1
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Alimohamadi H, Luo EWC, Yang R, Gupta S, Nolden KA, Mandal T, Hill RB, Wong GCL. Dynamins combine mechano-constriction and membrane remodeling to enable two-step mitochondrial fission via a 'snap-through' instability. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.08.19.608723. [PMID: 39229060 PMCID: PMC11370335 DOI: 10.1101/2024.08.19.608723] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 09/05/2024]
Abstract
Mitochondrial fission is controlled by dynamin proteins, the dysregulation of which is correlated with diverse diseases. Fission dynamins are GTP hydrolysis-driven mechanoenzymes that self-oligomerize into helical structures that constrict membrane to achieve fission, but details are not well understood. However, dynamins can also remodel membranes by inducing negative Gaussian curvature, the type of curvature required for completion of fission. Here, we examine how these drastically different mechanisms synergistically exert their influences on a membrane, via a mechanical model calibrated with small-angle X-ray scattering structural data. We find that free dynamin can trigger a "snap-through instability" that enforces a shape transition from an oligomer-confined cylindrical membrane to a drastically narrower catenoid-shaped neck within the spontaneous hemi-fission regime, in a manner that depends critically on the length of the confined tube. These results indicate how the combination of dynamin assembly, and paradoxically disassembly, can lead to diverse pathways to scission. Teaser Dynamin mechano-constriction by assembly and curvature-driven instability by free monomers synergistically drive mitochondrial fission.
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2
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Langley CA, Dietzen PA, Emerman M, Tenthorey JL, Malik HS. Antiviral Mx proteins have an ancient origin and widespread distribution among eukaryotes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.08.06.606855. [PMID: 39149278 PMCID: PMC11326297 DOI: 10.1101/2024.08.06.606855] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/17/2024]
Abstract
First identified in mammals, Mx proteins are potent antivirals against a broad swathe of viruses. Mx proteins arose within the Dynamin superfamily of proteins (DSP), mediating critical cellular processes, such as endocytosis and mitochondrial, plastid, and peroxisomal dynamics. And yet, the evolutionary origins of Mx proteins are poorly understood. Using a series of phylogenomic analyses with stepwise increments in taxonomic coverage, we show that Mx proteins predate the interferon signaling system in vertebrates. Our analyses find an ancient monophyletic DSP lineage in eukaryotes that groups vertebrate and invertebrate Mx proteins with previously undescribed fungal MxF proteins, the relatively uncharacterized plant and algal Dynamin 4A/4C proteins, and representatives from several early-branching eukaryotic lineages. Thus, Mx-like proteins date back close to the origin of Eukarya. Our phylogenetic analyses also reveal that host-encoded and NCLDV (nucleocytoplasmic large DNA viruses)-encoded DSPs are interspersed in four distinct DSP lineages, indicating recurrent viral theft of host DSPs. Our analyses thus reveal an ancient history of viral and antiviral functions encoded by the Dynamin superfamily in eukaryotes.
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Affiliation(s)
- Caroline A. Langley
- Molecular and Cellular Biology Graduate Program, University of Washington, Seattle, WA
- Division of Human Biology, Fred Hutchinson Cancer Center, Seattle, WA
- Division of Basic Science, Fred Hutchinson Cancer Center, Seattle, WA
| | - Peter A. Dietzen
- Molecular and Cellular Biology Graduate Program, University of Washington, Seattle, WA
- Division of Human Biology, Fred Hutchinson Cancer Center, Seattle, WA
- Division of Basic Science, Fred Hutchinson Cancer Center, Seattle, WA
| | - Michael Emerman
- Division of Human Biology, Fred Hutchinson Cancer Center, Seattle, WA
- Division of Basic Science, Fred Hutchinson Cancer Center, Seattle, WA
| | - Jeannette L. Tenthorey
- Division of Basic Science, Fred Hutchinson Cancer Center, Seattle, WA
- Cellular Molecular Pharmacology, University of California San Francisco, San Francisco, CA
| | - Harmit S. Malik
- Division of Basic Science, Fred Hutchinson Cancer Center, Seattle, WA
- Howard Hughes Medical Institute, Fred Hutchinson Cancer Center, Seattle, WA
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3
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Lv W, Tu Y, Xu T, Zhang Y, Chen J, Yang N, Wang Y. The Mitochondrial Distribution and Morphology Family 33 Gene FgMDM33 Is Involved in Autophagy and Pathogenesis in Fusarium graminearum. J Fungi (Basel) 2024; 10:579. [PMID: 39194905 DOI: 10.3390/jof10080579] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2024] [Revised: 08/05/2024] [Accepted: 08/06/2024] [Indexed: 08/29/2024] Open
Abstract
The mitochondrial distribution and morphology family 33 gene (MDM33) regulates mitochondrial homeostasis by mediating the mitochondrial fission process in yeast. The wheat head blight Fusarium graminearum contains an FgMdm33 protein that is orthologous to Saccharomyces cerevisiae Mdm33, albeit its function remains unknown. We have reported here the roles of FgMdm33 in regulating fungal morphogenesis, mitochondrial morphology, autophagy, apoptosis, and fungal pathogenicity. The ΔFgmdm33 mutants generated through a homologous recombination strategy in this study exhibited defects in terms of mycelial growth, conidia production, and virulence. Hyphal cells lacking FgMDM33 displayed elongated mitochondria and a dispensable respiratory-deficient growth phenotype, indicating the possible involvement of FgMDM33 in mitochondrial fission. The ΔFgmdm33 mutants displayed a remarkable reduction in the proteolysis of GFP-FgAtg8, whereas the formation of autophagic bodies in the hyphal cells of mutants was recorded under the induction of mitophagy. In addition, the transcriptional expression of the apoptosis-inducing factor 1 gene (FgAIF1) was significantly upregulated in the ΔFgmdm33 mutants. Cumulatively, these results indicate that FgMDM33 is involved in mitochondrial fission, non-selective macroautophagy, and apoptosis and that it regulates fungal growth, conidiation, and pathogenicity of the head blight pathogen.
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Affiliation(s)
- Wuyun Lv
- College of Tea Science and Tea Culture, Zhejiang A&F University, Hangzhou 311300, China
| | - Yiyi Tu
- College of Tea Science and Tea Culture, Zhejiang A&F University, Hangzhou 311300, China
| | - Ting Xu
- College of Tea Science and Tea Culture, Zhejiang A&F University, Hangzhou 311300, China
| | - You Zhang
- College of Tea Science and Tea Culture, Zhejiang A&F University, Hangzhou 311300, China
| | - Junjie Chen
- College of Tea Science and Tea Culture, Zhejiang A&F University, Hangzhou 311300, China
| | - Nan Yang
- The People's Government Office of Bengbu City, Bengbu 233000, China
| | - Yuchun Wang
- College of Tea Science and Tea Culture, Zhejiang A&F University, Hangzhou 311300, China
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Alimohamadi H, Luo EWC, Gupta S, de Anda J, Yang R, Mandal T, Wong GCL. Comparing Multifunctional Viral and Eukaryotic Proteins for Generating Scission Necks in Membranes. ACS NANO 2024; 18:15545-15556. [PMID: 38838261 DOI: 10.1021/acsnano.4c00277] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2024]
Abstract
Deterministic formation of membrane scission necks by protein machinery with multiplexed functions is critical in biology. A microbial example is M2 viroporin, a proton pump from the influenza A virus that is multiplexed with membrane remodeling activity to induce budding and scission in the host membrane during viral maturation. In comparison, the dynamin family constitutes a class of eukaryotic proteins implicated in mitochondrial fission, as well as various budding and endocytosis pathways. In the case of Dnm1, the mitochondrial fission protein in yeast, the membrane remodeling activity is multiplexed with mechanoenzyme activity to create fission necks. It is not clear why these functions are combined in these scission processes, which occur in drastically different compositions and solution conditions. In general, direct experimental access to changing neck sizes induced by individual proteins or peptide fragments is challenging due to the nanoscale dimensions and influence of thermal fluctuations. Here, we use a mechanical model to estimate the size of scission necks by leveraging small-angle X-ray scattering structural data of protein-lipid systems under different conditions. The influence of interfacial tension, lipid composition, and membrane budding morphology on the size of the induced scission necks is systematically investigated using our data and molecular dynamic simulations. We find that the M2 budding protein from the influenza A virus has robust pH-dependent membrane activity that induces nanoscopic necks within the range of spontaneous hemifission for a broad range of lipid compositions. In contrast, the sizes of scission necks generated by mitochondrial fission proteins strongly depend on lipid composition, which suggests a role for mechanical constriction.
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Affiliation(s)
- Haleh Alimohamadi
- Department of Bioengineering, University of California, Los Angeles, Los Angeles, California 90025, United States
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095, United States
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, California 90095, United States
- California NanoSystems Institute, University of California, Los Angeles, California 90095, United States
| | - Elizabeth Wei-Chia Luo
- Department of Bioengineering, University of California, Los Angeles, Los Angeles, California 90025, United States
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095, United States
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, California 90095, United States
- California NanoSystems Institute, University of California, Los Angeles, California 90095, United States
| | - Shivam Gupta
- Department of Physics, Indian Institute of Technology Kanpur, Kanpur 208016, India
| | - Jaime de Anda
- Department of Bioengineering, University of California, Los Angeles, Los Angeles, California 90025, United States
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095, United States
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, California 90095, United States
- California NanoSystems Institute, University of California, Los Angeles, California 90095, United States
| | - Rena Yang
- Department of Bioengineering, University of California, Los Angeles, Los Angeles, California 90025, United States
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095, United States
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, California 90095, United States
- California NanoSystems Institute, University of California, Los Angeles, California 90095, United States
| | - Taraknath Mandal
- Department of Physics, Indian Institute of Technology Kanpur, Kanpur 208016, India
| | - Gerard C L Wong
- Department of Bioengineering, University of California, Los Angeles, Los Angeles, California 90025, United States
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095, United States
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, California 90095, United States
- California NanoSystems Institute, University of California, Los Angeles, California 90095, United States
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5
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Furukawa K, Hayatsu M, Okuyama K, Fukuda T, Yamashita SI, Inoue K, Shibata S, Kanki T. Atg44/Mdi1/mitofissin facilitates Dnm1-mediated mitochondrial fission. Autophagy 2024:1-9. [PMID: 38818923 DOI: 10.1080/15548627.2024.2360345] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2023] [Accepted: 05/22/2024] [Indexed: 06/01/2024] Open
Abstract
Mitochondria undergo fission and fusion, and their coordinated balance is crucial for maintaining mitochondrial homeostasis. In yeast, the dynamin-related protein Dnm1 is a mitochondrial fission factor acting from outside the mitochondria. We recently reported the mitochondrial intermembrane space protein Atg44/mitofissin/Mdi1/Mco8 as a novel fission factor, but the relationship between Atg44 and Dnm1 remains elusive. Here, we show that Atg44 is required to complete Dnm1-mediated mitochondrial fission under homeostatic conditions. Atg44-deficient cells often exhibit enlarged mitochondria with accumulated Dnm1 and rosary-like mitochondria with Dnm1 foci at constriction sites. These mitochondrial constriction sites retain the continuity of both the outer and inner membranes within an extremely confined space, indicating that Dnm1 is unable to complete mitochondrial fission without Atg44. Moreover, accumulated Atg44 proteins are observed at mitochondrial constriction sites. These findings suggest that Atg44 and Dnm1 cooperatively execute mitochondrial fission from inside and outside the mitochondria, respectively.Abbreviation: ATG: autophagy related; CLEM: correlative light and electron microscopy; EM: electron microscopy; ER: endoplasmic reticulum; ERMES: endoplasmic reticulum-mitochondria encounter structure; GA: glutaraldehyde; GFP: green fluorescent protein; GTP: guanosine triphosphate: IMM: inner mitochondrial membrane; IMS: intermembrane space; OMM: outer mitochondrial membrane; PB: phosphate buffer; PBS: phosphate-buffered saline; PFA: paraformaldehyde; RFP: red fluorescent protein; WT: wild type.
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Affiliation(s)
- Kentaro Furukawa
- Department of Cellular Physiology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
- Department of Cellular Physiology, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - Manabu Hayatsu
- Division of Microscopic Anatomy, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - Kentaro Okuyama
- Division of Microscopic Anatomy, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - Tomoyuki Fukuda
- Department of Cellular Physiology, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - Shun-Ichi Yamashita
- Department of Cellular Physiology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
- Department of Cellular Physiology, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - Keiichi Inoue
- Department of Cellular Physiology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
- Department of Cellular Physiology, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - Shinsuke Shibata
- Division of Microscopic Anatomy, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - Tomotake Kanki
- Department of Cellular Physiology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
- Department of Cellular Physiology, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
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6
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Ma X, Niu M, Ni HM, Ding WX. Mitochondrial dynamics, quality control, and mtDNA in alcohol-associated liver disease and liver cancer. Hepatology 2024:01515467-990000000-00861. [PMID: 38683546 DOI: 10.1097/hep.0000000000000910] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/24/2024] [Accepted: 04/05/2024] [Indexed: 05/01/2024]
Abstract
Mitochondria are intracellular organelles responsible for energy production, glucose and lipid metabolism, cell death, cell proliferation, and innate immune response. Mitochondria are highly dynamic organelles that constantly undergo fission, fusion, and intracellular trafficking, as well as degradation and biogenesis. Mitochondrial dysfunction has been implicated in a variety of chronic liver diseases including alcohol-associated liver disease, metabolic dysfunction-associated steatohepatitis, and HCC. In this review, we provide a detailed overview of mitochondrial dynamics, mitophagy, and mitochondrial DNA-mediated innate immune response, and how dysregulation of these mitochondrial processes affects the pathogenesis of alcohol-associated liver disease and HCC. Mitochondrial dynamics and mitochondrial DNA-mediated innate immune response may thereby represent an attractive therapeutic target for ameliorating alcohol-associated liver disease and alcohol-associated HCC.
