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Su J, Tian X, Wang Z, Yang J, Sun S, Sui SF. Structure of the intact Tom20 receptor in the human translocase of the outer membrane complex. PNAS NEXUS 2024; 3:pgae269. [PMID: 39071881 PMCID: PMC11273160 DOI: 10.1093/pnasnexus/pgae269] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Accepted: 06/21/2024] [Indexed: 07/30/2024]
Abstract
The translocase of the outer membrane (TOM) complex serves as the main gate for preproteins entering mitochondria and thus plays a pivotal role in sustaining mitochondrial stability. Precursor proteins, featuring amino-terminal targeting signals (presequences) or internal targeting signals, are recognized by the TOM complex receptors Tom20, Tom22, and Tom70, and then translocated into mitochondria through Tom40. By using chemical cross-linking to stabilize Tom20 in the TOM complex, this study unveils the structure of the human TOM holo complex, encompassing the intact Tom20 component, at a resolution of approximately 6 Å by cryo-electron microscopy. Our structure shows the TOM holo complex containing only one Tom20 subunit, which is located right at the center of the complex and stabilized by extensive interactions with Tom22, Tom40, and Tom6. Based on the structure, we proposed a possible translocation mode of TOM complex, by which different receptors could work simultaneously to ensure that the preproteins recognized by them are all efficiently translocated into the mitochondria.
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Affiliation(s)
- Jiayue Su
- State Key Laboratory of Membrane Biology, Beijing Frontier Research Center for Biological Structure, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Xuyang Tian
- State Key Laboratory of Membrane Biology, Beijing Frontier Research Center for Biological Structure, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Ziyi Wang
- State Key Laboratory of Membrane Biology, Beijing Frontier Research Center for Biological Structure, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Jiawen Yang
- School of Life Sciences, Cryo-EM Center, Southern University of Science and Technology, Shenzhen 518055, Guangdong, China
| | - Shan Sun
- State Key Laboratory of Membrane Biology, Beijing Frontier Research Center for Biological Structure, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Sen-Fang Sui
- State Key Laboratory of Membrane Biology, Beijing Frontier Research Center for Biological Structure, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
- School of Life Sciences, Cryo-EM Center, Southern University of Science and Technology, Shenzhen 518055, Guangdong, China
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2
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Borgert L, Becker T, den Brave F. Conserved quality control mechanisms of mitochondrial protein import. J Inherit Metab Dis 2024. [PMID: 38790152 DOI: 10.1002/jimd.12756] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Revised: 04/15/2024] [Accepted: 05/08/2024] [Indexed: 05/26/2024]
Abstract
Mitochondria carry out essential functions for the cell, including energy production, various biosynthesis pathways, formation of co-factors and cellular signalling in apoptosis and inflammation. The functionality of mitochondria requires the import of about 900-1300 proteins from the cytosol in baker's yeast Saccharomyces cerevisiae and human cells, respectively. The vast majority of these proteins pass the outer membrane in a largely unfolded state through the translocase of the outer mitochondrial membrane (TOM) complex. Subsequently, specific protein translocases sort the precursor proteins into the outer and inner membranes, the intermembrane space and matrix. Premature folding of mitochondrial precursor proteins, defects in the mitochondrial protein translocases or a reduction of the membrane potential across the inner mitochondrial membrane can cause stalling of precursors at the protein import apparatus. Consequently, the translocon is clogged and non-imported precursor proteins accumulate in the cell, which in turn leads to proteotoxic stress and eventually cell death. To prevent such stress situations, quality control mechanisms remove non-imported precursor proteins from the TOM channel. The highly conserved ubiquitin-proteasome system of the cytosol plays a critical role in this process. Thus, the surveillance of protein import via the TOM complex involves the coordinated activity of mitochondria-localized and cytosolic proteins to prevent proteotoxic stress in the cell.
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Affiliation(s)
- Lion Borgert
- Faculty of Medicine, Institute of Biochemistry and Molecular Biology, University of Bonn, Bonn, Germany
| | - Thomas Becker
- Faculty of Medicine, Institute of Biochemistry and Molecular Biology, University of Bonn, Bonn, Germany
| | - Fabian den Brave
- Faculty of Medicine, Institute of Biochemistry and Molecular Biology, University of Bonn, Bonn, Germany
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3
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den Brave F, Pfanner N, Becker T. Mitochondrial entry gate as regulatory hub. BIOCHIMICA ET BIOPHYSICA ACTA. MOLECULAR CELL RESEARCH 2024; 1871:119529. [PMID: 37951505 DOI: 10.1016/j.bbamcr.2023.119529] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2023] [Revised: 06/18/2023] [Accepted: 06/23/2023] [Indexed: 11/14/2023]
Abstract
Mitochondria import 1000-1300 different precursor proteins from the cytosol. The main mitochondrial entry gate is formed by the translocase of the outer membrane (TOM complex). Molecular coupling and modification of TOM subunits control and modulate protein import in response to cellular signaling. The TOM complex functions as regulatory hub to integrate mitochondrial protein biogenesis and quality control into the cellular proteostasis network.
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Affiliation(s)
- Fabian den Brave
- Institute of Biochemistry and Molecular Biology, Faculty of Medicine, University of Bonn, 53115 Bonn, Germany
| | - Nikolaus Pfanner
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany; CIBSS Centre for Integrative Biological Signalling Studies, University of Freiburg, 79104 Freiburg, Germany; BIOSS Centre for Biological Signalling Studies, University of Freiburg, 79104 Freiburg, Germany.
| | - Thomas Becker
- Institute of Biochemistry and Molecular Biology, Faculty of Medicine, University of Bonn, 53115 Bonn, Germany.
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4
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Perez CM, Gong Z, Yoo C, Roy D, Deoraj A, Felty Q. Inhibitor of DNA Binding Protein 3 (ID3) and Nuclear Respiratory Factor 1 (NRF1) Mediated Transcriptional Gene Signatures are Associated with the Severity of Cerebral Amyloid Angiopathy. Mol Neurobiol 2024; 61:835-882. [PMID: 37668961 DOI: 10.1007/s12035-023-03541-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Accepted: 07/25/2023] [Indexed: 09/06/2023]
Abstract
Cerebral amyloid angiopathy (CAA) is a degenerative vasculopathy. We have previously shown that transcription regulating proteins- inhibitor of DNA binding protein 3 (ID3) and the nuclear respiratory factor 1 (NRF1) contribute to vascular dysregulation. In this study, we have identified sex specific ID3 and NRF1-mediated gene networks in CAA patients diagnosed with Alzheimer's Disease (AD). High expression of ID3 mRNA coupled with low NRF1 mRNA levels was observed in the temporal cortex of men and women CAA patients. Low NRF1 mRNA expression in the temporal cortex was found in men with severe CAA. High ID3 expression was found in women with the genetic risk factor APOE4. Low NRF1 expression was also associated with APOE4 in women with CAA. Genome wide transcriptional activity of both ID3 and NRF1 paralleled their mRNA expression levels. Sex specific differences in transcriptional gene signatures of both ID3 and NRF1 were observed. These findings were further corroborated by Bayesian machine learning and the GeNIe simulation models. Dynamic machine learning using a Monte Carlo Markov Chain (MCMC) gene ordering approach revealed that ID3 was associated with disease severity in women. NRF1 was associated with CAA and severity of this disease in men. These findings suggest that aberrant ID3 and NRF1 activity presumably plays a major role in the pathogenesis and severity of CAA. Further analyses of ID3- and NRF1-regulated molecular drivers of CAA may provide new targets for personalized medicine and/or prevention strategies against CAA.
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Affiliation(s)
- Christian Michael Perez
- Department of Environmental Health Sciences, Robert Stempel College of Public Health and Social Work, Florida International University, Miami, FL, USA
| | - Zhenghua Gong
- Department of Biostatistics, Robert Stempel College of Public Health and Social Work, Florida International University, Miami, FL, USA
| | - Changwon Yoo
- Department of Biostatistics, Robert Stempel College of Public Health and Social Work, Florida International University, Miami, FL, USA
| | - Deodutta Roy
- Department of Environmental Health Sciences, Robert Stempel College of Public Health and Social Work, Florida International University, Miami, FL, USA
| | - Alok Deoraj
- Department of Environmental Health Sciences, Robert Stempel College of Public Health and Social Work, Florida International University, Miami, FL, USA
| | - Quentin Felty
- Department of Environmental Health Sciences, Robert Stempel College of Public Health and Social Work, Florida International University, Miami, FL, USA.
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5
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Mitochondrial protein import and UPR mt in skeletal muscle remodeling and adaptation. Semin Cell Dev Biol 2023; 143:28-36. [PMID: 35063351 DOI: 10.1016/j.semcdb.2022.01.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Revised: 12/20/2021] [Accepted: 01/04/2022] [Indexed: 01/03/2023]
Abstract
The biogenesis of mitochondria requires the coordinated expression of the nuclear and the mitochondrial genomes. However, the vast majority of gene products within the organelle are encoded in the nucleus, synthesized in the cytosol, and imported into mitochondria via the protein import machinery, which permit the entry of proteins to expand the mitochondrial network. Once inside, proteins undergo a maturation and folding process brought about by enzymes comprising the unfolded protein response (UPRmt). Protein import and UPRmt activity must be synchronized and matched with mtDNA-encoded subunit synthesis for proper assembly of electron transport chain complexes to avoid proteotoxicity. This review discusses the functions of the import and UPRmt systems in mammalian skeletal muscle, as well as how exercise alters the equilibrium of these pathways in a time-dependent manner, leading to a new steady state of mitochondrial content resulting in enhanced oxidative capacity and improved muscle health.
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6
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Needs HI, Lorriman JS, Pereira GC, Henley JM, Collinson I. The MitoLuc Assay System for Accurate Real-Time Monitoring of Mitochondrial Protein Import Within Mammalian Cells. J Mol Biol 2023; 435:168129. [PMID: 37105499 PMCID: PMC7616392 DOI: 10.1016/j.jmb.2023.168129] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Revised: 03/31/2023] [Accepted: 04/19/2023] [Indexed: 04/29/2023]
Abstract
Mitochondrial protein import is critical for organelle biogenesis, bioenergetic function, and health. The mechanism of which is poorly understood, particularly of the mammalian system. To address this problem we have established an assay to quantitatively monitor mitochondrial import inside mammalian cells. The reporter is based on a split luciferase, whereby the large fragment is segregated in the mitochondrial matrix and the small complementary fragment is fused to the C-terminus of a purified recombinant precursor protein destined for import. Following import the complementary fragments combine to form an active luciferase-providing a sensitive, accurate and continuous measure of protein import. This advance allows detailed mechanistic examination of the transport process in live cells, including the analysis of import breakdown associated with disease, and high-throughput drug screening. Furthermore, the set-up has the potential to be adapted for the analysis of alternative protein transport systems within different cell types, and multicellular model organisms.
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Affiliation(s)
- Hope I Needs
- School of Biochemistry, University of Bristol, Bristol BS8 1TD, UK. https://twitter.com/hopeneeds
| | - James S Lorriman
- School of Biochemistry, University of Bristol, Bristol BS8 1TD, UK. https://twitter.com/JamesLorriman
| | - Gonçalo C Pereira
- School of Biochemistry, University of Bristol, Bristol BS8 1TD, UK. https://twitter.com/MitoPereira_GC
| | - Jeremy M Henley
- School of Biochemistry, University of Bristol, Bristol BS8 1TD, UK
| | - Ian Collinson
- School of Biochemistry, University of Bristol, Bristol BS8 1TD, UK.
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7
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Needs HI, Wilkinson KA, Henley JM, Collinson I. Aggregation-prone Tau impairs mitochondrial import, which affects organelle morphology and neuronal complexity. J Cell Sci 2023; 136:jcs260993. [PMID: 37303235 PMCID: PMC10357015 DOI: 10.1242/jcs.260993] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Accepted: 06/05/2023] [Indexed: 06/13/2023] Open
Abstract
Mitochondrial protein import is essential for organellar biogenesis, and thereby for the sufficient supply of cytosolic ATP - which is particularly important for cells with high energy demands like neurons. This study explores the prospect of import machinery perturbation as a cause of neurodegeneration instigated by the accumulation of aggregating proteins linked to disease. We found that the aggregation-prone Tau variant (TauP301L) reduces the levels of components of the import machinery of the outer (TOM20, encoded by TOMM20) and inner membrane (TIM23, encoded by TIMM23) while associating with TOM40 (TOMM40). Intriguingly, this interaction affects mitochondrial morphology, but not protein import or respiratory function; raising the prospect of an intrinsic rescue mechanism. Indeed, TauP301L induced the formation of tunnelling nanotubes (TNTs), potentially for the recruitment of healthy mitochondria from neighbouring cells and/or the disposal of mitochondria incapacitated by aggregated Tau. Consistent with this, inhibition of TNT formation (and rescue) reveals Tau-induced import impairment. In primary neuronal cultures, TauP301L induced morphological changes characteristic of neurodegeneration. Interestingly, these effects were mirrored in cells where the import sites were blocked artificially. Our results reveal a link between aggregation-prone Tau and defective mitochondrial import relevant to disease.
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Affiliation(s)
- Hope I. Needs
- School of Biochemistry, University of Bristol, Bristol BS8 1TD, UK
| | | | - Jeremy M. Henley
- School of Biochemistry, University of Bristol, Bristol BS8 1TD, UK
| | - Ian Collinson
- School of Biochemistry, University of Bristol, Bristol BS8 1TD, UK
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8
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Lionaki E, Gkikas I, Tavernarakis N. Mitochondrial protein import machinery conveys stress signals to the cytosol and beyond. Bioessays 2023; 45:e2200160. [PMID: 36709422 DOI: 10.1002/bies.202200160] [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: 08/16/2022] [Revised: 12/14/2022] [Accepted: 01/02/2023] [Indexed: 01/30/2023]
Abstract
Mitochondria hold diverse and pivotal roles in fundamental processes that govern cell survival, differentiation, and death, in addition to organismal growth, maintenance, and aging. The mitochondrial protein import system is a major contributor to mitochondrial biogenesis and lies at the crossroads between mitochondrial and cellular homeostasis. Recent findings highlight the mitochondrial protein import system as a signaling hub, receiving inputs from other cellular compartments and adjusting its function accordingly. Impairment of protein import, in a physiological, or disease context, elicits adaptive responses inside and outside mitochondria. In this review, we discuss recent developments, relevant to the mechanisms of mitochondrial protein import regulation, with a particular focus on quality control, proteostatic and metabolic cellular responses, triggered upon impairment of mitochondrial protein import.
