center for Cell Dynamics and Department of Cell Biology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Department of Chemical and Biomolecular Engineering, Whiting School of Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
- Mechanobiology Institute and Department of Biological Science, National University of Singapore, Singapore 117411, Singapore
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Abstract
Species-specific limits to lifespan (lifespan setpoint) determine the life expectancy of any given organism. Whether limiting lifespan provides an evolutionary benefit or is the result of an inevitable decline in fitness remains controversial. The identification of mutations extending lifespan suggests that aging is under genetic control, but the evolutionary driving forces limiting lifespan have not been defined. By examining the impact of lifespan on pathogen spread in a population, we propose that epidemics drive lifespan setpoints' evolution. Shorter lifespan limits infection spread and accelerates pathogen clearance when compared to populations with longer-lived individuals. Limiting longevity is particularly beneficial in the context of zoonotic transmissions, where pathogens must undergo adaptation to a new host. Strikingly, in populations exposed to pathogens, shorter-living variants outcompete individuals with longer lifespans. We submit that infection outbreaks can contribute to control the evolution of species' lifespan setpoints.
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Affiliation(s)
- Peter V Lidsky
- Department of Microbiology and Immunology, University of California, San Francisco, CA 94143-2280
| | - Raul Andino
- Department of Microbiology and Immunology, University of California, San Francisco, CA 94143-2280
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40
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Kohler V, Aufschnaiter A, Büttner S. Closing the Gap: Membrane Contact Sites in the Regulation of Autophagy. Cells 2020; 9:E1184. [PMID: 32397538 PMCID: PMC7290522 DOI: 10.3390/cells9051184] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Revised: 04/29/2020] [Accepted: 05/07/2020] [Indexed: 12/14/2022] Open
Abstract
In all eukaryotic cells, intracellular organization and spatial separation of incompatible biochemical processes is established by individual cellular subcompartments in form of membrane-bound organelles. Virtually all of these organelles are physically connected via membrane contact sites (MCS), allowing interorganellar communication and a functional integration of cellular processes. These MCS coordinate the exchange of diverse metabolites and serve as hubs for lipid synthesis and trafficking. While this of course indirectly impacts on a plethora of biological functions, including autophagy, accumulating evidence shows that MCS can also directly regulate autophagic processes. Here, we focus on the nexus between interorganellar contacts and autophagy in yeast and mammalian cells, highlighting similarities and differences. We discuss MCS connecting the ER to mitochondria or the plasma membrane, crucial for early steps of both selective and non-selective autophagy, the yeast-specific nuclear-vacuolar tethering system and its role in microautophagy, the emerging function of distinct autophagy-related proteins in organellar tethering as well as novel MCS transiently emanating from the growing phagophore and mature autophagosome.
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Affiliation(s)
- Verena Kohler
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, 106 91 Stockholm, Sweden;
| | - Andreas Aufschnaiter
- Department of Biochemistry and Biophysics, Stockholm University, 106 91 Stockholm, Sweden;
| | - Sabrina Büttner
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, 106 91 Stockholm, Sweden;
- Institute of Molecular Biosciences, University of Graz, 8010 Graz, Austria
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41
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Tharyan RG, Annibal A, Schiffer I, Laboy R, Atanassov I, Weber AL, Gerisch B, Antebi A. NFYB-1 regulates mitochondrial function and longevity via lysosomal prosaposin. Nat Metab 2020; 2:387-396. [PMID: 32694663 DOI: 10.1038/s42255-020-0200-2] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Accepted: 03/26/2020] [Indexed: 12/24/2022]
Abstract
Mitochondria are multidimensional organelles whose activities are essential to cellular vitality and organismal longevity, yet underlying regulatory mechanisms spanning these different levels of organization remain elusive1-5. Here we show that Caenorhabditis elegans nuclear transcription factor Y, beta subunit (NFYB-1), a subunit of the NF-Y transcriptional complex6-8, is a crucial regulator of mitochondrial function. Identified in RNA interference (RNAi) screens, NFYB-1 loss leads to perturbed mitochondrial gene expression, reduced oxygen consumption, mitochondrial fragmentation, disruption of mitochondrial stress pathways, decreased mitochondrial cardiolipin levels and abolition of organismal longevity triggered by mitochondrial impairment. Multi-omics analysis reveals that NFYB-1 is a potent repressor of lysosomal prosaposin, a regulator of glycosphingolipid metabolism. Limiting prosaposin expression unexpectedly restores cardiolipin production, mitochondrial function and longevity in the nfyb-1 background. Similarly, cardiolipin supplementation rescues nfyb-1 phenotypes. These findings suggest that the NFYB-1-prosaposin axis coordinates lysosomal to mitochondria signalling via lipid pools to enhance cellular mitochondrial function and organismal health.