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Affiliation(s)
- Xiaowen Ma
- Department of Pharmacology, Toxicology and Therapeutics, University of Kansas Medical Center, Kansas City, Kansas, USA
| | - Mengwei Niu
- Department of Pharmacology, Toxicology and Therapeutics, University of Kansas Medical Center, Kansas City, Kansas, USA
| | - Hong-Min Ni
- Department of Pharmacology, Toxicology and Therapeutics, University of Kansas Medical Center, Kansas City, Kansas, USA
| | - Wen-Xing Ding
- Department of Pharmacology, Toxicology and Therapeutics, University of Kansas Medical Center, Kansas City, Kansas, USA
- Department of Internal Medicine, Division of Gastroenterology, Hepatology and Mobility, University of Kansas Medical Center, Kansas City, Kansas, USA
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7
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Plank M, Carmiol N, Mitri B, Lipinski AA, Langlais PR, Capaldi AP. Systems level analysis of time and stimuli specific signaling through PKA. Mol Biol Cell 2024; 35:ar60. [PMID: 38446618 PMCID: PMC11064662 DOI: 10.1091/mbc.e23-02-0066] [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: 02/23/2023] [Revised: 02/13/2024] [Accepted: 03/01/2024] [Indexed: 03/08/2024] Open
Abstract
It is well known that eukaryotic cells create gradients of cAMP across space and time to regulate the cAMP dependent protein kinase (PKA) and, in turn, growth and metabolism. However, it is unclear how PKA responds to different concentrations of cAMP. Here, to address this question, we examine PKA signaling in Saccharomyces cerevisiae in different conditions, timepoints, and concentrations of the chemical inhibitor 1-NM-PP1, using phosphoproteomics. These experiments show that there are numerous proteins that are only phosphorylated when cAMP and PKA activity are at/near their maximum level, while other proteins are phosphorylated even when cAMP levels and PKA activity are low. The data also show that PKA drives cells into distinct growth states by acting on proteins with different thresholds for phosphorylation in different conditions. Analysis of the sequences surrounding the 118 PKA-dependent phosphosites suggests that the phosphorylation thresholds are set, at least in part, by the affinity of PKA for each site.
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Affiliation(s)
- Michael Plank
- Department of Molecular and Cellular Biology, University of Arizona, Tucson, AZ 85721
- The Bio5 Institute, University of Arizona, Tucson, AZ 85721
| | - Nicole Carmiol
- Department of Molecular and Cellular Biology, University of Arizona, Tucson, AZ 85721
| | - Bassam Mitri
- Department of Molecular and Cellular Biology, University of Arizona, Tucson, AZ 85721
| | | | - Paul R. Langlais
- The Department of Medicine, University of Arizona, Tucson, AZ 85721
| | - Andrew P. Capaldi
- Department of Molecular and Cellular Biology, University of Arizona, Tucson, AZ 85721
- The Bio5 Institute, University of Arizona, Tucson, AZ 85721
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8
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Shiino H, Tashiro S, Hashimoto M, Sakata Y, Hosoya T, Endo T, Kojima H, Tamura Y. Chemical inhibition of phosphatidylcholine biogenesis reveals its role in mitochondrial division. iScience 2024; 27:109189. [PMID: 38420588 PMCID: PMC10901091 DOI: 10.1016/j.isci.2024.109189] [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: 10/31/2023] [Revised: 12/19/2023] [Accepted: 02/06/2024] [Indexed: 03/02/2024] Open
Abstract
Phospholipids are major components of biological membranes and play structural and regulatory roles in various biological processes. To determine the biological significance of phospholipids, the use of chemical inhibitors of phospholipid metabolism offers an effective approach; however, the availability of such compounds is limited. In this study, we performed a chemical-genetic screening using yeast and identified small molecules capable of inhibiting phosphatidylcholine (PC) biogenesis, which we designated PC inhibitors 1, 2, 3, and 4 (PCiB-1, 2, 3, and 4). Biochemical analyses indicated that PCiB-2, 3, and 4 inhibited the phosphatidylethanolamine (PE) methyltransferase activity of Cho2, whereas PCiB-1 may inhibit PE transport from mitochondria to the endoplasmic reticulum (ER). Interestingly, we found that PCiB treatment resulted in mitochondrial fragmentation, which was suppressed by expression of a dominant-negative mutant of the mitochondrial division factor Dnm1. These results provide evidence that normal PC biogenesis is important for the regulation of mitochondrial division.
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Affiliation(s)
- Hiroya Shiino
- Graduate School of Global Symbiotic Sciences, Yamagata University, 1-4-12 Kojirakawa-machi, Yamagata 990-8560, Japan
| | - Shinya Tashiro
- Faculty of Science, Yamagata University, 1-4-12 Kojirakawa-machi, Yamagata, Yamagata 990-8560, Japan
| | - Michiko Hashimoto
- Faculty of Science, Yamagata University, 1-4-12 Kojirakawa-machi, Yamagata, Yamagata 990-8560, Japan
| | - Yuki Sakata
- Laboratory of Chemical Bioscience, Institute of Biomaterials and Bioengineering, Tokyo Medical and Dental University (TMDU), 2-3-10 Kanda-Surugadai, Chiyoda-ku, Tokyo 101-0062, Japan
| | - Takamitsu Hosoya
- Laboratory of Chemical Bioscience, Institute of Biomaterials and Bioengineering, Tokyo Medical and Dental University (TMDU), 2-3-10 Kanda-Surugadai, Chiyoda-ku, Tokyo 101-0062, Japan
| | - Toshiya Endo
- Faculty of Life Sciences, Kyoto Sangyo University, Kamigamo-motoyama, Kyoto 603-8555, Japan
- Institute for Protein Dynamics, Kyoto Sangyo University, Kamigamo-motoyama, Kyoto 603-8555, Japan
| | - Hirotatsu Kojima
- Drug Discovery Initiative, Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Yasushi Tamura
- Faculty of Science, Yamagata University, 1-4-12 Kojirakawa-machi, Yamagata, Yamagata 990-8560, Japan
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9
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Yoshii SR, Barral Y. Fission-independent compartmentalization of mitochondria during budding yeast cell division. J Cell Biol 2024; 223:e202211048. [PMID: 38180475 PMCID: PMC10783438 DOI: 10.1083/jcb.202211048] [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: 11/13/2022] [Revised: 07/14/2023] [Accepted: 12/14/2023] [Indexed: 01/06/2024] Open
Abstract
Lateral diffusion barriers compartmentalize membranes to generate polarity or asymmetrically partition membrane-associated macromolecules. Budding yeasts assemble such barriers in the endoplasmic reticulum (ER) and the outer nuclear envelope at the bud neck to retain aging factors in the mother cell and generate naïve and rejuvenated daughter cells. However, little is known about whether other organelles are similarly compartmentalized. Here, we show that the membranes of mitochondria are laterally compartmentalized at the bud neck and near the cell poles. The barriers in the inner mitochondrial membrane are constitutive, whereas those in the outer membrane form in response to stresses. The strength of mitochondrial diffusion barriers is regulated positively by spatial cues from the septin axis and negatively by retrograde (RTG) signaling. These data indicate that mitochondria are compartmentalized in a fission-independent manner. We propose that these diffusion barriers promote mitochondrial polarity and contribute to mitochondrial quality control.
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Affiliation(s)
- Saori R. Yoshii
- Department of Biology, Institute of Biochemistry, ETH Zürich, Zürich, Switzerland
- Department of Biochemistry and Molecular Biology, Graduate School and Faculty of Medicine, The University of Tokyo, Tokyo, Japan
| | - Yves Barral
- Department of Biology, Institute of Biochemistry, ETH Zürich, Zürich, Switzerland
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10
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Mannino PJ, Perun A, Surovstev I, Ader NR, Shao L, Melia TJ, King MC, Lusk CP. A quantitative ultrastructural timeline of nuclear autophagy reveals a role for dynamin-like protein 1 at the nuclear envelope. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.14.580336. [PMID: 38405892 PMCID: PMC10888867 DOI: 10.1101/2024.02.14.580336] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/27/2024]
Abstract
Autophagic mechanisms that maintain nuclear envelope homeostasis are bulwarks to aging and disease. By leveraging 4D lattice light sheet microscopy and correlative light and electron tomography, we define a quantitative and ultrastructural timeline of a nuclear macroautophagy (nucleophagy) pathway in yeast. Nucleophagy initiates with a rapid local accumulation of the nuclear cargo adaptor Atg39 at the nuclear envelope adjacent to the nucleus-vacuole junction and is delivered to the vacuole in ~300 seconds through an autophagosome intermediate. Mechanistically, nucleophagy incorporates two consecutive and genetically defined membrane fission steps: inner nuclear membrane (INM) fission generates a lumenal vesicle in the perinuclear space followed by outer nuclear membrane (ONM) fission to liberate a double membraned vesicle to the cytosol. ONM fission occurs independently of phagophore engagement and instead relies surprisingly on dynamin-like protein1 (Dnm1), which is recruited to sites of Atg39 accumulation at the nuclear envelope. Loss of Dnm1 compromises nucleophagic flux by stalling nucleophagy after INM fission. Our findings reveal how nuclear and INM cargo are removed from an intact nucleus without compromising its integrity, achieved in part by a non-canonical role for Dnm1 in nuclear envelope remodeling.
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Affiliation(s)
- Philip J. Mannino
- Department of Cell Biology, Yale School of Medicine, 295 Congress Ave, New Haven, CT, 06520
| | - Andrew Perun
- Department of Cell Biology, Yale School of Medicine, 295 Congress Ave, New Haven, CT, 06520
| | - Ivan Surovstev
- Department of Cell Biology, Yale School of Medicine, 295 Congress Ave, New Haven, CT, 06520
- Department of Physics, Yale University, New Haven, CT, 06511
| | - Nicholas R. Ader
- Department of Cell Biology, Yale School of Medicine, 295 Congress Ave, New Haven, CT, 06520
| | - Lin Shao
- Department of Cell Biology, Yale School of Medicine, 295 Congress Ave, New Haven, CT, 06520
| | - Thomas J. Melia
- Department of Cell Biology, Yale School of Medicine, 295 Congress Ave, New Haven, CT, 06520
| | - Megan C. King
- Department of Cell Biology, Yale School of Medicine, 295 Congress Ave, New Haven, CT, 06520
- Department of Molecular Cellular and Developmental Biology, Yale University, New Haven, CT, 06511
| | - C. Patrick Lusk
- Department of Cell Biology, Yale School of Medicine, 295 Congress Ave, New Haven, CT, 06520
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11
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Alimohamadi H, Luo EWC, Gupta S, de Anda J, Yang R, Mandal T, Wong GCL. Comparing multifunctional viral and eukaryotic proteins for generating scission necks in membranes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.05.574447. [PMID: 38260291 PMCID: PMC10802413 DOI: 10.1101/2024.01.05.574447] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
Deterministic formation of membrane scission necks by protein machinery with multiplexed functions is critical in biology. A microbial example is the M2 viroporin, a proton pump from the influenza A virus which is multiplexed with membrane remodeling activity to induce budding and scission in the host membrane during viral maturation. In comparison, the dynamin family constitutes a class of eukaryotic proteins implicated in mitochondrial fission, as well as various budding and endocytosis pathways. In the case of Dnm1, the mitochondrial fission protein in yeast, the membrane remodeling activity is multiplexed with mechanoenzyme activity to create fission necks. It is not clear why these functions are combined in these scission processes, which occur in drastically different compositions and solution conditions. In general, direct experimental access to changing neck sizes induced by individual proteins or peptide fragments is challenging due to the nanoscale dimensions and influence of thermal fluctuations. Here, we use a mechanical model to estimate the size of scission necks by leveraging Small-Angle X-ray Scattering (SAXS) structural data of protein-lipid systems under different conditions. The influence of interfacial tension, lipid composition, and membrane budding morphology on the size of the induced scission necks is systematically investigated using our data and molecular dynamic simulations. We find that the M2 budding protein from the influenza A virus has robust pH-dependent membrane activity that induces nanoscopic necks within the range of spontaneous hemi-fission for a broad range of lipid compositions. In contrast, the sizes of scission necks generated by mitochondrial fission proteins strongly depend on lipid composition, which suggests a role for mechanical constriction.