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Affiliation(s)
- Eirini Lionaki
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology - Hellas, Heraklion, Crete, Greece
| | - Ilias Gkikas
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology - Hellas, Heraklion, Crete, Greece
- Department of Biology, School of Sciences and Engineering, University of Crete, Heraklion, Crete, Greece
| | - Nektarios Tavernarakis
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology - Hellas, Heraklion, Crete, Greece
- Department of Basic Sciences, Faculty of Medicine, University of Crete, Heraklion, Crete, Greece
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9
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Shockley KR, Dunnick JK. Gene expression profiling after exposure to a chemical carcinogen, Pentabrominated Diphenyl Ether, at different life stages. FRONTIERS IN TOXICOLOGY 2023; 4:1028309. [PMID: 36687508 PMCID: PMC9847571 DOI: 10.3389/ftox.2022.1028309] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Accepted: 12/07/2022] [Indexed: 01/06/2023] Open
Abstract
Exposure to environmental hazards occurs at different stages of our lifetime-infant, child, adult. This study integrates recently published toxicogenomics data to examine how exposure to a known rat chemical carcinogen (pentabrominated diphenyl ether (PBDE)) upregulated liver transcriptomic changes at different life cycle stages (PND 4, PND 22, adult). We found that at all three life cycle stages PBDE exposure induced hepatocellular transcriptomic changes in disease pathways including cancer, metabolic, membrane function, and Nrf2 antioxidant pathways, pathways all characteristics of chemical carcinogens. In addition, in the adult rat after a 5-day exposure to the chemical carcinogen, there was upregulation of members of the Ras oncogenic pathway, a specific pathway found to be activated in the PBDE-induced tumors in rats in a previous hazard identification cancer study. The findings of liver transcript changes characteristic of carcinogenic activity after early life exposures and after short-term adult exposures provides data to support the use of transcriptomic data to predict the apical cancer endpoints in model studies. Using data from gene expression profiling studies after neonatal, young, or adult short-term chemical exposure helps to meet the 21st century toxicology goal of developing study designs to reduce, refine, and replace the use of traditional 2-year rodent cancer studies to provide hazard identification information. The studies reported here find that key transcripts associated with carcinogenesis were elevated in neonate (PND 4), young (PND 22) and adult animals after short-term exposure to PBDE, a known experimental chemical carcinogen in model systems.
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Affiliation(s)
- Keith R. Shockley
- Biostatistics and Computational Biology Branch, Division of Intramural Research, National Institute of Environmental Health Sciences, Research Triangle Park, Durham, NC, United States,*Correspondence: Keith R. Shockley,
| | - June K. Dunnick
- Systems Toxicology Branch, Division of Translational Toxicology, National Institute of Environmental Health Sciences, Research Triangle Park, Durham, NC, United States
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10
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Seike H, Ishimori K, Watanabe A, Kiryu M, Hatakeyama S, Tanaka S, Yoshihara R. Two high-mobility group domains of MHG1 are necessary to maintain mtDNA in Neurospora crassa. Fungal Biol 2022; 126:826-833. [PMID: 36517150 DOI: 10.1016/j.funbio.2022.11.001] [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: 05/03/2022] [Revised: 10/13/2022] [Accepted: 11/08/2022] [Indexed: 11/15/2022]
Abstract
The mhg1 (NCU02695/ada-23) gene encodes the mitochondrial high-mobility group box (HMG-box or HMGB) protein in Neurospora crassa. The mhg1 KO strain (mhg1KO) has mitochondrial DNA (mtDNA) instability and a short lifespan; however, the function of MHG1 remains unclear. To investigate the role of this protein in the maintenance of mtDNA, domain deleted MHG1 proteins were expressed in the mhg1KO strain, and their effects were analyzed. We identified two putative HMG-domains, HMGBI and HMGBII. Although deletion of the HMG-box did not abolish MHG1's mitochondrial localization, the mhg1KO phenotype of a severe growth defect and a high sensitivity to mutagens could not be restored by introduction of HMG-box deleted mhg1 gene into the KO strain. It was indicated that recombinant full-length MHG1, i.e., mitochondrial targeting sequence (MTS) containing protein, did not exhibit explicit DNA binding, whereas the MHG1 protein truncated for the MTS sequence did in vitro by an electrophoretic mobility shift assay. Furthermore, recombinant MHG1 protein lacking MTS and HMG-domains, either HMGBI or HMGBII, had DNA affinity and an altered band shift pattern compared with MTS-truncated MHG1 protein. These results suggest that cleavage of MTS and appropriate DNA binding via HMG-domains are indispensable for maintaining mtDNA in N. crassa.
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Affiliation(s)
- Hayami Seike
- Department of Regulatory Biology, Faculty of Science, Saitama University, Shimo-Ohkubo 255, Sakura-ku, Saitama, Saitama, 338-8570, Japan
| | - Keisuke Ishimori
- Department of Regulatory Biology, Faculty of Science, Saitama University, Shimo-Ohkubo 255, Sakura-ku, Saitama, Saitama, 338-8570, Japan
| | - Asagi Watanabe
- Department of Regulatory Biology, Faculty of Science, Saitama University, Shimo-Ohkubo 255, Sakura-ku, Saitama, Saitama, 338-8570, Japan
| | - Mao Kiryu
- Department of Regulatory Biology, Faculty of Science, Saitama University, Shimo-Ohkubo 255, Sakura-ku, Saitama, Saitama, 338-8570, Japan
| | - Shin Hatakeyama
- Department of Regulatory Biology, Faculty of Science, Saitama University, Shimo-Ohkubo 255, Sakura-ku, Saitama, Saitama, 338-8570, Japan
| | - Shuuitsu Tanaka
- Department of Regulatory Biology, Faculty of Science, Saitama University, Shimo-Ohkubo 255, Sakura-ku, Saitama, Saitama, 338-8570, Japan
| | - Ryouhei Yoshihara
- Department of Regulatory Biology, Faculty of Science, Saitama University, Shimo-Ohkubo 255, Sakura-ku, Saitama, Saitama, 338-8570, Japan.
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11
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Structural basis of Tom20 and Tom22 cytosolic domains as the human TOM complex receptors. Proc Natl Acad Sci U S A 2022; 119:e2200158119. [PMID: 35733257 PMCID: PMC9245660 DOI: 10.1073/pnas.2200158119] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Mitochondrial preproteins synthesized in cytosol are imported into mitochondria by a multisubunit translocase of the outer membrane (TOM) complex. Functioned as the receptor, the TOM complex components, Tom 20, Tom22, and Tom70, recognize the presequence and further guide the protein translocation. Their deficiency has been linked with neurodegenerative diseases and cardiac pathology. Although several structures of the TOM complex have been reported by cryoelectron microscopy (cryo-EM), how Tom22 and Tom20 function as TOM receptors remains elusive. Here we determined the structure of TOM core complex at 2.53 Å and captured the structure of the TOM complex containing Tom22 and Tom20 cytosolic domains at 3.74 Å. Structural analysis indicates that Tom20 and Tom22 share a similar three-helix bundle structural feature in the cytosolic domain. Further structure-guided biochemical analysis reveals that the Tom22 cytosolic domain is responsible for binding to the presequence, and the helix H1 is critical for this binding. Altogether, our results provide insights into the functional mechanism of the TOM complex recognizing and transferring preproteins across the mitochondrial membrane.
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12
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Liu W, Sun Y, Ge W, Zhang F, Gan L, Zhu Y, Guo T, Liu K. DIA-based Proteomics Identifies IDH2 as a Targetable Regulator of Acquired Drug Resistance in Chronic Myeloid Leukemia. Mol Cell Proteomics 2021; 21:100187. [PMID: 34922009 PMCID: PMC8800142 DOI: 10.1016/j.mcpro.2021.100187] [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: 04/06/2021] [Revised: 11/08/2021] [Accepted: 12/13/2021] [Indexed: 11/26/2022] Open
Abstract
Drug resistance is a critical obstacle to effective treatment in patients with chronic myeloid leukemia (CML). To understand the underlying resistance mechanisms in response to imatinib (IMA) and adriamycin (ADR), the parental K562 cells were treated with low doses of IMA or ADR for two months to generate derivative cells with mild, intermediate and severe resistance to the drugs as defined by their increasing resistance index (RI). PulseDIA-based quantitative proteomics was then employed to reveal the proteome changes in these resistant cells. In total, 7082 proteotypic proteins from 98,232 peptides were identified and quantified from the dataset using four DIA software tools including OpenSWATH, Spectronaut, DIA-NN, and EncyclopeDIA. Sirtuin Signaling Pathway was found to be significantly enriched in both ADR- and IMA-resistant K562 cells. In particular, IDH2 was identified as a potential drug target correlated with the drug resistance phenotype, and its inhibition by the antagonist AGI-6780 reversed the acquired resistance in K562 cells to either ADR or IMA. Together, our study has implicated IDH2 as a potential target that can be therapeutically leveraged to alleviate the drug resistance in K562 cells when treated with IMA and ADR.
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Affiliation(s)
- Wei Liu
- Department of Clinical Pharmacology, College of Pharmacy, Dalian Medical University, Dalian, Liaoning, China; Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China; Center for Infectious Disease Research, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China; Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, Zhejiang, China
| | - Yaoting Sun
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China; Center for Infectious Disease Research, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China; Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, Zhejiang, China
| | - Weigang Ge
- Westlake Omics (Hangzhou) Biotechnology Co., Ltd., Hangzhou 310024, China
| | - Fangfei Zhang
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China; Center for Infectious Disease Research, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China; Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, Zhejiang, China
| | - Lin Gan
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China; Center for Infectious Disease Research, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China; Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, Zhejiang, China
| | - Yi Zhu
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China; Center for Infectious Disease Research, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China; Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, Zhejiang, China
| | - Tiannan Guo
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China; Center for Infectious Disease Research, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China; Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, Zhejiang, China.
| | - Kexin Liu
- Department of Clinical Pharmacology, College of Pharmacy, Dalian Medical University, Dalian, Liaoning, China.
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13
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Bogorodskiy A, Okhrimenko I, Burkatovskii D, Jakobs P, Maslov I, Gordeliy V, Dencher NA, Gensch T, Voos W, Altschmied J, Haendeler J, Borshchevskiy V. Role of Mitochondrial Protein Import in Age-Related Neurodegenerative and Cardiovascular Diseases. Cells 2021; 10:3528. [PMID: 34944035 PMCID: PMC8699856 DOI: 10.3390/cells10123528] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Revised: 12/10/2021] [Accepted: 12/12/2021] [Indexed: 11/17/2022] Open
Abstract
Mitochondria play a critical role in providing energy, maintaining cellular metabolism, and regulating cell survival and death. To carry out these crucial functions, mitochondria employ more than 1500 proteins, distributed between two membranes and two aqueous compartments. An extensive network of dedicated proteins is engaged in importing and sorting these nuclear-encoded proteins into their designated mitochondrial compartments. Defects in this fundamental system are related to a variety of pathologies, particularly engaging the most energy-demanding tissues. In this review, we summarize the state-of-the-art knowledge about the mitochondrial protein import machinery and describe the known interrelation of its failure with age-related neurodegenerative and cardiovascular diseases.
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Affiliation(s)
- Andrey Bogorodskiy
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141701 Dolgoprudny, Russia; (A.B.); (I.O.); (D.B.); (I.M.); (V.G.); (N.A.D.)
| | - Ivan Okhrimenko
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141701 Dolgoprudny, Russia; (A.B.); (I.O.); (D.B.); (I.M.); (V.G.); (N.A.D.)
| | - Dmitrii Burkatovskii
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141701 Dolgoprudny, Russia; (A.B.); (I.O.); (D.B.); (I.M.); (V.G.); (N.A.D.)
| | - Philipp Jakobs
- Environmentally-Induced Cardiovascular Degeneration, Central Institute of Clinical Chemistry and Laboratory Medicine, Medical Faculty, University Hospital and Heinrich-Heine-University Düsseldorf, 40225 Düsseldorf, Germany; (P.J.); (J.A.); (J.H.)
| | - Ivan Maslov
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141701 Dolgoprudny, Russia; (A.B.); (I.O.); (D.B.); (I.M.); (V.G.); (N.A.D.)
| | - Valentin Gordeliy
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141701 Dolgoprudny, Russia; (A.B.); (I.O.); (D.B.); (I.M.); (V.G.); (N.A.D.)
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich, 52428 Jülich, Germany
- JuStruct: Jülich Center for Structural Biology, Forschungszentrum Jülich, 52428 Jülich, Germany
- Institut de Biologie Structurale (IBS), Université Grenoble Alpes, CEA, CNRS, 38400 Grenoble, France
| | - Norbert A. Dencher
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141701 Dolgoprudny, Russia; (A.B.); (I.O.); (D.B.); (I.M.); (V.G.); (N.A.D.)
- Physical Biochemistry, Chemistry Department, Technical University of Darmstadt, 64289 Darmstadt, Germany
| | - Thomas Gensch
- Institute of Biological Information Processing (IBI-1: Molecular and Cellular Physiology), Forschungszentrum Jülich, 52428 Jülich, Germany;
| | - Wolfgang Voos
- Institute of Biochemistry and Molecular Biology (IBMB), Faculty of Medicine, University of Bonn, 53113 Bonn, Germany;
| | - Joachim Altschmied
- Environmentally-Induced Cardiovascular Degeneration, Central Institute of Clinical Chemistry and Laboratory Medicine, Medical Faculty, University Hospital and Heinrich-Heine-University Düsseldorf, 40225 Düsseldorf, Germany; (P.J.); (J.A.); (J.H.)
- IUF—Leibniz Research Institute for Environmental Medicine, 40225 Düsseldorf, Germany
| | - Judith Haendeler
- Environmentally-Induced Cardiovascular Degeneration, Central Institute of Clinical Chemistry and Laboratory Medicine, Medical Faculty, University Hospital and Heinrich-Heine-University Düsseldorf, 40225 Düsseldorf, Germany; (P.J.); (J.A.); (J.H.)
| | - Valentin Borshchevskiy
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141701 Dolgoprudny, Russia; (A.B.); (I.O.); (D.B.); (I.M.); (V.G.); (N.A.D.)
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich, 52428 Jülich, Germany
- JuStruct: Jülich Center for Structural Biology, Forschungszentrum Jülich, 52428 Jülich, Germany
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14
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Zegallai HM, Abu-El-Rub E, Cole LK, Field J, Mejia EM, Gordon JW, Marshall AJ, Hatch GM. Tafazzin deficiency impairs mitochondrial metabolism and function of lipopolysaccharide activated B lymphocytes in mice. FASEB J 2021; 35:e22023. [PMID: 34767647 DOI: 10.1096/fj.202100811rr] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Revised: 10/05/2021] [Accepted: 10/19/2021] [Indexed: 01/21/2023]
Abstract
B lymphocytes are responsible for humoral immunity and play a key role in the immune response. Optimal mitochondrial function is required to support B cell activity during activation. We examined how deficiency of tafazzin, a cardiolipin remodeling enzyme required for mitochondrial function, alters the metabolic activity of B cells and their response to activation by lipopolysaccharide in mice. B cells were isolated from 3-month-old wild type or tafazzin knockdown mice and incubated for up to 72 h with lipopolysaccharide and cell proliferation, expression of cell surface markers, secretion of antibodies and chemokines, proteasome and immunoproteasome activities, and metabolic function determined. In addition, proteomic analysis was performed to identify altered levels of proteins involved in survival, immunogenic, proteasomal and mitochondrial processes. Compared to wild type lipopolysaccharide activated B cells, lipopolysaccharide activated tafazzin knockdown B cells exhibited significantly reduced proliferation, lowered expression of cluster of differentiation 86 and cluster of differentiation 69 surface markers, reduced secretion of immunoglobulin M antibody, reduced secretion of keratinocytes-derived chemokine and macrophage-inflammatory protein-2, reduced proteasome and immunoproteasome activities, and reduced mitochondrial respiration and glycolysis. Proteomic analysis revealed significant alterations in key protein targets that regulate cell survival, immunogenicity, proteasomal processing and mitochondrial function consistent with the findings of the above functional studies. The results indicate that the cardiolipin transacylase enzyme tafazzin plays a key role in regulating mouse B cell function and metabolic activity during activation through modulation of mitochondrial function.
