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Gomez-Pinilla F, Thapak P. Exercise epigenetics is fueled by cell bioenergetics: Supporting role on brain plasticity and cognition. Free Radic Biol Med 2024; 220:43-55. [PMID: 38677488 PMCID: PMC11144461 DOI: 10.1016/j.freeradbiomed.2024.04.237] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Revised: 04/04/2024] [Accepted: 04/24/2024] [Indexed: 04/29/2024]
Abstract
Exercise has the unique aptitude to benefit overall health of body and brain. Evidence indicates that the effects of exercise can be saved in the epigenome for considerable time to elevate the threshold for various diseases. The action of exercise on epigenetic regulation seems central to building an "epigenetic memory" to influence long-term brain function and behavior. As an intrinsic bioenergetic process, exercise engages the function of the mitochondria and redox pathways to impinge upon molecular mechanisms that regulate synaptic plasticity and learning and memory. We discuss how the action of exercise uses mechanisms of bioenergetics to support a "epigenetic memory" with long-term implications for neural and behavioral plasticity. This information is crucial for directing the power of exercise to reduce the burden of neurological and psychiatric disorders.
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Affiliation(s)
- Fernando Gomez-Pinilla
- Department of Integrative Biology and Physiology, University of California, Los Angeles, Los Angeles, CA, 90095, USA; Department of Neurosurgery, UCLA Brain Injury Research Center, University of California, Los Angeles, Los Angeles, CA, 90095, USA.
| | - Pavan Thapak
- Department of Integrative Biology and Physiology, University of California, Los Angeles, Los Angeles, CA, 90095, USA
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2
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Raghuram N, Hughes AL. Amino acids trigger MDC-dependent mitochondrial remodeling by altering mitochondrial function. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.09.602707. [PMID: 39026767 PMCID: PMC11257621 DOI: 10.1101/2024.07.09.602707] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/20/2024]
Abstract
Cells utilize numerous pathways to maintain mitochondrial homeostasis, including a recently identified mechanism that adjusts the content of the outer mitochondrial membrane (OMM) through formation of OMM-derived multilamellar domains called mitochondrial-derived compartments, or MDCs. MDCs are triggered by perturbations in mitochondrial lipid and protein content, as well as increases in intracellular amino acids. Here, we sought to understand how amino acids trigger MDCs. We show that amino acid-activation of MDCs is dependent on the functional state of mitochondria. While amino acid excess triggers MDC formation when cells are grown on fermentable carbon sources, stimulating mitochondrial biogenesis blocks MDC formation. Moreover, amino acid elevation depletes TCA cycle metabolites in yeast, and preventing consumption of TCA cycle intermediates for amino acid catabolism suppresses MDC formation. Finally, we show that directly impairing the TCA cycle is sufficient to trigger MDC formation in the absence of amino acid stress. These results demonstrate that amino acids stimulate MDC formation by perturbing mitochondrial metabolism.
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Affiliation(s)
- Nidhi Raghuram
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - Adam L. Hughes
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
- Lead Contact
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3
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Garrigós V, Vallejo B, Mollà-Martí E, Picazo C, Peltier E, Marullo P, Matallana E, Aranda A. Up-regulation of Retrograde Response in yeast increases glycerol and reduces ethanol during wine fermentation. J Biotechnol 2024; 390:28-38. [PMID: 38768686 DOI: 10.1016/j.jbiotec.2024.05.007] [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: 01/30/2024] [Revised: 05/13/2024] [Accepted: 05/15/2024] [Indexed: 05/22/2024]
Abstract
Nutrient signaling pathways play a pivotal role in regulating the balance among metabolism, growth and stress response depending on the available food supply. They are key factors for the biotechnological success of the yeast Saccharomyces cerevisiae during food-producing fermentations. One such pathway is Retrograde Response, which controls the alpha-ketoglutarate supply required for the synthesis of amino acids like glutamate and lysine. Repressor MKS1 is linked with the TORC1 complex and negatively regulates this pathway. Deleting MKS1 from a variety of industrial strains causes glycerol to increase during winemaking, brewing and baking. This increase is accompanied by a reduction in ethanol production during grape juice fermentation in four commercial wine strains. Interestingly, this does not lead volatile acidity to increase because acetic acid levels actually lower. Aeration during winemaking usually increases acetic acid levels, but this effect reduces in the MKS1 mutant. Despite the improvement in the metabolites of oenological interest, it comes at a cost given that the mutant shows slower fermentation kinetics when grown in grape juice, malt and laboratory media and using glucose, sucrose and maltose as carbon sources. The deletion of RTG2, an activator of Retrograde Response that acts as an antagonist of MKS1, also results in a defect in wine fermentation speed. These findings suggest that the deregulation of this pathway causes a fitness defect. Therefore, manipulating repressor MKS1 is a promising approach to modulate yeast metabolism and to produce low-ethanol drinks.
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Affiliation(s)
- Víctor Garrigós
- Institute for Integrative Systems Biology, Universitat de València-CSIC, Spain
| | - Beatriz Vallejo
- Institute for Integrative Systems Biology, Universitat de València-CSIC, Spain
| | | | - Cecilia Picazo
- Institute for Integrative Systems Biology, Universitat de València-CSIC, Spain
| | - Emilien Peltier
- Université de Bordeaux, Unité de Recherche Œnologie INRAE, Bordeaux INP, ISVV, France
| | - Philippe Marullo
- Université de Bordeaux, Unité de Recherche Œnologie INRAE, Bordeaux INP, ISVV, France; Biolaffort, France
| | - Emilia Matallana
- Institute for Integrative Systems Biology, Universitat de València-CSIC, Spain
| | - Agustín Aranda
- Institute for Integrative Systems Biology, Universitat de València-CSIC, Spain.
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4
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Flynn MJ, Harper NW, Li R, Zhu LJ, Lee MJ, Benanti JA. Calcineurin promotes adaptation to chronic stress through two distinct mechanisms. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.19.585797. [PMID: 38562881 PMCID: PMC10983906 DOI: 10.1101/2024.03.19.585797] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Adaptation to environmental stress requires coordination between stress-defense programs and cell cycle progression. The immediate response to many stressors has been well characterized, but how cells survive in challenging environments long-term is unknown. Here, we investigate the role of the stress-activated phosphatase calcineurin (CN) in adaptation to chronic CaCl2 stress in Saccharomyces cerevisiae. We find that prolonged exposure to CaCl2 impairs mitochondrial function and demonstrate that cells respond to this stressor using two CN-dependent mechanisms - one that requires the downstream transcription factor Crz1 and another that is Crz1-independent. Our data indicate that CN maintains cellular fitness by promoting cell cycle progression and preventing CaCl2-induced cell death. When Crz1 is present, transient CN activation suppresses cell death and promotes adaptation despite high levels of mitochondrial loss. However, in the absence of Crz1, prolonged activation of CN prevents mitochondrial loss and further cell death by upregulating glutathione (GSH) biosynthesis genes thereby mitigating damage from reactive oxygen species. These findings illustrate how cells maintain long-term fitness during chronic stress and suggest that CN promotes adaptation in challenging environments by multiple mechanisms.
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Affiliation(s)
- Mackenzie J Flynn
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Chan Medical School, Worcester, MA 01605
- Interdisciplinary Graduate Program, Morningside Graduate School of Biomedical Sciences, University of Massachusetts Chan Medical School, Worcester, MA 01605
| | - Nicholas W Harper
- Interdisciplinary Graduate Program, Morningside Graduate School of Biomedical Sciences, University of Massachusetts Chan Medical School, Worcester, MA 01605
- Department of Systems Biology, University of Massachusetts Chan Medical School, Worcester, MA 01605
| | - Rui Li
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Chan Medical School, Worcester, MA 01605
| | - Lihua Julie Zhu
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Chan Medical School, Worcester, MA 01605
- Department of Genomics and Computational Biology, University of Massachusetts Chan Medical School, Worcester MA 01605
- Program in Molecular Medicine, University of Massachusetts Chan Medical School, Worcester MA 01605
| | - Michael J Lee
- Department of Systems Biology, University of Massachusetts Chan Medical School, Worcester, MA 01605
| | - Jennifer A Benanti
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Chan Medical School, Worcester, MA 01605
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5
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Kim S, Ramalho TR, Haynes CM. Regulation of proteostasis and innate immunity via mitochondria-nuclear communication. J Cell Biol 2024; 223:e202310005. [PMID: 38335010 PMCID: PMC10857905 DOI: 10.1083/jcb.202310005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Revised: 01/29/2024] [Accepted: 01/30/2024] [Indexed: 02/10/2024] Open
Abstract
Mitochondria are perhaps best known as the "powerhouse of the cell" for their role in ATP production required for numerous cellular activities. Mitochondria have emerged as an important signaling organelle. Here, we first focus on signaling pathways mediated by mitochondria-nuclear communication that promote protein homeostasis (proteostasis). We examine the mitochondrial unfolded protein response (UPRmt) in C. elegans, which is regulated by a transcription factor harboring both a mitochondrial- and nuclear-targeting sequence, the integrated stress response in mammals, as well as the regulation of chromatin by mitochondrial metabolites. In the second section, we explore the role of mitochondria-to-nuclear communication in the regulation of innate immunity and inflammation. Perhaps related to their prokaryotic origin, mitochondria harbor molecules also found in viruses and bacteria. If these molecules accumulate in the cytosol, they elicit the same innate immune responses as viral or bacterial infection.
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Affiliation(s)
- Sookyung Kim
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Theresa R. Ramalho
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Cole M. Haynes
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Chan Medical School, Worcester, MA, USA
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6
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Min SH, Kang GM, Park JW, Kim MS. Beneficial Effects of Low-Grade Mitochondrial Stress on Metabolic Diseases and Aging. Yonsei Med J 2024; 65:55-69. [PMID: 38288646 PMCID: PMC10827639 DOI: 10.3349/ymj.2023.0131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Revised: 11/07/2023] [Accepted: 12/04/2023] [Indexed: 02/01/2024] Open
Abstract
Mitochondria function as platforms for bioenergetics, nutrient metabolism, intracellular signaling, innate immunity regulators, and modulators of stem cell activity. Thus, the decline in mitochondrial functions causes or correlates with diabetes mellitus and many aging-related diseases. Upon stress or damage, the mitochondria elicit a series of adaptive responses to overcome stress and restore their structural integrity and functional homeostasis. These adaptive responses to low-level or transient mitochondrial stress promote health and resilience to upcoming stress. Beneficial effects of low-grade mitochondrial stress, termed mitohormesis, have been observed in various organisms, including mammals. Accumulated evidence indicates that treatments boosting mitohormesis have therapeutic potential in various human diseases accompanied by mitochondrial stress. Here, we review multiple cellular signaling pathways and interorgan communication mechanisms through which mitochondrial stress leads to advantageous outcomes. We also discuss the relevance of mitohormesis in obesity, diabetes, metabolic liver disease, aging, and exercise.
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Affiliation(s)
- Se Hee Min
- Division of Endocrinology and Metabolism, Department of Internal Medicine, Diabetes Center, Asan Medical Center and University of Ulsan College of Medicine, Seoul, Korea
- Appetite Regulation Laboratory, Asan Institute for Life Science, Seoul, Korea
| | - Gil Myoung Kang
- Appetite Regulation Laboratory, Asan Institute for Life Science, Seoul, Korea
| | - Jae Woo Park
- Appetite Regulation Laboratory, Asan Institute for Life Science, Seoul, Korea
| | - Min-Seon Kim
- Division of Endocrinology and Metabolism, Department of Internal Medicine, Diabetes Center, Asan Medical Center and University of Ulsan College of Medicine, Seoul, Korea
- Appetite Regulation Laboratory, Asan Institute for Life Science, Seoul, Korea.
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7
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Ouyang Y, Jeong MY, Cunningham CN, Berg JA, Toshniwal AG, Hughes CE, Seiler K, Van Vranken JG, Cluntun AA, Lam G, Winter JM, Akdogan E, Dove KK, Nowinski SM, West M, Odorizzi G, Gygi SP, Dunn CD, Winge DR, Rutter J. Phosphate starvation signaling increases mitochondrial membrane potential through respiration-independent mechanisms. eLife 2024; 13:e84282. [PMID: 38251707 PMCID: PMC10846858 DOI: 10.7554/elife.84282] [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: 10/18/2022] [Accepted: 01/19/2024] [Indexed: 01/23/2024] Open
Abstract
Mitochondrial membrane potential directly powers many critical functions of mitochondria, including ATP production, mitochondrial protein import, and metabolite transport. Its loss is a cardinal feature of aging and mitochondrial diseases, and cells closely monitor membrane potential as an indicator of mitochondrial health. Given its central importance, it is logical that cells would modulate mitochondrial membrane potential in response to demand and environmental cues, but there has been little exploration of this question. We report that loss of the Sit4 protein phosphatase in yeast increases mitochondrial membrane potential, both by inducing the electron transport chain and the phosphate starvation response. Indeed, a similarly elevated mitochondrial membrane potential is also elicited simply by phosphate starvation or by abrogation of the Pho85-dependent phosphate sensing pathway. This enhanced membrane potential is primarily driven by an unexpected activity of the ADP/ATP carrier. We also demonstrate that this connection between phosphate limitation and enhancement of mitochondrial membrane potential is observed in primary and immortalized mammalian cells as well as in Drosophila. These data suggest that mitochondrial membrane potential is subject to environmental stimuli and intracellular signaling regulation and raise the possibility for therapeutic enhancement of mitochondrial function even in defective mitochondria.
