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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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Kim HJ, Jin SP, Kang J, Bae SH, Son JB, Oh JH, Youn H, Kim SK, Kang KW, Chung JH. Uncovering the impact of UV radiation on mitochondria in dermal cells: a STED nanoscopy study. Sci Rep 2024; 14:8675. [PMID: 38622160 PMCID: PMC11018800 DOI: 10.1038/s41598-024-55778-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Accepted: 02/26/2024] [Indexed: 04/17/2024] Open
Abstract
Mitochondria are essential organelles in cellular energy metabolism and other cellular functions. Mitochondrial dysfunction is closely linked to cellular damage and can potentially contribute to the aging process. The purpose of this study was to investigate the subcellular structure of mitochondria and their activities in various cellular environments using super-resolution stimulated emission depletion (STED) nanoscopy. We examined the morphological dispersion of mitochondria below the diffraction limit in sub-cultured human primary skin fibroblasts and mouse skin tissues. Confocal microscopy provides only the overall morphology of the mitochondrial membrane and an indiscerptible location of nucleoids within the diffraction limit. Conversely, super-resolution STED nanoscopy allowed us to resolve the nanoscale distribution of translocase clusters on the mitochondrial outer membrane and accurately quantify the number of nucleoids per cell in each sample. Comparable results were obtained by analyzing the translocase distribution in the mouse tissues. Furthermore, we precisely and quantitatively analyzed biomolecular distribution in nucleoids, such as the mitochondrial transcription factor A (TFAM), using STED nanoscopy. Our findings highlight the efficacy of super-resolution fluorescence imaging in quantifying aging-related changes on the mitochondrial sub-structure in cells and tissues.
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Affiliation(s)
- Hyung Jun Kim
- Department of Chemistry, Seoul National University, Seoul, 08826, South Korea.
- Institute of Radiation Medicine, Medical Research Center, Seoul National University, Seoul, 03080, South Korea.
| | - Seon-Pil Jin
- Department of Dermatology, Seoul National University Hospital, Seoul, 03080, South Korea
- Department of Dermatology, Seoul National University College of Medicine, Seoul, 03080, South Korea
- Institute of Human-Environment Interface Biology, Medical Research Center, Seoul National University, Seoul, 03080, South Korea
| | - Jooyoun Kang
- Department of Chemistry, Seoul National University, Seoul, 08826, South Korea
| | - So Hyeon Bae
- Department of Chemistry, Seoul National University, Seoul, 08826, South Korea
| | - Jung Bae Son
- Department of Chemistry, Seoul National University, Seoul, 08826, South Korea
| | - Jang-Hee Oh
- Department of Dermatology, Seoul National University Hospital, Seoul, 03080, South Korea
- Department of Dermatology, Seoul National University College of Medicine, Seoul, 03080, South Korea
- Institute of Human-Environment Interface Biology, Medical Research Center, Seoul National University, Seoul, 03080, South Korea
| | - Hyewon Youn
- Department of Nuclear Medicine, Seoul National University Hospital, Seoul, 03080, South Korea
- Department of Nuclear Medicine, Seoul National University College of Medicine, Seoul, 03080, South Korea
- Cancer Research Institute, Seoul National University College of Medicine, Seoul, 03080, South Korea
| | - Seong Keun Kim
- Department of Chemistry, Seoul National University, Seoul, 08826, South Korea
- Department of Biophysics and Chemical Biology, Seoul National University, Seoul, 08826, South Korea
| | - Keon Wook Kang
- Institute of Radiation Medicine, Medical Research Center, Seoul National University, Seoul, 03080, South Korea.
- Department of Nuclear Medicine, Seoul National University Hospital, Seoul, 03080, South Korea.
- Department of Nuclear Medicine, Seoul National University College of Medicine, Seoul, 03080, South Korea.
- Cancer Research Institute, Seoul National University College of Medicine, Seoul, 03080, South Korea.
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, 03080, South Korea.
- Bio-MAX Institute, Seoul National University, Seoul, 08826, South Korea.
| | - Jin Ho Chung
- Department of Dermatology, Seoul National University Hospital, Seoul, 03080, South Korea.
- Department of Dermatology, Seoul National University College of Medicine, Seoul, 03080, South Korea.
- Institute of Human-Environment Interface Biology, Medical Research Center, Seoul National University, Seoul, 03080, South Korea.
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3
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Zeng G, Xu X, Kok YJ, Deng FS, Ling Chow EW, Gao J, Bi X, Wang Y. Cytochrome c regulates hyphal morphogenesis by interfering with cAMP-PKA signaling in Candida albicans. Cell Rep 2023; 42:113473. [PMID: 37980562 DOI: 10.1016/j.celrep.2023.113473] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Revised: 10/17/2023] [Accepted: 11/06/2023] [Indexed: 11/21/2023] Open
Abstract
In the human fungal pathogen Candida albicans, invasive hyphal growth is a well-recognized virulence trait. We employed transposon-mediated genome-wide mutagenesis, revealing that inactivating CTM1 blocks hyphal growth. CTM1 encodes a lysine (K) methyltransferase, which trimethylates cytochrome c (Cyc1) at K79. Mutants lacking CTM1 or expressing cyc1K79A grow as yeast under hyphae-inducing conditions, indicating that unmethylated Cyc1 suppresses hyphal growth. Transcriptomic analyses detected increased levels of the hyphal repressor NRG1 and decreased levels of hyphae-specific genes in ctm1Δ/Δ and cyc1K79A mutants, suggesting cyclic AMP (cAMP)-protein kinase A (PKA) signaling suppression. Co-immunoprecipitation and in vitro kinase assays demonstrated that unmethylated Cyc1 inhibits PKA kinase activity. Surprisingly, hyphae-defective ctm1Δ/Δ and cyc1K79A mutants remain virulent in mice due to accelerated proliferation. Our results unveil a critical role for cytochrome c in maintaining the virulence of C. albicans by orchestrating proliferation, growth mode, and metabolism. Importantly, this study identifies a biological function for lysine methylation on cytochrome c.
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Affiliation(s)
- Guisheng Zeng
- A(∗)STAR Infectious Diseases Labs (A(∗)STAR ID Labs), Agency for Science, Technology and Research (A(∗)STAR), 8A Biomedical Grove, #05-13 Immunos, Singapore 138648, Singapore.
| | - Xiaoli Xu
- A(∗)STAR Infectious Diseases Labs (A(∗)STAR ID Labs), Agency for Science, Technology and Research (A(∗)STAR), 8A Biomedical Grove, #05-13 Immunos, Singapore 138648, Singapore
| | - Yee Jiun Kok
- Bioprocessing Technology Institute, 20 Biopolis Way, #06-01 Centros, Singapore 138668, Singapore
| | - Fu-Sheng Deng
- Department of Biochemical Science and Technology, College of Life Science, National Taiwan University, Taipei 10617, Taiwan
| | - Eve Wai Ling Chow
- A(∗)STAR Infectious Diseases Labs (A(∗)STAR ID Labs), Agency for Science, Technology and Research (A(∗)STAR), 8A Biomedical Grove, #05-13 Immunos, Singapore 138648, Singapore
| | - Jiaxin Gao
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Xuezhi Bi
- Bioprocessing Technology Institute, 20 Biopolis Way, #06-01 Centros, Singapore 138668, Singapore; Duke-NUS Medical School, National University of Singapore, Singapore 169857, Singapore
| | - Yue Wang
- A(∗)STAR Infectious Diseases Labs (A(∗)STAR ID Labs), Agency for Science, Technology and Research (A(∗)STAR), 8A Biomedical Grove, #05-13 Immunos, Singapore 138648, Singapore; Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117597, Singapore.
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Lee EG, Leong L, Chen S, Tulloch J, Yu CE. APOE Locus-Associated Mitochondrial Function and Its Implication in Alzheimer's Disease and Aging. Int J Mol Sci 2023; 24:10440. [PMID: 37445616 PMCID: PMC10341489 DOI: 10.3390/ijms241310440] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 06/13/2023] [Accepted: 06/19/2023] [Indexed: 07/15/2023] Open
Abstract
The Apolipoprotein E (APOE) locus has garnered significant clinical interest because of its association with Alzheimer's disease (AD) and longevity. This genetic association appears across multiple genes in the APOE locus. Despite the apparent differences between AD and longevity, both conditions share a commonality of aging-related changes in mitochondrial function. This commonality is likely due to accumulative biological effects partly exerted by the APOE locus. In this study, we investigated changes in mitochondrial structure/function-related markers using oxidative stress-induced human cellular models and postmortem brains (PMBs) from individuals with AD and normal controls. Our results reveal a range of expressional alterations, either upregulated or downregulated, in these genes in response to oxidative stress. In contrast, we consistently observed an upregulation of multiple APOE locus genes in all cellular models and AD PMBs. Additionally, the effects of AD status on mitochondrial DNA copy number (mtDNA CN) varied depending on APOE genotype. Our findings imply a potential coregulation of APOE locus genes possibly occurring within the same topologically associating domain (TAD) of the 3D chromosome conformation. The coordinated expression of APOE locus genes could impact mitochondrial function, contributing to the development of AD or longevity. Our study underscores the significant role of the APOE locus in modulating mitochondrial function and provides valuable insights into the underlying mechanisms of AD and aging, emphasizing the importance of this locus in clinical research.