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Affiliation(s)
- Hana M Zegallai
- Diabetes Research Envisioned and Accomplished in Manitoba (DREAM) Theme, Children's Hospital Research Institute of Manitoba, Winnipeg, Manitoba, Canada.,Department of Pharmacology & Therapeutics, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Ejlal Abu-El-Rub
- Department of Physiology and Pathophysiology, Yarmouk University, Irbid, Jordan.,Department of Basic Medical Sciences, Faculty of Medicine, Yarmouk University, Irbid, Jordan.,Department of Physiology and Pathophysiology, University of Manitoba, Winnipeg, Manitoba, Canada.,Department of Regenerative Medicine, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Laura K Cole
- Diabetes Research Envisioned and Accomplished in Manitoba (DREAM) Theme, Children's Hospital Research Institute of Manitoba, Winnipeg, Manitoba, Canada.,Department of Pharmacology & Therapeutics, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Jared Field
- Diabetes Research Envisioned and Accomplished in Manitoba (DREAM) Theme, Children's Hospital Research Institute of Manitoba, Winnipeg, Manitoba, Canada.,Department of Human Anatomy and Cell Science, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Edgard M Mejia
- Department of Immunology, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Joseph W Gordon
- Diabetes Research Envisioned and Accomplished in Manitoba (DREAM) Theme, Children's Hospital Research Institute of Manitoba, Winnipeg, Manitoba, Canada.,Department of Human Anatomy and Cell Science, University of Manitoba, Winnipeg, Manitoba, Canada.,College of Nursing, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Aaron J Marshall
- Department of Immunology, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Grant M Hatch
- Diabetes Research Envisioned and Accomplished in Manitoba (DREAM) Theme, Children's Hospital Research Institute of Manitoba, Winnipeg, Manitoba, Canada.,Department of Pharmacology & Therapeutics, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, Manitoba, Canada
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15
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Quality control of protein import into mitochondria. Biochem J 2021; 478:3125-3143. [PMID: 34436539 DOI: 10.1042/bcj20190584] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Revised: 07/29/2021] [Accepted: 08/03/2021] [Indexed: 12/19/2022]
Abstract
Mitochondria import about 1000 proteins that are produced as precursors on cytosolic ribosomes. Defects in mitochondrial protein import result in the accumulation of non-imported precursor proteins and proteotoxic stress. The cell is equipped with different quality control mechanisms to monitor protein transport into mitochondria. First, molecular chaperones guide unfolded proteins to mitochondria and deliver non-imported proteins to proteasomal degradation. Second, quality control factors remove translocation stalled precursor proteins from protein translocases. Third, protein translocases monitor protein sorting to mitochondrial subcompartments. Fourth, AAA proteases of the mitochondrial subcompartments remove mislocalized or unassembled proteins. Finally, impaired efficiency of protein transport is an important sensor for mitochondrial dysfunction and causes the induction of cellular stress responses, which could eventually result in the removal of the defective mitochondria by mitophagy. In this review, we summarize our current understanding of quality control mechanisms that govern mitochondrial protein transport.
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16
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Balaji S. The transferred translocases: An old wine in a new bottle. Biotechnol Appl Biochem 2021; 69:1587-1610. [PMID: 34324237 DOI: 10.1002/bab.2230] [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: 03/30/2021] [Accepted: 07/23/2021] [Indexed: 11/12/2022]
Abstract
The role of translocases was underappreciated and was not included as a separate class in the enzyme commission until August 2018. The recent research interests in proteomics of orphan enzymes, ionomics, and metallomics along with high-throughput sequencing technologies generated overwhelming data and revamped this enzyme into a separate class. This offers a great opportunity to understand the role of new or orphan enzymes in general and specifically translocases. The enzymes belonging to translocases regulate/permeate the transfer of ions or molecules across the membranes. These enzyme entries were previously associated with other enzyme classes, which are now transferred to a new enzyme class 7 (EC 7). The entries that are reclassified are important to extend the enzyme list, and it is the need of the hour. Accordingly, there is an upgradation of entries of this class of enzymes in several databases. This review is a concise compilation of translocases with reference to the number of entries currently available in the databases. This review also focuses on function as well as dysfunction of translocases during normal and disordered states, respectively.
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Affiliation(s)
- S Balaji
- Department of Biotechnology, Manipal Institute of Technology, Manipal Academy of Higher Education, Manipal, Karnataka, 576 104, India
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17
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Pitt AS, Buchanan SK. A Biochemical and Structural Understanding of TOM Complex Interactions and Implications for Human Health and Disease. Cells 2021; 10:cells10051164. [PMID: 34064787 PMCID: PMC8150904 DOI: 10.3390/cells10051164] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Revised: 05/01/2021] [Accepted: 05/07/2021] [Indexed: 12/15/2022] Open
Abstract
The central role mitochondria play in cellular homeostasis has made its study critical to our understanding of various aspects of human health and disease. Mitochondria rely on the translocase of the outer membrane (TOM) complex for the bulk of mitochondrial protein import. In addition to its role as the major entry point for mitochondrial proteins, the TOM complex serves as an entry pathway for viral proteins. TOM complex subunits also participate in a host of interactions that have been studied extensively for their function in neurodegenerative diseases, cardiovascular diseases, innate immunity, cancer, metabolism, mitophagy and autophagy. Recent advances in our structural understanding of the TOM complex and the protein import machinery of the outer mitochondrial membrane have made structure-based therapeutics targeting outer mitochondrial membrane proteins during mitochondrial dysfunction an exciting prospect. Here, we describe advances in understanding the TOM complex, the interactome of the TOM complex subunits, the implications for the development of therapeutics, and our understanding of the structure/function relationship between components of the TOM complex and mitochondrial homeostasis.
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18
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Maity S, Chakrabarti O. Mitochondrial protein import as a quality control sensor. Biol Cell 2021; 113:375-400. [PMID: 33870508 DOI: 10.1111/boc.202100002] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Revised: 03/04/2021] [Accepted: 04/09/2021] [Indexed: 12/17/2022]
Abstract
Mitochondria are organelles involved in various functions related to cellular metabolism and homoeostasis. Though mitochondria contain own genome, their nuclear counterparts encode most of the different mitochondrial proteins. These are synthesised as precursors in the cytosol and have to be delivered into the mitochondria. These organelles hence have elaborate machineries for the import of precursor proteins from cytosol. The protein import machineries present in both mitochondrial membrane and aqueous compartments show great variability in pre-protein recognition, translocation and sorting across or into it. Mitochondrial protein import machineries also interact transiently with other protein complexes of the respiratory chain or those involved in the maintenance of membrane architecture. Hence mitochondrial protein translocation is an indispensable part of the regulatory network that maintains protein biogenesis, bioenergetics, membrane dynamics and quality control of the organelle. Various stress conditions and diseases that are associated with mitochondrial import defects lead to changes in cellular transcriptomic and proteomic profiles. Dysfunction in mitochondrial protein import also causes over-accumulation of precursor proteins and their aggregation in the cytosol. Multiple pathways may be activated for buffering these harmful consequences. Here, we present a comprehensive picture of import machinery and its role in cellular quality control in response to defective mitochondrial import. We also discuss the pathological consequences of dysfunctional mitochondrial protein import in neurodegeneration and cancer.
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Affiliation(s)
- Sebabrata Maity
- Biophysics & Structural Genomics Division, Saha Institute of Nuclear Physics, Kolkata, 700064, India.,Homi Bhabha National Institute, India
| | - Oishee Chakrabarti
- Biophysics & Structural Genomics Division, Saha Institute of Nuclear Physics, Kolkata, 700064, India.,Homi Bhabha National Institute, India
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19
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Palmer CS, Anderson AJ, Stojanovski D. Mitochondrial protein import dysfunction: mitochondrial disease, neurodegenerative disease and cancer. FEBS Lett 2021; 595:1107-1131. [PMID: 33314127 DOI: 10.1002/1873-3468.14022] [Citation(s) in RCA: 48] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Revised: 10/12/2020] [Accepted: 10/17/2020] [Indexed: 12/13/2022]
Abstract
The majority of proteins localised to mitochondria are encoded by the nuclear genome, with approximately 1500 proteins imported into mammalian mitochondria. Dysfunction in this fundamental cellular process is linked to a variety of pathologies including neuropathies, cardiovascular disorders, myopathies, neurodegenerative diseases and cancer, demonstrating the importance of mitochondrial protein import machinery for cellular function. Correct import of proteins into mitochondria requires the co-ordinated activity of multimeric protein translocation and sorting machineries located in both the outer and inner mitochondrial membranes, directing the imported proteins to the destined mitochondrial compartment. This dynamic process maintains cellular homeostasis, and its dysregulation significantly affects cellular signalling pathways and metabolism. This review summarises current knowledge of the mammalian mitochondrial import machinery and the pathological consequences of mutation of its components. In addition, we will discuss the role of mitochondrial import in cancer, and our current understanding of the role of mitochondrial import in neurodegenerative diseases including Alzheimer's disease, Huntington's disease and Parkinson's disease.
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Affiliation(s)
- Catherine S Palmer
- Department of Biochemistry and Molecular Biology and The Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Australia
| | - Alexander J Anderson
- Department of Biochemistry and Molecular Biology and The Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Australia
| | - Diana Stojanovski
- Department of Biochemistry and Molecular Biology and The Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Australia
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20
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Yu X, Li Y, Ding Y, Zhang H, Ding N, Lu M. HuR Promotes Ovarian Cancer Cell Proliferation by Regulating TIMM44 mRNA Stability. Cell Biochem Biophys 2020; 78:447-453. [PMID: 32901414 DOI: 10.1007/s12013-020-00939-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2020] [Accepted: 08/26/2020] [Indexed: 12/13/2022]
Abstract
The human antigen R (HuR) could play an essential role in stabilizing the mRNAs of many tumor-associated genes. Little research is performed to investigate the relevant mechanism mediated by HuR to promote the progress of ovarian cancer. The Cancer Genome Atlas (TCGA) dataset was retrieved to calculate the correlation between HuR and translocase of inner mitochondrial membrane 44 (TIMM44) expression. HuR expression plasmid, TIMM44 expression plasmid, siRNA HuR, and TIMM44 siRNAs were further transfected into A2780 and SKOV3 cells. The 3'UTR of TIMM44 fragment was cloned into the back of Renilla luciferase in the pSicheck2 dual fluorescent reporter to indicate the interaction between HuR and TIMM44. Cell count and MTT assay were performed to assay the proliferation ability of A2780 and SKOV3 cells. High-level HuR expression in 56 ovarian cancer patients recruited in Zibo Central Hospital was positively correlated with metastasis status and poor prognosis revealed by Kaplan-Meier analysis. Both HuR and TIMM44 can promote the proliferation of SKOV3 and A2780 cells. A high correlation of HuR and TIMM44 expression was testified in the TCGA data. Luciferase reporter assay confirmed that HuR could bind to TIMM44 to maintain the mRNA stability. TIMM44 siRNA administration inhibited the proliferation of SKOV3 cells, which could not be rescued. All of these indicate that the main function of HuR on ovarian cancer proliferation is mediated by TIMM44 through mRNA stability regulation, and HuR/TIMM44 complex can be used as a target to inhibit the proliferation of ovarian cancer cells.
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Affiliation(s)
- Xiaohui Yu
- Department of Gynaecology, ZIBO Central Hospital, No. 54 Gongqingtuan West Road, Zhangdian District, Zibo, 255036, Shandong, China
| | - Yujiao Li
- Department of Gynaecology, ZIBO Central Hospital, No. 54 Gongqingtuan West Road, Zhangdian District, Zibo, 255036, Shandong, China
| | - Yumei Ding
- Department of Gynaecology, ZIBO Central Hospital, No. 54 Gongqingtuan West Road, Zhangdian District, Zibo, 255036, Shandong, China
| | - Hong Zhang
- Department of Gynaecology, ZIBO Central Hospital, No. 54 Gongqingtuan West Road, Zhangdian District, Zibo, 255036, Shandong, China
| | - Ning Ding
- Department of Gynaecology, ZIBO Central Hospital, No. 54 Gongqingtuan West Road, Zhangdian District, Zibo, 255036, Shandong, China
| | - Ming Lu
- Department of Gynaecology, ZIBO Central Hospital, No. 54 Gongqingtuan West Road, Zhangdian District, Zibo, 255036, Shandong, China.
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21
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Goyal S, Chaturvedi RK. Mitochondrial Protein Import Dysfunction in Pathogenesis of Neurodegenerative Diseases. Mol Neurobiol 2020; 58:1418-1437. [PMID: 33180216 DOI: 10.1007/s12035-020-02200-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Accepted: 11/03/2020] [Indexed: 02/06/2023]
Abstract
Mitochondria play an essential role in maintaining energy homeostasis and cellular survival. In the brain, higher ATP production is required by mature neurons for communication. Most of the mitochondrial proteins transcribe in the nucleus and import in mitochondria through different pathways of the mitochondrial protein import machinery. This machinery plays a crucial role in determining mitochondrial morphology and functions through mitochondrial biogenesis. Failure of this machinery and any alterations during mitochondrial biogenesis underlies neurodegeneration resulting in Alzheimer's disease (AD), amyotrophic lateral sclerosis (ALS), and Parkinson's disease (PD) etc. Current knowledge has revealed the different pathways of mitochondrial protein import machinery such as translocase of the outer mitochondrial membrane complex, the presequence pathway, carrier pathway, β-barrel pathway, and mitochondrial import and assembly machinery etc. In this review, we have discussed the recent studies regarding protein import machinery, beyond the well-known effects of increased oxidative stress and bioenergetics dysfunctions. We have elucidated in detail how these types of machinery help to import and locate the precursor proteins to their specific location inside the mitochondria and play a major role in mitochondrial biogenesis. We further discuss their involvement in mitochondrial dysfunctioning and the induction of toxic aggregates in neurodegenerative diseases like AD and PD. The review supports the importance of import machinery in neuronal functions and its association with toxic aggregated proteins in mitochondrial impairment, suggesting a critical role in fostering and maintaining neurodegeneration and therapeutic response.
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Affiliation(s)
- Shweta Goyal
- Developmental Toxicology Laboratory, Systems Toxicology and Health Risk Assessment Group, CSIR-Indian Institute of Toxicology Research (CSIR-IITR), Vishvigyan Bhavan, 31, Mahatma Gandhi Marg, Lucknow, Uttar Pradesh, 226001, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Rajnish Kumar Chaturvedi
- Developmental Toxicology Laboratory, Systems Toxicology and Health Risk Assessment Group, CSIR-Indian Institute of Toxicology Research (CSIR-IITR), Vishvigyan Bhavan, 31, Mahatma Gandhi Marg, Lucknow, Uttar Pradesh, 226001, India. .,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India.