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Affiliation(s)
| | - Andrea Annibal
- Max Planck Institute for Biology of Ageing, Cologne, Germany
| | - Isabelle Schiffer
- Max Planck Institute for Biology of Ageing, Cologne, Germany
- CECAD, University of Cologne, Cologne, Germany
| | - Raymond Laboy
- Max Planck Institute for Biology of Ageing, Cologne, Germany
- CECAD, University of Cologne, Cologne, Germany
| | - Ilian Atanassov
- Max Planck Institute for Biology of Ageing, Cologne, Germany
| | | | - Birgit Gerisch
- Max Planck Institute for Biology of Ageing, Cologne, Germany
| | - Adam Antebi
- Max Planck Institute for Biology of Ageing, Cologne, Germany.
- CECAD, University of Cologne, Cologne, Germany.
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42
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Du G, Xiong L, Li X, Zhuo Z, Zhuang X, Yu Z, Wu L, Xiao D, Liu Z, Jie M, Liu X, Luo G, Guo Z, Chen H. Peroxisome Elevation Induces Stem Cell Differentiation and Intestinal Epithelial Repair. Dev Cell 2020; 53:169-184.e11. [PMID: 32243783 DOI: 10.1016/j.devcel.2020.03.002] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Revised: 01/20/2020] [Accepted: 03/03/2020] [Indexed: 02/08/2023]
Abstract
Epithelial-repair-dependent mucosal healing (MH) is associated with a more favorable prognosis for patients with inflammatory bowel disease (IBD). MH is accomplished via repair and regeneration of the intestinal epithelium. However, the mechanism underlying MH is ill defined. We found a striking upregulation of peroxisomes in the injured crypts of IBD patients. By increasing peroxisome levels in Drosophila midguts, we found that peroxisome elevation enhanced RAB7-dependent late endosome maturation, which then promoted stem and/or progenitor-cell differentiation via modulation of Janus Kinase (JAK) and Signal Transducer and Activator of Transcription (STAT)-SOX21A signaling. This in turn enhanced ISC-mediated regeneration. Importantly, RAB7 and SOX21 were upregulated in the crypts of IBD patients. Moreover, administration of drugs that increased peroxisome levels reversed the symptoms of dextran sulfate sodium (DSS)-induced colitis in mice. This study demonstrates a peroxisome-mediated epithelial repair mechanism, which opens a therapeutic avenue for the enhancement of MH in IBD patients.
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Affiliation(s)
- Gang Du
- Key Laboratory of Gene Engineering of the Ministry of Education, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, Guangdong, China; Laboratory for Stem Cell and anti-Aging Research, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu 610041, Sichuan, China
| | - Lishou Xiong
- Department of Gastroenterology and Hepatology, the First Affiliated Hospital of Sun Yat-sen University, Guangzhou 510080, China
| | - Xiaorong Li
- Key Laboratory of Gene Engineering of the Ministry of Education, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, Guangdong, China
| | - Zhangpeng Zhuo
- Key Laboratory of Gene Engineering of the Ministry of Education, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, Guangdong, China
| | - Xiaojun Zhuang
- Department of Gastroenterology and Hepatology, the First Affiliated Hospital of Sun Yat-sen University, Guangzhou 510080, China
| | - Zihua Yu
- Key Laboratory of Gene Engineering of the Ministry of Education, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, Guangdong, China
| | - Lijian Wu
- Key Laboratory of Gene Engineering of the Ministry of Education, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, Guangdong, China
| | - Danqing Xiao
- Key Laboratory of Gene Engineering of the Ministry of Education, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, Guangdong, China
| | - Zhiming Liu
- Laboratory for Stem Cell and anti-Aging Research, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu 610041, Sichuan, China
| | - Minwen Jie
- Key Laboratory of Gene Engineering of the Ministry of Education, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, Guangdong, China
| | - Xuehong Liu
- Key Laboratory of Gene Engineering of the Ministry of Education, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, Guangdong, China
| | - Guanzheng Luo
- Key Laboratory of Gene Engineering of the Ministry of Education, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, Guangdong, China
| | - Zheng Guo
- Department of Medical Genetics, School of Basic Medicine, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Haiyang Chen
- Key Laboratory of Gene Engineering of the Ministry of Education, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, Guangdong, China; Laboratory for Stem Cell and anti-Aging Research, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu 610041, Sichuan, China.