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Affiliation(s)
- Eun-Gyung Lee
- Geriatric Research, Education, and Clinical Center, VA Puget Sound Health Care System, Seattle, WA 98108, USA
| | - Lesley Leong
- Geriatric Research, Education, and Clinical Center, VA Puget Sound Health Care System, Seattle, WA 98108, USA
| | - Sunny Chen
- Geriatric Research, Education, and Clinical Center, VA Puget Sound Health Care System, Seattle, WA 98108, USA
| | - Jessica Tulloch
- Geriatric Research, Education, and Clinical Center, VA Puget Sound Health Care System, Seattle, WA 98108, USA
| | - Chang-En Yu
- Geriatric Research, Education, and Clinical Center, VA Puget Sound Health Care System, Seattle, WA 98108, USA
- Department of Medicine, University of Washington, Seattle, WA 98195, USA
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5
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Chakraborty D, Zhuang Z, Xue H, Fiecas MB, Shen X, Pan W. Deep Learning-Based Feature Extraction with MRI Data in Neuroimaging Genetics for Alzheimer's Disease. Genes (Basel) 2023; 14:626. [PMID: 36980898 PMCID: PMC10047952 DOI: 10.3390/genes14030626] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 02/27/2023] [Accepted: 02/27/2023] [Indexed: 03/06/2023] Open
Abstract
The prognosis and treatment of patients suffering from Alzheimer's disease (AD) have been among the most important and challenging problems over the last few decades. To better understand the mechanism of AD, it is of great interest to identify genetic variants associated with brain atrophy. Commonly, in these analyses, neuroimaging features are extracted based on one of many possible brain atlases with FreeSurf and other popular software; this, however, may cause the loss of important information due to our incomplete knowledge about brain function embedded in these suboptimal atlases. To address the issue, we propose convolutional neural network (CNN) models applied to three-dimensional MRI data for the whole brain or multiple, divided brain regions to perform completely data-driven and automatic feature extraction. These image-derived features are then used as endophenotypes in genome-wide association studies (GWASs) to identify associated genetic variants. When we applied this method to ADNI data, we identified several associated SNPs that have been previously shown to be related to several neurodegenerative/mental disorders, such as AD, depression, and schizophrenia.
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Affiliation(s)
- Dipnil Chakraborty
- Division of Biostatistics, School of Public Health, University of Minnesota, Minneapolis, MN 55455, USA
| | - Zhong Zhuang
- Department of Electrical and Computer Engineering, University of Minnesota, Minneapolis, MN 55455, USA
| | - Haoran Xue
- Division of Biostatistics, School of Public Health, University of Minnesota, Minneapolis, MN 55455, USA
| | - Mark B. Fiecas
- Division of Biostatistics, School of Public Health, University of Minnesota, Minneapolis, MN 55455, USA
| | - Xiatong Shen
- School of Statistics, University of Minnesota, Minneapolis, MN 55455, USA
| | - Wei Pan
- Division of Biostatistics, School of Public Health, University of Minnesota, Minneapolis, MN 55455, USA
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6
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Vikramdeo KS, Sudan SK, Singh AP, Singh S, Dasgupta S. Mitochondrial respiratory complexes: Significance in human mitochondrial disorders and cancers. J Cell Physiol 2022; 237:4049-4078. [PMID: 36074903 DOI: 10.1002/jcp.30869] [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: 11/17/2021] [Revised: 07/18/2022] [Accepted: 08/23/2022] [Indexed: 11/07/2022]
Abstract
Mitochondria are pivotal organelles that govern cellular energy production through the oxidative phosphorylation system utilizing five respiratory complexes. In addition, mitochondria also contribute to various critical signaling pathways including apoptosis, damage-associated molecular patterns, calcium homeostasis, lipid, and amino acid biosynthesis. Among these diverse functions, the energy generation program oversee by mitochondria represents an immaculate orchestration and functional coordination between the mitochondria and nuclear encoded molecules. Perturbation in this program through respiratory complexes' alteration results in the manifestation of various mitochondrial disorders and malignancy, which is alarmingly becoming evident in the recent literature. Considering the clinical relevance and importance of this emerging medical problem, this review sheds light on the timing and nature of molecular alterations in various respiratory complexes and their functional consequences observed in various mitochondrial disorders and human cancers. Finally, we discussed how this wealth of information could be exploited and tailored to develop respiratory complex targeted personalized therapeutics and biomarkers for better management of various incurable human mitochondrial disorders and cancers.
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Affiliation(s)
- Kunwar Somesh Vikramdeo
- Department of Pathology, Mitchell Cancer Institute, University of South Alabama, Mobile, Alabama, USA.,Department of Pathology, College of Medicine, University of South Alabama, Mobile, Alabama, USA
| | - Sarabjeet Kour Sudan
- Department of Pathology, Mitchell Cancer Institute, University of South Alabama, Mobile, Alabama, USA.,Department of Pathology, College of Medicine, University of South Alabama, Mobile, Alabama, USA
| | - Ajay P Singh
- Department of Pathology, Mitchell Cancer Institute, University of South Alabama, Mobile, Alabama, USA.,Department of Pathology, College of Medicine, University of South Alabama, Mobile, Alabama, USA.,Department of Biochemistry and Molecular Biology, University of South Alabama, Mobile, Alabama, USA
| | - Seema Singh
- Department of Pathology, Mitchell Cancer Institute, University of South Alabama, Mobile, Alabama, USA.,Department of Pathology, College of Medicine, University of South Alabama, Mobile, Alabama, USA.,Department of Biochemistry and Molecular Biology, University of South Alabama, Mobile, Alabama, USA
| | - Santanu Dasgupta
- Department of Pathology, Mitchell Cancer Institute, University of South Alabama, Mobile, Alabama, USA.,Department of Pathology, College of Medicine, University of South Alabama, Mobile, Alabama, USA.,Department of Biochemistry and Molecular Biology, University of South Alabama, Mobile, Alabama, USA
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7
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Chen S, Sarasua SM, Davis NJ, DeLuca JM, Boccuto L, Thielke SM, Yu CE. TOMM40 genetic variants associated with healthy aging and longevity: a systematic review. BMC Geriatr 2022; 22:667. [PMID: 35964003 PMCID: PMC9375314 DOI: 10.1186/s12877-022-03337-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Accepted: 07/23/2022] [Indexed: 11/17/2022] Open
Abstract
Introduction Healthy aging relies on mitochondrial functioning because this organelle provides energy and diminishes oxidative stress. Single nucleotide polymorphisms (SNPs) in TOMM40, a critical gene that produces the outer membrane protein TOM40 of mitochondria, have been associated with mitochondrial dysfunction and neurodegenerative processes. Yet it is not clear whether or how the mitochondria may impact human longevity. We conducted this review to ascertain which SNPs have been associated with markers of healthy aging. Methods Using the PRISMA methodology, we conducted a systematic review on PubMed and Embase databases to identify associations between TOMM40 SNPs and measures of longevity and healthy aging. Results Twenty-four articles were selected. The TOMM40 SNPs rs2075650 and rs10524523 were the two most commonly identified and studied SNPs associated with longevity. The outcomes associated with the TOMM40 SNPs were changes in BMI, brain integrity, cognitive functions, altered inflammatory network, vulnerability to vascular risk factors, and longevity. Discussions Our systematic review identified multiple TOMM40 SNPs potentially associated with healthy aging. Additional research can help to understand mechanisms in aging, including resilience, prevention of disease, and adaptation to the environment.
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Affiliation(s)
- Sunny Chen
- Geriatric Research, Education, and Clinical Center, Puget Sound VA Medical Center, VA Puget Sound Healthcare System, 1660 S Columbian Way, Seattle, WA, 98108, USA. .,Healthcare Genetics Program, School of Nursing, Clemson University, Clemson, SC, USA.
| | - Sara M Sarasua
- Healthcare Genetics Program, School of Nursing, Clemson University, Clemson, SC, USA
| | - Nicole J Davis
- Healthcare Genetics Program, School of Nursing, Clemson University, Clemson, SC, USA
| | - Jane M DeLuca
- Healthcare Genetics Program, School of Nursing, Clemson University, Clemson, SC, USA
| | - Luigi Boccuto
- Healthcare Genetics Program, School of Nursing, Clemson University, Clemson, SC, USA
| | - Stephen M Thielke
- Department of Psychiatry and Behavioral Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Chang-En Yu
- Geriatric Research, Education, and Clinical Center, Puget Sound VA Medical Center, VA Puget Sound Healthcare System, 1660 S Columbian Way, Seattle, WA, 98108, USA.,Department of Medicine, Division of Gerontology and Geriatric Medicine, University of Washington, Seattle, WA, USA
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8
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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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9
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Wang Y, Niu H, Wang K, Wang G, Liu J, James TD, Zhang H. mtDNA-Specific Ultrasensitive Near-Infrared Fluorescent Probe Enables the Differentiation of Healthy and Apoptotic Cells. Anal Chem 2022; 94:7510-7519. [PMID: 35588727 DOI: 10.1021/acs.analchem.1c05582] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Mitochondrial DNA (mtDNA) as a class of important genetic material is easily damaged, which can result in a series of metabolic diseases, hereditary disease, and so on. mtDNA is an ultrasensitive indicator for the health of living cells due to the extremely short physiological response time of mtDNA toward damage (ca. 5.0 min). Therefore, the development of specific ultrasensitive fluorescent probes that can in real-time monitor mtDNA in vivo are of great value. With this research, we developed a near-infrared twisted intramolecular charge transfer (TICT) fluorescent probe YON. YON is a thread-like molecule with an A-π-D-π-A structure, based on the dicyanoisophorone fluorophore. The molecular design of YON enabled the specific binding with dsDNA (binding constant (K) = 8.5 × 105 M-1) within 1.3 min. And the appropriate water-oil amphiphilicity makes YON significantly accumulate in the mitochondria, enabling the specific binding to mtDNA. The fluorescence intensity at 640 nm of YON enhanced linearly with increasing concentrations of mtDNA. Dicyanoisophorone as the strong electron-withdrawing group that was introduced into both ends of the molecule resulted in YON being a classic quadrupole, so it could ultrasensitively detect trace mtDNA. The minimum detection limit was 71 ng/mL. Moreover, the large Stokes shift (λex = 435 nm, λem = 640 nm) makes YON suitable for "interference-free" imaging of mtDNA. Therefore, YON was used to monitor trace changes of mtDNA in living cells; more importantly, it could be used to evaluate the health of cells by monitoring microchanges of mtDNA, enabling the ultrasensitive evaluation of apoptosis.