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Affiliation(s)
- Yeyun Ouyang
- Department of Biochemistry, The University of UtahSalt Lake CityUnited States
| | - Mi-Young Jeong
- Department of Biochemistry, The University of UtahSalt Lake CityUnited States
| | - Corey N Cunningham
- Department of Biochemistry, The University of UtahSalt Lake CityUnited States
| | - Jordan A Berg
- Department of Biochemistry, The University of UtahSalt Lake CityUnited States
| | - Ashish G Toshniwal
- Department of Biochemistry, The University of UtahSalt Lake CityUnited States
| | - Casey E Hughes
- Department of Biochemistry, The University of UtahSalt Lake CityUnited States
| | - Kristina Seiler
- Department of Biochemistry, The University of UtahSalt Lake CityUnited States
| | | | - Ahmad A Cluntun
- Department of Biochemistry, The University of UtahSalt Lake CityUnited States
| | - Geanette Lam
- Department of Biochemistry, The University of UtahSalt Lake CityUnited States
| | - Jacob M Winter
- Department of Biochemistry, The University of UtahSalt Lake CityUnited States
| | - Emel Akdogan
- Department of Molecular Biology and Genetics, Koç UniversityİstanbulTurkey
| | - Katja K Dove
- Department of Biochemistry, The University of UtahSalt Lake CityUnited States
| | - Sara M Nowinski
- Department of Biochemistry, The University of UtahSalt Lake CityUnited States
| | - Matthew West
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado, BoulderBoulderUnited States
| | - Greg Odorizzi
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado, BoulderBoulderUnited States
| | - Steven P Gygi
- Department of Cell Biology, Harvard University School of MedicineBostonUnited States
| | - Cory D Dunn
- Department of Molecular Biology and Genetics, Koç UniversityİstanbulTurkey
- Institute of Biotechnology, University of HelsinkiHelsinkiFinland
| | - Dennis R Winge
- Department of Biochemistry, The University of UtahSalt Lake CityUnited States
- Department of Medicine, The University of UtahSalt Lake CityUnited States
| | - Jared Rutter
- Department of Biochemistry, The University of UtahSalt Lake CityUnited States
- Howard Hughes Medical Institute, University of UtahSalt Lake CityUnited States
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8
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Bui THD, Labedzka-Dmoch K. RetroGREAT signaling: The lessons we learn from yeast. IUBMB Life 2024; 76:26-37. [PMID: 37565710 DOI: 10.1002/iub.2775] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Accepted: 07/13/2023] [Indexed: 08/12/2023]
Abstract
The mitochondrial retrograde signaling (RTG) pathway of communication from mitochondria to the nucleus was first studied in yeast Saccharomyces cerevisiae. It rewires cellular metabolism according to the mitochondrial state by reprogramming nuclear gene expression in response to mitochondrial triggers. The main players involved in retrograde signaling are the Rtg1 and Rtg3 transcription factors, and a set of positive and negative regulators, including the Rtg2, Mks1, Lst8, and Bmh1/2 proteins. Retrograde regulation is integrated with other processes, including stress response, osmoregulation, and nutrient sensing through functional crosstalk with cellular pathways such as high osmolarity glycerol or target of rapamycin signaling. In this review, we summarize metabolic changes observed upon retrograde stimulation and analyze the progress made to uncover the mechanisms underlying the integration of regulatory circuits. Comparisons of the evolutionary adaptations of the retrograde pathway that have occurred in the different yeast groups can help to fully understand the process.
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Affiliation(s)
- Thi Hoang Diu Bui
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Karolina Labedzka-Dmoch
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Warsaw, Poland
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9
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Gorospe CM, Carvalho G, Herrera Curbelo A, Marchhart L, Mendes IC, Niedźwiecka K, Wanrooij PH. Mitochondrial membrane potential acts as a retrograde signal to regulate cell cycle progression. Life Sci Alliance 2023; 6:e202302091. [PMID: 37696576 PMCID: PMC10494934 DOI: 10.26508/lsa.202302091] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Revised: 08/29/2023] [Accepted: 08/30/2023] [Indexed: 09/13/2023] Open
Abstract
Mitochondria are central to numerous metabolic pathways whereby mitochondrial dysfunction has a profound impact and can manifest in disease. The consequences of mitochondrial dysfunction can be ameliorated by adaptive responses that rely on crosstalk from the mitochondria to the rest of the cell. Such mito-cellular signalling slows cell cycle progression in mitochondrial DNA-deficient (ρ0) Saccharomyces cerevisiae cells, but the initial trigger of the response has not been thoroughly studied. Here, we show that decreased mitochondrial membrane potential (ΔΨm) acts as the initial signal of mitochondrial stress that delays G1-to-S phase transition in both ρ0 and control cells containing mtDNA. Accordingly, experimentally increasing ΔΨm was sufficient to restore timely cell cycle progression in ρ0 cells. In contrast, cellular levels of oxidative stress did not correlate with the G1-to-S delay. Restored G1-to-S transition in ρ0 cells with a recovered ΔΨm is likely attributable to larger cell size, whereas the timing of G1/S transcription remained delayed. The identification of ΔΨm as a regulator of cell cycle progression may have implications for disease states involving mitochondrial dysfunction.
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Affiliation(s)
- Choco Michael Gorospe
- https://ror.org/05kb8h459 Department of Medical Biochemistry and Biophysics, Umeå University, Umeå, Sweden
| | - Gustavo Carvalho
- https://ror.org/05kb8h459 Department of Medical Biochemistry and Biophysics, Umeå University, Umeå, Sweden
| | - Alicia Herrera Curbelo
- https://ror.org/05kb8h459 Department of Medical Biochemistry and Biophysics, Umeå University, Umeå, Sweden
| | - Lisa Marchhart
- https://ror.org/05kb8h459 Department of Medical Biochemistry and Biophysics, Umeå University, Umeå, Sweden
| | - Isabela C Mendes
- https://ror.org/05kb8h459 Department of Medical Biochemistry and Biophysics, Umeå University, Umeå, Sweden
| | - Katarzyna Niedźwiecka
- https://ror.org/05kb8h459 Department of Medical Biochemistry and Biophysics, Umeå University, Umeå, Sweden
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Paulina H Wanrooij
- https://ror.org/05kb8h459 Department of Medical Biochemistry and Biophysics, Umeå University, Umeå, Sweden
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10
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Azbarova AV, Knorre DA. Role of Mitochondrial DNA in Yeast Replicative Aging. BIOCHEMISTRY. BIOKHIMIIA 2023; 88:1997-2006. [PMID: 38462446 DOI: 10.1134/s0006297923120040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Revised: 11/13/2023] [Accepted: 11/15/2023] [Indexed: 03/12/2024]
Abstract
Despite the diverse manifestations of aging across different species, some common aging features and underlying mechanisms are shared. In particular, mitochondria appear to be among the most vulnerable systems in both metazoa and fungi. In this review, we discuss how mitochondrial dysfunction is related to replicative aging in the simplest eukaryotic model, the baker's yeast Saccharomyces cerevisiae. We discuss a chain of events that starts from asymmetric distribution of mitochondria between mother and daughter cells. With age, yeast mother cells start to experience a decrease in mitochondrial transmembrane potential and, consequently, a decrease in mitochondrial protein import efficiency. This induces mitochondrial protein precursors in the cytoplasm, the loss of mitochondrial DNA (mtDNA), and at the later stages - cell death. Interestingly, yeast strains without mtDNA can have either increased or decreased lifespan compared to the parental strains with mtDNA. The direction of the effect depends on their ability to activate compensatory mechanisms preventing or mitigating negative consequences of mitochondrial dysfunction. The central role of mitochondria in yeast aging and death indicates that it is one of the most complex and, therefore, deregulation-prone systems in eukaryotic cells.
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Affiliation(s)
- Aglaia V Azbarova
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119991, Russia
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, 119991, Russia
| | - Dmitry A Knorre
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119991, Russia.
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11
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Capps D, Hunter A, Chiang M, Pracheil T, Liu Z. Ubiquitin-Conjugating Enzymes Ubc1 and Ubc4 Mediate the Turnover of Hap4, a Master Regulator of Mitochondrial Biogenesis in Saccharomyces cerevisiae. Microorganisms 2022; 10:microorganisms10122370. [PMID: 36557625 PMCID: PMC9787919 DOI: 10.3390/microorganisms10122370] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Revised: 11/21/2022] [Accepted: 11/26/2022] [Indexed: 12/05/2022] Open
Abstract
Mitochondrial biogenesis is tightly regulated in response to extracellular and intracellular signals, thereby adapting yeast cells to changes in their environment. The Hap2/3/4/5 complex is a master transcriptional regulator of mitochondrial biogenesis in yeast. Hap4 is the regulatory subunit of the complex and exhibits increased expression when the Hap2/3/4/5 complex is activated. In cells grown under glucose derepression conditions, both the HAP4 transcript level and Hap4 protein level are increased. As part of an inter-organellar signaling mechanism coordinating gene expression between the mitochondrial and nuclear genomes, the activity of the Hap2/3/4/5 complex is reduced in respiratory-deficient cells, such as ρ0 cells lacking mitochondrial DNA, as a result of reduced Hap4 protein levels. However, the underlying mechanism is unclear. Here, we show that reduced HAP4 expression in ρ0 cells is mediated through both transcriptional and post-transcriptional mechanisms. We show that loss of mitochondrial DNA increases the turnover of Hap4, which requires the 26S proteasome and ubiquitin-conjugating enzymes Ubc1 and Ubc4. Stabilization of Hap4 in the ubc1 ubc4 double mutant leads to increased expression of Hap2/3/4/5-target genes. Our results indicate that mitochondrial biogenesis in yeast is regulated by the functional state of mitochondria partly through ubiquitin/proteasome-dependent turnover of Hap4.
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12
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Liu S, Liu S, Jiang H. Multifaceted roles of mitochondrial stress responses under ETC dysfunction - repair, destruction and pathogenesis. FEBS J 2022; 289:6994-7013. [PMID: 34918460 DOI: 10.1111/febs.16323] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 12/08/2021] [Accepted: 12/15/2021] [Indexed: 01/13/2023]
Abstract
Electron transport chain (ETC) dysfunction is a common feature of mitochondrial diseases and induces severe cellular stresses, including mitochondrial membrane potential (Δψm ) reduction, mitochondrial matrix acidification, metabolic derangements and proteostatic stresses. Extensive studies of ETC dysfunction in yeast, Caenorhabditis elegans, cultured cells and mouse models have revealed multiple mitochondrial stress response pathways. Here, we summarise the current understanding of the triggers, sensors, signalling mechanisms and the functional outcomes of mitochondrial stress responses in different species. We highlight Δψm reduction as a major trigger of stress responses in different species, but the responses are species-specific and the outcomes are context-dependent. ETC dysfunction elicits a mitochondrial unfolded protein response (UPRmt ) to repair damaged mitochondria in C. elegans, and activates a global adaptive programme to maintain Δψm in yeast. Yeast and C. elegans responses are remarkably similar at the downstream responses, although they are activated by different signalling mechanisms. UPRmt generally protects ETC-defective worms, but its constitutive activation is toxic for wildtype worms and worms carrying mutant mtDNA. In contrast to lower organisms, ETC dysfunction in mammals mainly activates a mitochondrial integrated stress response (ISRmt ) to reprogramme metabolism and a PINK1-Parkin mitophagy pathway to degrade damaged mitochondria. Accumulating in vivo results suggest that the ATF4 branch of ISRmt exacerbates metabolic derangements to accelerate mitochondrial disease progression. The in vivo roles of mitophagy in mitochondrial diseases are also context-dependent. These results thus reveal the common and unique aspects of mitochondrial stress responses in different species and highlight their multifaceted roles in mitochondrial diseases.
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Affiliation(s)
- Shanshan Liu
- National Institute of Biological Sciences, Beijing, China.,Beijing Key Laboratory of Cell Biology for Animal Aging, China.,Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing, China
| | - Siqi Liu
- National Institute of Biological Sciences, Beijing, China.,Beijing Key Laboratory of Cell Biology for Animal Aging, China.,Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing, China
| | - Hui Jiang
- National Institute of Biological Sciences, Beijing, China.,Beijing Key Laboratory of Cell Biology for Animal Aging, China.,Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing, China
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13
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A High-Quality Genome Assembly of the Mitochondrial Genome of the Oil-Tea Tree Camellia gigantocarpa (Theaceae). DIVERSITY 2022. [DOI: 10.3390/d14100850] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Camellia gigantocarpa is one of the oil-tea trees whose seeds can be used to extract high-quality vegetable oil. To date, there are no data on the mitochondrial genome of the oil-tea tree, in contrast to the tea-tree C. sinensis, which belongs to the same genus. In this paper, we present the first complete mitochondrial genomes of C. gigantocarpa obtained using PacBio Hi-Fi (high-fidelity) and Hi-C sequencing technologies to anchor the 970,410 bp genome assembly into a single sequence. A set of 44 protein-coding genes, 22 non-coding genes, 746 simple sequence repeats (SSRs), and more than 201 kb of repetitive sequences were annotated in the genome assembly. The high percentage of repetitive sequences in the mitochondrial genome of C. gigantocarpa (20.81%) and C.sinensis (22.15%, tea tree) compared to Arabidopsis thaliana (4.96%) significantly increased the mitogenome size in the genus Camellia. The comparison of the mitochondrial genomes between C. gigantocarpa and C. sinensis revealed genes exhibit high variance in gene order and low substitution rate within the genus Camellia. Information on the mitochondrial genome provides a better understanding of the structure and evolution of the genome in Camellia and may contribute to further study of the after-ripening process of oil-tea trees.