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43
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Crane MM, Chen KL, Blue BW, Kaeberlein M. Trajectories of Aging: How Systems Biology in Yeast Can Illuminate Mechanisms of Personalized Aging. Proteomics 2020; 20:e1800420. [PMID: 31385433 PMCID: PMC7000301 DOI: 10.1002/pmic.201800420] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Revised: 07/02/2019] [Indexed: 02/02/2023]
Abstract
All organisms age, but the extent to which all organisms age the same way remains a fundamental unanswered question in biology. Across species, it is now clear that at least some aspects of aging are highly conserved and are perhaps universal, but other mechanisms of aging are private to individual species or sets of closely related species. Within the same species, however, it has generally been assumed that the molecular mechanisms of aging are largely invariant from one individual to the next. With the development of new tools for studying aging at the individual cell level in budding yeast, recent data has called this assumption into question. There is emerging evidence that individual yeast mother cells may undergo fundamentally different trajectories of aging. Individual trajectories of aging are difficult to study by traditional population level assays, but through the application of systems biology approaches combined with novel microfluidic technologies, it is now possible to observe and study these phenomena in real time. Understanding the spectrum of mechanisms that determine how different individuals age is a necessary step toward the goal of personalized geroscience, where healthy longevity is optimized for each individual.
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Affiliation(s)
- Matthew M Crane
- Department of Pathology, School of Medicine, University of Washington, Seattle, WA, USA
| | - Kenneth L Chen
- Department of Pathology, School of Medicine, University of Washington, Seattle, WA, USA,Department of Genome Sciences, University of Washington, Seattle, WA, USA,Medical Scientist Training Program, University of Washington, Seattle, WA, USA
| | - Ben W. Blue
- Department of Pathology, School of Medicine, University of Washington, Seattle, WA, USA
| | - Matt Kaeberlein
- Department of Pathology, School of Medicine, University of Washington, Seattle, WA, USA,Department of Genome Sciences, University of Washington, Seattle, WA, USA
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44
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Heine KB, Hood WR. Mitochondrial behaviour, morphology, and animal performance. Biol Rev Camb Philos Soc 2020; 95:730-737. [PMID: 32022456 DOI: 10.1111/brv.12584] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2019] [Revised: 01/10/2020] [Accepted: 01/14/2020] [Indexed: 12/14/2022]
Abstract
We have a limited understanding of the proximate mechanisms that are responsible for the development of variation in animal performance and life-history strategies. Provided that components of an organism's successful life history - for example, mate competition, gestation, lactation, etc. - are energetically demanding, increased energy production within mitochondria is likely the foundation from which organisms are able to perform these tasks. Mitochondrial behaviour (positioning within the cell and communication between mitochondria) and morphology affect variation in energy production at the molecular, cellular, and organismal levels. Therefore, adaptations in mitochondrial behaviour and morphology that favour efficient energy production likely influence variation in animal performance. Previous work has linked greater proportions of inter-mitochondrial junctions and density of the inner mitochondrial membrane, among other traits, with increased energetic demand. Future research should focus on how inter-mitochondrial junctions and morphology of the inner mitochondrial membrane, in particular, influence animal performance in accordance with mitochondrial density, fission, and fusion.