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Affiliation(s)
- Yafu Wang
- Key Laboratory of Green Chemical Media and Reactions, Ministry of Education; Collaborative Innovation Centre of Henan Province for Green Manufacturing of Fine Chemicals; Henan Key Laboratory of Organic Functional Molecule and Drug Innovation; School of Chemistry and Chemical Engineering, Henan Normal University, Xinxiang, Henan 453007, P. R. China
| | - Huiyu Niu
- Key Laboratory of Green Chemical Media and Reactions, Ministry of Education; Collaborative Innovation Centre of Henan Province for Green Manufacturing of Fine Chemicals; Henan Key Laboratory of Organic Functional Molecule and Drug Innovation; School of Chemistry and Chemical Engineering, Henan Normal University, Xinxiang, Henan 453007, P. R. China
| | - Kui Wang
- Key Laboratory of Green Chemical Media and Reactions, Ministry of Education; Collaborative Innovation Centre of Henan Province for Green Manufacturing of Fine Chemicals; Henan Key Laboratory of Organic Functional Molecule and Drug Innovation; School of Chemistry and Chemical Engineering, Henan Normal University, Xinxiang, Henan 453007, P. R. China
| | - Ge Wang
- Xinxiang Medical University, Xinxiang 453000, P. R. China
| | - Junwei Liu
- Key Laboratory of Green Chemical Media and Reactions, Ministry of Education; Collaborative Innovation Centre of Henan Province for Green Manufacturing of Fine Chemicals; Henan Key Laboratory of Organic Functional Molecule and Drug Innovation; School of Chemistry and Chemical Engineering, Henan Normal University, Xinxiang, Henan 453007, P. R. China
| | - Tony D James
- Key Laboratory of Green Chemical Media and Reactions, Ministry of Education; Collaborative Innovation Centre of Henan Province for Green Manufacturing of Fine Chemicals; Henan Key Laboratory of Organic Functional Molecule and Drug Innovation; School of Chemistry and Chemical Engineering, Henan Normal University, Xinxiang, Henan 453007, P. R. China.,Department of Chemistry, University of Bath, Bath BA2 7AY, U.K
| | - Hua Zhang
- Key Laboratory of Green Chemical Media and Reactions, Ministry of Education; Collaborative Innovation Centre of Henan Province for Green Manufacturing of Fine Chemicals; Henan Key Laboratory of Organic Functional Molecule and Drug Innovation; School of Chemistry and Chemical Engineering, Henan Normal University, Xinxiang, Henan 453007, P. R. China
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10
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Elsadany M, Elghaish RA, Khalil AS, Ahmed AS, Mansour RH, Badr E, Elserafy M. Transcriptional Analysis of Nuclear-Encoded Mitochondrial Genes in Eight Neurodegenerative Disorders: The Analysis of Seven Diseases in Reference to Friedreich’s Ataxia. Front Genet 2021; 12:749792. [PMID: 34987545 PMCID: PMC8721009 DOI: 10.3389/fgene.2021.749792] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Accepted: 10/20/2021] [Indexed: 11/25/2022] Open
Abstract
Neurodegenerative diseases (NDDs) are challenging to understand, diagnose, and treat. Revealing the genomic and transcriptomic changes in NDDs contributes greatly to the understanding of the diseases, their causes, and development. Moreover, it enables more precise genetic diagnosis and novel drug target identification that could potentially treat the diseases or at least ease the symptoms. In this study, we analyzed the transcriptional changes of nuclear-encoded mitochondrial (NEM) genes in eight NDDs to specifically address the association of these genes with the diseases. Previous studies show strong links between defects in NEM genes and neurodegeneration, yet connecting specific genes with NDDs is not well studied. Friedreich’s ataxia (FRDA) is an NDD that cannot be treated effectively; therefore, we focused first on FRDA and compared the outcome with seven other NDDs, including Alzheimer’s disease, amyotrophic lateral sclerosis, Creutzfeldt–Jakob disease, frontotemporal dementia, Huntington’s disease, multiple sclerosis, and Parkinson’s disease. First, weighted correlation network analysis was performed on an FRDA RNA-Seq data set, focusing only on NEM genes. We then carried out differential gene expression analysis and pathway enrichment analysis to pinpoint differentially expressed genes that are potentially associated with one or more of the analyzed NDDs. Our findings propose a strong link between NEM genes and NDDs and suggest that our identified candidate genes can be potentially used as diagnostic markers and therapeutic targets.
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Affiliation(s)
- Muhammad Elsadany
- University of Science and Technology, Zewail City of Science and Technology, Giza, Egypt
| | - Reem A. Elghaish
- University of Science and Technology, Zewail City of Science and Technology, Giza, Egypt
- Center for Genomics, Helmy Institute for Medical Sciences, Zewail City of Science and Technology, Giza, Egypt
| | - Aya S. Khalil
- Center for Genomics, Helmy Institute for Medical Sciences, Zewail City of Science and Technology, Giza, Egypt
| | - Alaa S. Ahmed
- University of Science and Technology, Zewail City of Science and Technology, Giza, Egypt
- Center for Genomics, Helmy Institute for Medical Sciences, Zewail City of Science and Technology, Giza, Egypt
| | - Rana H. Mansour
- Center for Genomics, Helmy Institute for Medical Sciences, Zewail City of Science and Technology, Giza, Egypt
| | - Eman Badr
- University of Science and Technology, Zewail City of Science and Technology, Giza, Egypt
- Faculty of Computers and Artificial Intelligence, Cairo University, Giza, Egypt
- *Correspondence: Eman Badr, ; Menattallah Elserafy,
| | - Menattallah Elserafy
- University of Science and Technology, Zewail City of Science and Technology, Giza, Egypt
- Center for Genomics, Helmy Institute for Medical Sciences, Zewail City of Science and Technology, Giza, Egypt
- *Correspondence: Eman Badr, ; Menattallah Elserafy,
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11
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TOMM40 RNA Transcription in Alzheimer's Disease Brain and Its Implication in Mitochondrial Dysfunction. Genes (Basel) 2021; 12:genes12060871. [PMID: 34204109 PMCID: PMC8226536 DOI: 10.3390/genes12060871] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Revised: 06/01/2021] [Accepted: 06/04/2021] [Indexed: 11/24/2022] Open
Abstract
Increasing evidence suggests that the Translocase of Outer Mitochondria Membrane 40 (TOMM40) gene may contribute to the risk of Alzheimer’s disease (AD). Currently, there is no consensus as to whether TOMM40 expression is up- or down-regulated in AD brains, hindering a clear interpretation of TOMM40’s role in this disease. The aim of this study was to determine if TOMM40 RNA levels differ between AD and control brains. We applied RT-qPCR to study TOMM40 transcription in human postmortem brain (PMB) and assessed associations of these RNA levels with genetic variants in APOE and TOMM40. We also compared TOMM40 RNA levels with mitochondrial functions in human cell lines. Initially, we found that the human genome carries multiple TOMM40 pseudogenes capable of producing highly homologous RNAs that can obscure precise TOMM40 RNA measurements. To circumvent this obstacle, we developed a novel RNA expression assay targeting the primary transcript of TOMM40. Using this assay, we showed that TOMM40 RNA was upregulated in AD PMB. Additionally, elevated TOMM40 RNA levels were associated with decreases in mitochondrial DNA copy number and mitochondrial membrane potential in oxidative stress-challenged cells. Overall, differential transcription of TOMM40 RNA in the brain is associated with AD and could be an indicator of mitochondrial dysfunction.