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14
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Stenberg S, Li J, Gjuvsland AB, Persson K, Demitz-Helin E, González Peña C, Yue JX, Gilchrist C, Ärengård T, Ghiaci P, Larsson-Berghund L, Zackrisson M, Smits S, Hallin J, Höög JL, Molin M, Liti G, Omholt SW, Warringer J. Genetically controlled mtDNA deletions prevent ROS damage by arresting oxidative phosphorylation. eLife 2022; 11:76095. [PMID: 35801695 PMCID: PMC9427111 DOI: 10.7554/elife.76095] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Accepted: 07/07/2022] [Indexed: 11/15/2022] Open
Abstract
Deletion of mitochondrial DNA in eukaryotes is currently attributed to rare accidental events associated with mitochondrial replication or repair of double-strand breaks. We report the discovery that yeast cells arrest harmful intramitochondrial superoxide production by shutting down respiration through genetically controlled deletion of mitochondrial oxidative phosphorylation genes. We show that this process critically involves the antioxidant enzyme superoxide dismutase 2 and two-way mitochondrial-nuclear communication through Rtg2 and Rtg3. While mitochondrial DNA homeostasis is rapidly restored after cessation of a short-term superoxide stress, long-term stress causes maladaptive persistence of the deletion process, leading to complete annihilation of the cellular pool of intact mitochondrial genomes and irrevocable loss of respiratory ability. This shows that oxidative stress-induced mitochondrial impairment may be under strict regulatory control. If the results extend to human cells, the results may prove to be of etiological as well as therapeutic importance with regard to age-related mitochondrial impairment and disease.
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Affiliation(s)
- Simon Stenberg
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Jing Li
- State Key Laboratory of Oncology in South China, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Arne B Gjuvsland
- Department of Animal and Aquacultural Sciences, Norwegian University of Life Sciences, Ås, Norway
| | - Karl Persson
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Erik Demitz-Helin
- Department of Chemistry and Molecular Biology, University of Gothenburg, erikdemitzhelin, Sweden
| | - Carles González Peña
- Department of Chemistry and Molecular Biology, University of Gothenburg, Argentona, Spain
| | - Jia-Xing Yue
- State Key Laboratory of Oncology in South China, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Ciaran Gilchrist
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Timmy Ärengård
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Payam Ghiaci
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Lisa Larsson-Berghund
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Martin Zackrisson
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Silvana Smits
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Johan Hallin
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Johanna L Höög
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Mikael Molin
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Gianni Liti
- Institute for Research on Cancer and Aging, Université Côte d'Azur, CNRS, INSERM, IRCAN, Nice, France
| | - Stig W Omholt
- Department of Animal and Aquacultural Sciences, Norwegian University of Life Sciences, Ås, Norway
| | - Jonas Warringer
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
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15
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Costanza A, Guaragnella N, Bobba A, Manzari C, L'Abbate A, Giudice CL, Picardi E, D'Erchia AM, Pesole G, Giannattasio S. Yeast as a Model to Unravel New BRCA2 Functions in Cell Metabolism. Front Oncol 2022; 12:908442. [PMID: 35734584 PMCID: PMC9207209 DOI: 10.3389/fonc.2022.908442] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Accepted: 05/06/2022] [Indexed: 11/13/2022] Open
Abstract
Mutations in BRCA2 gene increase the risk for breast cancer and for other cancer types, including pancreatic and prostate cancer. Since its first identification as an oncosupressor in 1995, the best-characterized function of BRCA2 is in the repair of DNA double-strand breaks (DSBs) by homologous recombination. BRCA2 directly interacts with both RAD51 and single-stranded DNA, mediating loading of RAD51 recombinase to sites of single-stranded DNA. In the absence of an efficient homologous recombination pathway, DSBs accumulate resulting in genome instability, thus supporting tumorigenesis. Yet the precise mechanism by which BRCA2 exerts its tumor suppressor function remains unclear. BRCA2 has also been involved in other biological functions including protection of telomere integrity and stalled replication forks, cell cycle progression, transcriptional control and mitophagy. Recently, we and others have reported a role of BRCA2 in modulating cell death programs through a molecular mechanism conserved in yeast and mammals. Here we hypothesize that BRCA2 is a multifunctional protein which exerts specific functions depending on cell stress response pathway. Based on a differential RNA sequencing analysis carried out on yeast cells either growing or undergoing a regulated cell death process, either in the absence or in the presence of BRCA2, we suggest that BRCA2 causes central carbon metabolism reprogramming in response to death stimuli and encourage further investigation on the role of metabolic reprogramming in BRCA2 oncosuppressive function.
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Affiliation(s)
- Alessandra Costanza
- Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, National Research Council, Bari, Italy
| | - Nicoletta Guaragnella
- Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, National Research Council, Bari, Italy.,Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari "Aldo Moro", Bari, Italy
| | - Antonella Bobba
- Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, National Research Council, Bari, Italy
| | - Caterina Manzari
- Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari "Aldo Moro", Bari, Italy
| | - Alberto L'Abbate
- Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, National Research Council, Bari, Italy
| | - Claudio Lo Giudice
- Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari "Aldo Moro", Bari, Italy
| | - Ernesto Picardi
- Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, National Research Council, Bari, Italy.,Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari "Aldo Moro", Bari, Italy
| | - Anna Maria D'Erchia
- Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, National Research Council, Bari, Italy.,Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari "Aldo Moro", Bari, Italy
| | - Graziano Pesole
- Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, National Research Council, Bari, Italy.,Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari "Aldo Moro", Bari, Italy
| | - Sergio Giannattasio
- Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, National Research Council, Bari, Italy
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16
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Increased peroxisome proliferation is associated with early yeast replicative ageing. Curr Genet 2022; 68:207-225. [DOI: 10.1007/s00294-022-01233-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2021] [Revised: 02/10/2022] [Accepted: 02/11/2022] [Indexed: 11/03/2022]
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17
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Hijazi I, Wang E, Orozco M, Pelton S, Chang A. Peroxisomal support of mitochondrial respiratory efficiency promotes ER stress survival. J Cell Sci 2022; 135:273605. [PMID: 34854901 PMCID: PMC8767275 DOI: 10.1242/jcs.259254] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Accepted: 11/18/2021] [Indexed: 01/12/2023] Open
Abstract
Endoplasmic reticulum stress (ERS) occurs when cellular demand for protein folding exceeds the capacity of the organelle. Adaptation and cell survival in response to ERS requires a critical contribution by mitochondria and peroxisomes. During ERS responses, mitochondrial respiration increases to ameliorate reactive oxygen species (ROS) accumulation. We now show in yeast that peroxisome abundance also increases to promote an adaptive response. In pox1Δ cells, which are defective in peroxisomal β-oxidation of fatty acids, the respiratory response to ERS is impaired and ROS accrues. However, the respiratory response to ERS is rescued and ROS production is mitigated in pox1Δ cells overexpressing Mpc1, the mitochondrial pyruvate carrier that provides another source of acetyl CoA to fuel the tricarboxylic acid cycle and oxidative phosphorylation. Using proteomics, select mitochondrial proteins were identified that undergo upregulation upon ERS to remodel the respiratory machinery. The abundance of several peroxisome-based proteins was also increased, corroborating the role of peroxisomes in ERS adaptation. Finally, ERS stimulates assembly of respiratory complexes into higher-order supercomplexes, underlying increased electron transfer efficiency. Our results highlight peroxisomal and mitochondrial support for ERS adaptation to favor cell survival.
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18
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Li J, Cullis C. The Multipartite Mitochondrial Genome of Marama ( Tylosema esculentum). FRONTIERS IN PLANT SCIENCE 2021; 12:787443. [PMID: 34956284 PMCID: PMC8692981 DOI: 10.3389/fpls.2021.787443] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Accepted: 11/15/2021] [Indexed: 06/14/2023]
Abstract
Tylosema esculentum (marama bean), a wild legume from tropical Africa, has long been considered as a potential crop for local farmers due to its rich nutritional value. Genomics research of marama is indispensable for the domestication and varietal improvement of the bean. The chloroplast genome of marama has been sequenced and assembled previously using a hybrid approach based on both Illumina and PacBio data. In this study, a similar method was used to assemble the mitochondrial genome of marama. The mitochondrial genome of the experimental individual has been confirmed to have two large circles OK638188 and OK638189, which do not recombine according to the data. However, they may be able to restructure into five smaller circles through recombination on the 4 pairs of long repeats (>1 kb). The total length of marama mitogenome is 399,572 bp. A 9,798 bp DNA fragment has been found that is homologous to the chloroplast genome of marama, accounting for 2.5% of the mitogenome. In the Fabaceae family, the mitogenome of Millettia pinnata is highly similar to marama, including for both the genes present and the total size. Some genes including cox2, rpl10, rps1, and sdh4 have been lost during the evolution of angiosperms and are absent in the mitogenomes of some legumes. However, these remain intact and functional in marama. Another set of genes, rpl2, rps2, rps7, rps11, rps13, and rps19 are either absent, or present as pseudogenes, in the mitogenome of marama.
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19
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Vowinckel J, Hartl J, Marx H, Kerick M, Runggatscher K, Keller MA, Mülleder M, Day J, Weber M, Rinnerthaler M, Yu JSL, Aulakh SK, Lehmann A, Mattanovich D, Timmermann B, Zhang N, Dunn CD, MacRae JI, Breitenbach M, Ralser M. The metabolic growth limitations of petite cells lacking the mitochondrial genome. Nat Metab 2021; 3:1521-1535. [PMID: 34799698 PMCID: PMC7612105 DOI: 10.1038/s42255-021-00477-6] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Accepted: 09/10/2021] [Indexed: 12/25/2022]
Abstract
Eukaryotic cells can survive the loss of their mitochondrial genome, but consequently suffer from severe growth defects. 'Petite yeasts', characterized by mitochondrial genome loss, are instrumental for studying mitochondrial function and physiology. However, the molecular cause of their reduced growth rate remains an open question. Here we show that petite cells suffer from an insufficient capacity to synthesize glutamate, glutamine, leucine and arginine, negatively impacting their growth. Using a combination of molecular genetics and omics approaches, we demonstrate the evolution of fast growth overcomes these amino acid deficiencies, by alleviating a perturbation in mitochondrial iron metabolism and by restoring a defect in the mitochondrial tricarboxylic acid cycle, caused by aconitase inhibition. Our results hence explain the slow growth of mitochondrial genome-deficient cells with a partial auxotrophy in four amino acids that results from distorted iron metabolism and an inhibited tricarboxylic acid cycle.
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Affiliation(s)
- Jakob Vowinckel
- Department of Biochemistry and Cambridge Systems Biology Centre, University of Cambridge, Cambridge, UK
- Biognosys AG, Schlieren, Switzerland
| | - Johannes Hartl
- Department of Biochemistry and Cambridge Systems Biology Centre, University of Cambridge, Cambridge, UK
- Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Department of Biochemistry, Berlin, Germany
| | - Hans Marx
- Department of Biotechnology, University of Natural Resources and Life Sciences Vienna, Vienna, Austria
| | - Martin Kerick
- Sequencing Core Facility, Max Planck Institute for Molecular Genetics and Max Planck Unit for the Science of Pathogens, Berlin, Germany
- Institute of Parasitology and Biomedicine 'López-Neyra' (IPBLN, CSIC), Granada, Spain
| | - Kathrin Runggatscher
- Department of Biochemistry and Cambridge Systems Biology Centre, University of Cambridge, Cambridge, UK
| | - Markus A Keller
- Department of Biochemistry and Cambridge Systems Biology Centre, University of Cambridge, Cambridge, UK
- Institute of Human Genetics, Medical University of Innsbruck, Innsbruck, Austria
| | - Michael Mülleder
- Department of Biochemistry and Cambridge Systems Biology Centre, University of Cambridge, Cambridge, UK
- Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Department of Biochemistry, Berlin, Germany
- The Molecular Biology of Metabolism Laboratory, The Francis Crick Institute, London, UK
| | - Jason Day
- Department of Earth Sciences, University of Cambridge, Cambridge, UK
| | - Manuela Weber
- Department of Biosciences, University of Salzburg, Salzburg, Austria
| | - Mark Rinnerthaler
- Department of Biosciences, University of Salzburg, Salzburg, Austria
| | - Jason S L Yu
- The Molecular Biology of Metabolism Laboratory, The Francis Crick Institute, London, UK
| | - Simran Kaur Aulakh
- The Molecular Biology of Metabolism Laboratory, The Francis Crick Institute, London, UK
| | - Andrea Lehmann
- Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Department of Biochemistry, Berlin, Germany
| | - Diethard Mattanovich
- Department of Biotechnology, University of Natural Resources and Life Sciences Vienna, Vienna, Austria
| | - Bernd Timmermann
- Sequencing Core Facility, Max Planck Institute for Molecular Genetics and Max Planck Unit for the Science of Pathogens, Berlin, Germany
| | - Nianshu Zhang
- Department of Biochemistry and Cambridge Systems Biology Centre, University of Cambridge, Cambridge, UK
| | - Cory D Dunn
- Institute of Biotechnology, Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland
- Department of Molecular Biology and Genetics, Koç University, İstanbul, Turkey
| | - James I MacRae
- Metabolomics Laboratory, The Francis Crick Institute, London, UK
| | | | - Markus Ralser
- Department of Biochemistry and Cambridge Systems Biology Centre, University of Cambridge, Cambridge, UK.
- Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Department of Biochemistry, Berlin, Germany.
- The Molecular Biology of Metabolism Laboratory, The Francis Crick Institute, London, UK.
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20
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Plocek V, Fadrhonc K, Maršíková J, Váchová L, Pokorná A, Hlaváček O, Wilkinson D, Palková Z. Mitochondrial Retrograde Signaling Contributes to Metabolic Differentiation in Yeast Colonies. Int J Mol Sci 2021; 22:ijms22115597. [PMID: 34070491 PMCID: PMC8198273 DOI: 10.3390/ijms22115597] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Revised: 05/19/2021] [Accepted: 05/21/2021] [Indexed: 12/16/2022] Open
Abstract
During development of yeast colonies, various cell subpopulations form, which differ in their properties and specifically localize within the structure. Three branches of mitochondrial retrograde (RTG) signaling play a role in colony development and differentiation, each of them activating the production of specific markers in different cell types. Here, aiming to identify proteins and processes controlled by the RTG pathway, we analyzed proteomes of individual cell subpopulations from colonies of strains, mutated in genes of the RTG pathway. Resulting data, along with microscopic analyses revealed that the RTG pathway predominantly regulates processes in U cells, long-lived cells with unique properties, which are localized in upper colony regions. Rtg proteins therein activate processes leading to amino acid biosynthesis, including transport of metabolic intermediates between compartments, but also repress expression of mitochondrial ribosome components, thus possibly contributing to reduced mitochondrial translation in U cells. The results reveal the RTG pathway's role in activating metabolic processes, important in U cell adaptation to altered nutritional conditions. They also point to the important role of Rtg regulators in repressing mitochondrial activity in U cells.