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12
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Banerjee R, Mukherjee A, Adhikary A, Sharma S, Hussain MS, Ali ME, Nagotu S. Insights into the role of the conserved GTPase domain residues T62 and S277 in yeast Dnm1. Int J Biol Macromol 2023; 253:127381. [PMID: 37838106 DOI: 10.1016/j.ijbiomac.2023.127381] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Revised: 09/10/2023] [Accepted: 10/09/2023] [Indexed: 10/16/2023]
Abstract
Mitochondrial division is a highly regulated process. The master regulator of this process is the multi-domain, conserved protein called Dnm1 in yeast. In this study, we systematically analyzed two residues, T62 and S277, reported to be putatively phosphorylated in the GTPase domain of the protein. These residues lie in the G2 and G5 motifs of the GTPase domain. Both residues are important for the function of the protein, as evident from in vivo and in vitro analysis of the non-phosphorylatable and phosphomimetic variants. Dnm1T62A/D and Dnm1S277A/D showed differences with respect to the protein localization and puncta dynamics in vivo, albeit both were non-functional as assessed by mitochondrial morphology and GTPase activity. Overall, the secondary structure of the protein variants was unaltered, but local conformational changes were observed. Interestingly, both Dnm1T62A/D and Dnm1S277A/D exhibited dominant-negative behavior when expressed in cells containing endogenous Dnm1. To our knowledge, we report for the first time a single residue (S277) change that does not alter the localization of Dnm1 but makes it non-functional in a dominant-negative manner. Intriguingly, the two residues analyzed in this study are present in the same domain but exhibit variable effects when mutated to alanine or aspartic acid.
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Affiliation(s)
- Riddhi Banerjee
- Organelle Biology and Cellular Ageing Lab, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati 781039, Assam, India
| | - Agradeep Mukherjee
- Organelle Biology and Cellular Ageing Lab, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati 781039, Assam, India
| | - Ankita Adhikary
- Organelle Biology and Cellular Ageing Lab, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati 781039, Assam, India
| | - Shikha Sharma
- Institute of Nano Science and Technology, Knowledge City, Sector-81, Mohali, Punjab 140306, India
| | - Md Saddam Hussain
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati 781039, Assam, India
| | - Md Ehesan Ali
- Institute of Nano Science and Technology, Knowledge City, Sector-81, Mohali, Punjab 140306, India
| | - Shirisha Nagotu
- Organelle Biology and Cellular Ageing Lab, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati 781039, Assam, India.
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13
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Nolden KA, Harwig MC, Hill RB. Human Fis1 directly interacts with Drp1 in an evolutionarily conserved manner to promote mitochondrial fission. J Biol Chem 2023; 299:105380. [PMID: 37866629 PMCID: PMC10694664 DOI: 10.1016/j.jbc.2023.105380] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2023] [Revised: 09/30/2023] [Accepted: 10/11/2023] [Indexed: 10/24/2023] Open
Abstract
Mitochondrial fission protein 1 (Fis1) and dynamin-related protein 1 (Drp1) are the only two proteins evolutionarily conserved for mitochondrial fission, and directly interact in Saccharomyces cerevisiae to facilitate membrane scission. However, it remains unclear if a direct interaction is conserved in higher eukaryotes as other Drp1 recruiters, not present in yeast, are known. Using NMR, differential scanning fluorimetry, and microscale thermophoresis, we determined that human Fis1 directly interacts with human Drp1 (KD = 12-68 μM), and appears to prevent Drp1 assembly, but not GTP hydrolysis. Similar to yeast, the Fis1-Drp1 interaction appears governed by two structural features of Fis1: its N-terminal arm and a conserved surface. Alanine scanning mutagenesis of the arm identified both loss-of-function and gain-of-function alleles with mitochondrial morphologies ranging from highly elongated (N6A) to highly fragmented (E7A), demonstrating a profound ability of Fis1 to govern morphology in human cells. An integrated analysis identified a conserved Fis1 residue, Y76, that upon substitution to alanine, but not phenylalanine, also caused highly fragmented mitochondria. The similar phenotypic effects of the E7A and Y76A substitutions, along with NMR data, support that intramolecular interactions occur between the arm and a conserved surface on Fis1 to promote Drp1-mediated fission as in S. cerevisiae. These findings indicate that some aspects of Drp1-mediated fission in humans derive from direct Fis1-Drp1 interactions that are conserved across eukaryotes.
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Affiliation(s)
- Kelsey A Nolden
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Megan C Harwig
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - R Blake Hill
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, Wisconsin, USA.
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14
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Datta D. Interrogating the Etiology of Sporadic Alzheimer's Disease Using Aging Rhesus Macaques: Cellular, Molecular, and Cortical Circuitry Perspectives. J Gerontol A Biol Sci Med Sci 2023; 78:1523-1534. [PMID: 37279946 PMCID: PMC10460555 DOI: 10.1093/gerona/glad134] [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: 11/16/2022] [Indexed: 06/08/2023] Open
Abstract
Aging is the most significant risk factor for neurodegenerative disorders such as Alzheimer's disease (AD) associated with profound socioeconomic and personal costs. Consequently, there is an urgent need for animal models that recapitulate the age-related spatial and temporal complexity and patterns of pathology identical to human AD. Our research in aging nonhuman primate models involving rhesus macaques has revealed naturally occurring amyloid and tau pathology, including the formation of amyloid plaques and neurofibrillary tangles comprising hyperphosphorylated tau. Moreover, rhesus macaques exhibit synaptic dysfunction in association cortices and cognitive impairments with advancing age, and thus can be used to interrogate the etiological mechanisms that generate neuropathological cascades in sporadic AD. Particularly, unique molecular mechanisms (eg, feedforward cyclic adenosine 3',5'-monophosphate [cAMP]-Protein kinase A (PKA)-calcium signaling) in the newly evolved primate dorsolateral prefrontal cortex are critical for persistent firing required for subserving higher-order cognition. For example, dendritic spines in primate dorsolateral prefrontal cortex contain a specialized repertoire of proteins to magnify feedforward cAMP-PKA-calcium signaling such as N-methyl-d-aspartic acid receptors and calcium channels on the smooth endoplasmic reticulum (eg, ryanodine receptors). This process is constrained by phosphodiesterases (eg, PDE4) that hydrolyze cAMP and calcium-buffering proteins (eg, calbindin) in the cytosol. However, genetic predispositions and age-related insults exacerbate feedforward cAMP-Protein kinase A-calcium signaling pathways that induce a myriad of downstream effects, including the opening of K+ channels to weaken network connectivity, calcium-mediated dysregulation of mitochondria, and activation of inflammatory cascades to eliminate synapses, thereby increasing susceptibility to atrophy. Therefore, aging rhesus macaques provide an invaluable model to explore novel therapeutic strategies in sporadic AD.
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Affiliation(s)
- Dibyadeep Datta
- Department of Psychiatry, Yale University School of Medicine, New Haven, Connecticut, USA
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15
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Nolden KA, Harwig MC, Hill RB. Human Fis1 directly interacts with Drp1 in an evolutionarily conserved manner to promote mitochondrial fission. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.03.539292. [PMID: 37205551 PMCID: PMC10187221 DOI: 10.1101/2023.05.03.539292] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Mitochondrial Fission Protein 1 (Fis1) and Dynamin Related Protein 1 (Drp1) are the only two proteins evolutionarily conserved for mitochondrial fission, and directly interact in S. cerevisiae to facilitate membrane scission. However, it remains unclear if a direct interaction is conserved in higher eukaryotes as other Drp1 recruiters, not present in yeast, are known. Using NMR, differential scanning fluorimetry, and microscale thermophoresis, we determined that human Fis1 directly interacts with human Drp1 ( K D = 12-68 µM), and appears to prevent Drp1 assembly, but not GTP hydrolysis. Similar to yeast, the Fis1-Drp1 interaction appears governed by two structural features of Fis1: its N-terminal arm and a conserved surface. Alanine scanning mutagenesis of the arm identified both loss- and gain-of-function alleles with mitochondrial morphologies ranging from highly elongated (N6A) to highly fragmented (E7A) demonstrating a profound ability of Fis1 to govern morphology in human cells. An integrated analysis identified a conserved Fis1 residue, Y76, that upon substitution to alanine, but not phenylalanine, also caused highly fragmented mitochondria. The similar phenotypic effects of the E7A and Y76A substitutions, along with NMR data, support that intramolecular interactions occur between the arm and a conserved surface on Fis1 to promote Drp1-mediated fission as in S. cerevisiae . These findings indicate that some aspects of Drp1-mediated fission in humans derive from direct Fis1-Drp1 interactions that are conserved across eukaryotes.
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16
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Quintana-Cabrera R, Scorrano L. Determinants and outcomes of mitochondrial dynamics. Mol Cell 2023; 83:857-876. [PMID: 36889315 DOI: 10.1016/j.molcel.2023.02.012] [Citation(s) in RCA: 58] [Impact Index Per Article: 58.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2022] [Revised: 01/13/2023] [Accepted: 02/13/2023] [Indexed: 03/09/2023]
Abstract
Mitochondria are not only central organelles in metabolism and energy conversion but are also platforms for cellular signaling cascades. Classically, the shape and ultrastructure of mitochondria were depicted as static. The discovery of morphological transitions during cell death and of conserved genes controlling mitochondrial fusion and fission contributed to establishing the concept that mitochondrial morphology and ultrastructure are dynamically regulated by mitochondria-shaping proteins. These finely tuned, dynamic changes in mitochondrial shape can in turn control mitochondrial function, and their alterations in human diseases suggest that this space can be explored for drug discovery. Here, we review the basic tenets and molecular mechanisms of mitochondrial morphology and ultrastructure, describing how they can coordinately define mitochondrial function.
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Affiliation(s)
| | - Luca Scorrano
- Veneto Institute of Molecular Medicine, Via Orus 2, 35129 Padova, Italy; Department of Biology, University of Padova, Via U. Bassi 58B, 35121 Padova, Italy.
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17
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Prem PN, Chellappan DR, Kurian GA. High-fat diet-induced mitochondrial dysfunction is associated with loss of protection from ischemic preconditioning in renal ischemia reperfusion. Pflugers Arch 2023; 475:637-653. [PMID: 36867229 DOI: 10.1007/s00424-023-02799-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Revised: 02/21/2023] [Accepted: 02/21/2023] [Indexed: 03/04/2023]
Abstract
Consumption of high-fat diet (HFD) promotes mitochondrial dysfunction and the latter act as a critical factor in determining the severity of ischemia-reperfusion (IR) injury in different cell types. Ischemic preconditioning (IPC), a well-known protocol that render IR protection in kidney works via mitochondria. In the present study, we evaluated how HFD kidney with underlying mitochondrial changes respond to precondition protocol after IR induction. Wistar male rats were used in this study and were divided into two groups: SD (standard diet; n = 18) and HFD (high-fat diet; n = 18), which were further subdivided into sham, ischemia-reperfusion, and precondition groups at the end of the dietary regimen. Blood biochemistry, renal injury marker, creatinine clearance (CrCl), mitochondrial quality (fission, fusion, and phagy), mitochondrial function via ETC enzyme activities and respiration, and signalling pathway were analysed. Sixteen weeks of HFD administration to the rat deteriorated the renal mitochondrial health measured via 10% decline in mitochondrial respiration index ADP/O (in GM), reduced mitochondrial copy number (55%), biogenesis (56%), low bioenergetics potential (19% complex I + III and 15% complex II + III), increased oxidative stress, and reduced expression of mitochondrial fusion genes compared with SD rats. IR procedure in HFD rat kidney inflicted significant mitochondrial dysfunction and further deteriorated copy number along with impaired mitophagy and mitochondrial dynamics. IPC could effectively ameliorate the renal ischemia injury in normal rat but failed to provide similar kind of protection in HFD rat kidney. Even though the IR-associated mitochondrial dysfunction in both normal and HFD rats were similar, the magnitude of overall dysfunction and corresponding renal injury and compromised physiology was high in HFD rats. This observation was further confirmed via in vitro protein translation assay in isolated mitochondria from normal and HFD rat kidney that showed significantly reduction in the response ability of mitochondria in HFD. In conclusion, the deteriorated mitochondrial function and its quality along with low mitochondrial copy number and downregulation of mitochondrial dynamic gene exhibited by HFD rat kidney augments the sensitivity of renal tissue towards the IR injury which leads to the compromised protective ability by ischemic preconditioning.
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Affiliation(s)
- Priyanka N Prem
- School of Chemical and Biotechnology, SASTRA Deemed University, Tirumalaisamudram, Thanjavur, Tamil Nadu, India
| | - David Raj Chellappan
- School of Chemical and Biotechnology, SASTRA Deemed University, Tirumalaisamudram, Thanjavur, Tamil Nadu, India
| | - Gino A Kurian
- School of Chemical and Biotechnology, SASTRA Deemed University, Tirumalaisamudram, Thanjavur, Tamil Nadu, India. .,Vascular Biology Lab, School of Chemical and Biotechnology, SASTRA Deemed University, Thanjavur, India.