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12
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Lopez Sanchez MIG, Ziemann M, Bachem A, Makam R, Crowston JG, Pinkert CA, McKenzie M, Bedoui S, Trounce IA. Nuclear response to divergent mitochondrial DNA genotypes modulates the interferon immune response. PLoS One 2020; 15:e0239804. [PMID: 33031404 PMCID: PMC7544115 DOI: 10.1371/journal.pone.0239804] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Accepted: 09/14/2020] [Indexed: 11/23/2022] Open
Abstract
Mitochondrial OXPHOS generates most of the energy required for cellular function. OXPHOS biogenesis requires the coordinated expression of the nuclear and mitochondrial genomes. This represents a unique challenge that highlights the importance of nuclear-mitochondrial genetic communication to cellular function. Here we investigated the transcriptomic and functional consequences of nuclear-mitochondrial genetic divergence in vitro and in vivo. We utilized xenomitochondrial cybrid cell lines containing nuclear DNA from the common laboratory mouse Mus musculus domesticus and mitochondrial DNA (mtDNA) from Mus musculus domesticus, or exogenous mtDNA from progressively divergent mouse species Mus spretus, Mus terricolor, Mus caroli and Mus pahari. These cybrids model a wide range of nuclear-mitochondrial genetic divergence that cannot be achieved with other research models. Furthermore, we used a xenomitochondrial mouse model generated in our laboratory that harbors wild-type, C57BL/6J Mus musculus domesticus nuclear DNA and homoplasmic mtDNA from Mus terricolor. RNA sequencing analysis of xenomitochondrial cybrids revealed an activation of interferon signaling pathways even in the absence of OXPHOS dysfunction or immune challenge. In contrast, xenomitochondrial mice displayed lower baseline interferon gene expression and an impairment in the interferon-dependent innate immune response upon immune challenge with herpes simplex virus, which resulted in decreased viral control. Our work demonstrates that nuclear-mitochondrial genetic divergence caused by the introduction of exogenous mtDNA can modulate the interferon immune response both in vitro and in vivo, even when OXPHOS function is not compromised. This work may lead to future insights into the role of mitochondrial genetic variation and the immune function in humans, as patients affected by mitochondrial disease are known to be more susceptible to immune challenges.
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Affiliation(s)
- M. Isabel G. Lopez Sanchez
- Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, Melbourne, Victoria, Australia
- Ophthalmology, Department of Surgery, University of Melbourne, Melbourne, Victoria, Australia
- * E-mail: (MIGLS); (IAT)
| | - Mark Ziemann
- Department of Diabetes, Monash University Central Clinical School, The Alfred Medical Research and Education Precinct, Melbourne, Victoria, Australia
- School of Life and Environmental Sciences, Deakin University, Victoria, Australia
| | - Annabell Bachem
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Rahul Makam
- Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, Melbourne, Victoria, Australia
| | - Jonathan G. Crowston
- Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, Melbourne, Victoria, Australia
- Ophthalmology, Department of Surgery, University of Melbourne, Melbourne, Victoria, Australia
| | - Carl A. Pinkert
- Department of Pathobiology, College of Veterinary Medicine, Auburn University, Auburn, Alabama, United States of America
| | - Matthew McKenzie
- School of Life and Environmental Sciences, Deakin University, Victoria, Australia
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Melbourne, Victoria, Australia
- Department of Molecular and Translational Science, Monash University, Melbourne, Victoria, Australia
| | - Sammy Bedoui
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Ian A. Trounce
- Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, Melbourne, Victoria, Australia
- Ophthalmology, Department of Surgery, University of Melbourne, Melbourne, Victoria, Australia
- * E-mail: (MIGLS); (IAT)
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13
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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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14
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Ahmed MAH, Ali MH, Abbas HH, Elatrash GA, Foda AAM. Expression of TOMM34 and Its Clinicopathological Correlations in Urothelial Carcinoma of the Bladder. Pathol Oncol Res 2018; 26:411-418. [PMID: 30382527 DOI: 10.1007/s12253-018-0524-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Accepted: 10/25/2018] [Indexed: 02/06/2023]
Abstract
The substantial difference between normal cells and cancer cells in terms of their energy metabolism in mitochondria provides an interesting basis for the development of novel therapeutic agents targeting energy machinery of tumour cells. TOMM34 is one of the Tom (translocase of the outer membrane of mitochondria) family that was found to be overexpressed in colorectal, hepatocellular, lung and early invasive breast carcinomas. The expression profile of mitochondrial translocases in bladder cancer compared to normal urinary bladder tissues has not been investigated yet. Therefore, the aim of the current study is to investigate the expression pattern of TOMM34 in bladder cancer tissues and explore its correlation with the clinico-pathological parameters of those cases. Sixty patients who underwent either transurethral resection or radical cystectomy for bladder cancer were included in this study with revision of all their clinicopathological data and tumor slides. Ten histologically normal urothelial biopsies were also included. Immunohistochemical staining for TOMM34 was done and semi-quantitatively scored using the modified H-score. All relations were analysed using established statistical methodologies. TOMM34 overexpression was significantly associated with high tumour stage, muscle invasion and high grade. Significant positive association was observed between TOMM34 expression and poor outcome in terms of shorter disease-specific survival. This study suggests TOMM34 as a biomarker of progression and poor prognosis in urothelial cell carcinoma patients. Furthermore, we suggest a role played by mitochondrial machinery in urothelial cell carcinoma progression, which is a potential target for the newly-discovered vaccine therapy for urothelial cell carcinoma.
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Affiliation(s)
- Mohamed A H Ahmed
- Department of Pathology, Faculty of Medicine, Suez Canal University, Ismailia, Egypt.,East Sussex Health Care Trust, Eastbourne District General Hospital, Eastbourne, UK
| | - Mohamed Hassan Ali
- Department of Urology, Faculty of Medicine, Suez Canal University, Ismailia, Egypt
| | - Hashem Hafez Abbas
- Department of Urology, Faculty of Medicine, Suez Canal University, Ismailia, Egypt
| | - Gamal Ali Elatrash
- Department of Urology, Faculty of Medicine, Suez Canal University, Ismailia, Egypt
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15
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Rivera-Mulia JC, Schwerer H, Besnard E, Desprat R, Trevilla-Garcia C, Sima J, Bensadoun P, Zouaoui A, Gilbert DM, Lemaitre JM. Cellular senescence induces replication stress with almost no affect on DNA replication timing. Cell Cycle 2018; 17:1667-1681. [PMID: 29963964 DOI: 10.1080/15384101.2018.1491235] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
Organismal aging entails a gradual decline of normal physiological functions and a major contributor to this decline is withdrawal of the cell cycle, known as senescence. Senescence can result from telomere diminution leading to a finite number of population doublings, known as replicative senescence (RS), or from oncogene overexpression, as a protective mechanism against cancer. Senescence is associated with large-scale chromatin re-organization and changes in gene expression. Replication stress is a complex phenomenon, defined as the slowing or stalling of replication fork progression and/or DNA synthesis, which has serious implications for genome stability, and consequently in human diseases. Aberrant replication fork structures activate the replication stress response leading to the activation of dormant origins, which is thought to be a safeguard mechanism to complete DNA replication on time. However, the relationship between replicative stress and the changes in the spatiotemporal program of DNA replication in senescence progression remains unclear. Here, we studied the DNA replication program during senescence progression in proliferative and pre-senescent cells from donors of various ages by single DNA fiber combing of replicated DNA, origin mapping by sequencing short nascent strands and genome-wide profiling of replication timing (TRT). We demonstrate that, progression into RS leads to reduced replication fork rates and activation of dormant origins, which are the hallmarks of replication stress. However, with the exception of a delay in RT of the CREB5 gene in all pre-senescent cells, RT was globally unaffected by replication stress during entry into either oncogene-induced or RS. Consequently, we conclude that RT alterations associated with physiological and accelerated aging, do not result from senescence progression. Our results clarify the interplay between senescence, aging and replication programs and demonstrate that RT is largely resistant to replication stress.
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Affiliation(s)
| | - Hélène Schwerer
- b Laboratory of Genome and Stem Cell Plasticity in Development and Aging , Institute of Regenerative Medicine, U1183, Université de Montpellier , Montpellier Cedex , France
| | - Emilie Besnard
- b Laboratory of Genome and Stem Cell Plasticity in Development and Aging , Institute of Regenerative Medicine, U1183, Université de Montpellier , Montpellier Cedex , France
| | - Romain Desprat
- c Stem cell Core Facility SAFE-iPS INGESTEM , CHU Montpellier, Saint Eloi Hospital , Montpellier Cedex , France
| | | | - Jiao Sima
- a Department of Biological Science , Florida State University , Tallahassee , FL , USA
| | - Paul Bensadoun
- b Laboratory of Genome and Stem Cell Plasticity in Development and Aging , Institute of Regenerative Medicine, U1183, Université de Montpellier , Montpellier Cedex , France
| | - Anissa Zouaoui
- c Stem cell Core Facility SAFE-iPS INGESTEM , CHU Montpellier, Saint Eloi Hospital , Montpellier Cedex , France
| | - David M Gilbert
- a Department of Biological Science , Florida State University , Tallahassee , FL , USA.,d Center for Genomics and Personalized Medicine , Florida State University , Tallahassee , FL , USA
| | - Jean-Marc Lemaitre
- b Laboratory of Genome and Stem Cell Plasticity in Development and Aging , Institute of Regenerative Medicine, U1183, Université de Montpellier , Montpellier Cedex , France.,c Stem cell Core Facility SAFE-iPS INGESTEM , CHU Montpellier, Saint Eloi Hospital , Montpellier Cedex , France
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16
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Sabharwal A, Sharma D, Vellarikkal SK, Jayarajan R, Verma A, Senthivel V, Scaria V, Sivasubbu S. Organellar transcriptome sequencing reveals mitochondrial localization of nuclear encoded transcripts. Mitochondrion 2018; 46:59-68. [PMID: 29486245 DOI: 10.1016/j.mito.2018.02.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2017] [Revised: 01/23/2018] [Accepted: 02/22/2018] [Indexed: 01/10/2023]
Abstract
Mitochondria are organelles involved in a variety of biological functions in the cell, apart from their principal role in generation of ATP, the cellular currency of energy. The mitochondria, in spite of being compact organelles, are capable of performing complex biological functions largely because of the ability to exchange proteins, RNA, chemical metabolites and other biomolecules between cellular compartments. A close network of biomolecular interactions are known to modulate the crosstalk between the mitochondria and the nuclear genome. Apart from the small repertoire of genes encoded by the mitochondrial genome, it is now known that the functionality of the organelle is highly reliant on a number of proteins encoded by the nuclear genome, which localize to the mitochondria. With exceptions to a few anecdotal examples, the transcripts that have the potential to localize to the mitochondria have been poorly studied. We used a deep sequencing approach to identify transcripts encoded by the nuclear genome which localize to the mitoplast in a zebrafish model. We prioritized 292 candidate transcripts of nuclear origin that are potentially localized to the mitochondrial matrix. We experimentally demonstrated that the transcript encoding the nuclear encoded ribosomal protein 11 (Rpl11) localizes to the mitochondria. This study represents a comprehensive analysis of the mitochondrial localization of nuclear encoded transcripts. Our analysis has provided insights into a new layer of biomolecular pathways modulating mitochondrial-nuclear cross-talk. This provides a starting point towards understanding the role of nuclear encoded transcripts that localize to mitochondria and their influence on mitochondrial function.