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Affiliation(s)
- Vítězslav Plocek
- Department of Genetics and Microbiology, Faculty of Science, Charles University, BIOCEV, 12800 Prague, Czech Republic; (V.P.); (K.F.); (J.M.); (D.W.)
| | - Kristýna Fadrhonc
- Department of Genetics and Microbiology, Faculty of Science, Charles University, BIOCEV, 12800 Prague, Czech Republic; (V.P.); (K.F.); (J.M.); (D.W.)
| | - Jana Maršíková
- Department of Genetics and Microbiology, Faculty of Science, Charles University, BIOCEV, 12800 Prague, Czech Republic; (V.P.); (K.F.); (J.M.); (D.W.)
| | - Libuše Váchová
- Institute of Microbiology of the Czech Academy of Sciences, BIOCEV, 14220 Prague, Czech Republic; (L.V.); (A.P.); (O.H.)
| | - Alexandra Pokorná
- Institute of Microbiology of the Czech Academy of Sciences, BIOCEV, 14220 Prague, Czech Republic; (L.V.); (A.P.); (O.H.)
| | - Otakar Hlaváček
- Institute of Microbiology of the Czech Academy of Sciences, BIOCEV, 14220 Prague, Czech Republic; (L.V.); (A.P.); (O.H.)
| | - Derek Wilkinson
- Department of Genetics and Microbiology, Faculty of Science, Charles University, BIOCEV, 12800 Prague, Czech Republic; (V.P.); (K.F.); (J.M.); (D.W.)
| | - Zdena Palková
- Department of Genetics and Microbiology, Faculty of Science, Charles University, BIOCEV, 12800 Prague, Czech Republic; (V.P.); (K.F.); (J.M.); (D.W.)
- Correspondence:
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21
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Liu S, Liu S, He B, Li L, Li L, Wang J, Cai T, Chen S, Jiang H. OXPHOS deficiency activates global adaptation pathways to maintain mitochondrial membrane potential. EMBO Rep 2021; 22:e51606. [PMID: 33655635 DOI: 10.15252/embr.202051606] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Revised: 01/18/2021] [Accepted: 01/27/2021] [Indexed: 12/19/2022] Open
Abstract
Reduction of mitochondrial membrane potential (Δψm ) is a hallmark of mitochondrial dysfunction. It activates adaptive responses in organisms from yeast to human to rewire metabolism, remove depolarized mitochondria, and degrade unimported precursor proteins. It remains unclear how cells maintain Δψm , which is critical for maintaining iron-sulfur cluster (ISC) synthesis, an indispensable function of mitochondria. Here, we show that yeast oxidative phosphorylation mutants deficient in complex III, IV, V, and mtDNA, respectively, exhibit activated stress responses and progressive reduction of Δψm . Extensive omics analyses of these mutants show that these mutants progressively activate adaptive responses, including transcriptional downregulation of ATP synthase inhibitor Inh1 and OXPHOS subunits, Puf3-mediated upregulation of import receptor Mia40 and global mitochondrial biogenesis, Snf1/AMPK-mediated upregulation of glycolysis and repression of ribosome biogenesis, and transcriptional upregulation of cytoplasmic chaperones. These adaptations disinhibit mitochondrial ATP hydrolysis, remodel mitochondrial proteome, and optimize ATP supply to mitochondria to convergently maintain Δψm , ISC biosynthesis, and cell proliferation.
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Affiliation(s)
- Siqi Liu
- Graduate School of Peking Union Medical College, Beijing, China.,National Institute of Biological Sciences, Beijing, China.,Beijing Key Laboratory of Cell Biology for Animal Aging, Beijing, China.,Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing, China
| | - Shanshan Liu
- Graduate School of Peking Union Medical College, Beijing, China.,National Institute of Biological Sciences, Beijing, China.,Beijing Key Laboratory of Cell Biology for Animal Aging, Beijing, China.,Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing, China
| | - Baiyu He
- National Institute of Biological Sciences, Beijing, China.,Beijing Key Laboratory of Cell Biology for Animal Aging, Beijing, China.,Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing, China.,College of Biological Sciences, China Agriculture University, Beijing, China
| | - Lanlan Li
- National Institute of Biological Sciences, Beijing, China.,Beijing Key Laboratory of Cell Biology for Animal Aging, Beijing, China.,Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing, China.,College of Life Sciences, Beijing Normal University, Beijing, China
| | - Lin Li
- National Institute of Biological Sciences, Beijing, China.,Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing, China
| | - Jiawen Wang
- National Institute of Biological Sciences, Beijing, China.,Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing, China
| | - Tao Cai
- National Institute of Biological Sciences, Beijing, China.,Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing, China
| | - She Chen
- National Institute of Biological Sciences, Beijing, China.,Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing, China
| | - Hui Jiang
- Graduate School of Peking Union Medical College, Beijing, China.,National Institute of Biological Sciences, Beijing, China.,Beijing Key Laboratory of Cell Biology for Animal Aging, Beijing, China.,Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing, China
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22
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Mutlu B, Puigserver P. GCN5 acetyltransferase in cellular energetic and metabolic processes. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2021; 1864:194626. [PMID: 32827753 PMCID: PMC7854474 DOI: 10.1016/j.bbagrm.2020.194626] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Revised: 07/29/2020] [Accepted: 08/14/2020] [Indexed: 12/23/2022]
Abstract
General Control Non-repressed 5 protein (GCN5), encoded by the mammalian gene Kat2a, is the first histone acetyltransferase discovered to link histone acetylation to transcriptional activation [1]. The enzymatic activity of GCN5 is linked to cellular metabolic and energetic states regulating gene expression programs. GCN5 has a major impact on energy metabolism by i) sensing acetyl-CoA, a central metabolite and substrate of the GCN5 catalytic reaction, and ii) acetylating proteins such as PGC-1α, a transcriptional coactivator that controls genes linked to energy metabolism and mitochondrial biogenesis. PGC-1α is biochemically associated with the GCN5 protein complex during active metabolic reprogramming. In the first part of the review, we examine how metabolism can change GCN5-dependent histone acetylation to regulate gene expression to adapt cells. In the second part, we summarize the GCN5 function as a nutrient sensor, focusing on non-histone protein acetylation, mainly the metabolic role of PGC-1α acetylation across different tissues.
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Affiliation(s)
- Beste Mutlu
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA; Department of Cell Biology, Harvard Medical School, Boston, MA, USA
| | - Pere Puigserver
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA; Department of Cell Biology, Harvard Medical School, Boston, MA, USA.
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23
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Lv XC, Chen M, Huang ZR, Guo WL, Ai LZ, Bai WD, Yu XD, Liu YL, Rao PF, Ni L. Potential mechanisms underlying the ameliorative effect of Lactobacillus paracasei FZU103 on the lipid metabolism in hyperlipidemic mice fed a high-fat diet. Food Res Int 2021; 139:109956. [DOI: 10.1016/j.foodres.2020.109956] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Revised: 11/26/2020] [Accepted: 11/27/2020] [Indexed: 12/12/2022]
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24
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25
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English J, Son JM, Cardamone MD, Lee C, Perissi V. Decoding the rosetta stone of mitonuclear communication. Pharmacol Res 2020; 161:105161. [PMID: 32846213 PMCID: PMC7755734 DOI: 10.1016/j.phrs.2020.105161] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Revised: 08/04/2020] [Accepted: 08/14/2020] [Indexed: 12/12/2022]
Abstract
Cellular homeostasis in eukaryotic cells requires synchronized coordination of multiple organelles. A key role in this stage is played by mitochondria, which have recently emerged as highly interconnected and multifunctional hubs that process and coordinate diverse cellular functions. Beyond producing ATP, mitochondria generate key metabolites and are central to apoptotic and metabolic signaling pathways. Because most mitochondrial proteins are encoded in the nuclear genome, the biogenesis of new mitochondria and the maintenance of mitochondrial functions and flexibility critically depend upon effective mitonuclear communication. This review addresses the complex network of signaling molecules and pathways allowing mitochondria-nuclear communication and coordinated regulation of their independent but interconnected genomes, and discusses the extent to which dynamic communication between the two organelles has evolved for mutual benefit and for the overall maintenance of cellular and organismal fitness.
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Affiliation(s)
- Justin English
- Department of Biochemistry, Boston University, Boston, MA, 02115, USA; Graduate Program in Biomolecular Pharmacology, Department of Pharmacology and Experimental Therapeutics, Boston University, Boston, MA, 02115, USA
| | - Jyung Mean Son
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA 90089, USA
| | | | - Changhan Lee
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA 90089, USA; USC Norris Comprehensive Cancer Center, Los Angeles, CA, 90089, USA; Biomedical Sciences, Graduate School, Ajou University, Suwon, 16499, South Korea
| | - Valentina Perissi
- Department of Biochemistry, Boston University, Boston, MA, 02115, USA.
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26
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Malecki M, Kamrad S, Ralser M, Bähler J. Mitochondrial respiration is required to provide amino acids during fermentative proliferation of fission yeast. EMBO Rep 2020; 21:e50845. [PMID: 32896087 PMCID: PMC7645267 DOI: 10.15252/embr.202050845] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Revised: 07/07/2020] [Accepted: 08/10/2020] [Indexed: 12/21/2022] Open
Abstract
When glucose is available, many organisms repress mitochondrial respiration in favour of aerobic glycolysis, or fermentation in yeast, that suffices for ATP production. Fission yeast cells, however, rely partially on respiration for rapid proliferation under fermentative conditions. Here, we determined the limiting factors that require respiratory function during fermentation. When inhibiting the electron transport chain, supplementation with arginine was necessary and sufficient to restore rapid proliferation. Accordingly, a systematic screen for mutants growing poorly without arginine identified mutants defective in mitochondrial oxidative metabolism. Genetic or pharmacological inhibition of respiration triggered a drop in intracellular levels of arginine and amino acids derived from the Krebs cycle metabolite alpha‐ketoglutarate: glutamine, lysine and glutamic acid. Conversion of arginine into these amino acids was required for rapid proliferation when blocking the respiratory chain. The respiratory block triggered an immediate gene expression response diagnostic of TOR inhibition, which was muted by arginine supplementation or without the AMPK‐activating kinase Ssp1. The TOR‐controlled proteins featured biased composition of amino acids reflecting their shortage after respiratory inhibition. We conclude that respiration supports rapid proliferation in fermenting fission yeast cells by boosting the supply of Krebs cycle‐derived amino acids.
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Affiliation(s)
- Michal Malecki
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Warsaw, Poland.,Institute of Healthy Ageing and Research Department of Genetics, Evolution & Environment, University College London, London, UK
| | - Stephan Kamrad
- Institute of Healthy Ageing and Research Department of Genetics, Evolution & Environment, University College London, London, UK.,Molecular Biology of Metabolism Laboratory, The Francis Crick Institute, London, UK
| | - Markus Ralser
- Molecular Biology of Metabolism Laboratory, The Francis Crick Institute, London, UK
| | - Jürg Bähler
- Institute of Healthy Ageing and Research Department of Genetics, Evolution & Environment, University College London, London, UK
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27
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Protonophore FCCP provides fitness advantage to PDR-deficient yeast cells. J Bioenerg Biomembr 2020; 52:383-395. [DOI: 10.1007/s10863-020-09849-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2020] [Accepted: 08/06/2020] [Indexed: 01/02/2023]
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28
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Magrì A, Di Rosa MC, Orlandi I, Guarino F, Reina S, Guarnaccia M, Morello G, Spampinato A, Cavallaro S, Messina A, Vai M, De Pinto V. Deletion of Voltage-Dependent Anion Channel 1 knocks mitochondria down triggering metabolic rewiring in yeast. Cell Mol Life Sci 2020; 77:3195-3213. [PMID: 31655859 PMCID: PMC11104908 DOI: 10.1007/s00018-019-03342-8] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2019] [Revised: 10/01/2019] [Accepted: 10/14/2019] [Indexed: 01/07/2023]
Abstract
The Voltage-Dependent Anion-selective Channel (VDAC) is the pore-forming protein of mitochondrial outer membrane, allowing metabolites and ions exchanges. In Saccharomyces cerevisiae, inactivation of POR1, encoding VDAC1, produces defective growth in the presence of non-fermentable carbon source. Here, we characterized the whole-genome expression pattern of a VDAC1-null strain (Δpor1) by microarray analysis, discovering that the expression of mitochondrial genes was completely abolished, as consequence of the dramatic reduction of mtDNA. To overcome organelle dysfunction, Δpor1 cells do not activate the rescue signaling retrograde response, as ρ0 cells, and rather carry out complete metabolic rewiring. The TCA cycle works in a "branched" fashion, shunting intermediates towards mitochondrial pyruvate generation via malic enzyme, and the glycolysis-derived pyruvate is pushed towards cytosolic utilization by PDH bypass rather than the canonical mitochondrial uptake. Overall, Δpor1 cells enhance phospholipid biosynthesis, accumulate lipid droplets, increase vacuoles and cell size, overproduce and excrete inositol. Such unexpected re-arrangement of whole metabolism suggests a regulatory role of VDAC1 in cell bioenergetics.