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18
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Pal A, Paripati A, Deolal P, Chatterjee A, Prasad PR, Adla P, Sepuri NBV. Eisosome protein Pil1 regulates mitochondrial morphology, mitophagy, and cell death in Saccharomyces cerevisiae. J Biol Chem 2022; 298:102533. [PMID: 36162502 PMCID: PMC9619184 DOI: 10.1016/j.jbc.2022.102533] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 09/18/2022] [Accepted: 09/19/2022] [Indexed: 12/06/2022] Open
Abstract
Mitochondrial morphology and dynamics maintain mitochondrial integrity by regulating its size, shape, distribution, and connectivity, thereby modulating various cellular processes. Several studies have established a functional link between mitochondrial dynamics, mitophagy, and cell death, but further investigation is needed to identify specific proteins involved in mitochondrial dynamics. Any alteration in the integrity of mitochondria has severe ramifications that include disorders like cancer and neurodegeneration. In this study, we used budding yeast as a model organism and found that Pil1, the major component of the eisosome complex, also localizes to the periphery of mitochondria. Interestingly, the absence of Pil1 causes the branched tubular morphology of mitochondria to be abnormally fused or aggregated, whereas its overexpression leads to mitochondrial fragmentation. Most importantly, pil1Δ cells are defective in mitophagy and bulk autophagy, resulting in elevated levels of reactive oxygen species and protein aggregates. In addition, we show that pil1Δ cells are more prone to cell death. Yeast two-hybrid analysis and co-immunoprecipitations show the interaction of Pil1 with two major proteins in mitochondrial fission, Fis1 and Dnm1. Additionally, our data suggest that the role of Pil1 in maintaining mitochondrial shape is dependent on Fis1 and Dnm1, but it functions independently in mitophagy and cell death pathways. Together, our data suggest that Pil1, an eisosome protein, is a novel regulator of mitochondrial morphology, mitophagy, and cell death.
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Affiliation(s)
- Amita Pal
- Department of Biochemistry, University of Hyderabad, Prof. C.R Rao Road, Gachibowli, Hyderabad, TS -500046
| | - Arunkumar Paripati
- Department of Biochemistry, University of Hyderabad, Prof. C.R Rao Road, Gachibowli, Hyderabad, TS -500046
| | - Pallavi Deolal
- Department of Biochemistry, University of Hyderabad, Prof. C.R Rao Road, Gachibowli, Hyderabad, TS -500046
| | - Arpan Chatterjee
- Department of Biochemistry, University of Hyderabad, Prof. C.R Rao Road, Gachibowli, Hyderabad, TS -500046
| | - Pushpa Rani Prasad
- Department of Biochemistry, University of Hyderabad, Prof. C.R Rao Road, Gachibowli, Hyderabad, TS -500046
| | - Priyanka Adla
- Department of Biochemistry, University of Hyderabad, Prof. C.R Rao Road, Gachibowli, Hyderabad, TS -500046
| | - Naresh Babu V Sepuri
- Department of Biochemistry, University of Hyderabad, Prof. C.R Rao Road, Gachibowli, Hyderabad, TS -500046.
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19
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The E3 Ubiquitin Ligase SYVN1 Plays an Antiapoptotic Role in Polycystic Ovary Syndrome by Regulating Mitochondrial Fission. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2022; 2022:3639302. [PMID: 36193086 PMCID: PMC9526636 DOI: 10.1155/2022/3639302] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Revised: 08/25/2022] [Accepted: 08/26/2022] [Indexed: 11/18/2022]
Abstract
Polycystic ovary syndrome (PCOS) is one of the most common hormonal disorders among premenopausal women. PCOS is accompanied by many other reproductive, endocrinal, and metabolic disorders thus amassing the difficulties encountered by the women affected. However, there is limited information on its molecular etiology. Synoviolin (SYVN1) is an E3 ubiquitin ligase that is thought to participate in the pathology of PCOS. However, the expression and function of SYVN1 in PCOS are unknown. In this study, we found that downregulation of SYVN1 expression was followed by increased apoptosis in the granulosa cells (GCs) of patients with PCOS. Subsequent in vitro experiments indicated that the overexpression of SYVN1 inhibited apoptosis and mitochondrial fission. Furthermore, using immunoprecipitation and western blotting, we identified that SYVN1 promoted the degradation of Drp1 via the proteasome-dependent pathway. Additionally, we generated a PCOS model in female Sprague Dawley rats and treated them with an SYVN1 inhibitor, LS-102. We observed that the inhibition of SYVN1 increased Drp1 levels and exacerbated the degeneration of GCs in the PCOS rat model. Finally, in vitro and in vivo experiments showed that SYVN1 inhibits apoptosis and mitochondrial fission by promoting Drp1 degradation in GCs. These results highlight the function of SYVN1 in PCOS and provide a potential target for the clinical treatment of PCOS.
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20
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Kondo W, Kitagawa T, Hoshida H, Akada R, Miyakawa I. Morphological Changes of Mitochondria and Actin Cytoskeleton in the Yeast <i>Saccharomyces cerevisiae</i> During Diauxic Growth and Glucose Depletion Culture. CYTOLOGIA 2022. [DOI: 10.1508/cytologia.87.157] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Affiliation(s)
- Wataru Kondo
- Department of Biology, Faculty of Science, Yamaguchi University
| | - Takao Kitagawa
- Department of Applied Chemistry, Graduate School of Sciences and Technology for Innovation, Yamaguchi University
| | - Hisashi Hoshida
- Department of Applied Chemistry, Graduate School of Sciences and Technology for Innovation, Yamaguchi University
| | - Rinji Akada
- Department of Applied Chemistry, Graduate School of Sciences and Technology for Innovation, Yamaguchi University
| | - Isamu Miyakawa
- Department of Biology, Faculty of Science, Yamaguchi University
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21
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Romero-Morales AI, Gama V. Revealing the Impact of Mitochondrial Fitness During Early Neural Development Using Human Brain Organoids. Front Mol Neurosci 2022; 15:840265. [PMID: 35571368 PMCID: PMC9102998 DOI: 10.3389/fnmol.2022.840265] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Accepted: 04/04/2022] [Indexed: 11/13/2022] Open
Abstract
Mitochondrial homeostasis -including function, morphology, and inter-organelle communication- provides guidance to the intrinsic developmental programs of corticogenesis, while also being responsive to environmental and intercellular signals. Two- and three-dimensional platforms have become useful tools to interrogate the capacity of cells to generate neuronal and glia progeny in a background of metabolic dysregulation, but the mechanistic underpinnings underlying the role of mitochondria during human neurogenesis remain unexplored. Here we provide a concise overview of cortical development and the use of pluripotent stem cell models that have contributed to our understanding of mitochondrial and metabolic regulation of early human brain development. We finally discuss the effects of mitochondrial fitness dysregulation seen under stress conditions such as metabolic dysregulation, absence of developmental apoptosis, and hypoxia; and the avenues of research that can be explored with the use of brain organoids.
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Affiliation(s)
| | - Vivian Gama
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN, United States
- Vanderbilt Center for Stem Cell Biology, Vanderbilt University, Nashville, TN, United States
- Vanderbilt Brain Institute, Vanderbilt University, Nashville, TN, United States
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22
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Quiring L, Walter B, Lohaus N, Schwan D, Rech A, Dlugos A, Rauen U. Characterisation of cold-induced mitochondrial fission in porcine aortic endothelial cells. Mol Med 2022; 28:13. [PMID: 35100966 PMCID: PMC8802553 DOI: 10.1186/s10020-021-00430-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Accepted: 12/27/2021] [Indexed: 12/21/2022] Open
Abstract
Background Previously, we observed that hypothermia, widely used for organ preservation, elicits mitochondrial fission in different cell types. However, temperature dependence, mechanisms and consequences of this cold-induced mitochondrial fission are unknown. Therefore, we here study cold-induced mitochondrial fission in endothelial cells, a cell type generally displaying a high sensitivity to cold-induced injury. Methods Porcine aortic endothelial cells were incubated at 4–25 °C in modified Krebs–Henseleit buffer (plus glucose to provide substrate and deferoxamine to prevent iron-dependent hypothermic injury). Results Cold-induced mitochondrial fission occurred as early as after 3 h at 4 °C and at temperatures below 21 °C, and was more marked after longer cold incubation periods. It was accompanied by the formation of unusual mitochondrial morphologies such as donuts, blobs, and lassos. Under all conditions, re-fusion was observed after rewarming. Cellular ATP content dropped to 33% after 48 h incubation at 4 °C, recovering after rewarming. Drp1 protein levels showed no significant change during cold incubation, but increased phosphorylation at both phosphorylation sites, activating S616 and inactivating S637. Drp1 receptor protein levels were unchanged. Instead of increased mitochondrial accumulation of Drp1 decreased mitochondrial localization was observed during hypothermia. Moreover, the well-known Drp1 inhibitor Mdivi-1 showed only partial protection against cold-induced mitochondrial fission. The inner membrane fusion-mediating protein Opa1 showed a late shift from the long to the fusion-incompetent short isoform during prolonged cold incubation. Oma1 cleavage was not observed. Conclusions Cold-induced mitochondrial fission appears to occur over almost the whole temperature range relevant for organ preservation. Unusual morphologies appear to be related to fission/auto-fusion. Fission appears to be associated with lower mitochondrial function/ATP decline, mechanistically unusual, and after cold incubation in physiological solutions reversible at 37 °C. Supplementary Information The online version contains supplementary material available at 10.1186/s10020-021-00430-z.
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23
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Maity S, Komal P, Kumar V, Saxena A, Tungekar A, Chandrasekar V. Impact of ER Stress and ER-Mitochondrial Crosstalk in Huntington's Disease. Int J Mol Sci 2022; 23:780. [PMID: 35054963 PMCID: PMC8775980 DOI: 10.3390/ijms23020780] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 12/30/2021] [Accepted: 01/03/2022] [Indexed: 02/07/2023] Open
Abstract
Accumulation of misfolded proteins is a common phenomenon of several neurodegenerative diseases. The misfolding of proteins due to abnormal polyglutamine (PolyQ) expansions are linked to the development of PolyQ diseases including Huntington's disease (HD). Though the genetic basis of PolyQ repeats in HD remains prominent, the primary molecular basis mediated by PolyQ toxicity remains elusive. Accumulation of misfolded proteins in the ER or disruption of ER homeostasis causes ER stress and activates an evolutionarily conserved pathway called Unfolded protein response (UPR). Protein homeostasis disruption at organelle level involving UPR or ER stress response pathways are found to be linked to HD. Due to dynamic intricate connections between ER and mitochondria, proteins at ER-mitochondria contact sites (mitochondria associated ER membranes or MAMs) play a significant role in HD development. The current review aims at highlighting the most updated information about different UPR pathways and their involvement in HD disease progression. Moreover, the role of MAMs in HD progression has also been discussed. In the end, the review has focused on the therapeutic interventions responsible for ameliorating diseased states via modulating either ER stress response proteins or modulating the expression of ER-mitochondrial contact proteins.
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Affiliation(s)
- Shuvadeep Maity
- Department of Biological Sciences, Birla Institute of Technology and Science (BITS)-Pilani (Hyderabad Campus), Shameerpet-Mandal, Hyderabad 500078, Telangana, India; (P.K.); (V.K.); (A.S.); (A.T.); (V.C.)
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24
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Banerjee R, Mukherjee A, Nagotu S. Mitochondrial dynamics and its impact on human health and diseases: inside the DRP1 blackbox. J Mol Med (Berl) 2021; 100:1-21. [PMID: 34657190 DOI: 10.1007/s00109-021-02150-7] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Revised: 08/24/2021] [Accepted: 10/06/2021] [Indexed: 01/01/2023]
Abstract
Mitochondria are essential organelles that play a significant role in various cellular processes apart from providing energy in eukaryotic cells. An intricate link between mitochondrial structure and function is now unequivocally accepted. Several molecular players have been identified, which are important in maintaining the structure of the organelle. Dynamin-related protein 1 (DRP1) is one such conserved protein that is a vital regulator of mitochondrial dynamics. Multidisciplinary studies have helped elucidate the structure of the protein and its mechanism of action in great detail. Mutations in various domains of the protein have been identified that are associated with debilitating conditions in patients. The involvement of the protein in disease conditions such as neurodegeneration, cancer, and cardiovascular disorders is also gaining attention. The purpose of this review is to highlight recent findings on the role of DRP1 in human disease conditions and address its importance as a therapeutic target.
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Affiliation(s)
- Riddhi Banerjee
- Organelle Biology and Cellular Ageing Lab, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati-781039, Assam, India
| | - Agradeep Mukherjee
- Organelle Biology and Cellular Ageing Lab, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati-781039, Assam, India
| | - Shirisha Nagotu
- Organelle Biology and Cellular Ageing Lab, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati-781039, Assam, India.