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Affiliation(s)
- Ankit Sabharwal
- Genomics and Molecular Medicine, CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), Mathura Road, Delhi 110 020, India; Academy of Scientific and Innovative Research (AcSIR), CSIR IGIB South Campus, Mathura Road, Delhi 110020, India
| | - Disha Sharma
- GN Ramachandran Knowledge Center for Genome Informatics, CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), Mathura Road, Delhi 110 020, India; Academy of Scientific and Innovative Research (AcSIR), CSIR IGIB South Campus, Mathura Road, Delhi 110020, India
| | - Shamsudheen Karuthedath Vellarikkal
- Genomics and Molecular Medicine, CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), Mathura Road, Delhi 110 020, India; Academy of Scientific and Innovative Research (AcSIR), CSIR IGIB South Campus, Mathura Road, Delhi 110020, India
| | - Rijith Jayarajan
- Genomics and Molecular Medicine, CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), Mathura Road, Delhi 110 020, India
| | - Ankit Verma
- Genomics and Molecular Medicine, CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), Mathura Road, Delhi 110 020, India
| | - Vigneshwar Senthivel
- Genomics and Molecular Medicine, CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), Mathura Road, Delhi 110 020, India
| | - Vinod Scaria
- GN Ramachandran Knowledge Center for Genome Informatics, CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), Mathura Road, Delhi 110 020, India; Academy of Scientific and Innovative Research (AcSIR), CSIR IGIB South Campus, Mathura Road, Delhi 110020, India.
| | - Sridhar Sivasubbu
- Genomics and Molecular Medicine, CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), Mathura Road, Delhi 110 020, India; Academy of Scientific and Innovative Research (AcSIR), CSIR IGIB South Campus, Mathura Road, Delhi 110020, India.
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17
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Williamson J, Petralia RS, Wang YX, Mattson MP, Yao PJ. Purine Biosynthesis Enzymes in Hippocampal Neurons. Neuromolecular Med 2017; 19:518-524. [PMID: 28866774 PMCID: PMC6085884 DOI: 10.1007/s12017-017-8466-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2017] [Accepted: 08/29/2017] [Indexed: 01/26/2023]
Abstract
Despite reports implicating disrupted purine metabolism in causing a wide spectrum of neurological defects, the mechanistic details of purine biosynthesis in neurons are largely unknown. As an initial step in filling that gap, we examined the expression and subcellular distribution of three purine biosynthesis enzymes (PFAS, PAICS and ATIC) in rat hippocampal neurons. Using immunoblotting and high-resolution light and electron microscopic analysis, we find that all three enzymes are broadly distributed in hippocampal neurons with pools of these enzymes associated with mitochondria. These findings suggest a potential link between purine metabolism and mitochondrial function in neurons and provide an impetus for further studies.
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Affiliation(s)
| | | | - Ya-Xian Wang
- Advanced Imaging Core, NIDCD/NIH, Bethesda, MD, 20892, USA
| | - Mark P Mattson
- Laboratory of Neurosciences, NIA/NIH, Baltimore, MD, 21224, USA
| | - Pamela J Yao
- Laboratory of Neurosciences, NIA/NIH, Baltimore, MD, 21224, USA.
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18
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Mitochondrial dysfunction in cancer: Potential roles of ATF5 and the mitochondrial UPR. Semin Cancer Biol 2017; 47:43-49. [PMID: 28499833 DOI: 10.1016/j.semcancer.2017.05.002] [Citation(s) in RCA: 74] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2017] [Revised: 04/26/2017] [Accepted: 05/03/2017] [Indexed: 12/14/2022]
Abstract
Mitochondria form a cellular network of organelles, or cellular compartments, that efficiently couple nutrients to energy production in the form of ATP. As cancer cells rely heavily on glycolysis, historically mitochondria and the cellular pathways in place to maintain mitochondrial activities were thought to be more relevant to diseases observed in non-dividing cells such as muscles and neurons. However, more recently it has become clear that cancers rely heavily on mitochondrial activities including lipid, nucleotide and amino acid synthesis, suppression of mitochondria-mediated apoptosis as well as oxidative phosphorylation (OXPHOS) for growth and survival. Considering the variety of conditions and stresses that cancer cell mitochondria may incur such as hypoxia, reactive oxygen species and mitochondrial genome mutagenesis, we examine potential roles for a mitochondrial-protective transcriptional response known as the mitochondrial unfolded protein response (UPRmt) in cancer cell biology.
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19
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20
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Formosa LE, Hofer A, Tischner C, Wenz T, Ryan MT. Translation and Assembly of Radiolabeled Mitochondrial DNA-Encoded Protein Subunits from Cultured Cells and Isolated Mitochondria. Methods Mol Biol 2016; 1351:115-29. [PMID: 26530678 DOI: 10.1007/978-1-4939-3040-1_9] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
Abstract
In higher eukaryotes, the mitochondrial electron transport chain consists of five multi-subunit membrane complexes responsible for the generation of cellular ATP. Of these, four complexes are under dual genetic control as they contain subunits encoded by both the mitochondrial and nuclear genomes, thereby adding another layer of complexity to the puzzle of respiratory complex biogenesis. These subunits must be synthesized and assembled in a coordinated manner in order to ensure correct biogenesis of different respiratory complexes. Here, we describe techniques to (1) specifically radiolabel proteins encoded by mtDNA to monitor the rate of synthesis using pulse labeling methods, and (2) analyze the stability, assembly, and turnover of subunits using pulse-chase methods in cultured cells and isolated mitochondria.
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Affiliation(s)
- Luke E Formosa
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC, 3086, Australia.,Department of Biochemistry and Molecular Biology, Monash University, Building 77, Level 2, Clayton Campus, Melbourne, VIC, 3800, Australia
| | - Annette Hofer
- Institute for Genetics and Cluster of Excellence: Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Zülpicher Str. 47A, Cologne, 50674, Germany
| | - Christin Tischner
- Institute for Genetics and Cluster of Excellence: Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Zülpicher Str. 47A, Cologne, 50674, Germany
| | - Tina Wenz
- Institute for Genetics and Cluster of Excellence: Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Zülpicher Str. 47A, Cologne, 50674, Germany
| | - Michael T Ryan
- Department of Biochemistry and Molecular Biology, Monash University, Building 77, Level 2, Clayton Campus, Melbourne, VIC, 3800, Australia.
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21
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Hoseini H, Pandey S, Jores T, Schmitt A, Franz-Wachtel M, Macek B, Buchner J, Dimmer KS, Rapaport D. The cytosolic cochaperone Sti1 is relevant for mitochondrial biogenesis and morphology. FEBS J 2016; 283:3338-52. [PMID: 27412066 DOI: 10.1111/febs.13813] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2016] [Revised: 06/30/2016] [Accepted: 07/12/2016] [Indexed: 11/28/2022]
Abstract
Most mitochondrial proteins are synthesized in the cytosol prior to their import into the organelle. It is commonly accepted that cytosolic factors are required for delivering precursor proteins to the mitochondrial surface and for keeping newly synthesized proteins in an import-competent conformation. However, the identity of such factors and their defined contribution to the import process are mostly unknown. Using a presequence-containing model protein and a site-directed photo-crosslinking approach in yeast cells we identified the cytosolic chaperones Hsp70 (Ssa1) and Hsp90 (Hsp82) as well as their cochaperones, Sti1 and Ydj1, as putative cytosolic factors involved in mitochondrial protein import. Deletion of STI1 caused both alterations in mitochondrial morphology and lower steady-state levels of a subset of mitochondrial proteins. In addition, double deletion of STI1 with the mitochondrial import factors, MIM1 or TOM20, showed a synthetic growth phenotype indicating a genetic interaction of STI1 with these genes. Moreover, recombinant cytosolic domains of the import receptors Tom20 and Tom70 were able to bind in vitro Sti1 and other cytosolic factors. In summary, our observations point to a, direct or indirect, role of Sti1 for mitochondrial functionality.