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22
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Kreimendahl S, Rassow J. The Mitochondrial Outer Membrane Protein Tom70-Mediator in Protein Traffic, Membrane Contact Sites and Innate Immunity. Int J Mol Sci 2020; 21:E7262. [PMID: 33019591 PMCID: PMC7583919 DOI: 10.3390/ijms21197262] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Revised: 09/25/2020] [Accepted: 09/28/2020] [Indexed: 02/08/2023] Open
Abstract
Tom70 is a versatile adaptor protein of 70 kDa anchored in the outer membrane of mitochondria in metazoa, fungi and amoeba. The tertiary structure was resolved for the Tom70 of yeast, showing 26 α-helices, most of them participating in the formation of 11 tetratricopeptide repeat (TPR) motifs. Tom70 serves as a docking site for cytosolic chaperone proteins and co-chaperones and is thereby involved in the uptake of newly synthesized chaperone-bound proteins in mitochondrial biogenesis. In yeast, Tom70 additionally mediates ER-mitochondria contacts via binding to sterol transporter Lam6/Ltc1. In mammalian cells, TOM70 promotes endoplasmic reticulum (ER) to mitochondria Ca2+ transfer by association with the inositol-1,4,5-triphosphate receptor type 3 (IP3R3). TOM70 is specifically targeted by the Bcl-2-related protein MCL-1 that acts as an anti-apoptotic protein in macrophages infected by intracellular pathogens, but also in many cancer cells. By participating in the recruitment of PINK1 and the E3 ubiquitin ligase Parkin, TOM70 can be implicated in the development of Parkinson's disease. TOM70 acts as receptor of the mitochondrial antiviral-signaling protein (MAVS) and thereby participates in the corresponding system of innate immunity against viral infections. The protein encoded by Orf9b in the genome of SARS-CoV-2 binds to TOM70, probably compromising the synthesis of type I interferons.
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Affiliation(s)
| | - Joachim Rassow
- Institute for Biochemistry and Pathobiochemistry, Ruhr-University Bochum, 44801 Bochum, Germany;
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23
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Wang W, Chen X, Zhang L, Yi J, Ma Q, Yin J, Zhuo W, Gu J, Yang M. Atomic structure of human TOM core complex. Cell Discov 2020; 6:67. [PMID: 33083003 PMCID: PMC7522991 DOI: 10.1038/s41421-020-00198-2] [Citation(s) in RCA: 58] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Accepted: 07/20/2020] [Indexed: 12/22/2022] Open
Abstract
The translocase of the outer mitochondrial membrane (TOM) complex is the main entry gate for mitochondrial precursor proteins synthesized on cytosolic ribosomes. Here we report the single-particle cryo-electron microscopy (cryo-EM) structure of the dimeric human TOM core complex (TOM-CC). Two Tom40 β-barrel proteins, connected by two Tom22 receptor subunits and one phospholipid, form the protein-conducting channels. The small Tom proteins Tom5, Tom6, and Tom7 surround the channel and have notable configurations. The distinct electrostatic features of the complex, including the pronounced negative interior and the positive regions at the periphery and center of the dimer on the intermembrane space (IMS) side, provide insight into the preprotein translocation mechanism. Further, two dimeric TOM complexes may associate to form tetramer in the shape of a parallelogram, offering a potential explanation into the unusual structural features of Tom subunits and a new perspective of viewing the import of mitochondrial proteins.
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Affiliation(s)
- Wenhe Wang
- Ministry of Education Key Laboratory of Protein Science, Beijing Advanced Innovation Center for Structural Biology & Frontier Research Center for Biological Structure, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, 100084 Beijing, China
| | - Xudong Chen
- Ministry of Education Key Laboratory of Protein Science, Beijing Advanced Innovation Center for Structural Biology & Frontier Research Center for Biological Structure, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, 100084 Beijing, China
| | - Laixing Zhang
- Ministry of Education Key Laboratory of Protein Science, Beijing Advanced Innovation Center for Structural Biology & Frontier Research Center for Biological Structure, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, 100084 Beijing, China
| | - Jingbo Yi
- Ministry of Education Key Laboratory of Protein Science, Beijing Advanced Innovation Center for Structural Biology & Frontier Research Center for Biological Structure, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, 100084 Beijing, China
| | - Qingxi Ma
- Ministry of Education Key Laboratory of Protein Science, Beijing Advanced Innovation Center for Structural Biology & Frontier Research Center for Biological Structure, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, 100084 Beijing, China
| | - Jian Yin
- Ministry of Education Key Laboratory of Protein Science, Beijing Advanced Innovation Center for Structural Biology & Frontier Research Center for Biological Structure, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, 100084 Beijing, China
| | - Wei Zhuo
- Ministry of Education Key Laboratory of Protein Science, Beijing Advanced Innovation Center for Structural Biology & Frontier Research Center for Biological Structure, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, 100084 Beijing, China
| | - Jinke Gu
- Ministry of Education Key Laboratory of Protein Science, Beijing Advanced Innovation Center for Structural Biology & Frontier Research Center for Biological Structure, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, 100084 Beijing, China
| | - Maojun Yang
- Ministry of Education Key Laboratory of Protein Science, Beijing Advanced Innovation Center for Structural Biology & Frontier Research Center for Biological Structure, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, 100084 Beijing, China
- School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030 Hubei China
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24
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Grevel A, Pfanner N, Becker T. Coupling of import and assembly pathways in mitochondrial protein biogenesis. Biol Chem 2020; 401:117-129. [PMID: 31513529 DOI: 10.1515/hsz-2019-0310] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2019] [Accepted: 08/13/2019] [Indexed: 12/14/2022]
Abstract
Biogenesis and function of mitochondria depend on the import of about 1000 precursor proteins that are produced on cytosolic ribosomes. The translocase of the outer membrane (TOM) forms the entry gate for most proteins. After passage through the TOM channel, dedicated preprotein translocases sort the precursor proteins into the mitochondrial subcompartments. Many proteins have to be assembled into oligomeric membrane-integrated complexes in order to perform their functions. In this review, we discuss a dual role of mitochondrial preprotein translocases in protein translocation and oligomeric assembly, focusing on the biogenesis of the TOM complex and the respiratory chain. The sorting and assembly machinery (SAM) of the outer mitochondrial membrane forms a dynamic platform for coupling transport and assembly of TOM subunits. The biogenesis of the cytochrome c oxidase of the inner membrane involves a molecular circuit to adjust translation of mitochondrial-encoded core subunits to the availability of nuclear-encoded partner proteins. Thus, mitochondrial protein translocases not only import precursor proteins but can also support their assembly into functional complexes.
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Affiliation(s)
- Alexander Grevel
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, D-79104 Freiburg, Germany.,Faculty of Biology, University of Freiburg, D-79104 Freiburg, Germany
| | - Nikolaus Pfanner
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, D-79104 Freiburg, Germany.,CIBSS Centre for Integrative Biological Signalling Studies, University of Freiburg, D-79104 Freiburg, Germany
| | - Thomas Becker
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, D-79104 Freiburg, Germany.,CIBSS Centre for Integrative Biological Signalling Studies, University of Freiburg, D-79104 Freiburg, Germany
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25
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Dores-Silva PR, Cauvi DM, Kiraly VTR, Borges JC, De Maio A. Human HSPA9 (mtHsp70, mortalin) interacts with lipid bilayers containing cardiolipin, a major component of the inner mitochondrial membrane. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2020; 1862:183436. [PMID: 32781155 DOI: 10.1016/j.bbamem.2020.183436] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Revised: 07/21/2020] [Accepted: 07/22/2020] [Indexed: 12/16/2022]
Abstract
Mitochondrial Hsp70 (HSPA9, mtHsp70, mortalin) in conjunction with a complex set of other proteins is involved in the transport of polypeptides across the mitochondrial matrix. This observation allows us to hypothesize that HSPA9 might interact with membranes directly, similarly to other Hsp70s. Thus, we investigated whether human HSPA9 could also get inserted into lipid membranes. Human HSPA9 was incubated with liposomes made of lipids found within the mitochondrial membrane, such as 1', 3'-bis [1, 2-dimyristoyl-sn-glycero-3-phospho]-glycerol (CL), palmitoyl-oleoyl phosphocholine (POPC), palmitoyl-oleoyl phosphoserine (POPS), and palmitoyl-oleoyl phosphoethanolamine (POPE). HSPA9 displayed a predilection for CL and POPS, and low affinity for POPC and POPE, suggesting that the proteins have high specificity for negatively charged phospholipids. Then, liposomes were made with a composition resembling either the outer or inner mitochondrial membrane (OMM or IMM, respectively). We observed that HSPA9 has a higher affinity for IMM than OMM, which is consistent with the higher content of CL in the IMM. A comparison for the incorporation into POPS or CL liposomes by HSPA9 or HSPA1 indicated that both proteins behaved very similarly when exposed to CL liposomes, but differently with POPS liposomes, which was further corroborated by their susceptibility to proteinase K digestion after incorporation into liposomes. The measurement of thermodynamic parameters also showed that the interaction of both proteins with CL and POPS liposomes was different. Overall, our data showed that HSPA9 is prone to interact with membranes resembling the IMM that may be important for its role in the translocation of proteins into the mitochondria.
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Affiliation(s)
- Paulo Roberto Dores-Silva
- Division of Trauma, Critical Care, Burns and Acute Care Surgery, Department of Surgery, School of Medicine, University of California San Diego, La Jolla, CA 92093, USA; São Carlos Institute of Chemistry, University of São Paulo, São Paulo, Brazil
| | - David M Cauvi
- Division of Trauma, Critical Care, Burns and Acute Care Surgery, Department of Surgery, School of Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Vanessa T R Kiraly
- São Carlos Institute of Chemistry, University of São Paulo, São Paulo, Brazil
| | - Júlio C Borges
- São Carlos Institute of Chemistry, University of São Paulo, São Paulo, Brazil
| | - Antonio De Maio
- Division of Trauma, Critical Care, Burns and Acute Care Surgery, Department of Surgery, School of Medicine, University of California San Diego, La Jolla, CA 92093, USA; Division of Trauma, Critical Care, Burns and Acute Care Surgery, Department of Neurosciences, School of Medicine, University of California San Diego, La Jolla, CA 92093, USA.
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26
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Ming H, Sun J, Pasquariello R, Gatenby L, Herrick JR, Yuan Y, Pinto CR, Bondioli KR, Krisher RL, Jiang Z. The landscape of accessible chromatin in bovine oocytes and early embryos. Epigenetics 2020; 16:300-312. [PMID: 32663104 DOI: 10.1080/15592294.2020.1795602] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Chromatin reorganization governs the regulation of gene expression during preimplantation development. However, the landscape of chromatin dynamics in this period has not been explored in bovine. In this study, we constructed a genome-wide map of accessible chromatin in bovine oocytes and early embryos using an improved assay for transposase-accessible chromatin with high-throughput sequencing (ATAC-seq) which revealed unique features of the accessible chromatin during bovine early embryo development. We found that chromatin accessibility is low in oocytes and 2-/4-cell embryos, followed by a significant increase in embryos during major embryonic genome activation (EGA), and peaked in elongating day 14 embryos. Genome-wide characteristics of open chromatin showed that ATAC-seq signals in both transcription start sites (TSS) and transcription end sites (TES) were strong. Additionally, the distal ATAC-seq peaks were enriched in repeat elements in a type-specific and stage-specific manner. We further unveiled a series of transcription factor (TF) motifs with distinct variation of enrichment from distal ATAC-seq peaks. By integrated analysis of chromatin accessibility with transcriptomes and DNA methylomes in bovine early embryos, we showed that promoter accessibility was positively correlated with gene expression, especially during major EGA, and was strongly correlated to DNA methylation and CpG density. Finally, we identified the critical chromatin signatures and TFs that differ between in vivo and in vitro derived blastocysts, which provides insights to the potential mechanisms leading to low quality of embryos produced in vitro. Together, this comprehensive analysis revealed critical features of chromatin landscape and epigenetic reprogramming during bovine preimplantation embryo development.
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Affiliation(s)
- Hao Ming
- School of Animal Sciences, AgCenter, Louisiana State University , Baton Rouge, LA, USA
| | - Jiangwen Sun
- Department of Computer Science, Old Dominion University , Norfolk, VA, USA
| | | | - Lauren Gatenby
- School of Animal Sciences, AgCenter, Louisiana State University , Baton Rouge, LA, USA
| | - Jason R Herrick
- Colorado Center for Reproductive Medicine , Lone Tree, CO, USA
| | - Ye Yuan
- Colorado Center for Reproductive Medicine , Lone Tree, CO, USA
| | - Carlos R Pinto
- Department of Theriogenology, School of Veterinary Medicine, Louisiana State University , Baton Rouge, LA, USA
| | - Kenneth R Bondioli
- School of Animal Sciences, AgCenter, Louisiana State University , Baton Rouge, LA, USA
| | | | - Zongliang Jiang
- School of Animal Sciences, AgCenter, Louisiana State University , Baton Rouge, LA, USA
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27
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Khanna S, Padhan P, Jaiswal KS, Jain AP, Ghosh A, Tripathy A, Gowda H, Raghav SK, Gupta B. Altered mitochondrial proteome and functional dynamics in patients with rheumatoid arthritis. Mitochondrion 2020; 54:8-14. [PMID: 32544466 DOI: 10.1016/j.mito.2020.06.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Revised: 05/03/2020] [Accepted: 06/10/2020] [Indexed: 02/05/2023]
Abstract
The autoimmune inflammatory disease, Rheumatoid arthritis (RA), has known imbalances in energy metabolism and superoxide levels thus may have an etiology associated with mitochondrial dysfunction. We thus evaluated the presence of a differential mitochondrial proteome as well as other characteristics including mitochondrial mass, membrane potential (Ψm), total cellular ATP and superoxide levels. Eighteen mitochondrial proteins were down-regulated while four were up-regulated in RA patients in comparison to the healthy controls (HC). A significant decrease in mitochondrial Ψm, superoxides and cellular ATP levels was observed in RA with constant mitochondrial mass suggesting mitochondrial dysfunction responsible for functional disparity in RA.
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Affiliation(s)
- Shweta Khanna
- Disease Biology Laboratory, School of Biotechnology, Kalinga Institute of Industrial Technology (KIIT), Deemed to be University, Bhubaneswar, Odisha, India
| | - Prasanta Padhan
- Department of Rheumatology, Kalinga Institute of Medical Sciences, Bhubaneswar, Odisha, India
| | - Kumar S Jaiswal
- Disease Biology Laboratory, School of Biotechnology, Kalinga Institute of Industrial Technology (KIIT), Deemed to be University, Bhubaneswar, Odisha, India
| | - Ankit P Jain
- Institute of Bioinformatics, International Tech Park, Bangalore, India
| | - Arup Ghosh
- Laboratory of Immuno-Genomics and Systems Biology, Institute of Life Sciences, Bhubaneswar, Odisha, India
| | - Archana Tripathy
- Disease Biology Laboratory, School of Biotechnology, Kalinga Institute of Industrial Technology (KIIT), Deemed to be University, Bhubaneswar, Odisha, India
| | - Harsha Gowda
- Institute of Bioinformatics, International Tech Park, Bangalore, India
| | - Sunil K Raghav
- Laboratory of Immuno-Genomics and Systems Biology, Institute of Life Sciences, Bhubaneswar, Odisha, India
| | - Bhawna Gupta
- Disease Biology Laboratory, School of Biotechnology, Kalinga Institute of Industrial Technology (KIIT), Deemed to be University, Bhubaneswar, Odisha, India.