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25
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Cdk8 Kinase Module: A Mediator of Life and Death Decisions in Times of Stress. Microorganisms 2021; 9:microorganisms9102152. [PMID: 34683473 PMCID: PMC8540245 DOI: 10.3390/microorganisms9102152] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2021] [Revised: 10/06/2021] [Accepted: 10/08/2021] [Indexed: 01/18/2023] Open
Abstract
The Cdk8 kinase module (CKM) of the multi-subunit mediator complex plays an essential role in cell fate decisions in response to different environmental cues. In the budding yeast S. cerevisiae, the CKM consists of four conserved subunits (cyclin C and its cognate cyclin-dependent kinase Cdk8, Med13, and Med12) and predominantly negatively regulates a subset of stress responsive genes (SRG’s). Derepression of these SRG’s is accomplished by disassociating the CKM from the mediator, thus allowing RNA polymerase II-directed transcription. In response to cell death stimuli, cyclin C translocates to the mitochondria where it induces mitochondrial hyper-fission and promotes regulated cell death (RCD). The nuclear release of cyclin C requires Med13 destruction by the ubiquitin-proteasome system (UPS). In contrast, to protect the cell from RCD following SRG induction induced by nutrient deprivation, cyclin C is rapidly destroyed by the UPS before it reaches the cytoplasm. This enables a survival response by two mechanisms: increased ATP production by retaining reticular mitochondrial morphology and relieving CKM-mediated repression on autophagy genes. Intriguingly, nitrogen starvation also stimulates Med13 destruction but through a different mechanism. Rather than destruction via the UPS, Med13 proteolysis occurs in the vacuole (yeast lysosome) via a newly identified Snx4-assisted autophagy pathway. Taken together, these findings reveal that the CKM regulates cell fate decisions by both transcriptional and non-transcriptional mechanisms, placing it at a convergence point between cell death and cell survival pathways.
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The 3D organisation of mitochondria in primate photoreceptors. Sci Rep 2021; 11:18863. [PMID: 34552195 PMCID: PMC8458444 DOI: 10.1038/s41598-021-98409-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Accepted: 08/17/2021] [Indexed: 11/08/2022] Open
Abstract
Vertebrate photoreceptors contain large numbers of closely-packed mitochondria which sustain the high metabolic demands of these cells. These mitochondria populations are dynamic and undergo fusion and fission events. This activity serves to maintain the population in a healthy state. In the event of mitochondrial damage, sub-domains, or indeed whole mitochondria, can be degraded and population homeostasis achieved. If this process is overwhelmed cell death may result. Death of photoreceptors contributes to loss of vision in aging individuals and is associated with many eye diseases. In this study we used serial block face scanning electron microscopy of adult Macaca fascicularis retinae to examine the 3D structure of mitochondria in rod and cone photoreceptors. We show that healthy-looking photoreceptors contain mitochondria exhibiting a range of shapes which are associated with different regions of the cell. In some photoreceptors we observe mitochondrial swelling and other changes often associated with cellular stress. In rods and cones that appear stressed we identify elongated domains of mitochondria with densely-packed normal cristae associated with photoreceptor ciliary rootlet bundles. We observe mitochondrial fission and mitochondrion fragments localised to these domains. Swollen mitochondria with few intact cristae are located towards the periphery of the photoreceptor inner-segment in rods, whilst they are found throughout the cell in cones. Swollen mitochondria exhibit sites on the mitochondrial inner membrane which have undergone complex invagination resulting in membranous, electron-dense aggregates. Membrane contact occurs between the mitochondrion and the photoreceptor plasma membrane in the vicinity of these aggregates, and a series of subsequent membrane fusions results in expulsion of the mitochondrial aggregate from the photoreceptor. These events are primarily associated with rods. The potential fate of this purged material and consequences of its clearance by retinal pigment epithelia are discussed.
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27
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Banerjee R, Kumar A, Satpati P, Nagotu S. Mimicking human Drp1 disease-causing mutations in yeast Dnm1 reveals altered mitochondrial dynamics. Mitochondrion 2021; 59:283-295. [PMID: 34157431 DOI: 10.1016/j.mito.2021.06.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 06/14/2021] [Accepted: 06/17/2021] [Indexed: 12/15/2022]
Abstract
The dynamin-related protein 1 (Drp1) and its homologs in various eukaryotes are essential to maintain mitochondrial morphology and regulate mitochondrial division. Several mutations in different domains of Drp1 have been reported, which result in debilitating conditions. Four such disease-causing mutations of the middle domain of Drp1 were mimicked in the yeast dynamin-related GTPase (Dnm1) and were characterized in this study. Mitochondrial morphology and protein function were observed to be altered to a variable extent in cells expressing the mutated variants of Dnm1. Several aspects related to the protein such as punctate formation, localization to mitochondria, dynamic behavior and structure were analyzed by microscopy, biochemical studies and molecular dynamics simulations. Significant effects on the protein structure and function were observed in cells expressing A430D and G397D mutations. Overall, our data provide insight into the molecular and cellular alterations resulting from middle domain mutations in Dnm1.
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Affiliation(s)
- Riddhi Banerjee
- Organelle Biology and Cellular Ageing Lab, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati 781039, Assam, India
| | - Abhishek Kumar
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati 781039, Assam, India
| | - Priyadarshi Satpati
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati 781039, Assam, India
| | - Shirisha Nagotu
- Organelle Biology and Cellular Ageing Lab, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati 781039, Assam, India.
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28
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Aretz I, Jakubke C, Osman C. Power to the daughters - mitochondrial and mtDNA transmission during cell division. Biol Chem 2021; 401:533-546. [PMID: 31812944 DOI: 10.1515/hsz-2019-0337] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Accepted: 11/08/2019] [Indexed: 11/15/2022]
Abstract
Mitochondria supply virtually all eukaryotic cells with energy through ATP production by oxidative phosphoryplation (OXPHOS). Accordingly, maintenance of mitochondrial function is fundamentally important to sustain cellular health and various diseases have been linked to mitochondrial dysfunction. Biogenesis of OXPHOS complexes crucially depends on mitochondrial DNA (mtDNA) that encodes essential subunits of the respiratory chain and is distributed in multiple copies throughout the mitochondrial network. During cell division, mitochondria, including mtDNA, need to be accurately apportioned to daughter cells. This process requires an intimate and coordinated interplay between the cell cycle, mitochondrial dynamics and the replication and distribution of mtDNA. Recent years have seen exciting advances in the elucidation of the mechanisms that facilitate these processes and essential key players have been identified. Moreover, segregation of qualitatively distinct mitochondria during asymmetric cell division is emerging as an important quality control step, which secures the maintenance of a healthy cell population.
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Affiliation(s)
- Ina Aretz
- Department of Biology II, Ludwig-Maximilians-University Munich, Großhaderner Str. 2, 82152Planegg-Martinsried, Germany
| | - Christopher Jakubke
- Department of Biology II, Ludwig-Maximilians-University Munich, Großhaderner Str. 2, 82152Planegg-Martinsried, Germany
| | - Christof Osman
- Department of Biology II, Ludwig-Maximilians-University Munich, Großhaderner Str. 2, 82152Planegg-Martinsried, Germany
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29
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Haeussler S, Yeroslaviz A, Rolland SG, Luehr S, Lambie EJ, Conradt B. Genome-wide RNAi screen for regulators of UPRmt in Caenorhabditis elegans mutants with defects in mitochondrial fusion. G3-GENES GENOMES GENETICS 2021; 11:6204483. [PMID: 33784383 PMCID: PMC8495942 DOI: 10.1093/g3journal/jkab095] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Accepted: 03/18/2021] [Indexed: 01/22/2023]
Abstract
Mitochondrial dynamics plays an important role in mitochondrial quality control and the adaptation of metabolic activity in response to environmental changes. The disruption of mitochondrial dynamics has detrimental consequences for mitochondrial and cellular homeostasis and leads to the activation of the mitochondrial unfolded protein response (UPRmt), a quality control mechanism that adjusts cellular metabolism and restores homeostasis. To identify genes involved in the induction of UPRmt in response to a block in mitochondrial fusion, we performed a genome-wide RNAi screen in Caenorhabditis elegans mutants lacking the gene fzo-1, which encodes the ortholog of mammalian Mitofusin, and identified 299 suppressors and 86 enhancers. Approximately 90% of these 385 genes are conserved in humans, and one third of the conserved genes have been implicated in human disease. Furthermore, many have roles in developmental processes, which suggests that mitochondrial function and the response to stress are defined during development and maintained throughout life. Our dataset primarily contains mitochondrial enhancers and non-mitochondrial suppressors of UPRmt, indicating that the maintenance of mitochondrial homeostasis has evolved as a critical cellular function, which, when disrupted, can be compensated for by many different cellular processes. Analysis of the subsets 'non-mitochondrial enhancers' and 'mitochondrial suppressors' suggests that organellar contact sites, especially between the ER and mitochondria, are of importance for mitochondrial homeostasis. In addition, we identified several genes involved in IP3 signaling that modulate UPRmt in fzo-1 mutants and found a potential link between pre-mRNA splicing and UPRmt activation.
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Affiliation(s)
- Simon Haeussler
- Faculty of Biology, Ludwig-Maximilians-University Munich, 82152 Planegg-Martinsried, Germany
| | - Assa Yeroslaviz
- Computational Biology Group, Max Planck Institute of Biochemistry, 82152 Planegg-Martinsried, Germany
| | - Stéphane G Rolland
- Faculty of Biology, Ludwig-Maximilians-University Munich, 82152 Planegg-Martinsried, Germany.,Center for Genomic Integrity, Institute for Basic Science (IBS), Ulsan 44919, South Korea
| | - Sebastian Luehr
- Faculty of Biology, Ludwig-Maximilians-University Munich, 82152 Planegg-Martinsried, Germany
| | - Eric J Lambie
- Center for Integrated Protein Science, Ludwig-Maximilians-University Munich, 82152 Planegg-Martinsried, Germany
| | - Barbara Conradt
- Faculty of Biology, Ludwig-Maximilians-University Munich, 82152 Planegg-Martinsried, Germany.,Center for Integrated Protein Science, Ludwig-Maximilians-University Munich, 82152 Planegg-Martinsried, Germany.,Research Department of Cell and Developmental Biology, Division of Biosciences, University College London, London WC1E 6AP, United Kingdom
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30
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Liaghati A, Pileggi CA, Parmar G, Patten DA, Hadzimustafic N, Cuillerier A, Menzies KJ, Burelle Y, Harper ME. Grx2 Regulates Skeletal Muscle Mitochondrial Structure and Autophagy. Front Physiol 2021; 12:604210. [PMID: 33762963 PMCID: PMC7982873 DOI: 10.3389/fphys.2021.604210] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Accepted: 01/29/2021] [Indexed: 12/24/2022] Open
Abstract
Glutathione is an important antioxidant that regulates cellular redox status and is disordered in many disease states. Glutaredoxin 2 (Grx2) is a glutathione-dependent oxidoreductase that plays a pivotal role in redox control by catalyzing reversible protein deglutathionylation. As oxidized glutathione (GSSG) can stimulate mitochondrial fusion, we hypothesized that Grx2 may contribute to the maintenance of mitochondrial dynamics and ultrastructure. Here, we demonstrate that Grx2 deletion results in decreased GSH:GSSG, with a marked increase of GSSG in primary muscle cells isolated from C57BL/6 Grx2-/- mice. The altered glutathione redox was accompanied by increased mitochondrial length, consistent with a more fused mitochondrial reticulum. Electron microscopy of Grx2-/- skeletal muscle fibers revealed decreased mitochondrial surface area, profoundly disordered ultrastructure, and the appearance of multi-lamellar structures. Immunoblot analysis revealed that autophagic flux was augmented in Grx2-/- muscle as demonstrated by an increase in the ratio of LC3II/I expression. These molecular changes resulted in impaired complex I respiration and complex IV activity, a smaller diameter of tibialis anterior muscle, and decreased body weight in Grx2 deficient mice. Together, these are the first results to show that Grx2 regulates skeletal muscle mitochondrial structure, and autophagy.
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Affiliation(s)
- Ava Liaghati
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, ON, Canada.,Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, ON, Canada
| | - Chantal A Pileggi
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, ON, Canada.,Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, ON, Canada
| | - Gaganvir Parmar
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, ON, Canada.,Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, ON, Canada
| | - David A Patten
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, ON, Canada.,Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, ON, Canada
| | - Nina Hadzimustafic
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, ON, Canada.,Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, ON, Canada
| | - Alexanne Cuillerier
- Faculty of Health Science, Interdisciplinary School of Health Sciences, University of Ottawa, Ottawa, ON, Canada
| | - Keir J Menzies
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, ON, Canada.,Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, ON, Canada.,Faculty of Health Science, Interdisciplinary School of Health Sciences, University of Ottawa, Ottawa, ON, Canada
| | - Yan Burelle
- Faculty of Health Science, Interdisciplinary School of Health Sciences, University of Ottawa, Ottawa, ON, Canada
| | - Mary-Ellen Harper
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, ON, Canada.,Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, ON, Canada
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31
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Ng MYW, Wai T, Simonsen A. Quality control of the mitochondrion. Dev Cell 2021; 56:881-905. [PMID: 33662258 DOI: 10.1016/j.devcel.2021.02.009] [Citation(s) in RCA: 161] [Impact Index Per Article: 53.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Revised: 01/06/2021] [Accepted: 02/08/2021] [Indexed: 12/22/2022]
Abstract
Mitochondria are essential organelles that execute and coordinate various metabolic processes in the cell. Mitochondrial dysfunction severely affects cell fitness and contributes to disease. Proper organellar function depends on the biogenesis and maintenance of mitochondria and its >1,000 proteins. As a result, the cell has evolved mechanisms to coordinate protein and organellar quality control, such as the turnover of proteins via mitochondria-associated degradation, the ubiquitin-proteasome system, and mitoproteases, as well as the elimination of mitochondria through mitophagy. Specific quality control mechanisms are engaged depending upon the nature and severity of mitochondrial dysfunction, which can also feed back to elicit transcriptional or proteomic remodeling by the cell. Here, we will discuss the current understanding of how these different quality control mechanisms are integrated and overlap to maintain protein and organellar quality and how they may be relevant for cellular and organismal health.