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Affiliation(s)
- Hoda Hoseini
- Interfaculty Institute of Biochemistry, University of Tübingen, Germany
| | - Saroj Pandey
- Interfaculty Institute of Biochemistry, University of Tübingen, Germany
| | - Tobias Jores
- Interfaculty Institute of Biochemistry, University of Tübingen, Germany
| | - Anja Schmitt
- Interfaculty Institute of Biochemistry, University of Tübingen, Germany
| | - Mirita Franz-Wachtel
- Proteome Center Tübingen, Interfaculty Institute for Cell Biology, University of Tübingen, Germany
| | - Boris Macek
- Proteome Center Tübingen, Interfaculty Institute for Cell Biology, University of Tübingen, Germany
| | - Johannes Buchner
- Department Chemie, Center for Integrated Protein Science, Technische Universität München, Garching, Germany
| | - Kai Stefan Dimmer
- Interfaculty Institute of Biochemistry, University of Tübingen, Germany
| | - Doron Rapaport
- Interfaculty Institute of Biochemistry, University of Tübingen, Germany.
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22
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Nuebel E, Manganas P, Tokatlidis K. Orphan proteins of unknown function in the mitochondrial intermembrane space proteome: New pathways and metabolic cross-talk. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2016; 1863:2613-2623. [PMID: 27425144 PMCID: PMC5404111 DOI: 10.1016/j.bbamcr.2016.07.004] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/24/2016] [Revised: 07/07/2016] [Accepted: 07/12/2016] [Indexed: 12/14/2022]
Abstract
The mitochondrial intermembrane space (IMS) is involved in protein transport, lipid homeostasis and metal ion exchange, while further acting in signalling pathways such as apoptosis. Regulation of these processes involves protein modifications, as well as stress-induced import or release of proteins and other signalling molecules. Even though the IMS is the smallest sub-compartment of mitochondria, its redox state seems to be tightly regulated. However, the way in which this compartment participates in the cross-talk between the multiple organelles and the cytosol is far from understood. Here we focus on newly identified IMS proteins that may represent future challenges in mitochondrial research. We present an overview of the import pathways, the recently discovered new components of the IMS proteome and how these relate to key aspects of cell signalling and progress made in stem cell and cancer research. A brief overview of the classic mitochondrial import pathways is featured Recent studies assigning a number of new proteins to the mitochondrial IMS are discussed Analysis of the expanded IMS proteomes can provide insights into organelle cross-talk and signalling pathways
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Affiliation(s)
- Esther Nuebel
- Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, UK
| | - Phanee Manganas
- Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, UK
| | - Kostas Tokatlidis
- Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, UK.
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23
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Abstract
Mitochondrion-related organelles (MROs) have arisen independently in a wide range of anaerobic protist lineages. Only a few of these organelles and their functions have been investigated in detail, and most of what is known about MROs comes from studies of parasitic organisms such as the parabasalid Trichomonas vaginalis. Here, we describe the MRO of a free-living anaerobic jakobid excavate, Stygiella incarcerata. We report an RNAseq-based reconstruction of S. incarcerata’s MRO proteome, with an associated biochemical map of the pathways predicted to be present in this organelle. The pyruvate metabolism and oxidative stress response pathways are strikingly similar to those found in the MROs of other anaerobic protists, such as Pygsuia and Trichomonas. This elegant example of convergent evolution is suggestive of an anaerobic biochemical ‘module’ of prokaryotic origins that has been laterally transferred among eukaryotes, enabling them to adapt rapidly to anaerobiosis. We also identified genes corresponding to a variety of mitochondrial processes not found in Trichomonas, including intermembrane space components of the mitochondrial protein import apparatus, and enzymes involved in amino acid metabolism and cardiolipin biosynthesis. In this respect, the MROs of S. incarcerata more closely resemble those of the much more distantly related free-living organisms Pygsuia biforma and Cantina marsupialis, likely reflecting these organisms’ shared lifestyle as free-living anaerobes.
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Affiliation(s)
- Michelle M Leger
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS, Canada
| | - Laura Eme
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS, Canada
| | - Laura A Hug
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS, Canada
| | - Andrew J Roger
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS, Canada
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Revisiting trends on mitochondrial mega-channels for the import of proteins and nucleic acids. J Bioenerg Biomembr 2016; 49:75-99. [DOI: 10.1007/s10863-016-9662-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2016] [Accepted: 04/25/2016] [Indexed: 12/14/2022]
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25
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Lasserre JP, Dautant A, Aiyar RS, Kucharczyk R, Glatigny A, Tribouillard-Tanvier D, Rytka J, Blondel M, Skoczen N, Reynier P, Pitayu L, Rötig A, Delahodde A, Steinmetz LM, Dujardin G, Procaccio V, di Rago JP. Yeast as a system for modeling mitochondrial disease mechanisms and discovering therapies. Dis Model Mech 2016; 8:509-26. [PMID: 26035862 PMCID: PMC4457039 DOI: 10.1242/dmm.020438] [Citation(s) in RCA: 101] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Mitochondrial diseases are severe and largely untreatable. Owing to the many essential processes carried out by mitochondria and the complex cellular systems that support these processes, these diseases are diverse, pleiotropic, and challenging to study. Much of our current understanding of mitochondrial function and dysfunction comes from studies in the baker's yeast Saccharomyces cerevisiae. Because of its good fermenting capacity, S. cerevisiae can survive mutations that inactivate oxidative phosphorylation, has the ability to tolerate the complete loss of mitochondrial DNA (a property referred to as ‘petite-positivity’), and is amenable to mitochondrial and nuclear genome manipulation. These attributes make it an excellent model system for studying and resolving the molecular basis of numerous mitochondrial diseases. Here, we review the invaluable insights this model organism has yielded about diseases caused by mitochondrial dysfunction, which ranges from primary defects in oxidative phosphorylation to metabolic disorders, as well as dysfunctions in maintaining the genome or in the dynamics of mitochondria. Owing to the high level of functional conservation between yeast and human mitochondrial genes, several yeast species have been instrumental in revealing the molecular mechanisms of pathogenic human mitochondrial gene mutations. Importantly, such insights have pointed to potential therapeutic targets, as have genetic and chemical screens using yeast. Summary: In this Review, we discuss the use of budding yeast to understand mitochondrial diseases and help in the search for their treatments.
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Affiliation(s)
- Jean-Paul Lasserre
- University Bordeaux-CNRS, IBGC, UMR 5095, 1 rue Camille Saint-Saëns, Bordeaux F-33000, France
| | - Alain Dautant
- University Bordeaux-CNRS, IBGC, UMR 5095, 1 rue Camille Saint-Saëns, Bordeaux F-33000, France
| | - Raeka S Aiyar
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Meyerhofstrasse 1, Heidelberg 69117, Germany
| | - Roza Kucharczyk
- Department of Genetics, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw 02-106, Poland
| | - Annie Glatigny
- Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CEA, CNRS, Université Paris-Sud, 1 avenue de la terrasse, Gif-sur-Yvette 91198, France
| | - Déborah Tribouillard-Tanvier
- Institut National de la Santé et de la Recherche Médicale UMR1078, Université de Bretagne Occidentale, Faculté de Médecine et des Sciences de la Santé, Etablissement Français du Sang (EFS) Bretagne, CHRU Brest, Hôpital Morvan, Laboratoire de Génétique Moléculaire, Brest F-29200, France
| | - Joanna Rytka
- Department of Genetics, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw 02-106, Poland
| | - Marc Blondel
- Institut National de la Santé et de la Recherche Médicale UMR1078, Université de Bretagne Occidentale, Faculté de Médecine et des Sciences de la Santé, Etablissement Français du Sang (EFS) Bretagne, CHRU Brest, Hôpital Morvan, Laboratoire de Génétique Moléculaire, Brest F-29200, France
| | - Natalia Skoczen
- University Bordeaux-CNRS, IBGC, UMR 5095, 1 rue Camille Saint-Saëns, Bordeaux F-33000, France Department of Genetics, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw 02-106, Poland
| | - Pascal Reynier
- UMR CNRS 6214-INSERM U1083, Angers 49933, Cedex 9, France Département de Biochimie et Génétique, Centre Hospitalier Universitaire d'Angers, Angers 49933, Cedex 9, France
| | - Laras Pitayu
- Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CEA, CNRS, Université Paris-Sud, rue Gregor Mendel, Orsay 91405, France
| | - Agnès Rötig
- Inserm U1163, Hôpital Necker-Enfants-Malades, Institut Imagine, Université Paris Descartes-Sorbonne Paris Cité, 149 rue de Sèvres, Paris 75015, France
| | - Agnès Delahodde
- Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CEA, CNRS, Université Paris-Sud, rue Gregor Mendel, Orsay 91405, France
| | - Lars M Steinmetz
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Meyerhofstrasse 1, Heidelberg 69117, Germany Stanford Genome Technology Center, Department of Biochemistry, Stanford University, Palo Alto, CA 94304, USA Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305-5301, USA
| | - Geneviève Dujardin
- Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CEA, CNRS, Université Paris-Sud, 1 avenue de la terrasse, Gif-sur-Yvette 91198, France
| | - Vincent Procaccio
- UMR CNRS 6214-INSERM U1083, Angers 49933, Cedex 9, France Département de Biochimie et Génétique, Centre Hospitalier Universitaire d'Angers, Angers 49933, Cedex 9, France
| | - Jean-Paul di Rago
- University Bordeaux-CNRS, IBGC, UMR 5095, 1 rue Camille Saint-Saëns, Bordeaux F-33000, France
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Roundhill E, Turnbull D, Burchill S. Localization of MRP-1 to the outer mitochondrial membrane by the chaperone protein HSP90β. FASEB J 2015; 30:1712-23. [PMID: 26722004 DOI: 10.1096/fj.15-283408] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2015] [Accepted: 12/08/2015] [Indexed: 12/29/2022]
Abstract
Overexpression of plasma membrane multidrug resistance-associated protein 1 (MRP-1) in Ewing's sarcoma (ES) predicts poor outcome. MRP-1 is also expressed in mitochondria, and we have examined the submitochondrial localization of MRP-1 and investigated the mechanism of MRP-1 transport and role of this organelle in the response to doxorubicin. The mitochondrial localization of MRP-1 was examined in ES cell lines by differential centrifugation and membrane solubilization by digitonin. Whether MRP-1 is chaperoned by heat shock proteins (HSPs) was investigated by immunoprecipitation, immunofluorescence microscopy, and HSP knockout using small hairpin RNA and inhibitors (apoptozole, 17-AAG, and NVPAUY). The effect of disrupting mitochondrial MRP-1-dependent efflux activity on the cytotoxic effect of doxorubicin was investigated by counting viable cell number. Mitochondrial MRP-1 is glycosylated and localized to the outer mitochondrial membrane, where it is coexpressed with HSP90. MRP-1 binds to both HSP90 and HSP70, although only inhibition of HSP90β decreases expression of MRP-1 in the mitochondria. Disruption of mitochondrial MRP-1-dependent efflux significantly increases the cytotoxic effect of doxorubicin (combination index, <0.9). For the first time, we have demonstrated that mitochondrial MRP-1 is expressed in the outer mitochondrial membrane and is a client protein of HSP90β, where it may play a role in the doxorubicin-induced resistance of ES.-Roundhill, E., Turnbull, D., Burchill, S. Localization of MRP-1 to the outer mitochondrial membrane by the chaperone protein HSP90β.