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Affiliation(s)
- Andrea Magrì
- Department of Biomedical and Biotechnological Sciences, University of Catania, Via S. Sofia, 64, Catania, Italy
- Department of Biological, Geological and Environmental Sciences, University of Catania, Via A. Longo, 19, Catania, Italy
- National Institute of Biostructures and Biosystems (INBB), Section of Catania, Rome, Italy
| | - Maria Carmela Di Rosa
- Department of Biomedical and Biotechnological Sciences, University of Catania, Via S. Sofia, 64, Catania, Italy
- National Institute of Biostructures and Biosystems (INBB), Section of Catania, Rome, Italy
| | - Ivan Orlandi
- Department of Biotechnologies and Biosciences, University of Milano-Bicocca, Piazza della Scienza, 2, Milan, Italy
| | - Francesca Guarino
- Department of Biomedical and Biotechnological Sciences, University of Catania, Via S. Sofia, 64, Catania, Italy
- National Institute of Biostructures and Biosystems (INBB), Section of Catania, Rome, Italy
| | - Simona Reina
- Department of Biomedical and Biotechnological Sciences, University of Catania, Via S. Sofia, 64, Catania, Italy
- Department of Biological, Geological and Environmental Sciences, University of Catania, Via A. Longo, 19, Catania, Italy
- National Institute of Biostructures and Biosystems (INBB), Section of Catania, Rome, Italy
| | - Maria Guarnaccia
- Institute for Biomedical Research and Innovation (IRIB), National Research Council (CNR), Via P. Gaifami, 18, Catania, Italy
| | - Giovanna Morello
- Institute for Biomedical Research and Innovation (IRIB), National Research Council (CNR), Via P. Gaifami, 18, Catania, Italy
| | - Antonio Spampinato
- Institute for Biomedical Research and Innovation (IRIB), National Research Council (CNR), Via P. Gaifami, 18, Catania, Italy
| | - Sebastiano Cavallaro
- Institute for Biomedical Research and Innovation (IRIB), National Research Council (CNR), Via P. Gaifami, 18, Catania, Italy
| | - Angela Messina
- Department of Biological, Geological and Environmental Sciences, University of Catania, Via A. Longo, 19, Catania, Italy
- National Institute of Biostructures and Biosystems (INBB), Section of Catania, Rome, Italy
| | - Marina Vai
- Department of Biotechnologies and Biosciences, University of Milano-Bicocca, Piazza della Scienza, 2, Milan, Italy.
| | - Vito De Pinto
- Department of Biomedical and Biotechnological Sciences, University of Catania, Via S. Sofia, 64, Catania, Italy.
- National Institute of Biostructures and Biosystems (INBB), Section of Catania, Rome, Italy.
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29
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Kessi-Pérez EI, Ponce B, Li J, Molinet J, Baeza C, Figueroa D, Bastías C, Gaete M, Liti G, Díaz-Barrera A, Salinas F, Martínez C. Differential Gene Expression and Allele Frequency Changes Favour Adaptation of a Heterogeneous Yeast Population to Nitrogen-Limited Fermentations. Front Microbiol 2020; 11:1204. [PMID: 32612585 PMCID: PMC7307137 DOI: 10.3389/fmicb.2020.01204] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Accepted: 05/12/2020] [Indexed: 12/18/2022] Open
Abstract
Alcoholic fermentation is fundamentally an adaptation process, in which the yeast Saccharomyces cerevisiae outperforms its competitors and takes over the fermentation process itself. Although wine yeast strains appear to be adapted to the stressful conditions of alcoholic fermentation, nitrogen limitations in grape must cause stuck or slow fermentations, generating significant economic losses for the wine industry. One way to discover the genetic bases that promote yeast adaptation to nitrogen-deficient environments are selection experiments, where a yeast population undergoes selection under conditions of nitrogen restriction for a number of generations, to then identify by sequencing the molecular characteristics that promote this adaptation. In this work, we carried out selection experiments in bioreactors imitating wine fermentation under nitrogen-limited fermentation conditions (SM60), using the heterogeneous SGRP-4X yeast population, to then sequence the transcriptome and the genome of the population at different time points of the selection process. The transcriptomic results showed an overexpression of genes from the NA strain (North American/YPS128), a wild, non-domesticated isolate. In addition, genome sequencing and allele frequency results allowed several QTLs to be mapped for adaptation to nitrogen-limited fermentation. Finally, we validated the ECM38 allele of NA strain as responsible for higher growth efficiency under nitrogen-limited conditions. Taken together, our results revealed a complex pattern of molecular signatures favouring adaptation of the yeast population to nitrogen-limited fermentations, including differential gene expression, allele frequency changes and loss of the mitochondrial genome. Finally, the results suggest that wild alleles from a non-domesticated isolate (NA) may have a relevant role in the adaptation to the assayed fermentation conditions, with the consequent potential of these alleles for the genetic improvement of wine yeast strains.
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Affiliation(s)
- Eduardo I Kessi-Pérez
- Departamento de Ciencia y Tecnología de los Alimentos, Universidad de Santiago de Chile (USACH), Santiago, Chile.,Centro de Estudios en Ciencia y Tecnología de Alimentos (CECTA), Universidad de Santiago de Chile (USACH), Santiago, Chile
| | - Belén Ponce
- Escuela de Ingeniería Bioquímica, Pontificia Universidad Católica de Valparaíso, Valparaíso, Chile
| | - Jing Li
- Université Côte d'Azur, CNRS, INSERM, IRCAN, Nice, France.,State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Jennifer Molinet
- Departamento de Ciencia y Tecnología de los Alimentos, Universidad de Santiago de Chile (USACH), Santiago, Chile
| | - Camila Baeza
- Centro de Estudios en Ciencia y Tecnología de Alimentos (CECTA), Universidad de Santiago de Chile (USACH), Santiago, Chile.,Millennium Institute for Integrative Biology (iBio), Santiago, Chile.,Instituto de Bioquímica y Microbiología, Facultad de Ciencias, Universidad Austral de Chile (UACH), Valdivia, Chile
| | - David Figueroa
- Centro de Estudios en Ciencia y Tecnología de Alimentos (CECTA), Universidad de Santiago de Chile (USACH), Santiago, Chile.,Millennium Institute for Integrative Biology (iBio), Santiago, Chile.,Instituto de Bioquímica y Microbiología, Facultad de Ciencias, Universidad Austral de Chile (UACH), Valdivia, Chile
| | - Camila Bastías
- Centro de Estudios en Ciencia y Tecnología de Alimentos (CECTA), Universidad de Santiago de Chile (USACH), Santiago, Chile.,Millennium Institute for Integrative Biology (iBio), Santiago, Chile
| | - Marco Gaete
- Departamento de Ciencia y Tecnología de los Alimentos, Universidad de Santiago de Chile (USACH), Santiago, Chile
| | - Gianni Liti
- Université Côte d'Azur, CNRS, INSERM, IRCAN, Nice, France
| | - Alvaro Díaz-Barrera
- Escuela de Ingeniería Bioquímica, Pontificia Universidad Católica de Valparaíso, Valparaíso, Chile
| | - Francisco Salinas
- Centro de Estudios en Ciencia y Tecnología de Alimentos (CECTA), Universidad de Santiago de Chile (USACH), Santiago, Chile.,Millennium Institute for Integrative Biology (iBio), Santiago, Chile.,Instituto de Bioquímica y Microbiología, Facultad de Ciencias, Universidad Austral de Chile (UACH), Valdivia, Chile
| | - Claudio Martínez
- Departamento de Ciencia y Tecnología de los Alimentos, Universidad de Santiago de Chile (USACH), Santiago, Chile.,Centro de Estudios en Ciencia y Tecnología de Alimentos (CECTA), Universidad de Santiago de Chile (USACH), Santiago, Chile
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30
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Chalermwat C, Thosapornvichai T, Wongkittichote P, Phillips JD, Cox JE, Jensen AN, Wattanasirichaigoon D, Jensen LT. Overexpression of the peroxin Pex34p suppresses impaired acetate utilization in yeast lacking the mitochondrial aspartate/glutamate carrier Agc1p. FEMS Yeast Res 2020; 19:5621492. [PMID: 31711143 DOI: 10.1093/femsyr/foz078] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Accepted: 11/10/2019] [Indexed: 12/19/2022] Open
Abstract
PEX34, encoding a peroxisomal protein implicated in regulating peroxisome numbers, was identified as a high copy suppressor, capable of bypassing impaired acetate utilization of agc1∆ yeast. However, improved growth of agc1∆ yeast on acetate is not mediated through peroxisome proliferation. Instead, stress to the endoplasmic reticulum and mitochondria from PEX34 overexpression appears to contribute to enhanced acetate utilization of agc1∆ yeast. The citrate/2-oxoglutarate carrier Yhm2p is required for PEX34 stimulated growth of agc1∆ yeast on acetate medium, suggesting that the suppressor effect is mediated through increased activity of a redox shuttle involving mitochondrial citrate export. Metabolomic analysis also revealed redirection of acetyl-coenzyme A (CoA) from synthetic reactions for amino acids in PEX34 overexpressing yeast. We propose a model in which increased formation of products from the glyoxylate shunt, together with enhanced utilization of acetyl-CoA, promotes the activity of an alternative mitochondrial redox shuttle, partially substituting for loss of yeast AGC1.
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Affiliation(s)
- Chalongchai Chalermwat
- Graduate Program in Molecular Medicine, Faculty of Science, Mahidol University, 272 Rama 6 Road, Ratchathewi, Bangkok 10400 Thailand
| | - Thitipa Thosapornvichai
- Department of Biochemistry, Faculty of Science, Mahidol University, 272 Rama 6 Road, Ratchathewi, Bangkok 10400 Thailand
| | - Parith Wongkittichote
- Department of Pediatrics, Faculty of Medicine, Ramathibodi Hospital, Mahidol University, 270 Rama 6 Road, Ratchathewi, Bangkok 10400, Thailand.,Department of Pediatrics, St. Louis Children's Hospital, Washington University School of Medicine, 1 Brookings Drive, St. Louis, MO 63130, USA
| | - John D Phillips
- Department of Internal Medicine, Division of Hematology, University of Utah, 30 N 1900 E, Salt Lake City, UT 84132, USA
| | - James E Cox
- Metabolomics Core Research Facility, University of Utah, 15 N Medical Drive East, Salt Lake City, UT 84112, USA.,Department of Biochemistry, University of Utah, 15 N Medical Drive East, Salt Lake City, UT 84112, USA
| | - Amornrat N Jensen
- Department of Pathobiology, Faculty of Science, Mahidol University, 272 Rama 6 Road, Ratchathewi, Bangkok 10400, Thailand
| | - Duangrurdee Wattanasirichaigoon
- Department of Pediatrics, Faculty of Medicine, Ramathibodi Hospital, Mahidol University, 270 Rama 6 Road, Ratchathewi, Bangkok 10400, Thailand
| | - Laran T Jensen
- Department of Biochemistry, Faculty of Science, Mahidol University, 272 Rama 6 Road, Ratchathewi, Bangkok 10400 Thailand
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31
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Ulgherait M, Chen A, McAllister SF, Kim HX, Delventhal R, Wayne CR, Garcia CJ, Recinos Y, Oliva M, Canman JC, Picard M, Owusu-Ansah E, Shirasu-Hiza M. Circadian regulation of mitochondrial uncoupling and lifespan. Nat Commun 2020; 11:1927. [PMID: 32317636 PMCID: PMC7174288 DOI: 10.1038/s41467-020-15617-x] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2019] [Accepted: 03/11/2020] [Indexed: 12/24/2022] Open
Abstract
Because old age is associated with defects in circadian rhythm, loss of circadian regulation is thought to be pathogenic and contribute to mortality. We show instead that loss of specific circadian clock components Period (Per) and Timeless (Tim) in male Drosophila significantly extends lifespan. This lifespan extension is not mediated by canonical diet-restriction longevity pathways but is due to altered cellular respiration via increased mitochondrial uncoupling. Lifespan extension of per mutants depends on mitochondrial uncoupling in the intestine. Moreover, upregulated uncoupling protein UCP4C in intestinal stem cells and enteroblasts is sufficient to extend lifespan and preserve proliferative homeostasis in the gut with age. Consistent with inducing a metabolic state that prevents overproliferation, mitochondrial uncoupling drugs also extend lifespan and inhibit intestinal stem cell overproliferation due to aging or even tumorigenesis. These results demonstrate that circadian-regulated intestinal mitochondrial uncoupling controls longevity in Drosophila and suggest a new potential anti-aging therapeutic target.
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Affiliation(s)
- Matt Ulgherait
- Department of Genetics and Development, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, 10032, USA
| | - Anna Chen
- Columbia College, New York, NY, 10027, USA
| | | | - Han X Kim
- Department of Genetics and Development, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, 10032, USA
| | - Rebecca Delventhal
- Department of Genetics and Development, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, 10032, USA
| | - Charlotte R Wayne
- Department of Neurology, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, 10032, USA
| | - Christian J Garcia
- Department of Physiology and Cellular Biophysics, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, 10032, USA
| | - Yocelyn Recinos
- Department of Systems Biology, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, 10032, USA
| | | | - Julie C Canman
- Department of Pathology and Cell Biology, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, 10032, USA
| | - Martin Picard
- Departments of Psychiatry and Neurology, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, 10032, USA
| | - Edward Owusu-Ansah
- Department of Physiology and Cellular Biophysics, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, 10032, USA
| | - Mimi Shirasu-Hiza
- Department of Genetics and Development, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, 10032, USA.
