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McNamara JT, Zhu J, Wang Y, Li R. Gene dosage adaptations to mtDNA depletion and mitochondrial protein stress in budding yeast. G3 (BETHESDA, MD.) 2024; 14:jkad272. [PMID: 38126114 PMCID: PMC10849340 DOI: 10.1093/g3journal/jkad272] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2023] [Accepted: 11/14/2023] [Indexed: 12/23/2023]
Abstract
Mitochondria contain a local genome (mtDNA) comprising a small number of genes necessary for respiration, mitochondrial transcription and translation, and other vital functions. Various stressors can destabilize mtDNA leading to mtDNA loss. While some cells can survive mtDNA loss, they exhibit various deficiencies. Here, we investigated the impact of proteotoxicity on mitochondrial function by inducing mitochondrial unfolded protein stress in budding yeast. This led to rapid mtDNA loss, but aerobic conditioning imparted transient resistance to mitochondrial protein stress. We present a quantitative model of mtDNA loss in a growing cell population and measure its parameters. To identify genetic adaptations to mtDNA depletion, we performed a genome-wide screen for gene dosage increases that affect the growth of cells lacking mtDNA. The screen revealed a set of dosage suppressors that alleviate the growth impairment in mtDNA-deficient cells. Additionally, we show that these suppressors of mtDNA stress both bolster cell proliferation and prevent mtDNA loss during mitochondrial protein stress.
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Affiliation(s)
- Joshua T McNamara
- Center for Cell Dynamics and Department of Cell Biology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Biochemistry, Cellular and Molecular Biology (BCMB) Graduate Program, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Jin Zhu
- Mechanobiology Institute, National University of Singapore, Singapore 117411, Singapore
| | - Yuhao Wang
- Center for Cell Dynamics and Department of Cell Biology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Biochemistry, Cellular and Molecular Biology (BCMB) Graduate Program, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Rong Li
- Center for Cell Dynamics and Department of Cell Biology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Mechanobiology Institute, National University of Singapore, Singapore 117411, Singapore
- Department of Biological Sciences, National University of Singapore, Singapore 117411, Singapore
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Akgul R, Morgil H, Kizilkaya IT, Sarayloo E, Cevahir G, Akgul F, Kavakli IH. Transcriptomic and fatty acid analyses of Neochloris aquatica grown under different nitrogen concentration. Funct Integr Genomics 2022; 22:407-421. [PMID: 35286570 DOI: 10.1007/s10142-022-00838-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 02/25/2022] [Accepted: 02/28/2022] [Indexed: 11/28/2022]
Abstract
In this study, we characterized the fatty acid production in Neochloris aquatica at transcriptomics and biochemical levels under limiting, normal, and excess nitrate concentrations in different growth phases. At the stationary phase, N. aquatica mainly produced saturated fatty acids such as stearic acid under the limiting nitrate concentration, which is suitable for biodiesel production. However, it produced polyunsaturated fatty acids such as α-linolenic acid under the excess nitrate concentration, which has nutritional values as food supplements. In addition, RNA-seq was employed to identify genes and pathways that were being affected in N. aquatica for three growth phases in the presence of the different nitrate amounts. Genes that are responsible for the production of saturated fatty acids were upregulated in the cells grown under a limiting nitrogen amount while genes that are responsible for the production of polyunsaturated fatty acid were upregulated in the cells grown under excess nitrogen amount. Further analysis showed more genes differentially expressed (DEGs) at the logarithmic phase in all conditions while a relatively steady trend was observed during the transition from the logarithmic phase to the stationary phase under limiting and excess nitrogen. Our results provide a foundation for identifying developmentally important genes and understanding the biological processes in the different growth phases of the N. aquatica in terms of biomass and lipid production.