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Affiliation(s)
- Kyle B Heine
- Department of Biological Sciences, Auburn University, 101 Rouse Life Sciences Building, Auburn, AL, 36849, U.S.A
| | - Wendy R Hood
- Department of Biological Sciences, Auburn University, 101 Rouse Life Sciences Building, Auburn, AL, 36849, U.S.A
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45
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Wesley CC, Mishra S, Levy DL. Organelle size scaling over embryonic development. WILEY INTERDISCIPLINARY REVIEWS-DEVELOPMENTAL BIOLOGY 2020; 9:e376. [PMID: 32003549 DOI: 10.1002/wdev.376] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Revised: 12/19/2019] [Accepted: 01/08/2020] [Indexed: 12/13/2022]
Abstract
Cell division without growth results in progressive cell size reductions during early embryonic development. How do the sizes of intracellular structures and organelles scale with cell size and what are the functional implications of such scaling relationships? Model organisms, in particular Caenorhabditis elegans worms, Drosophila melanogaster flies, Xenopus laevis frogs, and Mus musculus mice, have provided insights into developmental size scaling of the nucleus, mitotic spindle, and chromosomes. Nuclear size is regulated by nucleocytoplasmic transport, nuclear envelope proteins, and the cytoskeleton. Regulators of microtubule dynamics and chromatin compaction modulate spindle and mitotic chromosome size scaling, respectively. Developmental scaling relationships for membrane-bound organelles, like the endoplasmic reticulum, Golgi, mitochondria, and lysosomes, have been less studied, although new imaging approaches promise to rectify this deficiency. While models that invoke limiting components and dynamic regulation of assembly and disassembly can account for some size scaling relationships in early embryos, it will be exciting to investigate the contribution of newer concepts in cell biology such as phase separation and interorganellar contacts. With a growing understanding of the underlying mechanisms of organelle size scaling, future studies promise to uncover the significance of proper scaling for cell function and embryonic development, as well as how aberrant scaling contributes to disease. This article is categorized under: Establishment of Spatial and Temporal Patterns > Regulation of Size, Proportion, and Timing Early Embryonic Development > Fertilization to Gastrulation Comparative Development and Evolution > Model Systems.
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Affiliation(s)
- Chase C Wesley
- Department of Molecular Biology, University of Wyoming, Laramie, Wyoming
| | - Sampada Mishra
- Department of Molecular Biology, University of Wyoming, Laramie, Wyoming
| | - Daniel L Levy
- Department of Molecular Biology, University of Wyoming, Laramie, Wyoming
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46
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Mondino S, Schmidt S, Rolando M, Escoll P, Gomez-Valero L, Buchrieser C. Legionnaires’ Disease: State of the Art Knowledge of Pathogenesis Mechanisms of Legionella. ANNUAL REVIEW OF PATHOLOGY-MECHANISMS OF DISEASE 2020; 15:439-466. [DOI: 10.1146/annurev-pathmechdis-012419-032742] [Citation(s) in RCA: 72] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Legionella species are environmental gram-negative bacteria able to cause a severe form of pneumonia in humans known as Legionnaires’ disease. Since the identification of Legionella pneumophila in 1977, four decades of research on Legionella biology and Legionnaires’ disease have brought important insights into the biology of the bacteria and the molecular mechanisms that these intracellular pathogens use to cause disease in humans. Nowadays, Legionella species constitute a remarkable model of bacterial adaptation, with a genus genome shaped by their close coevolution with amoebae and an ability to exploit many hosts and signaling pathways through the secretion of a myriad of effector proteins, many of which have a eukaryotic origin. This review aims to discuss current knowledge of Legionella infection mechanisms and future research directions to be taken that might answer the many remaining open questions. This research will without a doubt be a terrific scientific journey worth taking.
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Affiliation(s)
- Sonia Mondino
- Institut Pasteur, Biologie des Bactéries Intracellulaires, CNRS UMR 3525, 75015 Paris, France;, , , , ,
| | - Silke Schmidt
- Institut Pasteur, Biologie des Bactéries Intracellulaires, CNRS UMR 3525, 75015 Paris, France;, , , , ,
- Sorbonne Université, Collège doctoral, 75005 Paris, France
| | - Monica Rolando
- Institut Pasteur, Biologie des Bactéries Intracellulaires, CNRS UMR 3525, 75015 Paris, France;, , , , ,
| | - Pedro Escoll
- Institut Pasteur, Biologie des Bactéries Intracellulaires, CNRS UMR 3525, 75015 Paris, France;, , , , ,
| | - Laura Gomez-Valero
- Institut Pasteur, Biologie des Bactéries Intracellulaires, CNRS UMR 3525, 75015 Paris, France;, , , , ,
| | - Carmen Buchrieser
- Institut Pasteur, Biologie des Bactéries Intracellulaires, CNRS UMR 3525, 75015 Paris, France;, , , , ,
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47
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Waller TC, Berg JA, Lex A, Chapman BE, Rutter J. Compartment and hub definitions tune metabolic networks for metabolomic interpretations. Gigascience 2020; 9:giz137. [PMID: 31972021 PMCID: PMC6977586 DOI: 10.1093/gigascience/giz137] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2018] [Revised: 08/31/2019] [Accepted: 10/27/2019] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Metabolic networks represent all chemical reactions that occur between molecular metabolites in an organism's cells. They offer biological context in which to integrate, analyze, and interpret omic measurements, but their large scale and extensive connectivity present unique challenges. While it is practical to simplify these networks by placing constraints on compartments and hubs, it is unclear how these simplifications alter the structure of metabolic networks and the interpretation of metabolomic experiments. RESULTS We curated and adapted the latest systemic model of human metabolism and developed customizable tools to define metabolic networks with and without compartmentalization in subcellular organelles and with or without inclusion of prolific metabolite hubs. Compartmentalization made networks larger, less dense, and more modular, whereas hubs made networks larger, more dense, and less modular. When present, these hubs also dominated shortest paths in the network, yet their exclusion exposed the subtler prominence of other metabolites that are typically more relevant to metabolomic experiments. We applied the non-compartmental network without metabolite hubs in a retrospective, exploratory analysis of metabolomic measurements from 5 studies on human tissues. Network clusters identified individual reactions that might experience differential regulation between experimental conditions, several of which were not apparent in the original publications. CONCLUSIONS Exclusion of specific metabolite hubs exposes modularity in both compartmental and non-compartmental metabolic networks, improving detection of relevant clusters in omic measurements. Better computational detection of metabolic network clusters in large data sets has potential to identify differential regulation of individual genes, transcripts, and proteins.