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32
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Saquib Q, Xia P, Siddiqui MA, Zhang J, Xie Y, Faisal M, Ansari SM, Alwathnani HA, Alatar AA, Al-Khedhairy AA, Zhang X. High-throughput transcriptomics: An insight on the pathways affected in HepG2 cells exposed to nickel oxide nanoparticles. CHEMOSPHERE 2020; 244:125488. [PMID: 31812053 DOI: 10.1016/j.chemosphere.2019.125488] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Revised: 11/24/2019] [Accepted: 11/26/2019] [Indexed: 06/10/2023]
Abstract
Nickel oxide nanoparticles (NiO-NPs) have been used in several consumer goods, reported to demonstrate the hepatotoxic effects in vitro and in vivo test models. Nonetheless the molecular mechanism of hepatotoxicity is still missing. Hence, a toxicogenomic approach integrating microscopic techniques and high-throughput RNA sequencing (RNA-Seq) was applied to reveal hepatotoxicity in human hepatocellular carcinoma cells (HepG2). NiO-NPs induced a concentration dependent (5-100 μg/ml) cytotoxicity, with a No observed effect level (NOEL) of 5 μg/ml. Hypoxia-inducible transcription factor-1α (HIF-1α) and miR-210 microRNA were upregulated at 25 and 100 μg/ml, while significant alteration on transcriptome at mRNA and pathway level was observed at non-toxic level of NiO-NPs treatment. The treated cells also showed activation of glycolysis, glutathione, lysosomes and autophagy pathways by a pathway-driven analysis. Flow cytometric analysis affirmed the elevation in nitric oxide (NO), Ca++ influx, esterase, and disruption of mitochondrial membrane potential (ΔΨm). Cell cycle dysregulation was affirmed by the appearance of 30.5% subG1 apoptotic peak in NiO-NPs (100 μg/ml) treated cells. The molecular responses were consistent with the microscopic observation that NiO-NPs induced subcellular alterations in HepG2 cells. We conclude that hypoxia stress played a pivotal role in NiO-NPs induced hepatoxicity in HepG2 cells. Concentration dependent effects on transcriptomics specify a powerful tool to evaluate the molecular mechanisms of nanoparticle induced cytotoxicity. Overall our study unequivocally affirmed the transcriptomic alterations in human cells, consequently the prevalent usage of NiO-NPs should be given subtle consideration owing to its effects on biological processes.
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Affiliation(s)
- Quaiser Saquib
- Zoology Department, College of Sciences, King Saud University, P.O. Box 2455, Riyadh, 11451, Saudi Arabia; A.R. Al-Jeraisy Chair for DNA Research, Zoology Department, College of Sciences, King Saud University, P.O. Box 2455, Riyadh, 11451, Saudi Arabia
| | - Pu Xia
- State Key Laboratory of Pollution Control & Resource Reuse, School of the Environment, Nanjing University, Nanjing, 210023, PR China
| | - Maqsood A Siddiqui
- A.R. Al-Jeraisy Chair for DNA Research, Zoology Department, College of Sciences, King Saud University, P.O. Box 2455, Riyadh, 11451, Saudi Arabia
| | - Junjiang Zhang
- State Key Laboratory of Pollution Control & Resource Reuse, School of the Environment, Nanjing University, Nanjing, 210023, PR China
| | - Yuwei Xie
- State Key Laboratory of Pollution Control & Resource Reuse, School of the Environment, Nanjing University, Nanjing, 210023, PR China
| | - Mohammad Faisal
- Department of Botany & Microbiology, College of Sciences, King Saud University, P.O Box 2455, Riyadh, 11451, Saudi Arabia
| | - Sabiha M Ansari
- Department of Botany & Microbiology, College of Sciences, King Saud University, P.O Box 2455, Riyadh, 11451, Saudi Arabia
| | - Hend A Alwathnani
- Department of Botany & Microbiology, College of Sciences, King Saud University, P.O Box 2455, Riyadh, 11451, Saudi Arabia
| | - Abdulrahman A Alatar
- Department of Botany & Microbiology, College of Sciences, King Saud University, P.O Box 2455, Riyadh, 11451, Saudi Arabia
| | - Abdulaziz A Al-Khedhairy
- Zoology Department, College of Sciences, King Saud University, P.O. Box 2455, Riyadh, 11451, Saudi Arabia
| | - Xiaowei Zhang
- State Key Laboratory of Pollution Control & Resource Reuse, School of the Environment, Nanjing University, Nanjing, 210023, PR China.
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33
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Hijazi I, Knupp J, Chang A. Retrograde signaling mediates an adaptive survival response to endoplasmic reticulum stress in Saccharomyces cerevisiae. J Cell Sci 2020; 133:jcs.241539. [PMID: 32005698 DOI: 10.1242/jcs.241539] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Accepted: 01/23/2020] [Indexed: 12/11/2022] Open
Abstract
One major cause of endoplasmic reticulum (ER) stress is homeostatic imbalance between biosynthetic protein folding and protein folding capacity. Cells utilize mechanisms such as the unfolded protein response (UPR) to cope with ER stress. Nevertheless, when ER stress is prolonged or severe, cell death may occur, accompanied by production of mitochondrial reactive oxygen species (ROS). Using a yeast model (Saccharomyces cerevisiae), we describe an innate, adaptive response to ER stress to increase select mitochondrial proteins, O2 consumption and cell survival. The mitochondrial response allows cells to resist additional ER stress. The ER stress-induced mitochondrial response is mediated by activation of retrograde (RTG) signaling to enhance anapleurotic reactions of the tricarboxylic acid cycle. Mitochondrial response to ER stress is accompanied by inactivation of the conserved TORC1 pathway, and activation of Snf1/AMPK, the conserved energy sensor and regulator of metabolism. Our results provide new insight into the role of respiration in cell survival in the face of ER stress, and should help in developing therapeutic strategies to limit cell death in disorders linked to ER stress.This article has an associated First Person interview with the first author of the paper.
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Affiliation(s)
- Imadeddin Hijazi
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, 1105 N University, Ann Arbor, MI 48109, USA
| | - Jeffrey Knupp
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, 1105 N University, Ann Arbor, MI 48109, USA
| | - Amy Chang
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, 1105 N University, Ann Arbor, MI 48109, USA
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34
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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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35
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Nair A, Chauhan P, Saha B, Kubatzky KF. Conceptual Evolution of Cell Signaling. Int J Mol Sci 2019; 20:E3292. [PMID: 31277491 PMCID: PMC6651758 DOI: 10.3390/ijms20133292] [Citation(s) in RCA: 68] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Revised: 06/26/2019] [Accepted: 06/28/2019] [Indexed: 12/27/2022] Open
Abstract
During the last 100 years, cell signaling has evolved into a common mechanism for most physiological processes across systems. Although the majority of cell signaling principles were initially derived from hormonal studies, its exponential growth has been supported by interdisciplinary inputs, e.g., from physics, chemistry, mathematics, statistics, and computational fields. As a result, cell signaling has grown out of scope for any general review. Here, we review how the messages are transferred from the first messenger (the ligand) to the receptor, and then decoded with the help of cascades of second messengers (kinases, phosphatases, GTPases, ions, and small molecules such as cAMP, cGMP, diacylglycerol, etc.). The message is thus relayed from the membrane to the nucleus where gene expression ns, subsequent translations, and protein targeting to the cell membrane and other organelles are triggered. Although there are limited numbers of intracellular messengers, the specificity of the response profiles to the ligands is generated by the involvement of a combination of selected intracellular signaling intermediates. Other crucial parameters in cell signaling are its directionality and distribution of signaling strengths in different pathways that may crosstalk to adjust the amplitude and quality of the final effector output. Finally, we have reflected upon its possible developments during the coming years.
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Affiliation(s)
- Arathi Nair
- National Center for Cell Science (NCCS), Ganeshkhind, Pune 411007, India
| | - Prashant Chauhan
- National Center for Cell Science (NCCS), Ganeshkhind, Pune 411007, India
| | - Bhaskar Saha
- National Center for Cell Science (NCCS), Ganeshkhind, Pune 411007, India.
| | - Katharina F Kubatzky
- Zentrum für Infektiologie, Medizinische Mikrobiologie und Hygiene, Universitätsklinikum Heidelberg, Im Neuenheimer Feld 324, 69120 Heidelberg, Germany.
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36
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Guaragnella N, Coyne LP, Chen XJ, Giannattasio S. Mitochondria-cytosol-nucleus crosstalk: learning from Saccharomyces cerevisiae. FEMS Yeast Res 2019; 18:5066171. [PMID: 30165482 DOI: 10.1093/femsyr/foy088] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Accepted: 08/02/2018] [Indexed: 12/16/2022] Open
Abstract
Mitochondria are key cell organelles with a prominent role in both energetic metabolism and the maintenance of cellular homeostasis. Since mitochondria harbor their own genome, which encodes a limited number of proteins critical for oxidative phosphorylation and protein translation, their function and biogenesis strictly depend upon nuclear control. The yeast Saccharomyces cerevisiae has been a unique model for understanding mitochondrial DNA organization and inheritance as well as for deciphering the process of assembly of mitochondrial components. In the last three decades, yeast also provided a powerful tool for unveiling the communication network that coordinates the functions of the nucleus, the cytosol and mitochondria. This crosstalk regulates how cells respond to extra- and intracellular changes either to maintain cellular homeostasis or to activate cell death. This review is focused on the key pathways that mediate nucleus-cytosol-mitochondria communications through both transcriptional regulation and proteostatic signaling. We aim to highlight yeast that likely continues to serve as a productive model organism for mitochondrial research in the years to come.
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Affiliation(s)
- Nicoletta Guaragnella
- Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, CNR, Via Amendola 165/A, 70126 Bari, Italy
| | - Liam P Coyne
- Department of Biochemistry and Molecular Biology, State University of New York Upstate Medical University, 750 East Adams Street, Syracuse, NY 13210, USA
| | - Xin Jie Chen
- Department of Biochemistry and Molecular Biology, State University of New York Upstate Medical University, 750 East Adams Street, Syracuse, NY 13210, USA
| | - Sergio Giannattasio
- Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, CNR, Via Amendola 165/A, 70126 Bari, Italy
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37
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Weidling I, Swerdlow RH. Mitochondrial Dysfunction and Stress Responses in Alzheimer's Disease. BIOLOGY 2019; 8:biology8020039. [PMID: 31083585 PMCID: PMC6627276 DOI: 10.3390/biology8020039] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Revised: 01/04/2019] [Accepted: 01/16/2019] [Indexed: 02/04/2023]
Abstract
Alzheimer's disease (AD) patients display widespread mitochondrial defects. Brain hypometabolism occurs alongside mitochondrial defects, and correlates well with cognitive decline. Numerous theories attempt to explain AD mitochondrial dysfunction. Groups propose AD mitochondrial defects stem from: (1) mitochondrial-nuclear DNA interactions/variations; (2) amyloid and neurofibrillary tangle interactions with mitochondria, and (3) mitochondrial quality control defects and oxidative damage. Cells respond to mitochondrial dysfunction through numerous retrograde responses including the Integrated Stress Response (ISR) involving eukaryotic initiation factor 2α (eIF2α), activating transcription factor 4 (ATF4) and C/EBP homologous protein (CHOP). AD brains activate the ISR and we hypothesize mitochondrial defects may contribute to ISR activation. Here we review current recognized contributions of the mitochondria to AD, with an emphasis on their potential contribution to brain stress responses.
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Affiliation(s)
- Ian Weidling
- University of Kansas Alzheimer's Disease Center, Fairway, KS 66205, USA.
- Department of Integrated and Molecular Physiology, University of Kansas Medical Center, Kansas City, KS 66160, USA.
| | - Russell H Swerdlow
- University of Kansas Alzheimer's Disease Center, Fairway, KS 66205, USA.
- Department of Integrated and Molecular Physiology, University of Kansas Medical Center, Kansas City, KS 66160, USA.
- Department of Neurology, University of Kansas Medical Center, Kansas City, KS 66160, USA.
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, KS 66160, USA.
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Muid KA, Kimyon Ö, Reza SH, Karakaya HC, Koc A. Characterization of long living yeast deletion mutants that lack mitochondrial metabolism genes DSS1, PPA2 and AFG3. Gene 2019; 706:172-180. [PMID: 31082499 DOI: 10.1016/j.gene.2019.05.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Revised: 04/15/2019] [Accepted: 05/01/2019] [Indexed: 02/06/2023]
Abstract
Molecular mechanisms of aging and longevity are still mostly unknown. Mitochondria play central roles in cellular metabolism and aging. In this study, we identified three deletion mutants of mitochondrial metabolism genes (ppa2∆, dss1∆, and afg3∆) that live longer than wild-type cells. These long-lived cells harbored significantly decreased amount of mitochondrial DNA (mtDNA) and reactive oxygen species (ROS). Compared to the serpentine nature of wild-type mitochondria, a different dynamics and distribution pattern of mitochondria were observed in the mutants. Both young and old long-lived cells produced relatively low but adequate levels of ATP for cellular activities. The status of the retrograde signaling was checked by expression of CIT2 gene and found activated in long-lived mutants. The mutant cells were also profiled for their gene expression patterns, and genes that were differentially regulated were determined. All long-lived cells comprised similar pleiotropic phenotype regarding mitochondrial dynamics and functions. Thus, this study suggests that DSS1, PPA2, and AFG3 genes modulate the lifespan by altering the mitochondrial morphology and functions.
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Affiliation(s)
- K A Muid
- Izmir Institute of Technology, Department of Molecular Biology and Genetics, 35430 Urla, Izmir, Turkey
| | - Önder Kimyon
- Izmir Institute of Technology, Department of Molecular Biology and Genetics, 35430 Urla, Izmir, Turkey
| | - Shahadat Hasan Reza
- Izmir Institute of Technology, Department of Molecular Biology and Genetics, 35430 Urla, Izmir, Turkey
| | - Huseyin Caglar Karakaya
- Izmir Institute of Technology, Department of Molecular Biology and Genetics, 35430 Urla, Izmir, Turkey
| | - Ahmet Koc
- Izmir Institute of Technology, Department of Molecular Biology and Genetics, 35430 Urla, Izmir, Turkey; Inonu University, Medical School, Department of Medical Biology and Genetics, Battalgazi, Malatya, Turkey.