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Affiliation(s)
- Elizabeth Roundhill
- Children's Cancer Research Group, Leeds Institute of Cancer and Pathology, St. James's University Hospital, Leeds, United Kingdom; and
| | - Doug Turnbull
- Wellcome Trust Centre for Mitochondrial Research, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Susan Burchill
- Children's Cancer Research Group, Leeds Institute of Cancer and Pathology, St. James's University Hospital, Leeds, United Kingdom; and
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27
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Chen ZP, Li M, Zhang LJ, He JY, Wu L, Xiao YY, Duan JA, Cai T, Li WD. Mitochondria-targeted drug delivery system for cancer treatment. J Drug Target 2015; 24:492-502. [DOI: 10.3109/1061186x.2015.1108325] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Affiliation(s)
- Zhi-Peng Chen
- Department of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, P.R. China and
| | - Man Li
- Department of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, P.R. China and
| | - Liu-Jie Zhang
- Department of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, P.R. China and
| | - Jia-Yu He
- Department of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, P.R. China and
| | - Li Wu
- Department of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, P.R. China and
| | - Yan-Yu Xiao
- Department of Pharmacy, China Pharmaceutical University, Nanjing, P.R. China
| | - Jin-Ao Duan
- Department of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, P.R. China and
| | - Ting Cai
- Department of Pharmacy, China Pharmaceutical University, Nanjing, P.R. China
| | - Wei-Dong Li
- Department of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, P.R. China and
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Martinez F, Olvera-Sanchez S, Esparza-Perusquia M, Gomez-Chang E, Flores-Herrera O. Multiple functions of syncytiotrophoblast mitochondria. Steroids 2015; 103:11-22. [PMID: 26435077 DOI: 10.1016/j.steroids.2015.09.006] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/02/2015] [Revised: 09/16/2015] [Accepted: 09/27/2015] [Indexed: 12/17/2022]
Abstract
The human placenta plays a central role in pregnancy, and the syncytiotrophoblast cells are the main components of the placenta that support the relationship between the mother and fetus, in apart through the production of progesterone. In this review, the metabolic processes performed by syncytiotrophoblast mitochondria associated with placental steroidogenesis are described. The metabolism of cholesterol, specifically how this steroid hormone precursor reaches the mitochondria, and its transformation into progesterone are reviewed. The role of nucleotides in steroidogenesis, as well as the mechanisms associated with signal transduction through protein phosphorylation and dephosphorylation of proteins is discussed. Finally, topics that require further research are identified, including the need for new techniques to study the syncytiotrophoblast in situ using non-invasive methods.
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Affiliation(s)
- Federico Martinez
- Departamento de Bioquímica, Facultad de Medicina, Universidad Nacional Autónoma de México, Apdo. Postal 70-159, Coyoacan 04510, México, D.F., Mexico.
| | - Sofia Olvera-Sanchez
- Departamento de Bioquímica, Facultad de Medicina, Universidad Nacional Autónoma de México, Apdo. Postal 70-159, Coyoacan 04510, México, D.F., Mexico
| | - Mercedes Esparza-Perusquia
- Departamento de Bioquímica, Facultad de Medicina, Universidad Nacional Autónoma de México, Apdo. Postal 70-159, Coyoacan 04510, México, D.F., Mexico
| | - Erika Gomez-Chang
- Departamento de Bioquímica, Facultad de Medicina, Universidad Nacional Autónoma de México, Apdo. Postal 70-159, Coyoacan 04510, México, D.F., Mexico
| | - Oscar Flores-Herrera
- Departamento de Bioquímica, Facultad de Medicina, Universidad Nacional Autónoma de México, Apdo. Postal 70-159, Coyoacan 04510, México, D.F., Mexico
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29
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Wojtkowska M, Buczek D, Stobienia O, Karachitos A, Antoniewicz M, Slocinska M, Makałowski W, Kmita H. The TOM Complex of Amoebozoans: the Cases of the Amoeba Acanthamoeba castellanii and the Slime Mold Dictyostelium discoideum. Protist 2015; 166:349-62. [PMID: 26074248 DOI: 10.1016/j.protis.2015.05.005] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2014] [Revised: 05/10/2015] [Accepted: 05/14/2015] [Indexed: 11/29/2022]
Abstract
Protein import into mitochondria requires a wide variety of proteins, forming complexes in both mitochondrial membranes. The TOM complex (translocase of the outer membrane) is responsible for decoding of targeting signals, translocation of imported proteins across or into the outer membrane, and their subsequent sorting. Thus the TOM complex is regarded as the main gate into mitochondria for imported proteins. Available data indicate that mitochondria of representative organisms from across the major phylogenetic lineages of eukaryotes differ in subunit organization of the TOM complex. The subunit organization of the TOM complex in the Amoebozoa is still elusive, so we decided to investigate its organization in the soil amoeba Acanthamoeba castellanii and the slime mold Dictyostelium discoideum. They represent two major subclades of the Amoebozoa: the Lobosa and Conosa, respectively. Our results confirm the presence of Tom70, Tom40 and Tom7 in the A. castellanii and D. discoideum TOM complex, while the presence of Tom22 and Tom20 is less supported. Interestingly, the Tom proteins display the highest similarity to Opisthokonta cognate proteins, with the exception of Tom40. Thus representatives of two major subclades of the Amoebozoa appear to be similar in organization of the TOM complex, despite differences in their lifestyle.
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Affiliation(s)
- Małgorzata Wojtkowska
- Adam Mickiewicz University, Faculty of Biology, Institute of Molecular Biology and Biotechnology, Department of Bioenergetics, Poznań, Poland.
| | - Dorota Buczek
- Adam Mickiewicz University, Faculty of Biology, Institute of Molecular Biology and Biotechnology, Department of Bioenergetics, Poznań, Poland; University of Muenster, Faculty of Medicine Institute of Bioinformatics, Muenster, Germany
| | - Olgierd Stobienia
- Adam Mickiewicz University, Faculty of Biology, Institute of Molecular Biology and Biotechnology, Department of Bioenergetics, Poznań, Poland
| | - Andonis Karachitos
- Adam Mickiewicz University, Faculty of Biology, Institute of Molecular Biology and Biotechnology, Department of Bioenergetics, Poznań, Poland
| | - Monika Antoniewicz
- Adam Mickiewicz University, Faculty of Biology, Institute of Molecular Biology and Biotechnology, Department of Bioenergetics, Poznań, Poland
| | - Małgorzata Slocinska
- Adam Mickiewicz University, Faculty of Biology, Institute of Experimental Biology, Department of Animal Physiology and Development, Poznań, Poland
| | - Wojciech Makałowski
- University of Muenster, Faculty of Medicine Institute of Bioinformatics, Muenster, Germany
| | - Hanna Kmita
- Adam Mickiewicz University, Faculty of Biology, Institute of Molecular Biology and Biotechnology, Department of Bioenergetics, Poznań, Poland
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30
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Formosa LE, Mimaki M, Frazier AE, McKenzie M, Stait TL, Thorburn DR, Stroud DA, Ryan MT. Characterization of mitochondrial FOXRED1 in the assembly of respiratory chain complex I. Hum Mol Genet 2015; 24:2952-65. [DOI: 10.1093/hmg/ddv058] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2014] [Accepted: 02/09/2015] [Indexed: 11/12/2022] Open
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31
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Aiyar RS, Bohnert M, Duvezin-Caubet S, Voisset C, Gagneur J, Fritsch ES, Couplan E, von der Malsburg K, Funaya C, Soubigou F, Courtin F, Suresh S, Kucharczyk R, Evrard J, Antony C, St Onge RP, Blondel M, di Rago JP, van der Laan M, Steinmetz LM. Mitochondrial protein sorting as a therapeutic target for ATP synthase disorders. Nat Commun 2014; 5:5585. [PMID: 25519239 PMCID: PMC4284804 DOI: 10.1038/ncomms6585] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2014] [Accepted: 10/16/2014] [Indexed: 11/09/2022] Open
Abstract
Mitochondrial diseases are systemic, prevalent and often fatal; yet treatments remain scarce. Identifying molecular intervention points that can be therapeutically targeted remains a major challenge, which we confronted via a screening assay we developed. Using yeast models of mitochondrial ATP synthase disorders, we screened a drug repurposing library, and applied genomic and biochemical techniques to identify pathways of interest. Here we demonstrate that modulating the sorting of nuclear-encoded proteins into mitochondria, mediated by the TIM23 complex, proves therapeutic in both yeast and patient-derived cells exhibiting ATP synthase deficiency. Targeting TIM23-dependent protein sorting improves an array of phenotypes associated with ATP synthase disorders, including biogenesis and activity of the oxidative phosphorylation machinery. Our study establishes mitochondrial protein sorting as an intervention point for ATP synthase disorders, and because of the central role of this pathway in mitochondrial biogenesis, it holds broad value for the treatment of mitochondrial diseases.