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28
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Dutta D, Briere LC, Kanca O, Marcogliese PC, Walker MA, High FA, Vanderver A, Krier J, Carmichael N, Callahan C, Taft RJ, Simons C, Helman G, Network UD, Wangler MF, Yamamoto S, Sweetser DA, Bellen HJ. De novo mutations in TOMM70, a receptor of the mitochondrial import translocase, cause neurological impairment. Hum Mol Genet 2020; 29:1568-1579. [PMID: 32356556 PMCID: PMC7268787 DOI: 10.1093/hmg/ddaa081] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Revised: 04/02/2020] [Accepted: 04/24/2020] [Indexed: 12/20/2022] Open
Abstract
The translocase of outer mitochondrial membrane (TOMM) complex is the entry gate for virtually all mitochondrial proteins and is essential to build the mitochondrial proteome. TOMM70 is a receptor that assists mainly in mitochondrial protein import. Here, we report two individuals with de novo variants in the C-terminal region of TOMM70. While both individuals exhibited shared symptoms including hypotonia, hyper-reflexia, ataxia, dystonia and significant white matter abnormalities, there were differences between the two individuals, most prominently the age of symptom onset. Both individuals were undiagnosed despite extensive genetics workups. Individual 1 was found to have a p.Thr607Ile variant while Individual 2 was found to have a p.Ile554Phe variant in TOMM70. To functionally assess both TOMM70 variants, we replaced the Drosophila Tom70 coding region with a Kozak-mini-GAL4 transgene using CRISPR-Cas9. Homozygous mutant animals die as pupae, but lethality is rescued by the mini-GAL4-driven expression of human UAS-TOMM70 cDNA. Both modeled variants lead to significantly less rescue indicating that they are loss-of-function alleles. Similarly, RNAi-mediated knockdown of Tom70 in the developing eye causes roughening and synaptic transmission defect, common findings in neurodegenerative and mitochondrial disorders. These phenotypes were rescued by the reference, but not the variants, of TOMM70. Altogether, our data indicate that de novo loss-of-function variants in TOMM70 result in variable white matter disease and neurological phenotypes in affected individuals.
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Affiliation(s)
- Debdeep Dutta
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Jan and Dan Duncan Neurological Research Institute, Texas Children’s Hospital, Houston, TX 77030, USA
| | - Lauren C Briere
- Division of Medical Genetics and Metabolism, Department of Pediatrics, Massachusetts General Hospital for Children, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Oguz Kanca
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Jan and Dan Duncan Neurological Research Institute, Texas Children’s Hospital, Houston, TX 77030, USA
| | - Paul C Marcogliese
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Jan and Dan Duncan Neurological Research Institute, Texas Children’s Hospital, Houston, TX 77030, USA
| | - Melissa A Walker
- Department of Neurology, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Frances A High
- Division of Medical Genetics and Metabolism, Department of Pediatrics, Massachusetts General Hospital for Children, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Adeline Vanderver
- Division of Neurology, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Department of Neurology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Joel Krier
- Brigham Genomic Medicine, Brigham and Women’s Hospital, Boston, MA 02115, USA
| | - Nikkola Carmichael
- Brigham Genomic Medicine, Brigham and Women’s Hospital, Boston, MA 02115, USA
| | - Christine Callahan
- Department of Medicine, Brigham and Women’s Hospital, Boston, MA 02115, USA
| | | | - Cas Simons
- Murdoch Children's Research Institute, The Royal Children’s Hospital, Parkville, Victoria 3052, Australia
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Guy Helman
- Murdoch Children's Research Institute, The Royal Children’s Hospital, Parkville, Victoria 3052, Australia
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
| | | | - Michael F Wangler
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Jan and Dan Duncan Neurological Research Institute, Texas Children’s Hospital, Houston, TX 77030, USA
- Program in Developmental Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Shinya Yamamoto
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Jan and Dan Duncan Neurological Research Institute, Texas Children’s Hospital, Houston, TX 77030, USA
- Program in Developmental Biology, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Neuroscience, Baylor College of Medicine, Houston, TX 77030, USA
| | - David A Sweetser
- Division of Medical Genetics and Metabolism, Department of Pediatrics, Massachusetts General Hospital for Children, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Hugo J Bellen
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Jan and Dan Duncan Neurological Research Institute, Texas Children’s Hospital, Houston, TX 77030, USA
- Program in Developmental Biology, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Neuroscience, Baylor College of Medicine, Houston, TX 77030, USA
- Howard Hughes Medical Institute, Baylor College of Medicine, Houston, TX 77030, USA
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29
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Identification of mecciRNAs and their roles in the mitochondrial entry of proteins. SCIENCE CHINA-LIFE SCIENCES 2020; 63:1429-1449. [PMID: 32048164 DOI: 10.1007/s11427-020-1631-9] [Citation(s) in RCA: 99] [Impact Index Per Article: 24.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Accepted: 01/19/2020] [Indexed: 12/23/2022]
Abstract
Mammalian mitochondria have small genomes encoding very limited numbers of proteins. Over one thousand proteins and noncoding RNAs encoded by the nuclear genome must be imported from the cytosol into the mitochondria. Here, we report the identification of hundreds of circular RNAs (mecciRNAs) encoded by the mitochondrial genome. We provide both in vitro and in vivo evidence to show that mecciRNAs facilitate the mitochondrial entry of nuclear-encoded proteins by serving as molecular chaperones in the folding of imported proteins. Known components involved in mitochondrial protein and RNA importation, such as TOM40 and PNPASE, interact with mecciRNAs and regulate protein entry. The expression of mecciRNAs is regulated, and these transcripts are critical for the adaption of mitochondria to physiological conditions and diseases such as stresses and cancers by modulating mitochondrial protein importation. mecciRNAs and their associated physiological roles add categories and functions to the known eukaryotic circular RNAs and shed novel light on the communication between mitochondria and the nucleus.
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30
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Kumar A, Matta SK, D'Silva P. Role of conserved regions of Tim22 in the structural organization of the carrier translocase. J Cell Sci 2020; 133:jcs.244632. [DOI: 10.1242/jcs.244632] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Accepted: 06/15/2020] [Indexed: 11/20/2022] Open
Abstract
Mitochondrial biogenesis requires efficient sorting of various proteins into different mitochondrial sub-compartments mediated by dedicated protein machinery present in the outer and inner membrane. Among them, the TIM22 complex enables the integration of complex membrane proteins with internal targeting signals into the inner membrane. Although the Tim22 forms the core of the complex, the dynamic recruitment of subunits to the channel is still enigmatic. The present study first-time highlights that IMS and TM4 regions of Tim22 are critically required for the interaction of the membrane-embedded subunits including, Tim54, Tim18, and Sdh3, thereby maintain the functional architecture of TIM22 translocase. On the other hand, TM1 and TM2 regions of Tim22 are important for the Tim18 association, while TM3 is exclusively required for the Sdh3 interaction. Moreover, the impairment in TIM22 complex assembly influences its translocase activity, mitochondrial network, and the viability of cells lacking mitochondrial DNA. Overall our findings provide compelling evidence to highlight the significance of conserved regions of Tim22 that are important for the maintenance of the TIM22 complex and mitochondrial integrity.
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Affiliation(s)
- Abhishek Kumar
- Department of Biochemistry, New Biological Sciences Building, Indian Institute of Science, C V Raman Avenue, Bangalore-560012, India
| | - Srujan Kumar Matta
- Department of Biochemistry, New Biological Sciences Building, Indian Institute of Science, C V Raman Avenue, Bangalore-560012, India
| | - Patrick D'Silva
- Department of Biochemistry, New Biological Sciences Building, Indian Institute of Science, C V Raman Avenue, Bangalore-560012, India
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31
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Monteuuis G, Miścicka A, Świrski M, Zenad L, Niemitalo O, Wrobel L, Alam J, Chacinska A, Kastaniotis AJ, Kufel J. Non-canonical translation initiation in yeast generates a cryptic pool of mitochondrial proteins. Nucleic Acids Res 2019; 47:5777-5791. [PMID: 31216041 PMCID: PMC6582344 DOI: 10.1093/nar/gkz301] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Revised: 04/12/2019] [Accepted: 04/16/2019] [Indexed: 12/15/2022] Open
Abstract
Utilization of non-AUG alternative translation start sites is most common in bacteria and viruses, but it has been also reported in other organisms. This phenomenon increases proteome complexity by allowing expression of multiple protein isoforms from a single gene. In Saccharomyces cerevisiae, a few described cases concern proteins that are translated from upstream near-cognate start codons as N-terminally extended variants that localize to mitochondria. Using bioinformatics tools, we provide compelling evidence that in yeast the potential for producing alternative protein isoforms by non-AUG translation initiation is much more prevalent than previously anticipated and may apply to as many as a few thousand proteins. Several hundreds of candidates are predicted to gain a mitochondrial targeting signal (MTS), generating an unrecognized pool of mitochondrial proteins. We confirmed mitochondrial localization of a subset of proteins previously not identified as mitochondrial, whose standard forms do not carry an MTS. Our data highlight the potential of non-canonical translation initiation in expanding the capacity of the mitochondrial proteome and possibly also other cellular features.
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Affiliation(s)
- Geoffray Monteuuis
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, P.O. Box 5400, FIN-90014 Finland
| | - Anna Miścicka
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, 02-106 Warsaw, Poland
| | - Michał Świrski
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, 02-106 Warsaw, Poland
| | - Lounis Zenad
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, 02-106 Warsaw, Poland
| | - Olli Niemitalo
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, P.O. Box 5400, FIN-90014 Finland
| | - Lidia Wrobel
- International Institute of Molecular and Cell Biology, 02-109 Warsaw, Poland
| | - Jahangir Alam
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, P.O. Box 5400, FIN-90014 Finland
| | - Agnieszka Chacinska
- International Institute of Molecular and Cell Biology, 02-109 Warsaw, Poland.,Centre of New Technologies, University of Warsaw, 02-097 Warsaw, Poland
| | - Alexander J Kastaniotis
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, P.O. Box 5400, FIN-90014 Finland
| | - Joanna Kufel
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, 02-106 Warsaw, Poland
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32
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Lautenschäger J, Kaminski Schierle GS. Mitochondrial degradation of amyloidogenic proteins - A new perspective for neurodegenerative diseases. Prog Neurobiol 2019; 181:101660. [PMID: 31301323 DOI: 10.1016/j.pneurobio.2019.101660] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2018] [Revised: 06/02/2019] [Accepted: 07/04/2019] [Indexed: 01/09/2023]
Abstract
This perspective article outlines mechanisms of mitochondrial import and protein degradation and how these have been linked to alpha-synuclein and Amyloid beta (Aβ) homeostasis. Our aim is to underpin and stimulate the debate on the recent conception of mitochondria as protein degrading organelles, which suggests that mitochondria are more directly involved in neurodegenerative diseases than previously assumed.
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Affiliation(s)
- Janin Lautenschäger
- Molecular Neuroscience Group, Department of Chemical Engineering and Biotechnology, University of Cambridge, West Cambridge Site, Philippa Fawcett Drive, Cambridge, CB3 0AS, UK.
| | - Gabriele S Kaminski Schierle
- Molecular Neuroscience Group, Department of Chemical Engineering and Biotechnology, University of Cambridge, West Cambridge Site, Philippa Fawcett Drive, Cambridge, CB3 0AS, UK
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33
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Artika IM. Allotopic expression of mitochondrial genes: Basic strategy and progress. Genes Dis 2019; 7:578-584. [PMID: 33335957 PMCID: PMC7729113 DOI: 10.1016/j.gendis.2019.08.001] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Revised: 07/23/2019] [Accepted: 08/01/2019] [Indexed: 12/11/2022] Open
Abstract
Allotopic expression of mitochondrial genes is a deliberate functional relocation of mitochondrial genes into the nucleus followed by import of the gene-encoded polypeptide from the cytoplasm into the mitochondria. For successful allotopic expression of a mitochondrial gene, several key aspects must be considered. These include the different codon dictionary used by the mitochondrial and nuclear genomes, different codon preferences between mitochondrial and nuclear-cytosolic translation systems, and the provision of an import signal to ensure that the newly translated protein in the cytosol is successfully imported into mitochondria. The allotopic expression strategy was first developed in yeast, a useful model organism for studying human and other eukaryotic cells. Currently, a number of mitochondrial genes have been successfully recoded and nuclearly expressed in yeast and human cells. In addition to its use in evolutionary and molecular biology studies, the allotopic expression strategy has been developed as a potential approach to treat mitochondrial genetic disorders. Substantial progress has been recently achieved, and the development of this technique for therapy of the mitochondrial disease Leber's hereditary optic neuropathy (LHON) has entered phase III clinical trials. However, a number of challenges remain to be overcome to accelerate the successful application of this technique. These include improvement of nuclear gene expression, import into mitochondria, processing, and functional integration of the allotopically expressed polypeptides into mitochondrial protein complexes. This review discusses the current basic strategy, progress, challenges, and prospects of the allotopic expression strategy for mitochondrial genes.
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Affiliation(s)
- I. Made Artika
- Department of Biochemistry, Faculty of Mathematics and Natural Sciences, Bogor Agricultural University, Darmaga Campus, Bogor 16680, Indonesia
- Eijkman Institute for Molecular Biology, Jalan Diponegoro 69, Jakarta, 10430, Indonesia
- Department of Biochemistry, Faculty of Mathematics and Natural Sciences, Bogor Agricultural University, Darmaga Campus, Bogor 16680, Indonesia
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34
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Artika IM. Current understanding of structure, function and biogenesis of yeast mitochondrial ATP synthase. J Bioenerg Biomembr 2019; 51:315-328. [DOI: 10.1007/s10863-019-09809-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2019] [Accepted: 08/01/2019] [Indexed: 10/26/2022]
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35
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Jacoupy M, Hamon-Keromen E, Ordureau A, Erpapazoglou Z, Coge F, Corvol JC, Nosjean O, Mannoury la Cour C, Millan MJ, Boutin JA, Harper JW, Brice A, Guedin D, Gautier CA, Corti O. The PINK1 kinase-driven ubiquitin ligase Parkin promotes mitochondrial protein import through the presequence pathway in living cells. Sci Rep 2019; 9:11829. [PMID: 31413265 PMCID: PMC6694185 DOI: 10.1038/s41598-019-47352-9] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Accepted: 05/28/2019] [Indexed: 01/05/2023] Open
Abstract
Most of over a thousand mitochondrial proteins are encoded by nuclear genes and must be imported from the cytosol. Little is known about the cytosolic events regulating mitochondrial protein import, partly due to the lack of appropriate tools for its assessment in living cells. We engineered an inducible biosensor for monitoring the main presequence-mediated import pathway with a quantitative, luminescence-based readout. This tool was used to explore the regulation of mitochondrial import by the PINK1 kinase-driven Parkin ubiquitin ligase, which is dysfunctional in autosomal recessive Parkinson's disease. We show that mitochondrial import was stimulated by Parkin, but not by disease-causing Parkin variants. This effect was dependent on Parkin activation by PINK1 and accompanied by an increase in the abundance of K11 ubiquitin chains on mitochondria and by ubiquitylation of subunits of the translocase of outer mitochondrial membrane. Mitochondrial import efficiency was abnormally low in cells from patients with PINK1- and PARK2-linked Parkinson's disease and was restored by phosphomimetic ubiquitin in cells with residual Parkin activity. Altogether, these findings uncover a role of ubiquitylation in mitochondrial import regulation and suggest that loss of this regulatory loop may underlie the pathophysiology of Parkinson's disease, providing novel opportunities for therapeutic intervention.