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Filamentation Regulatory Pathways Control Adhesion-Dependent Surface Responses in Yeast. Genetics 2019; 212:667-690. [PMID: 31053593 DOI: 10.1534/genetics.119.302004] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Accepted: 04/18/2019] [Indexed: 01/07/2023] Open
Abstract
Signaling pathways can regulate biological responses by the transcriptional regulation of target genes. In yeast, multiple signaling pathways control filamentous growth, a morphogenetic response that occurs in many species including fungal pathogens. Here, we examine the role of signaling pathways that control filamentous growth in regulating adhesion-dependent surface responses, including mat formation and colony patterning. Expression profiling and mutant phenotype analysis showed that the major pathways that regulate filamentous growth [filamentous growth MAPK (fMAPK), RAS, retrograde (RTG), RIM101, RPD3, ELP, SNF1, and PHO85] also regulated mat formation and colony patterning. The chromatin remodeling complex, SAGA, also regulated these responses. We also show that the RAS and RTG pathways coregulated a common set of target genes, and that SAGA regulated target genes known to be controlled by the fMAPK, RAS, and RTG pathways. Analysis of surface growth-specific targets identified genes that respond to low oxygen, high temperature, and desiccation stresses. We also explore the question of why cells make adhesive contacts in colonies. Cell adhesion contacts mediated by the coregulated target and adhesion molecule, Flo11p, deterred entry into colonies by macroscopic predators and impacted colony temperature regulation. The identification of new regulators (e.g., SAGA), and targets of surface growth in yeast may provide insights into fungal pathogenesis in settings where surface growth and adhesion contributes to virulence.
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Druseikis M, Ben-Ari J, Covo S. The Goldilocks effect of respiration on canavanine tolerance in Saccharomyces cerevisiae. Curr Genet 2019; 65:1199-1215. [PMID: 31011791 DOI: 10.1007/s00294-019-00974-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2018] [Revised: 03/30/2019] [Accepted: 04/13/2019] [Indexed: 12/12/2022]
Abstract
When glucose is available, Saccharomyces cerevisiae prefers fermentation to respiration. In fact, it can live without respiration at all. Here, we study the role of respiration in stress tolerance in yeast. We found that colony growth of respiratory-deficient yeast (petite) is greatly inhibited by canavanine, the toxic analog of arginine that causes proteotoxic stress. We found lower amounts of the amino acids involved in arginine biosynthesis in petites compared with WT. This finding may be explained by the fact that petite cells exposed to canavanine show reduction in the efficiency of targeting of proteins required for arginine biosynthesis. The retrograde (RTG) pathway signals mitochondrial stress. It positively controls production of arginine precursors. We show that canavanine abrogates RTG signaling especially in petite cells, and mutants in the RTG pathway are extremely sensitive to canavanine. We suggest that petite cells are naturally ineffective in production of some amino acids; combination of this fact with the effect of canavanine on the RTG pathway is the simplest explanation why petite cells are inhibited by canavanine. Surprisingly, we found that canavanine greatly inhibits colony formation when WT cells are forced to respire. Our research proposes a novel connection between respiration and proteotoxic stress.
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Affiliation(s)
- Marina Druseikis
- Department of Plant Pathology and Microbiology, Robert H. Smith Faculty of Agriculture, Food and Environment, Hebrew University, 76100, Rehovot, Israel
| | - Julius Ben-Ari
- Interdepartmental Equipment Unit, Robert H. Smith Faculty of Agriculture, Food and Environment, Hebrew University, 76100, Rehovot, Israel
| | - Shay Covo
- Department of Plant Pathology and Microbiology, Robert H. Smith Faculty of Agriculture, Food and Environment, Hebrew University, 76100, Rehovot, Israel.
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Ning X, Ji X, Li G, Sang N. Ambient PM 2.5 causes lung injuries and coupled energy metabolic disorder. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2019; 170:620-626. [PMID: 30579162 DOI: 10.1016/j.ecoenv.2018.12.028] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Revised: 12/04/2018] [Accepted: 12/11/2018] [Indexed: 05/05/2023]
Abstract
Ambient fine particulate matter (PM2.5) is a challenge to public health worldwide. Although increasing numbers of recent epidemiological studies have emphasized the critical role of PM2.5 in promoting respiratory diseases, the precise mechanism behind PM2.5-mediated lung obstruction remains obscure. In the present study, we analyzed lung structure and function and further investigated mitochondrial morphology and transcription-modulated energy metabolism in mice following PM2.5 aspiration. The results showed that PM2.5 exposure reduced pulmonary function and induced severe pathological alterations, including alveolar endothelial disruption and airway obstruction. Based on ultrastructural observations, we also found mitochondrial vacuolation and mitochondrial membrane rupture in alveolar type II epithelial cells. Importantly, the abnormality of mitochondrial structure was coupled with energy metabolism disorders, as evidenced by the decrease in ATP levels, the accumulation of pyruvate and lactate content, and the altered transcription of related genes. Moreover, the reduction in mitochondrial markers, including PGC-1α, NRF-1, and TFAM, were involved in mitochondrial dysfunction. These findings suggest that energy metabolic disorders and mitochondrial dysfunction may be the important contributors to pulmonary injuries in response to PM2.5 exposure, indicating possible targets for protection and therapy in polluted areas.
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Affiliation(s)
- Xia Ning
- College of Environment and Resource, Research Center of Environment and Health, Shanxi University, Taiyuan, Shanxi 030006, PR China
| | - Xiaotong Ji
- College of Environment and Resource, Research Center of Environment and Health, Shanxi University, Taiyuan, Shanxi 030006, PR China
| | - Guangke Li
- College of Environment and Resource, Research Center of Environment and Health, Shanxi University, Taiyuan, Shanxi 030006, PR China.
| | - Nan Sang
- College of Environment and Resource, Research Center of Environment and Health, Shanxi University, Taiyuan, Shanxi 030006, PR China
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Esposito M, Hermann-Le Denmat S, Delahodde A. Contribution of ERMES subunits to mature peroxisome abundance. PLoS One 2019; 14:e0214287. [PMID: 30908556 PMCID: PMC6433259 DOI: 10.1371/journal.pone.0214287] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2018] [Accepted: 03/11/2019] [Indexed: 11/26/2022] Open
Abstract
Eukaryotic organelles share different components and establish physical contacts to communicate throughout the cell. One of the best-recognized examples of such interplay is the metabolic cooperation and crosstalk between mitochondria and peroxisomes, both organelles being functionally and physically connected and linked to the endoplasmic reticulum (ER). In Saccharomyces cerevisiae, mitochondria are linked to the ER by the ERMES complex that facilitates inter-organelle calcium and phospholipid exchanges. Recently, peroxisome-mitochondria contact sites (PerMit) have been reported and among Permit tethers, one component of the ERMES complex (Mdm34) was shown to interact with the peroxin Pex11, suggesting that the ERMES complex or part of it may be involved in two membrane contact sites (ER-mitochondria and peroxisome- mitochondria). This opens the possibility of exchanges between these three membrane compartments. Here, we investigated in details the role of each ERMES subunit on peroxisome abundance. First, we confirmed previous studies from other groups showing that absence of Mdm10 or Mdm12 leads to an increased number of mature peroxisomes. Secondly, we showed that this is not simply due to respiratory function defect, mitochondrial DNA (mtDNA) loss or mitochondrial network alteration. Finally, we present evidence that the contribution of ERMES subunits Mdm10 and Mdm12 to peroxisome number involves two different mechanisms.
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Affiliation(s)
- Michela Esposito
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris‐Sud, Université Paris‐Saclay, Gif‐sur‐Yvette cedex, France
| | - Sylvie Hermann-Le Denmat
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris‐Sud, Université Paris‐Saclay, Gif‐sur‐Yvette cedex, France
- Ecole Normale Supérieure, PSL Research University, Paris, France
| | - Agnès Delahodde
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris‐Sud, Université Paris‐Saclay, Gif‐sur‐Yvette cedex, France
- * E-mail:
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Cirigliano A, Macone A, Bianchi MM, Oliaro-Bosso S, Balliano G, Negri R, Rinaldi T. Ergosterol reduction impairs mitochondrial DNA maintenance in S. cerevisiae. Biochim Biophys Acta Mol Cell Biol Lipids 2019; 1864:290-303. [DOI: 10.1016/j.bbalip.2018.12.002] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2018] [Revised: 11/27/2018] [Accepted: 12/10/2018] [Indexed: 12/20/2022]
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Gayen D, Gayali S, Barua P, Lande NV, Varshney S, Sengupta S, Chakraborty S, Chakraborty N. Dehydration-induced proteomic landscape of mitochondria in chickpea reveals large-scale coordination of key biological processes. J Proteomics 2019; 192:267-279. [PMID: 30243939 DOI: 10.1016/j.jprot.2018.09.008] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Revised: 08/09/2018] [Accepted: 09/11/2018] [Indexed: 12/28/2022]
Abstract
Mitochondria play crucial roles in regulating multiple biological processes particularly electron transfer and energy metabolism in eukaryotic cells. Exposure to water-deficit or dehydration may affect mitochondrial function, and dehydration response may dictate cell fate decisions. iTRAQ-based quantitative proteome of a winter legume, chickpea, demonstrated the central metabolic alterations in mitochondria, presumably involved in dehydration adaptation. Three-week-old chickpea seedlings were subjected to progressive dehydration and the magnitude of dehydration-induced compensatory physiological responses was monitored in terms of physicochemical characteristics and mitochondrial architecture. The proteomics analysis led to the identification of 40 dehydration-responsive proteins whose expressions were significantly modulated by dehydration. The differentially expressed proteins were implicated in different metabolic processes, with obvious functional tendencies toward purine-thiamine metabolic network, pathways of carbon fixation and oxidative phosphorylation. The linearity of dehydration-induced proteome alteration was examined with transcript abundance of randomly selected candidates under multivariate stress conditions. The differentially regulated proteins were validated through sequence analysis. An extensive sequence based localization prediction revealed >62.5% proteins to be mitochondrial resident by, at least, one prediction algorithm. The results altogether provide intriguing insights into the dehydration-responsive metabolic pathways and useful clues to identify crucial proteins linked to stress tolerance. BIOLOGICAL SIGNIFICANCE: Investigation on plant mitochondrial proteome is of significance because it would allow a better understanding of mitochondrial function in plant adaptation to stress. Mitochondria are the unique organelles, which play a crucial role in energy metabolism and cellular homeostasis, particularly when exposed to stress conditions. Chickpea is one of the cultivated winter legumes, which enriches soil nitrogen and has very low water footprint and thus contributes to fortification of sustainable agriculture. We therefore examined the dehydration-responsive mitochondrial proteome landscape of chickpea and queried whether molecular interplay of mitochondrial proteins modulate dehydration tolerance. A total of 40 dehydration-induced mitochondrial proteins were identified, predicted to be involved in key metabolic processes. Our future efforts would focus on understanding both posttranslational modification and processing for comprehensive characterization of mitochondrial protein function. This approach will facilitate mining of more biomarkers linked to the tolerance trait and contribute to crop adaptation to climate change.
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Affiliation(s)
- Dipak Gayen
- National Institute of Plant Genome Research, Jawaharlal Nehru University Campus, Aruna, Asaf Ali Marg, New Delhi, India
| | - Saurabh Gayali
- National Institute of Plant Genome Research, Jawaharlal Nehru University Campus, Aruna, Asaf Ali Marg, New Delhi, India
| | - Pragya Barua
- National Institute of Plant Genome Research, Jawaharlal Nehru University Campus, Aruna, Asaf Ali Marg, New Delhi, India
| | - Nilesh Vikram Lande
- National Institute of Plant Genome Research, Jawaharlal Nehru University Campus, Aruna, Asaf Ali Marg, New Delhi, India
| | - Swati Varshney
- CSIR-Institute of Genomics and Integrative Biology, Mathura Road, New Delhi, India
| | - Shantanu Sengupta
- CSIR-Institute of Genomics and Integrative Biology, Mathura Road, New Delhi, India
| | - Subhra Chakraborty
- National Institute of Plant Genome Research, Jawaharlal Nehru University Campus, Aruna, Asaf Ali Marg, New Delhi, India
| | - Niranjan Chakraborty
- National Institute of Plant Genome Research, Jawaharlal Nehru University Campus, Aruna, Asaf Ali Marg, New Delhi, India.
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Raja V, Salsaa M, Joshi AS, Li Y, van Roermund CWT, Saadat N, Lazcano P, Schmidtke M, Hüttemann M, Gupta SV, Wanders RJA, Greenberg ML. Cardiolipin-deficient cells depend on anaplerotic pathways to ameliorate defective TCA cycle function. Biochim Biophys Acta Mol Cell Biol Lipids 2019; 1864:654-661. [PMID: 30731133 DOI: 10.1016/j.bbalip.2019.02.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2018] [Revised: 10/22/2018] [Accepted: 02/02/2019] [Indexed: 01/01/2023]
Abstract
Previous studies have shown that the cardiolipin (CL)-deficient yeast mutant, crd1Δ, has decreased levels of acetyl-CoA and decreased activities of the TCA cycle enzymes aconitase and succinate dehydrogenase. These biochemical phenotypes are expected to lead to defective TCA cycle function. In this study, we report that signaling and anaplerotic metabolic pathways that supplement defects in the TCA cycle are essential in crd1Δ mutant cells. The crd1Δ mutant is synthetically lethal with mutants in the TCA cycle, retrograde (RTG) pathway, glyoxylate cycle, and pyruvate carboxylase 1. Glutamate levels were decreased, and the mutant exhibited glutamate auxotrophy. Glyoxylate cycle genes were up-regulated, and the levels of glyoxylate metabolites succinate and citrate were increased in crd1Δ. Import of acetyl-CoA from the cytosol into mitochondria is essential in crd1Δ, as deletion of the carnitine-acetylcarnitine translocase led to lethality in the CL mutant. β-oxidation was functional in the mutant, and oleate supplementation rescued growth defects. These findings suggest that TCA cycle deficiency caused by the absence of CL necessitates activation of anaplerotic pathways to replenish acetyl-CoA and TCA cycle intermediates. Implications for Barth syndrome, a genetic disorder of CL metabolism, are discussed.