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Affiliation(s)
- T Cameron Waller
- Division of Medical Genetics, Department of Medicine, School of Medicine, University of California San Diego, Room 1318A, 9500 Gilman Drive #0606, La Jolla, California 92093-0606, United States of America
- Department of Biochemistry, School of Medicine, University of Utah, Room 4100, 15 North Medical Drive East, Salt Lake City, Utah 84112, USA
| | - Jordan A Berg
- Department of Biochemistry, School of Medicine, University of Utah, Room 4100, 15 North Medical Drive East, Salt Lake City, Utah 84112, USA
| | - Alexander Lex
- School of Computing, University of Utah, Room 3190, 50 South Central Campus Drive, Salt Lake City, Utah 84112, USA
- Scientific Computing and Imaging Institute, University of Utah, Room 3750, 72 South Central Campus Drive, Salt Lake City, Utah 84112, USA
| | - Brian E Chapman
- Department of Radiology and Imaging Sciences, School of Medicine, University of Utah, Room 1A071, 30 North 1900 East, Salt Lake City, Utah 84132, USA
- Department of Biomedical Informatics, School of Medicine, University of Utah, Suite 140, 421 Wakara Way, Salt Lake City, Utah 84108, USA
| | - Jared Rutter
- Department of Biochemistry, School of Medicine, University of Utah, Room 4100, 15 North Medical Drive East, Salt Lake City, Utah 84112, USA
- Howard Hughes Medical Institute, School of Medicine, University of Utah, Room AC101, 30 North 1900 East, Salt Lake City, Utah 84132, USA
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Ba Q, Raghavan G, Kiselyov K, Yang G. Whole-Cell Scale Dynamic Organization of Lysosomes Revealed by Spatial Statistical Analysis. Cell Rep 2019; 23:3591-3606. [PMID: 29925001 DOI: 10.1016/j.celrep.2018.05.079] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2017] [Revised: 04/14/2018] [Accepted: 05/23/2018] [Indexed: 01/22/2023] Open
Abstract
In eukaryotic cells, lysosomes are distributed in the cytoplasm as individual membrane-bound compartments to degrade macromolecules and to control cellular metabolism. A fundamental yet unanswered question is whether and, if so, how individual lysosomes are organized spatially to coordinate and integrate their functions. To address this question, we analyzed their collective behavior in cultured cells using spatial statistical techniques. We found that in single cells, lysosomes maintain non-random, stable, yet distinct spatial distributions mediated by the cytoskeleton, the endoplasmic reticulum (ER), and lysosomal biogenesis. Throughout the intracellular space, lysosomes form dynamic clusters that significantly increase their interactions with endosomes. Cluster formation is associated with local increases in ER spatial density but does not depend on fusion with endosomes or spatial exclusion by mitochondria. Taken together, our findings reveal whole-cell scale spatial organization of lysosomes and provide insights into how organelle interactions are mediated and regulated across the entire intracellular space.
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Affiliation(s)
- Qinle Ba
- Department of Biomedical Engineering, Carnegie Mellon University, Pittsburgh, PA 15213, USA
| | - Guruprasad Raghavan
- Department of Biomedical Engineering, Carnegie Mellon University, Pittsburgh, PA 15213, USA
| | - Kirill Kiselyov
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Ge Yang
- Department of Biomedical Engineering, Carnegie Mellon University, Pittsburgh, PA 15213, USA; Department of Computational Biology, Carnegie Mellon University, Pittsburgh, PA 15213, USA.