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Affiliation(s)
- Matthew Yoke Wui Ng
- Department of Molecular Medicine, Institute of Basic Medical Sciences, University of Oslo, 0372 Oslo, Norway; Centre for Cancer Cell Reprogramming, Institute of Clinical Medicine, University of Oslo, 0316 Oslo, Norway
| | - Timothy Wai
- Institut Pasteur CNRS UMR 3691, 25-28 Rue du Docteur Roux, Paris, France.
| | - Anne Simonsen
- Department of Molecular Medicine, Institute of Basic Medical Sciences, University of Oslo, 0372 Oslo, Norway; Centre for Cancer Cell Reprogramming, Institute of Clinical Medicine, University of Oslo, 0316 Oslo, Norway.
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32
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Ludl AA, Michoel T. Comparison between instrumental variable and mediation-based methods for reconstructing causal gene networks in yeast. Mol Omics 2021; 17:241-251. [PMID: 33438713 DOI: 10.1039/d0mo00140f] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Causal gene networks model the flow of information within a cell. Reconstructing causal networks from omics data is challenging because correlation does not imply causation. When genomics and transcriptomics data from a segregating population are combined, genomic variants can be used to orient the direction of causality between gene expression traits. Instrumental variable methods use a local expression quantitative trait locus (eQTL) as a randomized instrument for a gene's expression level, and assign target genes based on distal eQTL associations. Mediation-based methods additionally require that distal eQTL associations are mediated by the source gene. A detailed comparison between these methods has not yet been conducted, due to the lack of a standardized implementation of different methods, the limited sample size of most multi-omics datasets, and the absence of ground-truth networks for most organisms. Here we used Findr, a software package providing uniform implementations of instrumental variable, mediation, and coexpression-based methods, a recent dataset of 1012 segregants from a cross between two budding yeast strains, and the Yeastract database of known transcriptional interactions to compare causal gene network inference methods. We found that causal inference methods result in a significant overlap with the ground-truth, whereas coexpression did not perform better than random. A subsampling analysis revealed that the performance of mediation saturates at large sample sizes, due to a loss of sensitivity when residual correlations become significant. Instrumental variable methods on the other hand contain false positive predictions, due to genomic linkage between eQTL instruments. Instrumental variable and mediation-based methods also have complementary roles for identifying causal genes underlying transcriptional hotspots. Instrumental variable methods correctly predicted STB5 targets for a hotspot centred on the transcription factor STB5, whereas mediation failed due to Stb5p auto-regulating its own expression. Mediation suggests a new candidate gene, DNM1, for a hotspot on Chr XII, whereas instrumental variable methods could not distinguish between multiple genes located within the hotspot. In conclusion, causal inference from genomics and transcriptomics data is a powerful approach for reconstructing causal gene networks, which could be further improved by the development of methods to control for residual correlations in mediation analyses, and for genomic linkage and pleiotropic effects from transcriptional hotspots in instrumental variable analyses.
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Affiliation(s)
- Adriaan-Alexander Ludl
- Computational Biology Unit, Department of Informatics, University of Bergen, PO Box 7803, 5020 Bergen, Norway.
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33
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Zhang H, Ye Y, Li W. Perspectives of Molecular Therapy-Targeted Mitochondrial Fission in Hepatocellular Carcinoma. BIOMED RESEARCH INTERNATIONAL 2020; 2020:1039312. [PMID: 33457401 PMCID: PMC7785342 DOI: 10.1155/2020/1039312] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 12/16/2020] [Accepted: 12/21/2020] [Indexed: 12/21/2022]
Abstract
Current advances of molecular-targeting therapies for hepatocellular carcinoma (HCC) have improved the overall survival significantly, whereas the results still remain unsatisfied. Recently, much attention has been focused on organelles, such as the mitochondria, to reveal novel strategies to control the cancers. The mitochondria are vital organelles which supply energy and maintain metabolism in most of the eukaryotic cells. They not only execute critical bioenergetic and biosynthetic functions but also regulate ROS homeostasis and apoptosis. Existing in a dynamic equilibrium state, mitochondria constantly undergo the fission and fusion processes in normal situation. Increasing evidences have showed that mitochondrial fission is highly related to the diseases and cancers. Distinctive works have proved the significant effects of mitochondrial fission on HCC behaviors and the crosstalks with other molecular pathways. Here, we provide an overview of the mitochondrial fission and the link with HCC, emphasizing on the underlying molecular pathways and several novel materials that modulate HCC behaviors.
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Affiliation(s)
- Hanwen Zhang
- Department of Hepatobiliary-Pancreatic Surgery, China-Japan Union Hospital of Jilin University, Changchun 130033, China
| | - Yanshuo Ye
- Department of Hepatobiliary-Pancreatic Surgery, China-Japan Union Hospital of Jilin University, Changchun 130033, China
| | - Wei Li
- Department of Hepatobiliary-Pancreatic Surgery, China-Japan Union Hospital of Jilin University, Changchun 130033, China
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34
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Lysosomal activity regulates Caenorhabditis elegans mitochondrial dynamics through vitamin B12 metabolism. Proc Natl Acad Sci U S A 2020; 117:19970-19981. [PMID: 32737159 DOI: 10.1073/pnas.2008021117] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Mitochondrial fission and fusion are highly regulated by energy demand and physiological conditions to control the production, activity, and movement of these organelles. Mitochondria are arrayed in a periodic pattern in Caenorhabditis elegans muscle, but this pattern is disrupted by mutations in the mitochondrial fission component dynamin DRP-1. Here we show that the dramatically disorganized mitochondria caused by a mitochondrial fission-defective dynamin mutation is strongly suppressed to a more periodic pattern by a second mutation in lysosomal biogenesis or acidification. Vitamin B12 is normally imported from the bacterial diet via lysosomal degradation of B12-binding proteins and transport of vitamin B12 to the mitochondrion and cytoplasm. We show that the lysosomal dysfunction induced by gene inactivations of lysosomal biogenesis or acidification factors causes vitamin B12 deficiency. Growth of the C. elegans dynamin mutant on an Escherichia coli strain with low vitamin B12 also strongly suppressed the mitochondrial fission defect. Of the two C. elegans enzymes that require B12, gene inactivation of methionine synthase suppressed the mitochondrial fission defect of a dynamin mutation. We show that lysosomal dysfunction induced mitochondrial biogenesis, which is mediated by vitamin B12 deficiency and methionine restriction. S-adenosylmethionine, the methyl donor of many methylation reactions, including histones, is synthesized from methionine by S-adenosylmethionine synthase; inactivation of the sams-1 S-adenosylmethionine synthase also suppresses the drp-1 fission defect, suggesting that vitamin B12 regulates mitochondrial biogenesis and then affects mitochondrial fission via chromatin pathways.
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35
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Imoto Y, Itoh K, Fujiki Y. Molecular Basis of Mitochondrial and Peroxisomal Division Machineries. Int J Mol Sci 2020; 21:E5452. [PMID: 32751702 PMCID: PMC7432047 DOI: 10.3390/ijms21155452] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 07/28/2020] [Accepted: 07/28/2020] [Indexed: 12/20/2022] Open
Abstract
Mitochondria and peroxisomes are ubiquitous subcellular organelles that are highly dynamic and possess a high degree of plasticity. These organelles proliferate through division of pre-existing organelles. Studies on yeast, mammalian cells, and unicellular algae have led to a surprising finding that mitochondria and peroxisomes share the components of their division machineries. At the heart of the mitochondrial and peroxisomal division machineries is a GTPase dynamin-like protein, Dnm1/Drp1, which forms a contractile ring around the neck of the dividing organelles. During division, Dnm1/Drp1 functions as a motor protein and constricts the membrane. This mechanochemical work is achieved by utilizing energy from GTP hydrolysis. Over the last two decades, studies have focused on the structure and assembly of Dnm1/Drp1 molecules around the neck. However, the regulation of GTP during the division of mitochondrion and peroxisome is not well understood. Here, we review the current understanding of Dnm1/Drp1-mediated divisions of mitochondria and peroxisomes, exploring the mechanisms of GTP regulation during the Dnm1/Drp1 function, and provide new perspectives on their potential contribution to mitochondrial and peroxisomal biogenesis.
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Grants
- 14J04556 Japan Society for the Promotion of Science Fellowships
- P24247038, JP25112518, JP25116717, JP26116007, JP15K14511, JP15K21743, JP17H03675 Ministry of Education, Culture, Sports, Science, and Technology of Japan, Grants-in-Aid for Scientific Research
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Affiliation(s)
- Yuuta Imoto
- Department of Cell Biology, Johns Hopkins University School of Medicine, 725 N. Wolfe Street, Baltimore, MD 21205, USA;
| | - Kie Itoh
- Department of Cell Biology, Johns Hopkins University School of Medicine, 725 N. Wolfe Street, Baltimore, MD 21205, USA;
| | - Yukio Fujiki
- Division of Organelle Homeostasis, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
- Institute of Rheological Functions of Food, Hisayama-cho, Fukuoka 811-2501, Japan
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36
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Mnatsakanyan N, Jonas EA. The new role of F 1F o ATP synthase in mitochondria-mediated neurodegeneration and neuroprotection. Exp Neurol 2020; 332:113400. [PMID: 32653453 DOI: 10.1016/j.expneurol.2020.113400] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 05/23/2020] [Accepted: 07/07/2020] [Indexed: 02/08/2023]
Abstract
The mitochondrial F1Fo ATP synthase is one of the most abundant proteins of the mitochondrial inner membrane, which catalyzes the final step of oxidative phosphorylation to synthesize ATP from ADP and Pi. ATP synthase uses the electrochemical gradient of protons (ΔμH+) across the mitochondrial inner membrane to synthesize ATP. Under certain pathophysiological conditions, ATP synthase can run in reverse to hydrolyze ATP and build the necessary ΔμH+ across the mitochondrial inner membrane. Tight coupling between these two processes, proton translocation and ATP synthesis, is achieved by the unique rotational mechanism of ATP synthase and is necessary for efficient cellular metabolism and cell survival. The uncoupling of these processes, dissipation of mitochondrial inner membrane potential, elevated levels of ROS, low matrix content of ATP in combination with other cellular malfunction trigger the opening of the mitochondrial permeability transition pore in the mitochondrial inner membrane. In this review we will discuss the new role of ATP synthase beyond oxidative phosphorylation. We will highlight its function as a unique regulator of cell life and death and as a key target in mitochondria-mediated neurodegeneration and neuroprotection.
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Affiliation(s)
- Nelli Mnatsakanyan
- Section of Endocrinology, Department of Internal Medicine, Yale University, New Haven, CT, USA.
| | - Elizabeth Ann Jonas
- Section of Endocrinology, Department of Internal Medicine, Yale University, New Haven, CT, USA
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37
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Kalia R, Frost A. Open and cut: allosteric motion and membrane fission by dynamin superfamily proteins. Mol Biol Cell 2020; 30:2097-2104. [PMID: 31365329 PMCID: PMC6743466 DOI: 10.1091/mbc.e16-10-0709] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Cells have evolved diverse protein-based machinery to reshape, cut, or fuse their membrane-delimited compartments. Dynamin superfamily proteins are principal components of this machinery and use their ability to hydrolyze GTP and to polymerize into helices and rings to achieve these goals. Nucleotide-binding, hydrolysis, and exchange reactions drive significant conformational changes across the dynamin family, and these changes alter the shape and stability of supramolecular dynamin oligomers, as well as the ability of dynamins to bind receptors and membranes. Mutations that interfere with the conformational repertoire of these enzymes, and hence with membrane fission, exist in several inherited human diseases. Here, we discuss insights from new x-ray crystal structures and cryo-EM reconstructions that have enabled us to infer some of the allosteric dynamics for these proteins. Together, these studies help us to understand how dynamins perform mechanical work, as well as how specific mutants of dynamin family proteins exhibit pathogenic properties.