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Affiliation(s)
- Riza Akgul
- Burdur Food, Agriculture and Livestock Vocational High School, Mehmet Akif Ersoy University, Burdur, Turkey
| | - Hande Morgil
- Department of Biology, Istanbul University, Istanbul, Turkey.,Istanbul University Centre for Plant and Herbal Products Research-Development, 34126, Istanbul, Turkey
| | | | - Ehsan Sarayloo
- Department of Chemical and Biological Engineering, TUPRAS Energy Research Center, Koc University, Rumelifeneri Yolu, Sariyer, Istanbul, Turkey
| | - Gul Cevahir
- Department of Biology, Istanbul University, Istanbul, Turkey.,Istanbul University Centre for Plant and Herbal Products Research-Development, 34126, Istanbul, Turkey
| | - Fusun Akgul
- Department of Molecular Biology and Genetic, Faculty of Science and Arts, Mehmet Akif Ersoy University, Burdur, Turkey.
| | - Ibrahim Halil Kavakli
- Department of Chemical and Biological Engineering, TUPRAS Energy Research Center, Koc University, Rumelifeneri Yolu, Sariyer, Istanbul, Turkey. .,Department of Molecular Biology and Genetics, Koc University, Rumelifeneri Yolu, Sariyer, Istanbul, Turkey.
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Lewis AG, Caldwell R, Rogers JV, Ingaramo M, Wang RY, Soifer I, Hendrickson DG, McIsaac RS, Botstein D, Gibney PA. Loss of major nutrient sensing and signaling pathways suppresses starvation lethality in electron transport chain mutants. Mol Biol Cell 2021; 32:ar39. [PMID: 34668730 PMCID: PMC8694083 DOI: 10.1091/mbc.e21-06-0314] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022] Open
Abstract
The electron transport chain (ETC) is a well-studied and highly conserved metabolic pathway that produces ATP through generation of a proton gradient across the inner mitochondrial membrane coupled to oxidative phosphorylation. ETC mutations are associated with a wide array of human disease conditions and to aging-related phenotypes in a number of different organisms. In this study, we sought to better understand the role of the ETC in aging using a yeast model. A panel of ETC mutant strains that fail to survive starvation was used to isolate suppressor mutants that survive. These suppressors tend to fall into major nutrient sensing and signaling pathways, suggesting that the ETC is involved in proper starvation signaling to these pathways in yeast. These suppressors also partially restore ETC-associated gene expression and pH homeostasis defects, though it remains unclear whether these phenotypes directly cause the suppression or are simply effects. This work further highlights the complex cellular network connections between metabolic pathways and signaling events in the cell and their potential roles in aging and age-related diseases.
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Affiliation(s)
- Alisha G Lewis
- Department of Food Science, Cornell University, Ithaca, NY 14853
| | | | | | | | | | - Ilya Soifer
- Calico Life Sciences LLC, South San Francisco, CA 94080
| | | | | | | | - Patrick A Gibney
- Department of Food Science, Cornell University, Ithaca, NY 14853.,Calico Life Sciences LLC, South San Francisco, CA 94080
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Pkh1p-Ypk1p and Pkh1p-Sch9p Pathways Are Activated by Acetic Acid to Induce a Mitochondrial-Dependent Regulated Cell Death. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2020; 2020:7095078. [PMID: 32318242 PMCID: PMC7154982 DOI: 10.1155/2020/7095078] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Revised: 02/20/2020] [Accepted: 02/28/2020] [Indexed: 12/14/2022]
Abstract
The yeast Saccharomyces cerevisiae undergoes a mitochondrial-dependent regulated cell death (RCD) exhibiting typical markers of mammalian apoptosis. We have previously shown that ceramide production contributes to RCD induced by acetic acid and is involved in mitochondrial outer membrane permeabilization and cytochrome c release, especially through hydrolysis of complex sphingolipids catalyzed by Isc1p. Recently, we also showed that Sch9p regulates the translocation of Isc1p from the endoplasmic reticulum into mitochondria, perturbing sphingolipid balance and determining cell fate. In this study, we addressed the role of other signaling proteins in acetic acid-induced RCD. We found that single deletion of PKH1 or YPK1, as shown for SCH9 and ISC1, leads to an increase in cell survival in response to acetic acid and that Pkh1/2p-dependent phosphorylation of Ypk1p and Sch9p increases under these conditions. These results indicate that Pkh1p regulates acetic acid-induced RCD through Ypk1p and Sch9p. In addition, our results suggest that Pkh1p-Ypk1p is necessary for isc1Δ resistance to acetic acid-induced RCD. Moreover, double deletion of ISC1 and PKH1 has a drastic effect on cell survival associated with increased ROS accumulation and release of cytochrome c, which is counteracted by overexpression of the PKA pathway negative regulator PDE2. Overall, our results suggest that Pkh1p-Ypk1p and Pkh1p-Sch9p pathways contribute to RCD induced by acetic acid.