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Affiliation(s)
- M Jacoupy
- Inserm, U1127, F-75013, Paris, France.,CNRS, UMR 7225, F-75013, Paris, France.,Sorbonne Universités, UPMC Univ Paris 06, UMR S 1127, F-75013, Paris, France.,Institut du Cerveau et de la Moelle épinière, ICM, F-75013, Paris, France
| | - E Hamon-Keromen
- Inserm, U1127, F-75013, Paris, France.,CNRS, UMR 7225, F-75013, Paris, France.,Sorbonne Universités, UPMC Univ Paris 06, UMR S 1127, F-75013, Paris, France.,Institut du Cerveau et de la Moelle épinière, ICM, F-75013, Paris, France
| | - A Ordureau
- Department of Cell Biology, Harvard Medical School, Boston, MA, 02115, USA
| | - Z Erpapazoglou
- Inserm, U1127, F-75013, Paris, France.,CNRS, UMR 7225, F-75013, Paris, France.,Sorbonne Universités, UPMC Univ Paris 06, UMR S 1127, F-75013, Paris, France.,Institut du Cerveau et de la Moelle épinière, ICM, F-75013, Paris, France
| | - F Coge
- Institut du Cerveau et de la Moelle épinière, ICM, F-75013, Paris, France.,Laboratoire de Chémogénétique Servier, F-75013, Paris, France.,Institut de Recherches Servier, Croissy-sur-Seine, France
| | - J-C Corvol
- Inserm, U1127, F-75013, Paris, France.,CNRS, UMR 7225, F-75013, Paris, France.,Sorbonne Universités, UPMC Univ Paris 06, UMR S 1127, F-75013, Paris, France.,Institut du Cerveau et de la Moelle épinière, ICM, F-75013, Paris, France.,Assistance-Publique Hôpitaux de Paris, Inserm, CIC-1422, Department of Neurology, Hôpital Pitié-Salpêtrière, F-75013, Paris, France
| | - O Nosjean
- Institut de Recherches Servier, Croissy-sur-Seine, France
| | | | - M J Millan
- Institut de Recherches Servier, Croissy-sur-Seine, France
| | - J A Boutin
- Institut de Recherches Servier, Croissy-sur-Seine, France
| | - J W Harper
- Department of Cell Biology, Harvard Medical School, Boston, MA, 02115, USA
| | - A Brice
- Inserm, U1127, F-75013, Paris, France.,CNRS, UMR 7225, F-75013, Paris, France.,Sorbonne Universités, UPMC Univ Paris 06, UMR S 1127, F-75013, Paris, France.,Institut du Cerveau et de la Moelle épinière, ICM, F-75013, Paris, France
| | - D Guedin
- Institut du Cerveau et de la Moelle épinière, ICM, F-75013, Paris, France.,Laboratoire de Chémogénétique Servier, F-75013, Paris, France.,Institut de Recherches Servier, Croissy-sur-Seine, France
| | - C A Gautier
- Institut du Cerveau et de la Moelle épinière, ICM, F-75013, Paris, France. .,Laboratoire de Chémogénétique Servier, F-75013, Paris, France. .,Institut de Recherches Servier, Croissy-sur-Seine, France.
| | - O Corti
- Inserm, U1127, F-75013, Paris, France. .,CNRS, UMR 7225, F-75013, Paris, France. .,Sorbonne Universités, UPMC Univ Paris 06, UMR S 1127, F-75013, Paris, France. .,Institut du Cerveau et de la Moelle épinière, ICM, F-75013, Paris, France.
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36
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Nicolas E, Tricarico R, Savage M, Golemis EA, Hall MJ. Disease-Associated Genetic Variation in Human Mitochondrial Protein Import. Am J Hum Genet 2019; 104:784-801. [PMID: 31051112 PMCID: PMC6506819 DOI: 10.1016/j.ajhg.2019.03.019] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Accepted: 03/19/2019] [Indexed: 12/14/2022] Open
Abstract
Mitochondrial dysfunction has consequences not only for cellular energy output but also for cellular signaling pathways. Mitochondrial dysfunction, often based on inherited gene variants, plays a role in devastating human conditions such as mitochondrial neuropathies, myopathies, cardiovascular disorders, and Parkinson and Alzheimer diseases. Of the proteins essential for mitochondrial function, more than 98% are encoded in the cell nucleus, translated in the cytoplasm, sorted based on the presence of encoded mitochondrial targeting sequences (MTSs), and imported to specific mitochondrial sub-compartments based on the integrated activity of a series of mitochondrial translocases, proteinases, and chaperones. This import process is typically dynamic; as cellular homeostasis is coordinated through communication between the mitochondria and the nucleus, many of the adaptive responses to stress depend on modulation of mitochondrial import. We here describe an emerging class of disease-linked gene variants that are found to impact the mitochondrial import machinery itself or to affect the proteins during their import into mitochondria. As a whole, this class of rare defects highlights the importance of correct trafficking of mitochondrial proteins in the cell and the potential implications of failed targeting on metabolism and energy production. The existence of this variant class could have importance beyond rare neuromuscular disorders, given an increasing body of evidence suggesting that aberrant mitochondrial function may impact cancer risk and therapeutic response.
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Affiliation(s)
- Emmanuelle Nicolas
- Molecular Therapeutics Program, Fox Chase Cancer Center, Philadelphia, PA 19111, USA
| | - Rossella Tricarico
- Molecular Therapeutics Program, Fox Chase Cancer Center, Philadelphia, PA 19111, USA
| | - Michelle Savage
- Cancer Prevention and Control Program, Department of Clinical Genetics, Fox Chase Cancer Center, Philadelphia, PA 19111, USA
| | - Erica A Golemis
- Molecular Therapeutics Program, Fox Chase Cancer Center, Philadelphia, PA 19111, USA
| | - Michael J Hall
- Cancer Prevention and Control Program, Department of Clinical Genetics, Fox Chase Cancer Center, Philadelphia, PA 19111, USA.
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37
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Cai T, Hua B, Luo D, Xu L, Cheng Q, Yuan G, Yan Z, Sun N, Hua L, Lu C. The circadian protein CLOCK regulates cell metabolism via the mitochondrial carrier SLC25A10. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2019; 1866:1310-1321. [PMID: 30943427 DOI: 10.1016/j.bbamcr.2019.03.016] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Revised: 03/11/2019] [Accepted: 03/29/2019] [Indexed: 12/17/2022]
Abstract
Physiological function and metabolic regulation are the most important outputs of circadian clock controls in mammals. Mitochondrial respiration and ROS production show rhythmic activity. Mitochondrial carriers, which are responsible for mitochondrial substance transfer, are vital for mitochondrial metabolism. Clock (Circadian Locomotor Output Cycles Kaput) is the first core circadian gene identified in mammalian animals. However, whether CLOCK protein can regulate mitochondrial functions via mitochondrial carriers is unclear. Here, we showed that CLOCK can bind to the mitochondrial carrier SLC25A10. For further analysis, we established a Slc25a10-/--Hepa1-6 cell line using CRISPR/Cas9 gene-editing technology. Slc25a10-/--Hepa1-6 cells showed disordered glucose homeostasis, increased oxidative stress levels, and damaged electron transport chains. Next, using an immunoprecipitation assay, we found that amino acids 43-84 and 169-210 in SLC25A10 are key sites that respond to CLOCK binding. Finally, forced expression of wild-type SLC25A10 in Slc25a10-/--Hepa1-6 cells could compensate for the loss of SLC25A10; the decreased glucose metabolism, severe oxidative stress and damaged electron transport chain were recovered. In addition, a mutant Slc25a10 with changes in two key sites did not show a rescue effect. In conclusion, we identified a new protein-protein interaction mechanism in which CLOCK can directly regulate cell metabolism via the mitochondrial membrane transporter SLC25A10. Our study might provide some new insights into the relationship between circadian clock and mitochondrial metabolism.
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Affiliation(s)
- Tingting Cai
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Fudan University, Shanghai, China; Research Center on Aging and Medicine, Fudan University, Shanghai, China
| | - Bingxuan Hua
- Department of Orthopedics, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Dawei Luo
- Department of Ophthalmology, Shanghai First People's Hospital affiliated with Shanghai Jiaotong University, Shanghai, China
| | - Lirong Xu
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Fudan University, Shanghai, China; Research Center on Aging and Medicine, Fudan University, Shanghai, China
| | - Qianyun Cheng
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Fudan University, Shanghai, China; Research Center on Aging and Medicine, Fudan University, Shanghai, China
| | - Gongsheng Yuan
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Fudan University, Shanghai, China; Research Center on Aging and Medicine, Fudan University, Shanghai, China
| | - Zuoqin Yan
- Department of Orthopedics, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Ning Sun
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Fudan University, Shanghai, China; Research Center on Aging and Medicine, Fudan University, Shanghai, China; State Key Laboratory of Medical Neurobiology, Fudan University, Shanghai, China
| | - Luchun Hua
- Department of Surgery, Huashan Hospital, Fudan University, Shanghai, China.
| | - Chao Lu
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Fudan University, Shanghai, China; Research Center on Aging and Medicine, Fudan University, Shanghai, China; Shanghai Key Laboratory of Clinical Geriatric Medicine, Shanghai, China.
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38
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Mitochondrial presequence import: Multiple regulatory knobs fine-tune mitochondrial biogenesis and homeostasis. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2019; 1866:930-944. [PMID: 30802482 DOI: 10.1016/j.bbamcr.2019.02.012] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2019] [Revised: 02/14/2019] [Accepted: 02/19/2019] [Indexed: 12/22/2022]
Abstract
Mitochondria are pivotal organelles for cellular signaling and metabolism, and their dysfunction leads to severe cellular stress. About 60-70% of the mitochondrial proteome consists of preproteins synthesized in the cytosol with an amino-terminal cleavable presequence targeting signal. The TIM23 complex transports presequence signals towards the mitochondrial matrix. Ultimately, the mature protein segments are either transported into the matrix or sorted to the inner membrane. To ensure accurate preprotein import into distinct mitochondrial sub-compartments, the TIM23 machinery adopts specific functional conformations and interacts with different partner complexes. Regulatory subunits modulate the translocase dynamics, tailoring the import reaction to the incoming preprotein. The mitochondrial membrane potential and the ATP generated via oxidative phosphorylation are key energy sources in driving the presequence import pathway. Thus, mitochondrial dysfunctions have rapid repercussions on biogenesis. Cellular mechanisms exploit the presequence import pathway to monitor mitochondrial dysfunctions and mount transcriptional and proteostatic responses to restore functionality.
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39
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Richter F, Dennerlein S, Nikolov M, Jans DC, Naumenko N, Aich A, MacVicar T, Linden A, Jakobs S, Urlaub H, Langer T, Rehling P. ROMO1 is a constituent of the human presequence translocase required for YME1L protease import. J Cell Biol 2018; 218:598-614. [PMID: 30598479 PMCID: PMC6363466 DOI: 10.1083/jcb.201806093] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Revised: 10/18/2018] [Accepted: 11/26/2018] [Indexed: 01/15/2023] Open
Abstract
Mitochondria are the powerhouses of eukaryotic cells and rely on protein import from the cytosol. Richter et al. found ROMO1 as a new constituent of the human mitochondrial import machinery linking protein import to quality control and mitochondrial morphology. The mitochondrial presequence translocation machinery (TIM23 complex) is conserved between the yeast Saccharomyces cerevisiae and humans; however, functional characterization has been mainly performed in yeast. Here, we define the constituents of the human TIM23 complex using mass spectrometry and identified ROMO1 as a new translocase constituent with an exceptionally short half-life. Analyses of a ROMO1 knockout cell line revealed aberrant inner membrane structure and altered processing of the GTPase OPA1. We show that in the absence of ROMO1, mitochondria lose the inner membrane YME1L protease, which participates in OPA1 processing and ROMO1 turnover. While ROMO1 is dispensable for general protein import along the presequence pathway, we show that it participates in the dynamics of TIM21 during respiratory chain biogenesis and is specifically required for import of YME1L. This selective import defect can be linked to charge distribution in the unusually long targeting sequence of YME1L. Our analyses establish an unexpected link between mitochondrial protein import and inner membrane protein quality control.
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Affiliation(s)
- Frank Richter
- Department of Cellular Biochemistry, University Medical Center Göttingen, Göttingen, Germany
| | - Sven Dennerlein
- Department of Cellular Biochemistry, University Medical Center Göttingen, Göttingen, Germany
| | - Miroslav Nikolov
- Bioanalytical Mass Spectrometry Group, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Daniel C Jans
- Department of NanoBiophotonics, Mitochondrial Structure and Dynamics Group, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany.,Department of Neurology, University Medical Center, Göttingen, Germany
| | - Nataliia Naumenko
- Department of Cellular Biochemistry, University Medical Center Göttingen, Göttingen, Germany
| | - Abhishek Aich
- Department of Cellular Biochemistry, University Medical Center Göttingen, Göttingen, Germany
| | - Thomas MacVicar
- Department of Mitochondrial Proteostasis, Max Planck Institute for Biology of Ageing, Cologne, Germany
| | - Andreas Linden
- Bioanalytical Mass Spectrometry Group, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany.,Bioanalytics Group, Department of Clinical Chemistry, University Medical Center Göttingen, Göttingen, Germany
| | - Stefan Jakobs
- Department of NanoBiophotonics, Mitochondrial Structure and Dynamics Group, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany.,Department of Neurology, University Medical Center, Göttingen, Germany
| | - Henning Urlaub
- Bioanalytical Mass Spectrometry Group, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany.,Bioanalytics Group, Department of Clinical Chemistry, University Medical Center Göttingen, Göttingen, Germany
| | - Thomas Langer
- Department of Mitochondrial Proteostasis, Max Planck Institute for Biology of Ageing, Cologne, Germany
| | - Peter Rehling
- Department of Cellular Biochemistry, University Medical Center Göttingen, Göttingen, Germany .,Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
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40
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Heinemeyer T, Stemmet M, Bardien S, Neethling A. Underappreciated Roles of the Translocase of the Outer and Inner Mitochondrial Membrane Protein Complexes in Human Disease. DNA Cell Biol 2018; 38:23-40. [PMID: 30481057 DOI: 10.1089/dna.2018.4292] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Mitochondria are critical for cellular survival, and for their proper functioning, translocation of ∼1500 proteins across the mitochondrial membranes is required. The translocase of the outer (TOMM) and inner mitochondrial membrane (TIMM) complexes are major components of this translocation machinery. Through specific processes, preproteins and other molecules are imported, translocated, and directed to specific mitochondrial compartments for their function. In this study, we review the association of subunits of these complexes with human disease. Pathogenic mutations have been identified in the TIMM8A (DDP) and DNAJC19 (TIMM14) genes and are linked to Mohr-Tranebjærg syndrome and dilated cardiomyopathy syndrome (with and without ataxia), respectively. Polymorphisms in TOMM40 have been associated with Alzheimer's disease, frontotemporal lobar degeneration, Parkinson's disease with dementia, dementia with Lewy bodies, nonpathological cognitive aging, and various cardiovascular-related traits. Furthermore, reduced protein expression levels of several complex subunits have been associated with Parkinson's disease, Meniere's disease, and cardiovascular disorders. However, increased mRNA and protein levels of complex subunits are found in cancers. This review highlights the importance of the mitochondrial import machinery in human disease and stresses the need for further studies. Ultimately, this knowledge may prove to be critical for the development of therapeutic modalities for these conditions.