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Affiliation(s)
- Raghav Kalia
- Department of Physiology, University of California, San Francisco, San Francisco, CA 94158.,Department of Biochemistry, University of Utah, Salt Lake City, UT 84132
| | - Adam Frost
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158.,Department of Biochemistry, University of Utah, Salt Lake City, UT 84132.,Chan-Zuckerberg Biohub, San Francisco, CA 94158
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38
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Mollo N, Cicatiello R, Aurilia M, Scognamiglio R, Genesio R, Charalambous M, Paladino S, Conti A, Nitsch L, Izzo A. Targeting Mitochondrial Network Architecture in Down Syndrome and Aging. Int J Mol Sci 2020; 21:E3134. [PMID: 32365535 PMCID: PMC7247689 DOI: 10.3390/ijms21093134] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Revised: 04/26/2020] [Accepted: 04/27/2020] [Indexed: 12/12/2022] Open
Abstract
Mitochondria are organelles that mainly control energy conversion in the cell. In addition, they also participate in many relevant activities, such as the regulation of apoptosis and calcium levels, and other metabolic tasks, all closely linked to cell viability. Functionality of mitochondria appears to depend upon their network architecture that may dynamically pass from an interconnected structure with long tubular units, to a fragmented one with short separate fragments. A decline in mitochondrial quality, which presents itself as an altered structural organization and a function of mitochondria, has been observed in Down syndrome (DS), as well as in aging and in age-related pathologies. This review provides a basic overview of mitochondrial dynamics, from fission/fusion mechanisms to mitochondrial homeostasis. Molecular mechanisms determining the disruption of the mitochondrial phenotype in DS and aging are discussed. The impaired activity of the transcriptional co-activator PGC-1α/PPARGC1A and the hyperactivation of the mammalian target of rapamycin (mTOR) kinase are emerging as molecular underlying causes of these mitochondrial alterations. It is, therefore, likely that either stimulating the PGC-1α activity or inhibiting mTOR signaling could reverse mitochondrial dysfunction. Evidence is summarized suggesting that drugs targeting either these pathways or other factors affecting the mitochondrial network may represent therapeutic approaches to improve and/or prevent the effects of altered mitochondrial function. Overall, from all these studies it emerges that the implementation of such strategies may exert protective effects in DS and age-related diseases.
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Affiliation(s)
- Nunzia Mollo
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, 80131 Naples, Italy
| | - Rita Cicatiello
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, 80131 Naples, Italy
| | - Miriam Aurilia
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, 80131 Naples, Italy
| | - Roberta Scognamiglio
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, 80131 Naples, Italy
| | - Rita Genesio
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, 80131 Naples, Italy
| | - Maria Charalambous
- Institute of Experimental Endocrinology and Oncology “G. Salvatore”, National Research Council, 80131 Naples, Italy
| | - Simona Paladino
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, 80131 Naples, Italy
| | - Anna Conti
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, 80131 Naples, Italy
| | - Lucio Nitsch
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, 80131 Naples, Italy
- Institute of Experimental Endocrinology and Oncology “G. Salvatore”, National Research Council, 80131 Naples, Italy
| | - Antonella Izzo
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, 80131 Naples, Italy
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Axonal transport dysfunction of mitochondria in traumatic brain injury: A novel therapeutic target. Exp Neurol 2020; 329:113311. [PMID: 32302676 DOI: 10.1016/j.expneurol.2020.113311] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Revised: 03/27/2020] [Accepted: 04/10/2020] [Indexed: 01/05/2023]
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40
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Structural analysis of a trimeric assembly of the mitochondrial dynamin-like GTPase Mgm1. Proc Natl Acad Sci U S A 2020; 117:4061-4070. [PMID: 32041880 PMCID: PMC7049166 DOI: 10.1073/pnas.1919116117] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Mitochondria are dynamic double-membraned organelles, which undergo cycles of division and fusion mediated by dynamin-related GTPases. How dynamins mediate mitochondrial inner membrane fusion is not understood. In humans, defective inner membrane fusion causes a degenerative form of blindness termed dominant optic atrophy. Here, we solve the structure of a trimer assembly of an inner membrane fusion dynamin. Our observations underscore the structural plasticity of dynamins and suggest a previously unidentified mode of how they might mediate membrane fusion events. The fusion of inner mitochondrial membranes requires dynamin-like GTPases, Mgm1 in yeast and OPA1 in mammals, but how they mediate membrane fusion is poorly understood. Here, we determined the crystal structure of Saccharomyces cerevisiae short Mgm1 (s-Mgm1) in complex with GDP. It revealed an N-terminal GTPase (G) domain followed by two helix bundles (HB1 and HB2) and a unique C-terminal lipid-interacting stalk (LIS). Dimers can form through antiparallel HB interactions. Head-to-tail trimers are built by intermolecular interactions between the G domain and HB2-LIS. Biochemical and in vivo analyses support the idea that the assembly interfaces observed here are native and critical for Mgm1 function. We also found that s-Mgm1 interacts with negatively charged lipids via both the G domain and LIS. Based on these observations, we propose that membrane targeting via the G domain and LIS facilitates the in cis assembly of Mgm1, potentially generating a highly curved membrane tip to allow inner membrane fusion.
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Prieto J, Ponsoda X, Izpisua Belmonte JC, Torres J. Mitochondrial dynamics and metabolism in induced pluripotency. Exp Gerontol 2020; 133:110870. [PMID: 32045634 DOI: 10.1016/j.exger.2020.110870] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Revised: 12/20/2019] [Accepted: 02/05/2020] [Indexed: 12/15/2022]
Abstract
Somatic cells can be reprogrammed to pluripotency by either ectopic expression of defined factors or exposure to chemical cocktails. During reprogramming, somatic cells undergo dramatic changes in a wide range of cellular processes, such as metabolism, mitochondrial morphology and function, cell signaling pathways or immortalization. Regulation of these processes during cell reprograming lead to the acquisition of a pluripotent state, which enables indefinite propagation by symmetrical self-renewal without losing the ability of reprogrammed cells to differentiate into all cell types of the adult. In this review, recent data from different laboratories showing how these processes are controlled during the phenotypic transformation of a somatic cell into a pluripotent stem cell will be discussed.
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Affiliation(s)
- Javier Prieto
- Departamento Biología Celular, Biología Funcional y Antropología Física, Universitat de València, Calle Dr. Moliner 50, 46100 Burjassot, Spain; Gene Expression Laboratory, Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA.
| | - Xavier Ponsoda
- Departamento Biología Celular, Biología Funcional y Antropología Física, Universitat de València, Calle Dr. Moliner 50, 46100 Burjassot, Spain; Instituto de Investigación Sanitaria (INCLIVA), Avenida de Menéndez y Pelayo 4, 46010, Valencia, Spain
| | - Juan Carlos Izpisua Belmonte
- Gene Expression Laboratory, Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Josema Torres
- Departamento Biología Celular, Biología Funcional y Antropología Física, Universitat de València, Calle Dr. Moliner 50, 46100 Burjassot, Spain; Instituto de Investigación Sanitaria (INCLIVA), Avenida de Menéndez y Pelayo 4, 46010, Valencia, Spain.
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Changes in the Expression of Mitochondrial Morphology-Related Genes during the Differentiation of Murine Embryonic Stem Cells. Stem Cells Int 2020; 2020:9369268. [PMID: 32399055 PMCID: PMC7204333 DOI: 10.1155/2020/9369268] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Revised: 12/17/2019] [Accepted: 01/07/2020] [Indexed: 02/06/2023] Open
Abstract
During embryonic development, cells undergo changes in gene expression, signaling pathway activation/inactivation, metabolism, and intracellular organelle structures, which are mediated by mitochondria. Mitochondria continuously switch their morphology between elongated tubular and fragmented globular via mitochondrial fusion and fission. Mitochondrial fusion is mediated by proteins encoded by Mfn1, Mfn2, and Opa1, whereas mitochondrial fission is mediated by proteins encoded by Fis1 and Dnm1L. Here, we investigated the expression patterns of mitochondria-related genes during the differentiation of mouse embryonic stem cells (ESCs). Pluripotent ESCs maintain stemness in the presence of leukemia inhibitory factor (LIF) via the JAK-STAT3 pathway but lose pluripotency and differentiate in response to the withdrawal of LIF. We analyzed the expression levels of mitochondrial fusion- and fission-related genes during the differentiation of ESCs. We hypothesized that mitochondrial fusion genes would be overexpressed while the fission genes would be downregulated during the differentiation of ESCs. Though the mitochondria exhibited an elongated morphology in ESCs differentiating in response to LIF withdrawal, only the expression of Mfn2 was increased and that of Dnm1L was decreased as expected, the other exceptions being Mfn1, Opa1, and Fis1. Next, by comparing gene expression and mitochondrial morphology, we proposed an index that could precisely represent mitochondrial changes during the differentiation of pluripotent stem cells by analyzing the expression ratios of three fusion- and two fission-related genes. Surprisingly, increased Mfn2/Dnm1L ratio was correlated with elongation of mitochondria during the differentiation of ESCs. Moreover, application of this index to other specialized cell types revealed that neural stems cells (NSCs) and mouse embryonic fibroblasts (MEFs) showed increased Mfn2/Dnm1L ratio compared to ESCs. Thus, we suggest that the Mfn2/Dnm1L ratio could reflect changes in mitochondrial morphology according to the extent of differentiation.
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43
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Tornabene BA, Varlakhanova NV, Hosford CJ, Chappie JS, Ford MGJ. Structural and functional characterization of the dominant negative P-loop lysine mutation in the dynamin superfamily protein Vps1. Protein Sci 2020; 29:1416-1428. [PMID: 31981262 DOI: 10.1002/pro.3830] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Revised: 01/16/2020] [Accepted: 01/16/2020] [Indexed: 12/15/2022]
Abstract
Dynamin-superfamily proteins (DSPs) are large self-assembling mechanochemical GTPases that harness GTP hydrolysis to drive membrane remodeling events needed for many cellular processes. Mutation to alanine of a fully conserved lysine within the P-loop of the DSP GTPase domain results in abrogation of GTPase activity. This mutant has been widely used in the context of several DSPs as a dominant-negative to impair DSP-dependent processes. However, the precise deficit of the P-loop K to A mutation remains an open question. Here, we use biophysical, biochemical and structural approaches to characterize this mutant in the context of the endosomal DSP Vps1. We show that the Vps1 P-loop K to A mutant binds nucleotide with an affinity similar to wild type but exhibits defects in the organization of the GTPase active site that explain the lack of hydrolysis. In cells, Vps1 and Dnm1 bearing the P-loop K to A mutation are defective in disassembly. These mutants become trapped in assemblies at the typical site of action of the DSP. This work provides mechanistic insight into the widely-used DSP P-loop K to A mutation and the basis of its dominant-negative effects in the cell.
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Affiliation(s)
- Bryan A Tornabene
- Department of Cell Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - Natalia V Varlakhanova
- Department of Cell Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | | | - Joshua S Chappie
- Department of Molecular Medicine, Cornell University, Ithaca, New York
| | - Marijn G J Ford
- Department of Cell Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
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Kulek AR, Anzell A, Wider JM, Sanderson TH, Przyklenk K. Mitochondrial Quality Control: Role in Cardiac Models of Lethal Ischemia-Reperfusion Injury. Cells 2020; 9:cells9010214. [PMID: 31952189 PMCID: PMC7016592 DOI: 10.3390/cells9010214] [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: 12/11/2019] [Revised: 01/10/2020] [Accepted: 01/12/2020] [Indexed: 02/07/2023] Open
Abstract
The current standard of care for acute myocardial infarction or 'heart attack' is timely restoration of blood flow to the ischemic region of the heart. While reperfusion is essential for the salvage of ischemic myocardium, re-introduction of blood flow paradoxically kills (rather than rescues) a population of previously ischemic cardiomyocytes-a phenomenon referred to as 'lethal myocardial ischemia-reperfusion (IR) injury'. There is long-standing and exhaustive evidence that mitochondria are at the nexus of lethal IR injury. However, during the past decade, the paradigm of mitochondria as mediators of IR-induced cardiomyocyte death has been expanded to include the highly orchestrated process of mitochondrial quality control. Our aims in this review are to: (1) briefly summarize the current understanding of the pathogenesis of IR injury, and (2) incorporating landmark data from a broad spectrum of models (including immortalized cells, primary cardiomyocytes and intact hearts), provide a critical discussion of the emerging concept that mitochondrial dynamics and mitophagy (the components of mitochondrial quality control) may contribute to the pathogenesis of cardiomyocyte death in the setting of ischemia-reperfusion.
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Affiliation(s)
- Andrew R. Kulek
- Cardiovascular Research Institute, Wayne State University School of Medicine, Detroit, MI 48201, USA; (A.R.K.); (A.A.); (T.H.S.)
- Department of Biochemistry, Microbiology and Immunology, Wayne State University School of Medicine, Detroit, MI 48201, USA
| | - Anthony Anzell
- Cardiovascular Research Institute, Wayne State University School of Medicine, Detroit, MI 48201, USA; (A.R.K.); (A.A.); (T.H.S.)
- Department of Physiology, Wayne State University School of Medicine, Detroit, MI 48201, USA
- Departments of Emergency Medicine and Molecular & Integrative Physiology, University of Michigan Medical School, Ann Arbor, MI 48109, USA;
| | - Joseph M. Wider
- Departments of Emergency Medicine and Molecular & Integrative Physiology, University of Michigan Medical School, Ann Arbor, MI 48109, USA;
| | - Thomas H. Sanderson
- Cardiovascular Research Institute, Wayne State University School of Medicine, Detroit, MI 48201, USA; (A.R.K.); (A.A.); (T.H.S.)
- Departments of Emergency Medicine and Molecular & Integrative Physiology, University of Michigan Medical School, Ann Arbor, MI 48109, USA;
| | - Karin Przyklenk
- Cardiovascular Research Institute, Wayne State University School of Medicine, Detroit, MI 48201, USA; (A.R.K.); (A.A.); (T.H.S.)