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Coyne LP, Chen XJ. mPOS is a novel mitochondrial trigger of cell death - implications for neurodegeneration. FEBS Lett 2017; 592:759-775. [PMID: 29090463 DOI: 10.1002/1873-3468.12894] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2017] [Revised: 10/14/2017] [Accepted: 10/26/2017] [Indexed: 12/14/2022]
Abstract
In addition to its central role in energy metabolism, the mitochondrion has many other functions essential for cell survival. When stressed, the multifunctional mitochondria are expected to engender multifaceted cell stress with complex physiological consequences. Potential extra-mitochondrial proteostatic burdens imposed by inefficient protein import have been largely overlooked. Accumulating evidence suggests that a diverse range of pathogenic mitochondrial stressors, which do not directly target the core protein import machinery, can reduce cell fitness by disrupting the proteostatic network in the cytosol. The resulting stress, named mitochondrial precursor overaccumulation stress (mPOS), is characterized by the toxic accumulation of unimported mitochondrial proteins in the cytosol. Here, we review our current understanding of how mitochondrial dysfunction can impact the cytosolic proteome and proteostatic signaling. We also discuss the intriguing possibility that the mPOS model may help untangle the cause-effect relationship between mitochondrial dysfunction and cytosolic protein aggregation, which are probably the two most prominent molecular hallmarks of neurodegenerative disease.
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Affiliation(s)
- Liam P Coyne
- Department of Biochemistry and Molecular Biology, State University of New York Upstate Medical University, Syracuse, NY, USA
| | - Xin Jie Chen
- Department of Biochemistry and Molecular Biology, State University of New York Upstate Medical University, Syracuse, NY, USA.,Department of Neuroscience and Physiology, State University of New York Upstate Medical University, Syracuse, NY, USA
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Eisenberg-Bord M, Schuldiner M. Ground control to major TOM: mitochondria-nucleus communication. FEBS J 2016; 284:196-210. [PMID: 27283924 DOI: 10.1111/febs.13778] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2016] [Revised: 05/23/2016] [Accepted: 06/08/2016] [Indexed: 01/13/2023]
Abstract
Mitochondria have crucial functions in the cell, including ATP generation, iron-sulfur cluster biogenesis, nucleotide biosynthesis, and amino acid metabolism. All of these functions require tight regulation on mitochondrial activity and homeostasis. As mitochondria biogenesis is controlled by the nucleus and almost all mitochondrial proteins are encoded by nuclear genes, a tight communication network between mitochondria and the nucleus has evolved, which includes signaling cascades, proteins which are dual-localized to the two compartments, and sensing of mitochondrial products by nuclear proteins. All of these enable a crosstalk between mitochondria and the nucleus that allows the 'ground control' to get information on mitochondria's status. Such information facilitates the creation of a cellular balance of mitochondrial status with energetic needs. This communication also allows a transcriptional response in case mitochondrial function is impaired aimed to restore mitochondrial homeostasis. As mitochondrial dysfunction is related to a growing number of genetic diseases as well as neurodegenerative conditions and aging, elucidating the mechanisms governing the mitochondrial/nuclear communication should progress a better understanding of mitochondrial dysfunctions.
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Affiliation(s)
| | - Maya Schuldiner
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
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