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Affiliation(s)
- Vaishnavi Raja
- Department of Biological Sciences, Wayne State University, Detroit, MI 48202, United States of America
| | - Michael Salsaa
- Department of Biological Sciences, Wayne State University, Detroit, MI 48202, United States of America
| | - Amit S Joshi
- Department of Biological Sciences, Wayne State University, Detroit, MI 48202, United States of America
| | - Yiran Li
- Department of Biological Sciences, Wayne State University, Detroit, MI 48202, United States of America
| | - Carlo W T van Roermund
- Laboratory Genetic Metabolic Diseases, Department of Clinical Chemistry, Academic Medical Center, Amsterdam, the Netherlands
| | - Nadia Saadat
- Department of Nutrition and Food Science, Wayne State University, Detroit, MI 48202, United States of America
| | - Pablo Lazcano
- Department of Biological Sciences, Wayne State University, Detroit, MI 48202, United States of America
| | - Michael Schmidtke
- Department of Biological Sciences, Wayne State University, Detroit, MI 48202, United States of America
| | - Maik Hüttemann
- Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, Michigan 48201
| | - Smiti V Gupta
- Department of Nutrition and Food Science, Wayne State University, Detroit, MI 48202, United States of America
| | - Ronald J A Wanders
- Laboratory Genetic Metabolic Diseases, Department of Clinical Chemistry, Academic Medical Center, Amsterdam, the Netherlands
| | - Miriam L Greenberg
- Department of Biological Sciences, Wayne State University, Detroit, MI 48202, United States of America.
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Aw WC, Towarnicki SG, Melvin RG, Youngson NA, Garvin MR, Hu Y, Nielsen S, Thomas T, Pickford R, Bustamante S, Vila-Sanjurjo A, Smyth GK, Ballard JWO. Genotype to phenotype: Diet-by-mitochondrial DNA haplotype interactions drive metabolic flexibility and organismal fitness. PLoS Genet 2018; 14:e1007735. [PMID: 30399141 PMCID: PMC6219761 DOI: 10.1371/journal.pgen.1007735] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Accepted: 10/02/2018] [Indexed: 02/07/2023] Open
Abstract
Diet may be modified seasonally or by biogeographic, demographic or cultural shifts. It can differentially influence mitochondrial bioenergetics, retrograde signalling to the nuclear genome, and anterograde signalling to mitochondria. All these interactions have the potential to alter the frequencies of mtDNA haplotypes (mitotypes) in nature and may impact human health. In a model laboratory system, we fed four diets varying in Protein: Carbohydrate (P:C) ratio (1:2, 1:4, 1:8 and 1:16 P:C) to four homoplasmic Drosophila melanogaster mitotypes (nuclear genome standardised) and assayed their frequency in population cages. When fed a high protein 1:2 P:C diet, the frequency of flies harbouring Alstonville mtDNA increased. In contrast, when fed the high carbohydrate 1:16 P:C food the incidence of flies harbouring Dahomey mtDNA increased. This result, driven by differences in larval development, was generalisable to the replacement of the laboratory diet with fruits having high and low P:C ratios, perturbation of the nuclear genome and changes to the microbiome. Structural modelling and cellular assays suggested a V161L mutation in the ND4 subunit of complex I of Dahomey mtDNA was mildly deleterious, reduced mitochondrial functions, increased oxidative stress and resulted in an increase in larval development time on the 1:2 P:C diet. The 1:16 P:C diet triggered a cascade of changes in both mitotypes. In Dahomey larvae, increased feeding fuelled increased β-oxidation and the partial bypass of the complex I mutation. Conversely, Alstonville larvae upregulated genes involved with oxidative phosphorylation, increased glycogen metabolism and they were more physically active. We hypothesise that the increased physical activity diverted energy from growth and cell division and thereby slowed development. These data further question the use of mtDNA as an assumed neutral marker in evolutionary and population genetic studies. Moreover, if humans respond similarly, we posit that individuals with specific mtDNA variations may differentially metabolise carbohydrates, which has implications for a variety of diseases including cardiovascular disease, obesity, and perhaps Parkinson's Disease.
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Affiliation(s)
- Wen C. Aw
- School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, NSW, Australia
| | - Samuel G. Towarnicki
- School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, NSW, Australia
| | - Richard G. Melvin
- School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, NSW, Australia
| | - Neil A. Youngson
- School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, NSW, Australia
| | - Michael R. Garvin
- School of Biological Sciences, Washington State University, Pullman, Washington, United States of America
| | - Yifang Hu
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria, Australia
| | - Shaun Nielsen
- Centre for Marine Bio-Innovation and School of Biological, Earth and Environmental Sciences, The University of New South Wales, Sydney, NSW, Australia
| | - Torsten Thomas
- Centre for Marine Bio-Innovation and School of Biological, Earth and Environmental Sciences, The University of New South Wales, Sydney, NSW, Australia
| | - Russell Pickford
- Bioanalytical Mass Spectrometry Facility, Mark Wainwright Analytical Center, The University of New South Wales, Sydney, NSW, Australia
| | - Sonia Bustamante
- Bioanalytical Mass Spectrometry Facility, Mark Wainwright Analytical Center, The University of New South Wales, Sydney, NSW, Australia
| | - Antón Vila-Sanjurjo
- Grupo GIBE, Bioloxía Celular e Molecular, Facultade de Ciencias, Universidade da Coruña (UDC), Campus Zapateira s/n, A Coruña, Spain
| | - Gordon K. Smyth
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria, Australia
- School of Mathematics and Statistics, The University of Melbourne, Melbourne, Victoria, Australia
| | - J. William O. Ballard
- School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, NSW, Australia
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Dual roles of mitochondrial fusion gene FZO1 in yeast age asymmetry and in longevity mediated by a novel ATG32-dependent retrograde response. Biogerontology 2018; 20:93-107. [PMID: 30298458 DOI: 10.1007/s10522-018-9779-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2018] [Accepted: 10/04/2018] [Indexed: 12/27/2022]
Abstract
The replicative lifespan of the yeast Saccharomyces cerevisiae models the aging of stem cells. Age asymmetry between the mother and daughter cells is established during each cell division, such that the daughter retains the capacity for self-renewal while this ability is diminished in the mother. The segregation of fully-functional mitochondria to daughter cells is one mechanism that underlies this age asymmetry. In this study, we have examined the role of mitochondrial dynamics in this phenomenon. Mitochondrial dynamics involve the processes of fission and fusion. Out of the three fusion and three fission genes tested, we have found that only FZO1 is required for the segregation of fully-functional mitochondria to daughter cells and in the maintenance of age asymmetry as manifested in the potential of daughters for a full replicative lifespan despite its deterioration in their mothers. The quality of mitochondria is determined by their turnover, and we have also discovered that deletion of FZO1 reduces mitophagy. Mitochondrial dysfunction elicits a compensatory retrograde response that extends replicative lifespan. Typically, the dysfunction that triggers this response encompasses energy production. The disruption of mitochondrial dynamics by deletion of FZO1 also activates the retrograde response to extend replicative lifespan. We call this novel pathway the mitochondrial dynamics-associated retrograde response (MDARR) because it is distinct in the signal proximal to the mitochondrion that initiates it. Furthermore, the MDARR engages the mitophagy receptor Atg32 on the mitochondrial surface, and we propose that this is due to the accumulation of Atg32-Atg11-Dnm1 complexes on the mitochondrion in the absence of Fzo1 activity. MDARR can be masked by the operation of the 'classic' retrograde response.
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Kasai S, Yamazaki H, Tanji K, Engler MJ, Matsumiya T, Itoh K. Role of the ISR-ATF4 pathway and its cross talk with Nrf2 in mitochondrial quality control. J Clin Biochem Nutr 2018; 64:1-12. [PMID: 30705506 PMCID: PMC6348405 DOI: 10.3164/jcbn.18-37] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2018] [Accepted: 06/11/2018] [Indexed: 12/17/2022] Open
Abstract
Recent investigations have clarified the importance of mitochondria in various age-related degenerative diseases, including late-onset Alzheimer’s disease and Parkinson’s disease. Although mitochondrial disturbances can be involved in every step of disease progression, several observations have demonstrated that a subtle mitochondrial functional disturbance is observed preceding the actual appearance of pathophysiological alterations and can be the target of early therapeutic intervention. The signals from damaged mitochondria are transferred to the nucleus, leading to the altered expression of nuclear-encoded genes, which includes mitochondrial proteins (i.e., mitochondrial retrograde signaling). Mitochondrial retrograde signaling improves mitochondrial perturbation (i.e., mitohormesis) and is considered a homeostatic stress response against intrinsic (ex. aging or pathological mutations) and extrinsic (ex. chemicals and pathogens) stimuli. There are several branches of the mitochondrial retrograde signaling, including mitochondrial unfolded protein response (UPRMT), but recent observations increasingly show the importance of the ISR-ATF4 pathway in mitochondrial retrograde signaling. Furthermore, Nrf2, a master regulator of the oxidative stress response, interacts with ATF4 and cooperatively upregulates a battery of antioxidant and antiapoptotic genes while repressing the ATF4-mediated proapoptotic gene, CHOP. In this review article, we summarized the upstream and downstream mechanisms of ATF4 activation during mitochondrial stresses and disturbances and discuss therapeutic intervention against degenerative diseases by using Nrf2 activators.
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Affiliation(s)
- Shuya Kasai
- Department of Stress Response Science, Center for Advanced Medical Research, Hirosaki University Graduate School of Medicine, 5 Zaifu-cho, Hirosaki 036-8562, Japan
| | - Hiromi Yamazaki
- Department of Stress Response Science, Center for Advanced Medical Research, Hirosaki University Graduate School of Medicine, 5 Zaifu-cho, Hirosaki 036-8562, Japan
| | - Kunikazu Tanji
- Department of Neuropathology, Hirosaki University Graduate School of Medicine, 5 Zaifu-cho, Hirosaki 036-8562, Japan
| | - Máté János Engler
- Department of Stress Response Science, Center for Advanced Medical Research, Hirosaki University Graduate School of Medicine, 5 Zaifu-cho, Hirosaki 036-8562, Japan
| | - Tomoh Matsumiya
- Department of Vascular Biology, Hirosaki University Graduate School of Medicine, 5 Zaifu-cho, Hirosaki 036-8562, Japan
| | - Ken Itoh
- Department of Stress Response Science, Center for Advanced Medical Research, Hirosaki University Graduate School of Medicine, 5 Zaifu-cho, Hirosaki 036-8562, Japan
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Abstract
FOXO transcription factors are evolutionally conserved regulators of organismal life span downstream of insulin signaling. After integrating cellular signals from various stimuli such as growth factors, oxidative stress, and energy deprivation, FOXO factors induce expression of a specific set of genes that regulate various cellular processes to maintain homeostasis at a cellular or organismal level. In this review, we discuss roles of FOXO proteins in the maintenance of mitochondria, organelles critical for cellular quality control. FOXO factors protect mitochondria by activating mitochondrial antioxidant enzymes and they help remodel damaged mitochondria by inducing remodeling processes such as mitophagy. Furthermore, we also review the recently identified FOXO-dependent retrograde signaling from stressed mitochondria to the nucleus, which suggest that FOXO mediates the crosstalk between these two important organelles to maintain cell homeostasis. In addition, we introduce a mitohormetic role of gamitrinib-triphenylphosphonium (G-TPP), a mitochondrial heat shock protein (Hsp) inhibitor that can induce mild mitochondrial stress to protect cells from future insults in a FOXO-dependent manner.
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Truong T, Suriyanarayanan T, Zeng G, Le TD, Liu L, Li J, Tong C, Wang Y, Seneviratne CJ. Use of Haploid Model of Candida albicans to Uncover Mechanism of Action of a Novel Antifungal Agent. Front Cell Infect Microbiol 2018; 8:164. [PMID: 29938200 PMCID: PMC6002804 DOI: 10.3389/fcimb.2018.00164] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2018] [Accepted: 05/01/2018] [Indexed: 11/13/2022] Open
Abstract
Antifungal agents for the treatment of Candida albicans infections are limited. We recently discovered a novel antifungal small molecule, SM21, with promising in vivo activity. Herein, we employed the newly developed C. albicans haploid toolbox to uncover the mechanism of action of SM21. Comprehensive RNA-Seq analyses of the haploid susceptible GZY803 strain revealed significant gene expression changes related to mitochondria when exposed to SM21. Mitochondrial structure visualization and measurement of ATP generation, reactive oxygen species (ROS) levels, and the antioxidant potential of SM21-treated and untreated GZY803, mitochondrial structure defective haploid mutant (dnm1Δ), and wild-type diploid SC5314 strains confirmed defects in mitochondria. Exploiting the advantage of C. albicans haploids as a single ploidy model, we further exposed GZY803 to repetitive treatments of SM21 in order to generate resistant mutants. Three colonies designated S3, S5 and S6, which displayed resistance to SM21, were isolated. All resistant strains exhibited enhanced transcriptomic responses for peptide and protein metabolism and secreted aspartate proteases (SAPs) activity under SM21 treatment compared to the parent strain GZY803. Consistently, supplementing the resistant strains, GZY803, and SC5314 with peptone, a form of digested peptides, decreased susceptibility to SM21. The present study demonstrates the usefulness of haploid C. albicans model in antifungal drug discovery. The findings will be invaluable to develop SM21 as a novel antifungal agent, which will benefit millions of patients suffering from Candida infections.
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Affiliation(s)
- Thuyen Truong
- Oral Sciences, Faculty of Dentistry, National University of Singapore, Singapore, Singapore
| | | | - Guisheng Zeng
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research, Singapore, Singapore
| | - Thuc D Le
- School of Information Technology and Mathematical Sciences, University of South Australia, Adelaide, SA, Australia
| | - Lin Liu
- School of Information Technology and Mathematical Sciences, University of South Australia, Adelaide, SA, Australia
| | - Jiuyong Li
- School of Information Technology and Mathematical Sciences, University of South Australia, Adelaide, SA, Australia
| | - Cao Tong
- Oral Sciences, Faculty of Dentistry, National University of Singapore, Singapore, Singapore
| | - Yue Wang
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research, Singapore, Singapore.,Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Chaminda J Seneviratne
- Oral Sciences, Faculty of Dentistry, National University of Singapore, Singapore, Singapore
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