- Department of Physiology, Wayne State University School of Medicine, Detroit, MI 48201, USA
- Department of Emergency Medicine, Wayne State University School of Medicine, Detroit, MI 48201, USA
- Correspondence: ; Tel.: +1-313-577-9047
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45
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Yu R, Lendahl U, Nistér M, Zhao J. Regulation of Mammalian Mitochondrial Dynamics: Opportunities and Challenges. Front Endocrinol (Lausanne) 2020; 11:374. [PMID: 32595603 PMCID: PMC7300174 DOI: 10.3389/fendo.2020.00374] [Citation(s) in RCA: 92] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Accepted: 05/12/2020] [Indexed: 01/01/2023] Open
Abstract
Mitochondria are highly dynamic organelles and important for a variety of cellular functions. They constantly undergo fission and fusion events, referred to as mitochondrial dynamics, which affects the shape, size, and number of mitochondria in the cell, as well as mitochondrial subcellular transport, mitochondrial quality control (mitophagy), and programmed cell death (apoptosis). Dysfunctional mitochondrial dynamics is associated with various human diseases. Mitochondrial dynamics is mediated by a set of mitochondria-shaping proteins in both yeast and mammals. In this review, we describe recent insights into the potential molecular mechanisms underlying mitochondrial fusion and fission, particularly highlighting the coordinating roles of different mitochondria-shaping proteins in the processes, as well as the roles of the endoplasmic reticulum (ER), the actin cytoskeleton and membrane phospholipids in the regulation of mitochondrial dynamics. We particularly focus on emerging roles for the mammalian mitochondrial proteins Fis1, Mff, and MIEFs (MIEF1 and MIEF2) in regulating the recruitment of the cytosolic Drp1 to the surface of mitochondria and how these proteins, especially Fis1, mediate crosstalk between the mitochondrial fission and fusion machineries. In summary, this review provides novel insights into the molecular mechanisms of mammalian mitochondrial dynamics and the involvement of these mechanisms in apoptosis and autophagy.
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Affiliation(s)
- Rong Yu
- Department of Oncology-Pathology, Karolinska Institutet, Karolinska University Hospital Solna, Stockholm, Sweden
| | - Urban Lendahl
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | - Monica Nistér
- Department of Oncology-Pathology, Karolinska Institutet, Karolinska University Hospital Solna, Stockholm, Sweden
- *Correspondence: Monica Nistér
| | - Jian Zhao
- Department of Oncology-Pathology, Karolinska Institutet, Karolinska University Hospital Solna, Stockholm, Sweden
- Jian Zhao
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46
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Kennedy NW, Picton LK, Hill RB. Isolation and Analysis of Mitochondrial Fission Enzyme DNM1 from Saccharomyces cerevisiae. Methods Mol Biol 2020; 2159:3-15. [PMID: 32529359 PMCID: PMC8040746 DOI: 10.1007/978-1-0716-0676-6_1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
Mitochondrial fission, an essential process for mitochondrial and cellular homeostasis, is accomplished by evolutionarily conserved members of the dynamin superfamily of large GTPases. These enzymes couple the hydrolysis of guanosine triphosphate to the mechanical work of membrane remodeling that ultimately leads to membrane scission. The importance of mitochondrial dynamins is exemplified by mutations in the human family member that causes neonatal lethality. In this chapter, we describe the subcloning, purification, and preliminary characterization of the budding yeast mitochondrial dynamin, DNM1, from Saccharomyces cerevisiae, which is the first mitochondrial dynamin isolated from native sources. The yeast-purified enzyme exhibits assembly-stimulated hydrolysis of GTP similar to other fission dynamins, but differs from the enzyme isolated from non-native sources.
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Affiliation(s)
- Nolan W Kennedy
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Lora K Picton
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI, USA
| | - R Blake Hill
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI, USA.
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47
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Ota A, Ishihara T, Ishihara N. Mitochondrial nucleoid morphology and respiratory function are altered in Drp1-deficient HeLa cells. J Biochem 2019; 167:287-294. [DOI: 10.1093/jb/mvz112] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Accepted: 12/04/2019] [Indexed: 12/22/2022] Open
Abstract
Abstract
Mitochondria are dynamic organelles that frequently divide and fuse with each other. The dynamin-related GTPase protein Drp1 has a key role in mitochondrial fission. To analyse the physiological roles of Drp1 in cultured human cells, we analysed Drp1-deficient HeLa cells established by genome editing using CRISPR/Cas9. Under fluorescent microscopy, not only mitochondria were elongated but their DNA (mtDNA) nucleoids were extremely enlarged in bulb-like mitochondrial structures (‘mito-bulbs’) in the Drp1-deficient HeLa cells. We further found that respiratory activity, as measured by oxygen consumption rates, was severely repressed in Drp1-deficient HeLa cells and that this was reversible by the co-repression of mitochondrial fusion factors. Although mtDNA copy number was not affected, several respiratory subunits were repressed in Drp1-deficient HeLa cells. These results suggest that mitochondrial fission is required for the maintenance of active respiratory activity and the morphology of mtDNA nucleoids in human cells.
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Affiliation(s)
- Azusa Ota
- Department of Biological Sciences, Graduate School of Science, Osaka University, 1-1 Machikaneyama-machi, Toyonaka, Osaka 560-0043, Japan
- Department of Protein Biochemistry, Institute of Life Science, Kurume University, 67 Asahi-machi, Kurume, Fukuoka 830-0011, Japan
| | - Takaya Ishihara
- Department of Biological Sciences, Graduate School of Science, Osaka University, 1-1 Machikaneyama-machi, Toyonaka, Osaka 560-0043, Japan
- Department of Protein Biochemistry, Institute of Life Science, Kurume University, 67 Asahi-machi, Kurume, Fukuoka 830-0011, Japan
| | - Naotada Ishihara
- Department of Biological Sciences, Graduate School of Science, Osaka University, 1-1 Machikaneyama-machi, Toyonaka, Osaka 560-0043, Japan
- Department of Protein Biochemistry, Institute of Life Science, Kurume University, 67 Asahi-machi, Kurume, Fukuoka 830-0011, Japan
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48
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Truong T, Zeng G, Lim TK, Cao T, Pang LM, Lee YM, Lin Q, Wang Y, Seneviratne CJ. Proteomics Analysis ofCandida albicans dnm1Haploid Mutant Unraveled the Association between Mitochondrial Fission and Antifungal Susceptibility. Proteomics 2019; 20:e1900240. [DOI: 10.1002/pmic.201900240] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Revised: 11/05/2019] [Indexed: 12/16/2022]
Affiliation(s)
- Thuyen Truong
- Oral Sciences, Faculty of DentistryNational University of Singapore 9 Lower Kent Ridge Road Singapore 119085
| | - Guisheng Zeng
- Institute of Molecular and Cell BiologyAgency for Science, Technology and Research 61 Biopolis Drive, Proteos Singapore 138673
| | - Teck Kwang Lim
- Department of Biological SciencesFaculty of Science, National University of Singapore 16 Science Drive 4, S2 Singapore 117558
| | - Tong Cao
- Oral Sciences, Faculty of DentistryNational University of Singapore 9 Lower Kent Ridge Road Singapore 119085
| | - Li Mei Pang
- National Dental Research Institute SingaporeSinghealth Duke NUS, Singapore 5 Second Hospital Ave Singapore 168938
| | - Yew Mun Lee
- Department of Biological SciencesFaculty of Science, National University of Singapore 16 Science Drive 4, S2 Singapore 117558
| | - Qingsong Lin
- Department of Biological SciencesFaculty of Science, National University of Singapore 16 Science Drive 4, S2 Singapore 117558
| | - Yue Wang
- Institute of Molecular and Cell BiologyAgency for Science, Technology and Research 61 Biopolis Drive, Proteos Singapore 138673
- Department of Biochemistry, Yong Loo Lin School of MedicineNational University of Singapore 10 Medical Dr Singapore 117597
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49
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Plummer JD, Johnson JE. Extension of Cellular Lifespan by Methionine Restriction Involves Alterations in Central Carbon Metabolism and Is Mitophagy-Dependent. Front Cell Dev Biol 2019; 7:301. [PMID: 31850341 PMCID: PMC6892753 DOI: 10.3389/fcell.2019.00301] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2019] [Accepted: 11/08/2019] [Indexed: 01/01/2023] Open
Abstract
Methionine restriction (MR) is one of only a few dietary manipulations known to robustly extend healthspan in mammals. For example, rodents fed a methionine-restricted diet are up to 45% longer-lived than control-fed animals. Tantalizingly, ongoing studies suggest that humans could enjoy similar benefits from this intervention. While the benefits of MR are likely due, at least in part, to improved cellular stress tolerance, it remains to be determined exactly how MR extends organismal healthspan. In previous work, we made use of the yeast chronological lifespan (CLS) assay to model the extension of cellular lifespan conferred by MR and explore the genetic requirements for this extension. In these studies, we demonstrated that both dietary MR (D-MR) and genetic MR (G-MR) (i.e., impairment of the cell’s methionine biosynthetic machinery) significantly extend the CLS of yeast. This extension was found to require the mitochondria-to-nucleus retrograde (RTG) stress signaling pathway, and was associated with a multitude of gene expression changes, a significant proportion of which was also dependent on RTG signaling. Here, we show work aimed at understanding how a subset of the observed expression changes are causally related to MR-dependent CLS extension. Specifically, we find that multiple autophagy-related genes are upregulated by MR, likely resulting in an increased autophagic capacity. Consistent with activated autophagy being important for the benefits of MR, we also find that loss of any of several core autophagy factors abrogates the extended CLS observed for methionine-restricted cells. In addition, epistasis analyses provide further evidence that autophagy activation underlies the benefits of MR to yeast. Strikingly, of the many types of selective autophagy known, our data clearly demonstrate that MR-mediated CLS extension requires only the autophagic recycling of mitochondria (i.e., mitophagy). Indeed, we find that functional mitochondria are required for the full benefit of MR to CLS. Finally, we observe substantial alterations in carbon metabolism for cells undergoing MR, and provide evidence that such changes are directly responsible for the extended lifespan of methionine-restricted yeast. In total, our data indicate that MR produces changes in carbon metabolism that, together with the oxidative metabolism of mitochondria, result in extended cellular lifespan.
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Affiliation(s)
- Jason D Plummer
- Department of Biology, Orentreich Foundation for the Advancement of Science, Cold Spring, NY, United States
| | - Jay E Johnson
- Department of Biology, Orentreich Foundation for the Advancement of Science, Cold Spring, NY, United States
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50
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De Vecchis D, Brandner A, Baaden M, Cohen MM, Taly A. A Molecular Perspective on Mitochondrial Membrane Fusion: From the Key Players to Oligomerization and Tethering of Mitofusin. J Membr Biol 2019; 252:293-306. [PMID: 31485701 DOI: 10.1007/s00232-019-00089-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Accepted: 08/14/2019] [Indexed: 12/29/2022]
Abstract
Mitochondria are dynamic organelles characterized by an ultrastructural organization which is essential in maintaining their quality control and ensuring functional efficiency. The complex mitochondrial network is the result of the two ongoing forces of fusion and fission of inner and outer membranes. Understanding the functional details of mitochondrial dynamics is physiologically relevant as perturbations of this delicate equilibrium have critical consequences and involved in several neurological disorders. Molecular actors involved in this process are large GTPases from the dynamin-related protein family. They catalyze nucleotide-dependent membrane remodeling and are widely conserved from bacteria to higher eukaryotes. Although structural characterization of different family members has contributed in understanding molecular mechanisms of mitochondrial dynamics in more detail, the complete structure of some members as well as the precise assembly of functional oligomers remains largely unknown. As increasing structural data become available, the domain modularity across the dynamin superfamily emerged as a foundation for transfering the knowledge towards less characterized members. In this review, we will first provide an overview of the main actors involved in mitochondrial dynamics. We then discuss recent example of computational methodologies for the study of mitofusin oligomers, and present how the usage of integrative modeling in conjunction with biochemical data can be an asset in progressing the still challenging field of membrane dynamics.
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Affiliation(s)
- Dario De Vecchis
- School of Medicine, Leeds Institute of Cardiovascular and Metabolic Medicine, University of Leeds, LIGHT Building, Leeds, LS2 9JT, UK.
| | - Astrid Brandner
- CNRS, Université de Paris, UPR 9080, Laboratoire de Biochimie Théorique, 13 Rue Pierre et Marie Curie, 75005, Paris, France.,Institut de Biologie Physico-Chimique - Fondation Edmond de Rothschild, PSL Research University, Paris, France
| | - Marc Baaden
- CNRS, Université de Paris, UPR 9080, Laboratoire de Biochimie Théorique, 13 Rue Pierre et Marie Curie, 75005, Paris, France.,Institut de Biologie Physico-Chimique - Fondation Edmond de Rothschild, PSL Research University, Paris, France
| | - Mickael M Cohen
- Institut de Biologie Physico-Chimique - Fondation Edmond de Rothschild, PSL Research University, Paris, France.,Laboratoire de Biologie Cellulaire et Moléculaire des Eucaryotes, Sorbonne Université, CNRS, UMR 8226, Paris, France
| | - Antoine Taly
- CNRS, Université de Paris, UPR 9080, Laboratoire de Biochimie Théorique, 13 Rue Pierre et Marie Curie, 75005, Paris, France. .,Institut de Biologie Physico-Chimique - Fondation Edmond de Rothschild, PSL Research University, Paris, France.
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