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Affiliation(s)
- Thea Heinemeyer
- Division of Molecular Biology and Human Genetics, Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Stellenbosch University , Cape Town, South Africa
| | - Monique Stemmet
- Division of Molecular Biology and Human Genetics, Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Stellenbosch University , Cape Town, South Africa
| | - Soraya Bardien
- Division of Molecular Biology and Human Genetics, Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Stellenbosch University , Cape Town, South Africa
| | - Annika Neethling
- Division of Molecular Biology and Human Genetics, Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Stellenbosch University , Cape Town, South Africa
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41
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Sokol AM, Uszczynska-Ratajczak B, Collins MM, Bazala M, Topf U, Lundegaard PR, Sugunan S, Guenther S, Kuenne C, Graumann J, Chan SSL, Stainier DYR, Chacinska A. Loss of the Mia40a oxidoreductase leads to hepato-pancreatic insufficiency in zebrafish. PLoS Genet 2018; 14:e1007743. [PMID: 30457989 PMCID: PMC6245507 DOI: 10.1371/journal.pgen.1007743] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2018] [Accepted: 10/05/2018] [Indexed: 02/07/2023] Open
Abstract
Development and function of tissues and organs are powered by the activity of mitochondria. In humans, inherited genetic mutations that lead to progressive mitochondrial pathology often manifest during infancy and can lead to death, reflecting the indispensable nature of mitochondrial biogenesis and function. Here, we describe a zebrafish mutant for the gene mia40a (chchd4a), the life-essential homologue of the evolutionarily conserved Mia40 oxidoreductase which drives the biogenesis of cysteine-rich mitochondrial proteins. We report that mia40a mutant animals undergo progressive cellular respiration defects and develop enlarged mitochondria in skeletal muscles before their ultimate death at the larval stage. We generated a deep transcriptomic and proteomic resource that allowed us to identify abnormalities in the development and physiology of endodermal organs, in particular the liver and pancreas. We identify the acinar cells of the exocrine pancreas to be severely affected by mutations in the MIA pathway. Our data contribute to a better understanding of the molecular, cellular and organismal effects of mitochondrial deficiency, important for the accurate diagnosis and future treatment strategies of mitochondrial diseases. Mitochondrial pathologies which result from mutations in the nuclear DNA remain incurable and often lead to death. As mitochondria play various roles in cellular and tissue-specific contexts, the symptoms of mitochondrial pathologies can differ between patients. Thus, diagnosis and treatment of mitochondrial disorders remain challenging. To enhance this, the generation of new models that explore and define the consequences of mitochondria insufficiencies is of central importance. Here, we present a mia40a zebrafish mutant as a model for mitochondrial dysfunction, caused by an imbalance in mitochondrial protein biogenesis. This mutant shares characteristics with existing reports on mitochondria dysfunction, and has led us to identify novel phenotypes such as enlarged mitochondrial clusters in skeletal muscles. In addition, our transcriptomics and proteomics data contribute important findings to the existing knowledge on how faulty mitochondria impinge on vertebrate development in molecular, tissue and organ specific contexts.
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Affiliation(s)
- Anna M. Sokol
- International Institute of Molecular and Cell Biology, Warsaw, Poland
- Department of Developmental Genetics, Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany
- Biomolecular Mass Spectrometry, Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany
- * E-mail: (AMS); (AC)
| | | | - Michelle M. Collins
- Department of Developmental Genetics, Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany
| | - Michal Bazala
- International Institute of Molecular and Cell Biology, Warsaw, Poland
| | - Ulrike Topf
- International Institute of Molecular and Cell Biology, Warsaw, Poland
- Centre of New Technologies, University of Warsaw, Warsaw, Poland
| | - Pia R. Lundegaard
- Department of Biomedical Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Sreedevi Sugunan
- International Institute of Molecular and Cell Biology, Warsaw, Poland
- Centre of New Technologies, University of Warsaw, Warsaw, Poland
| | - Stefan Guenther
- Bioinformatics and Deep Sequencing Platform, Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany
| | - Carsten Kuenne
- Bioinformatics and Deep Sequencing Platform, Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany
| | - Johannes Graumann
- Biomolecular Mass Spectrometry, Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany
| | - Sherine S. L. Chan
- Department of Drug Discovery and Biomedical Sciences, College of Pharmacy, Medical University of South Carolina, Charleston, South Carolina, United States of America
| | - Didier Y. R. Stainier
- Department of Developmental Genetics, Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany
| | - Agnieszka Chacinska
- International Institute of Molecular and Cell Biology, Warsaw, Poland
- Centre of New Technologies, University of Warsaw, Warsaw, Poland
- * E-mail: (AMS); (AC)
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42
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Mitoproteomics: Tackling Mitochondrial Dysfunction in Human Disease. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2018; 2018:1435934. [PMID: 30533169 PMCID: PMC6250043 DOI: 10.1155/2018/1435934] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Accepted: 08/29/2018] [Indexed: 12/11/2022]
Abstract
Mitochondria are highly dynamic and regulated organelles that historically have been defined based on their crucial role in cell metabolism. However, they are implicated in a variety of other important functions, making mitochondrial dysfunction an important axis in several pathological contexts. Despite that conventional biochemical and molecular biology approaches have provided significant insight into mitochondrial functionality, innovative techniques that provide a global view of the mitochondrion are still necessary. Proteomics fulfils this need by enabling accurate, systems-wide quantitative analysis of protein abundance. More importantly, redox proteomics approaches offer unique opportunities to tackle oxidative stress, a phenomenon that is intimately linked to aging, cardiovascular disease, and cancer. In addition, cutting-edge proteomics approaches reveal how proteins exert their functions in complex interaction networks where even subtle alterations stemming from early pathological states can be monitored. Here, we describe the proteomics approaches that will help to deepen the role of mitochondria in health and disease by assessing not only changes to mitochondrial protein composition but also alterations to their redox state and how protein interaction networks regulate mitochondrial function and dynamics. This review is aimed at showing the reader how the application of proteomics approaches during the last 20 years has revealed crucial mitochondrial roles in the context of aging, neurodegenerative disorders, metabolic disease, and cancer.
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43
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Mitochondrial diseases caused by dysfunctional mitochondrial protein import. Biochem Soc Trans 2018; 46:1225-1238. [PMID: 30287509 DOI: 10.1042/bst20180239] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2018] [Revised: 08/20/2018] [Accepted: 08/31/2018] [Indexed: 12/18/2022]
Abstract
Mitochondria are essential organelles which perform complex and varied functions within eukaryotic cells. Maintenance of mitochondrial health and functionality is thus a key cellular priority and relies on the organelle's extensive proteome. The mitochondrial proteome is largely encoded by nuclear genes, and mitochondrial proteins must be sorted to the correct mitochondrial sub-compartment post-translationally. This essential process is carried out by multimeric and dynamic translocation and sorting machineries, which can be found in all four mitochondrial compartments. Interestingly, advances in the diagnosis of genetic disease have revealed that mutations in various components of the human import machinery can cause mitochondrial disease, a heterogenous and often severe collection of disorders associated with energy generation defects and a multisystem presentation often affecting the cardiovascular and nervous systems. Here, we review our current understanding of mitochondrial protein import systems in human cells and the molecular basis of mitochondrial diseases caused by defects in these pathways.
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44
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Reyes A, Melchionda L, Burlina A, Robinson AJ, Ghezzi D, Zeviani M. Mutations in TIMM50 compromise cell survival in OxPhos-dependent metabolic conditions. EMBO Mol Med 2018; 10:emmm.201708698. [PMID: 30190335 PMCID: PMC6180300 DOI: 10.15252/emmm.201708698] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
TIMM50 is an essential component of the TIM23 complex, the mitochondrial inner membrane machinery that imports cytosolic proteins containing a mitochondrial targeting presequence into the mitochondrial inner compartment. Whole exome sequencing (WES) identified compound heterozygous pathogenic mutations in TIMM50 in an infant patient with rapidly progressive, severe encephalopathy. Patient fibroblasts presented low levels of TIMM50 and other components of the TIM23 complex, lower mitochondrial membrane potential, and impaired TIM23-dependent protein import. As a consequence, steady-state levels of several components of mitochondrial respiratory chain were decreased, resulting in decreased respiration and increased ROS production. Growth of patient fibroblasts in galactose shifted energy production metabolism toward oxidative phosphorylation (OxPhos), producing an apparent improvement in most of the above features but also increased apoptosis. Complementation of patient fibroblasts with TIMM50 improved or restored these features to control levels. Moreover, RNASEH1 and ISCU mutant fibroblasts only shared a few of these features with TIMM50 mutant fibroblasts. Our results indicate that mutations in TIMM50 cause multiple mitochondrial bioenergetic dysfunction and that functional TIMM50 is essential for cell survival in OxPhos-dependent conditions.
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Affiliation(s)
- Aurelio Reyes
- MRC Mitochondrial Biology UnitUniversity of CambridgeCambridgeUK
| | - Laura Melchionda
- Unit of Molecular NeurogeneticsFoundation Carlo Besta Neurological Institute‐IRCCSMilanItaly
| | - Alberto Burlina
- Division of Inherited Metabolic DiseasesDepartment of PediatricsUniversity Hospital PadovaPadovaItaly
| | - Alan J Robinson
- MRC Mitochondrial Biology UnitUniversity of CambridgeCambridgeUK
| | - Daniele Ghezzi
- Unit of Molecular NeurogeneticsFoundation Carlo Besta Neurological Institute‐IRCCSMilanItaly
| | - Massimo Zeviani
- MRC Mitochondrial Biology UnitUniversity of CambridgeCambridgeUK
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45
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Matic S, Muders V, Meisinger C. Tuning the mitochondrial protein import machinery by reversible phosphorylation: from metabolic switches to cell cycle regulation. CURRENT OPINION IN PHYSIOLOGY 2018. [DOI: 10.1016/j.cophys.2018.02.011] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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46
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Jin D, Gu B, Xiong D, Huang G, Huang X, Liu L, Xiao J. A Transcriptomic Analysis of Saccharomyces cerevisiae Under the Stress of 2-Phenylethanol. Curr Microbiol 2018; 75:1068-1076. [PMID: 29666939 DOI: 10.1007/s00284-018-1488-y] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2017] [Accepted: 03/30/2018] [Indexed: 12/11/2022]
Abstract
2-Phenylethanol (2-PE) is a kind of advanced aromatic alcohol with rose fragrance, which is wildly used for the deployment of flavors and fragrances. Microbial transformation is the most feasible method for the production of natural 2-PE. But a bottleneck problem is the toxicity of 2-PE on the cells. The molecular mechanisms of the toxic effect of 2-PE to Saccharomyces cerevisiae are not well studied. In this study, we analyzed the transcriptomes of S. cerevisiae in the media with and without 2-PE, respectively, using Illumina RNA-Seq technology. We identified 580 differentially expressed genes between S. cerevisiae in two different treatments. GO and KEGG enrichment analyses of these genes suggested that most genes encoding mitochondrial proteins, cytoplasmic, and plasma membrane proteins were significantly up-regulated, whereas the enzymes related to amino acid metabolism were down-regulated. These results indicated that 2-PE suppressed the synthesis of plasma membrane proteins, which suppressed the transport of nutrients required for growth. The findings in this study will provide insight into the inhibitory mechanism of 2-PE to yeast and other microbes.
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Affiliation(s)
- Danfeng Jin
- Institute of Microbiology, Jiangxi Academy of Sciences, Nanchang, 330096, People's Republic of China.
| | - Bintao Gu
- Institute of Microbiology, Jiangxi Academy of Sciences, Nanchang, 330096, People's Republic of China
| | - Dawei Xiong
- Institute of Microbiology, Jiangxi Academy of Sciences, Nanchang, 330096, People's Republic of China
| | - Guochang Huang
- Institute of Microbiology, Jiangxi Academy of Sciences, Nanchang, 330096, People's Republic of China
| | - Xiaoping Huang
- Institute of Microbiology, Jiangxi Academy of Sciences, Nanchang, 330096, People's Republic of China
| | - Lan Liu
- Institute of Microbiology, Jiangxi Academy of Sciences, Nanchang, 330096, People's Republic of China
| | - Jun Xiao
- The First Affiliated Hospital of Nanchang University, Nanchang, 330006, People's Republic of China.
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47
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Kolli R, Soll J, Carrie C. Plant Mitochondrial Inner Membrane Protein Insertion. Int J Mol Sci 2018; 19:E641. [PMID: 29495281 PMCID: PMC5855863 DOI: 10.3390/ijms19020641] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2018] [Revised: 02/20/2018] [Accepted: 02/22/2018] [Indexed: 02/06/2023] Open
Abstract
During the biogenesis of the mitochondrial inner membrane, most nuclear-encoded inner membrane proteins are laterally released into the membrane by the TIM23 and the TIM22 machinery during their import into mitochondria. A subset of nuclear-encoded mitochondrial inner membrane proteins and all the mitochondrial-encoded inner membrane proteins use the Oxa machinery-which is evolutionarily conserved from the endosymbiotic bacterial ancestor of mitochondria-for membrane insertion. Compared to the mitochondria from other eukaryotes, plant mitochondria have several unique features, such as a larger genome and a branched electron transport pathway, and are also involved in additional cellular functions such as photorespiration and stress perception. This review focuses on the unique aspects of plant mitochondrial inner membrane protein insertion machinery, which differs from that in yeast and humans, and includes a case study on the biogenesis of Cox2 in yeast, humans, two plant species, and an algal species to highlight lineage-specific similarities and differences. Interestingly, unlike mitochondria of other eukaryotes but similar to bacteria and chloroplasts, plant mitochondria appear to use the Tat machinery for membrane insertion of the Rieske Fe/S protein.
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Affiliation(s)
- Renuka Kolli
- Department of Biology I, Botany, Ludwig-Maximilians-Universität München, Großhaderner Strasse 2-4, D-82152 Planegg-Martinsried, Germany.
| | - Jürgen Soll
- Department of Biology I, Botany, Ludwig-Maximilians-Universität München, Großhaderner Strasse 2-4, D-82152 Planegg-Martinsried, Germany.
- Munich Center for Integrated Protein Science, CiPSM, Ludwig-Maximilians-Universität München, Feodor-Lynen-Strasse 25, D-81377 Munich, Germany.
| | - Chris Carrie
- Department of Biology I, Botany, Ludwig-Maximilians-Universität München, Großhaderner Strasse 2-4, D-82152 Planegg-Martinsried, Germany.