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49
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Crane MM, Russell AE, Schafer BJ, Blue BW, Whalen R, Almazan J, Hong MG, Nguyen B, Goings JE, Chen KL, Kelly R, Kaeberlein M. DNA damage checkpoint activation impairs chromatin homeostasis and promotes mitotic catastrophe during aging. eLife 2019; 8:e50778. [PMID: 31714209 PMCID: PMC6850777 DOI: 10.7554/elife.50778] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Accepted: 10/30/2019] [Indexed: 02/01/2023] Open
Abstract
Genome instability is a hallmark of aging and contributes to age-related disorders such as cancer and Alzheimer's disease. The accumulation of DNA damage during aging has been linked to altered cell cycle dynamics and the failure of cell cycle checkpoints. Here, we use single cell imaging to study the consequences of increased genomic instability during aging in budding yeast and identify striking age-associated genome missegregation events. This breakdown in mitotic fidelity results from the age-related activation of the DNA damage checkpoint and the resulting degradation of histone proteins. Disrupting the ability of cells to degrade histones in response to DNA damage increases replicative lifespan and reduces genomic missegregations. We present several lines of evidence supporting a model of antagonistic pleiotropy in the DNA damage response where histone degradation, and limited histone transcription are beneficial to respond rapidly to damage but reduce lifespan and genomic stability in the long term.
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Affiliation(s)
- Matthew M Crane
- Department of PathologyUniversity of WashingtonSeattleUnited States
| | - Adam E Russell
- Department of PathologyUniversity of WashingtonSeattleUnited States
| | - Brent J Schafer
- Department of PathologyUniversity of WashingtonSeattleUnited States
| | - Ben W Blue
- Department of PathologyUniversity of WashingtonSeattleUnited States
| | - Riley Whalen
- Department of PathologyUniversity of WashingtonSeattleUnited States
| | - Jared Almazan
- Department of PathologyUniversity of WashingtonSeattleUnited States
| | - Mung Gi Hong
- Department of PathologyUniversity of WashingtonSeattleUnited States
| | - Bao Nguyen
- Department of PathologyUniversity of WashingtonSeattleUnited States
| | - Joslyn E Goings
- Department of PathologyUniversity of WashingtonSeattleUnited States
| | - Kenneth L Chen
- Department of PathologyUniversity of WashingtonSeattleUnited States
- Department of Genome SciencesUniversity of WashingtonSeattleUnited States
- Medical Scientist Training ProgramUniversity of WashingtonSeattleUnited States
| | - Ryan Kelly
- Department of PathologyUniversity of WashingtonSeattleUnited States
| | - Matt Kaeberlein
- Department of PathologyUniversity of WashingtonSeattleUnited States
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50
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Andréasson C, Ott M, Büttner S. Mitochondria orchestrate proteostatic and metabolic stress responses. EMBO Rep 2019; 20:e47865. [PMID: 31531937 PMCID: PMC6776902 DOI: 10.15252/embr.201947865] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Revised: 05/13/2019] [Accepted: 08/27/2019] [Indexed: 01/06/2023] Open
Abstract
The eukaryotic cell is morphologically and functionally organized as an interconnected network of organelles that responds to stress and aging. Organelles communicate via dedicated signal transduction pathways and the transfer of information in form of metabolites and energy levels. Recent data suggest that the communication between organellar proteostasis systems is a cornerstone of cellular stress responses in eukaryotic cells. Here, we discuss the integration of proteostasis and energy fluxes in the regulation of cellular stress and aging. We emphasize the molecular architecture of the regulatory transcriptional pathways that both sense and control metabolism and proteostasis. A special focus is placed on mechanistic insights gained from the model organism budding yeast in signaling from mitochondria to the nucleus and how this shapes cellular fitness.
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Affiliation(s)
- Claes Andréasson
- Department of Molecular BiosciencesThe Wenner‐Gren InstituteStockholm UniversityStockholmSweden
| | - Martin Ott
- Department of Biochemistry and BiophysicsStockholm UniversityStockholmSweden
| | - Sabrina Büttner
- Department of Molecular BiosciencesThe Wenner‐Gren InstituteStockholm UniversityStockholmSweden
- Institute of Molecular BiosciencesUniversity of GrazGrazAustria
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