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48
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Zuber V, Jönsson EG, Frei O, Witoelar A, Thompson WK, Schork AJ, Bettella F, Wang Y, Djurovic S, Smeland OB, Dieset I, Fanous AH, Desikan RS, Küry S, Bézieau S, Dale AM, Mills IG, Andreassen OA. Identification of shared genetic variants between schizophrenia and lung cancer. Sci Rep 2018; 8:674. [PMID: 29330379 PMCID: PMC5766533 DOI: 10.1038/s41598-017-16481-4] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2017] [Accepted: 11/14/2017] [Indexed: 02/02/2023] Open
Abstract
Epidemiology studies suggest associations between schizophrenia and cancer. However, the underlying genetic mechanisms are not well understood, and difficult to identify from epidemiological data. We investigated if there is a shared genetic architecture between schizophrenia and cancer, with the aim to identify specific overlapping genetic loci. First, we performed genome-wide enrichment analysis and second, we analyzed specific loci jointly associated with schizophrenia and cancer by the conjunction false discovery rate. We analyzed the largest genome-wide association studies of schizophrenia and lung, breast, prostate, ovary, and colon-rectum cancer including more than 220,000 subjects, and included genetic association with smoking behavior. Polygenic enrichment of associations with lung cancer was observed in schizophrenia, and weak enrichment for the remaining cancer sites. After excluding the major histocompatibility complex region, we identified three independent loci jointly associated with schizophrenia and lung cancer. The strongest association included nicotinic acetylcholine receptors and is an established pleiotropic locus shared between lung cancer and smoking. The two other loci were independent of genetic association with smoking. Functional analysis identified downstream pleiotropic effects on epigenetics and gene-expression in lung and brain tissue. These findings suggest that genetic factors may explain partly the observed epidemiological association of lung cancer and schizophrenia.
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Affiliation(s)
- Verena Zuber
- 0000 0004 1936 8921grid.5510.1NORMENT, KG Jebsen Centre for Psychosis Research, Institute of Clinical Medicine, University of Oslo, Oslo, Norway ,0000 0004 0389 8485grid.55325.34Division of Mental Health and Addiction, Oslo University Hospital, Oslo, Norway ,0000 0004 0389 8485grid.55325.34Centre for Molecular Medicine Norway, Nordic EMBL Partnership, University of Oslo and Oslo University Hospital, Oslo, Norway ,0000000121885934grid.5335.0MRC Biostatistics Unit, University of Cambridge, Cambridge, UK
| | - Erik G. Jönsson
- 0000 0004 1936 8921grid.5510.1NORMENT, KG Jebsen Centre for Psychosis Research, Institute of Clinical Medicine, University of Oslo, Oslo, Norway ,0000 0004 1937 0626grid.4714.6Department of Clinical Neuroscience, Centre for Psychiatry Research, Karolinska Institutet, Stockholm, Sweden
| | - Oleksandr Frei
- 0000 0004 1936 8921grid.5510.1NORMENT, KG Jebsen Centre for Psychosis Research, Institute of Clinical Medicine, University of Oslo, Oslo, Norway ,0000 0004 0389 8485grid.55325.34Division of Mental Health and Addiction, Oslo University Hospital, Oslo, Norway
| | - Aree Witoelar
- 0000 0004 1936 8921grid.5510.1NORMENT, KG Jebsen Centre for Psychosis Research, Institute of Clinical Medicine, University of Oslo, Oslo, Norway ,0000 0004 0389 8485grid.55325.34Division of Mental Health and Addiction, Oslo University Hospital, Oslo, Norway
| | - Wesley K. Thompson
- 0000 0001 2107 4242grid.266100.3Department of Psychiatry, University of California, San Diego, La Jolla, CA USA
| | - Andrew J. Schork
- 0000 0001 2107 4242grid.266100.3Multimodal Imaging Laboratory, University of California at San Diego, La Jolla, CA USA ,0000 0001 2107 4242grid.266100.3Cognitive Sciences Graduate Program, University of California, San Diego, La Jolla, CA USA ,0000 0001 2107 4242grid.266100.3Center for Human Development, University of California at San Diego, La Jolla, CA USA
| | - Francesco Bettella
- 0000 0004 1936 8921grid.5510.1NORMENT, KG Jebsen Centre for Psychosis Research, Institute of Clinical Medicine, University of Oslo, Oslo, Norway ,0000 0004 0389 8485grid.55325.34Division of Mental Health and Addiction, Oslo University Hospital, Oslo, Norway
| | - Yunpeng Wang
- 0000 0004 1936 8921grid.5510.1NORMENT, KG Jebsen Centre for Psychosis Research, Institute of Clinical Medicine, University of Oslo, Oslo, Norway ,0000 0004 0389 8485grid.55325.34Division of Mental Health and Addiction, Oslo University Hospital, Oslo, Norway
| | - Srdjan Djurovic
- 0000 0004 1936 7443grid.7914.bNORMENT, KG Jebsen Centre for Psychosis Research, Department of Clinical Science, University of Bergen, Bergen, Norway ,0000 0004 0389 8485grid.55325.34Department of Medical Genetics, Oslo University Hospital, Oslo, Norway
| | - Olav B. Smeland
- 0000 0004 1936 8921grid.5510.1NORMENT, KG Jebsen Centre for Psychosis Research, Institute of Clinical Medicine, University of Oslo, Oslo, Norway ,0000 0004 0389 8485grid.55325.34Division of Mental Health and Addiction, Oslo University Hospital, Oslo, Norway
| | - Ingrid Dieset
- 0000 0004 1936 8921grid.5510.1NORMENT, KG Jebsen Centre for Psychosis Research, Institute of Clinical Medicine, University of Oslo, Oslo, Norway ,0000 0004 0389 8485grid.55325.34Division of Mental Health and Addiction, Oslo University Hospital, Oslo, Norway
| | - Ayman H. Fanous
- 0000 0001 0693 2202grid.262863.bDepartment of Psychiatry, SUNY Downstate Medical Center, Brooklyn, NY USA
| | - Rahul S. Desikan
- 0000 0001 2297 6811grid.266102.1Department of Radiology, University of California, San Francisco, San Francisco, CA USA
| | - Sébastien Küry
- 0000 0004 0472 0371grid.277151.7CHU Nantes, Service de Génétique Médicale, 9 quai Moncousu, 44093, Nantes, CEDEX 1 France
| | - Stéphane Bézieau
- 0000 0004 0472 0371grid.277151.7CHU Nantes, Service de Génétique Médicale, 9 quai Moncousu, 44093, Nantes, CEDEX 1 France
| | - Anders M. Dale
- 0000 0001 2107 4242grid.266100.3Department of Psychiatry, University of California, San Diego, La Jolla, CA USA ,0000 0001 2107 4242grid.266100.3Multimodal Imaging Laboratory, University of California at San Diego, La Jolla, CA USA ,0000 0001 2107 4242grid.266100.3Center for Human Development, University of California at San Diego, La Jolla, CA USA ,0000 0001 2107 4242grid.266100.3Department of Neurosciences, University of California, San Diego, La Jolla, CA USA
| | - Ian G. Mills
- 0000 0004 0389 8485grid.55325.34Centre for Molecular Medicine Norway, Nordic EMBL Partnership, University of Oslo and Oslo University Hospital, Oslo, Norway ,0000 0004 0389 8485grid.55325.34Department of Cancer Prevention, Institute of Cancer Research and Department of Urology, Oslo University Hospital, Oslo, Norway ,0000 0004 0374 7521grid.4777.3Prostate Cancer UK/Movember Centre of Excellence for Prostate Cancer Research, Centre for Cancer Research and Cell Biology, Queen’s University Belfast, Belfast, BT9 7AE UK ,0000 0004 1936 8948grid.4991.5Nuffield Department of Surgical Sciences, University of Oxford, Oxford, United Kingdom
| | - Ole A. Andreassen
- 0000 0004 1936 8921grid.5510.1NORMENT, KG Jebsen Centre for Psychosis Research, Institute of Clinical Medicine, University of Oslo, Oslo, Norway ,0000 0004 0389 8485grid.55325.34Division of Mental Health and Addiction, Oslo University Hospital, Oslo, Norway
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49
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Wojtkowska M, Buczek D, Suzuki Y, Shabardina V, Makałowski W, Kmita H. The emerging picture of the mitochondrial protein import complexes of Amoebozoa supergroup. BMC Genomics 2017; 18:997. [PMID: 29284403 PMCID: PMC5747110 DOI: 10.1186/s12864-017-4383-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2017] [Accepted: 12/14/2017] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND The existence of mitochondria-related organelles (MROs) is proposed for eukaryotic organisms. The Amoebozoa includes some organisms that are known to have mitosomes but also organisms that have aerobic mitochondria. However, the mitochondrial protein apparatus of this supergroup remains largely unsampled, except for the mitochondrial outer membrane import complexes studied recently. Therefore, in this study we investigated the mitochondrial inner membrane and intermembrane space complexes, using the available genome and transcriptome sequences. RESULTS When compared with the canonical cognate complexes described for the yeast Saccharomyces cerevisiae, amoebozoans with aerobic mitochondria, display lower differences in the number of subunits predicted for these complexes than the mitochondrial outer membrane complexes, although the predicted subunits appear to display different levels of diversity in regard to phylogenetic position and isoform numbers. For the putative mitosome-bearing amoebozoans, the number of predicted subunits suggests the complex elimination distinctly more pronounced than in the case of the outer membrane ones. CONCLUSION The results concern the problem of mitochondrial and mitosome protein import machinery structural variability and the reduction of their complexity within the currently defined supergroup of Amoebozoa. This results are crucial for better understanding of the Amoebozoa taxa of both biomedical and evolutionary importance.
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Affiliation(s)
- Małgorzata Wojtkowska
- Laboratory of Bioenergetics, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Umultowska 89, 61-614 Poznan, Poland
| | - Dorota Buczek
- Laboratory of Bioenergetics, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Umultowska 89, 61-614 Poznan, Poland
- Institute of Bioinformatics, Faculty of Medicine, University of Muenster, Niels Stensen Strasse 14, 48149 Muenster, Germany
| | - Yutaka Suzuki
- Department of Medical Genome Sciences, Graduate School of Frontier Sciences, University of Tokyo, Kashiwa, Chiba 277-8562 Japan
| | - Victoria Shabardina
- Institute of Bioinformatics, Faculty of Medicine, University of Muenster, Niels Stensen Strasse 14, 48149 Muenster, Germany
| | - Wojciech Makałowski
- Institute of Bioinformatics, Faculty of Medicine, University of Muenster, Niels Stensen Strasse 14, 48149 Muenster, Germany
| | - Hanna Kmita
- Laboratory of Bioenergetics, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Umultowska 89, 61-614 Poznan, Poland
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50
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Chatre L, Fernandes J, Michel V, Fiette L, Avé P, Arena G, Jain U, Haas R, Wang TC, Ricchetti M, Touati E. Helicobacter pylori targets mitochondrial import and components of mitochondrial DNA replication machinery through an alternative VacA-dependent and a VacA-independent mechanisms. Sci Rep 2017; 7:15901. [PMID: 29162845 PMCID: PMC5698309 DOI: 10.1038/s41598-017-15567-3] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2017] [Accepted: 10/30/2017] [Indexed: 12/31/2022] Open
Abstract
Targeting mitochondria is a powerful strategy for pathogens to subvert cell physiology and establish infection. Helicobacter pylori is a bacterial pathogen associated with gastric cancer development that is known to target mitochondria directly and exclusively through its pro-apoptotic and vacuolating cytotoxin VacA. By in vitro infection of gastric epithelial cells with wild-type and VacA-deficient H. pylori strains, treatment of cells with purified VacA proteins and infection of a mouse model, we show that H. pylori deregulates mitochondria by two novel mechanisms, both rather associated with host cell survival. First, early upon infection VacA induces transient increase of mitochondrial translocases and a dramatic accumulation of the mitochondrial DNA replication and maintenance factors POLG and TFAM. These events occur when VacA is not detected intracellularly, therefore do not require the direct interaction of the cytotoxin with the organelle, and are independent of the toxin vacuolating activity. In vivo, these alterations coincide with the evolution of gastric lesions towards severity. Second, H. pylori also induces VacA-independent alteration of mitochondrial replication and import components, suggesting the involvement of additional H. pylori activities in mitochondria-mediated effects. These data unveil two novel mitochondrial effectors in H. pylori-host interaction with links on gastric pathogenesis.
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Affiliation(s)
- Laurent Chatre
- Stem Cells and Development, Team Stability of Nuclear and Mitochondrial DNA, Institut Pasteur, 25-28 Rue du Dr. Roux, Paris, France.,CNRS UMR3738, Paris, France
| | - Julien Fernandes
- Unit of Helicobacter Pathogenesis, Team Genotoxicity, Infection and Cancer, Institut Pasteur, 25-28 Rue du Dr. Roux, Paris, France.,CNRS ERL3526, Paris, France.,UTechS PBI-CiTech, Institut Pasteur, Paris, 75015, France
| | - Valérie Michel
- Unit of Helicobacter Pathogenesis, Team Genotoxicity, Infection and Cancer, Institut Pasteur, 25-28 Rue du Dr. Roux, Paris, France.,CNRS ERL3526, Paris, France
| | - Laurence Fiette
- Unit of Human Pathology and Animal Models, Institut Pasteur, 25-28 Rue du Dr. Roux, Paris, France.,Paris Descartes University, PRES Sorbonne-Paris-Cité, Paris, France
| | - Patrick Avé
- Unit of Human Pathology and Animal Models, Institut Pasteur, 25-28 Rue du Dr. Roux, Paris, France.,Paris Descartes University, PRES Sorbonne-Paris-Cité, Paris, France
| | - Giuseppe Arena
- Stem Cells and Development, Team Stability of Nuclear and Mitochondrial DNA, Institut Pasteur, 25-28 Rue du Dr. Roux, Paris, France.,IRCM (Institut de Recherche en Cancérologie de Montpellier), Université de Montpellier, 34298, Montpellier, France.,INSERM U1194, Montpellier, France
| | - Utkarsh Jain
- Max von Pettenkofer-Institute for Hygiene and Medical Microbiology, Ludwig-Maximilians-University, Pettenkoferstraße 9a, D-80336, Munich, Germany.,Amity Institute of Nanotechnology, Amity University, Sector 125, Noida, Uttar Pradesh, 201313, India
| | - Rainer Haas
- Max von Pettenkofer-Institute for Hygiene and Medical Microbiology, Ludwig-Maximilians-University, Pettenkoferstraße 9a, D-80336, Munich, Germany.,German Center for Infection Research [DZIF], LMU, Munich, Germany
| | - Timothy C Wang
- Division of Digestive and Liver Diseases, College of Physicians and Surgeons, Columbia University, New York, USA
| | - Miria Ricchetti
- Stem Cells and Development, Team Stability of Nuclear and Mitochondrial DNA, Institut Pasteur, 25-28 Rue du Dr. Roux, Paris, France. .,CNRS UMR3738, Paris, France.
| | - Eliette Touati
- Unit of Helicobacter Pathogenesis, Team Genotoxicity, Infection and Cancer, Institut Pasteur, 25-28 Rue du Dr. Roux, Paris, France. .,CNRS ERL3526, Paris, France.
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