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Affiliation(s)
- Raeka S Aiyar
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, 69117 Heidelberg, Germany
| | - Maria Bohnert
- Institut für Biochemie und Molekularbiologie, ZBMZ, Universität Freiburg, 79104 Freiburg, Germany
| | - Stéphane Duvezin-Caubet
- 1] Université Bordeaux, IBGC, UMR 5095, F-33000 Bordeaux, France [2] CNRS, IBGC, UMR 5095, F-33000 Bordeaux, France
| | - Cécile Voisset
- Institut National de la Santé et de la Recherche Médicale UMR1078; Université de Bretagne Occidentale, Faculté de Médecine et des Sciences de la Santé; Etablissement Français du Sang (EFS) Bretagne; CHRU Brest, Hôpital Morvan, Laboratoire de Génétique Moléculaire, Brest F-29200, France
| | - Julien Gagneur
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, 69117 Heidelberg, Germany
| | - Emilie S Fritsch
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, 69117 Heidelberg, Germany
| | - Elodie Couplan
- Institut National de la Santé et de la Recherche Médicale UMR1078; Université de Bretagne Occidentale, Faculté de Médecine et des Sciences de la Santé; Etablissement Français du Sang (EFS) Bretagne; CHRU Brest, Hôpital Morvan, Laboratoire de Génétique Moléculaire, Brest F-29200, France
| | - Karina von der Malsburg
- 1] Institut für Biochemie und Molekularbiologie, ZBMZ, Universität Freiburg, 79104 Freiburg, Germany [2] BIOSS Centre for Biological Signalling Studies, Universität Freiburg, 79104 Freiburg, Germany
| | - Charlotta Funaya
- European Molecular Biology Laboratory (EMBL), Electron Microscopy Core Facility, 69117 Heidelberg, Germany
| | - Flavie Soubigou
- Institut National de la Santé et de la Recherche Médicale UMR1078; Université de Bretagne Occidentale, Faculté de Médecine et des Sciences de la Santé; Etablissement Français du Sang (EFS) Bretagne; CHRU Brest, Hôpital Morvan, Laboratoire de Génétique Moléculaire, Brest F-29200, France
| | - Florence Courtin
- 1] Université Bordeaux, IBGC, UMR 5095, F-33000 Bordeaux, France [2] CNRS, IBGC, UMR 5095, F-33000 Bordeaux, France
| | - Sundari Suresh
- Stanford Genome Technology Center, Stanford University, Palo Alto, California 94304, USA
| | - Roza Kucharczyk
- Department of Genetics, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Justine Evrard
- Institut National de la Santé et de la Recherche Médicale UMR1078; Université de Bretagne Occidentale, Faculté de Médecine et des Sciences de la Santé; Etablissement Français du Sang (EFS) Bretagne; CHRU Brest, Hôpital Morvan, Laboratoire de Génétique Moléculaire, Brest F-29200, France
| | - Claude Antony
- European Molecular Biology Laboratory (EMBL), Electron Microscopy Core Facility, 69117 Heidelberg, Germany
| | - Robert P St Onge
- Stanford Genome Technology Center, Stanford University, Palo Alto, California 94304, USA
| | - Marc Blondel
- Institut National de la Santé et de la Recherche Médicale UMR1078; Université de Bretagne Occidentale, Faculté de Médecine et des Sciences de la Santé; Etablissement Français du Sang (EFS) Bretagne; CHRU Brest, Hôpital Morvan, Laboratoire de Génétique Moléculaire, Brest F-29200, France
| | - Jean-Paul di Rago
- 1] Université Bordeaux, IBGC, UMR 5095, F-33000 Bordeaux, France [2] CNRS, IBGC, UMR 5095, F-33000 Bordeaux, France
| | - Martin van der Laan
- 1] Institut für Biochemie und Molekularbiologie, ZBMZ, Universität Freiburg, 79104 Freiburg, Germany [2] BIOSS Centre for Biological Signalling Studies, Universität Freiburg, 79104 Freiburg, Germany
| | - Lars M Steinmetz
- 1] European Molecular Biology Laboratory (EMBL), Genome Biology Unit, 69117 Heidelberg, Germany [2] Stanford Genome Technology Center, Stanford University, Palo Alto, California 94304, USA [3] Department of Genetics, Stanford University School of Medicine, Stanford, California, USA
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Saleem A, Iqbal S, Zhang Y, Hood DA. Effect of p53 on mitochondrial morphology, import, and assembly in skeletal muscle. Am J Physiol Cell Physiol 2014; 308:C319-29. [PMID: 25472962 DOI: 10.1152/ajpcell.00253.2014] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The purpose of this study was to investigate whether p53 regulates mitochondrial function via changes in mitochondrial protein import, complex IV (COX) assembly, or the expression of key proteins involved in mitochondrial dynamics and degradation. Mitochondria from p53 KO mice displayed ultra-structural alterations and were more punctate in appearance. This was accompanied by protein-specific alterations in fission, fusion, and mitophagy-related proteins. However, matrix-destined protein import into subsarcolemmal or intermyofibrillar mitochondria was unaffected in the absence of p53, despite mitochondrial subfraction-specific reductions in Tom20, Tim23, mtHsp70, and mtHsp60 in the knockout (KO) mitochondria. Complex IV activity in isolated mitochondria was also unchanged in KO mice, but two-dimensional blue native-PAGE revealed a reduction in the assembly of complex IV within the IMF fractions from KO mice in tandem with lower levels of the assembly protein Surf1. This observed defect in complex IV assembly may facilitate the previously documented impairment in mitochondrial function in p53 KO mice. We suspect that these morphological and functional impairments in mitochondria drive a decreased reliance on mitochondrial respiration as a means of energy production in skeletal muscle in the absence of p53.
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Affiliation(s)
- Ayesha Saleem
- School of Kinesiology and Health Science, York University, Toronto, Ontario, Canada; and Muscle Health Research Centre, York University, Toronto, Ontario, Canada
| | - Sobia Iqbal
- School of Kinesiology and Health Science, York University, Toronto, Ontario, Canada; and Muscle Health Research Centre, York University, Toronto, Ontario, Canada
| | - Yuan Zhang
- School of Kinesiology and Health Science, York University, Toronto, Ontario, Canada; and Muscle Health Research Centre, York University, Toronto, Ontario, Canada
| | - David A Hood
- School of Kinesiology and Health Science, York University, Toronto, Ontario, Canada; and Muscle Health Research Centre, York University, Toronto, Ontario, Canada
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Lackey SWK, Taylor RD, Go NE, Wong A, Sherman EL, Nargang FE. Evidence supporting the 19 β-strand model for Tom40 from cysteine scanning and protease site accessibility studies. J Biol Chem 2014; 289:21640-50. [PMID: 24947507 DOI: 10.1074/jbc.m114.578765] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Most proteins found in mitochondria are translated in the cytosol and enter the organelle via the TOM complex (translocase of the outer mitochondrial membrane). Tom40 is the pore forming component of the complex. Although the three-dimensional structure of Tom40 has not been determined, the structure of porin, a related protein, has been shown to be a β-barrel containing 19 membrane spanning β-strands and an N-terminal α-helical region. The evolutionary relationship between the two proteins has allowed modeling of Tom40 into a similar structure by several laboratories. However, it has been suggested that the 19-strand porin structure does not represent the native form of the protein. If true, modeling of Tom40 based on the porin structure would also be invalid. We have used substituted cysteine accessibility mapping to identify several potential β-strands in the Tom40 protein in isolated mitochondria. These data, together with protease accessibility studies, support the 19 β-strand model for Tom40 with the C-terminal end of the protein localized to the intermembrane space.
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Affiliation(s)
- Sebastian W K Lackey
- From the Department of Biological Sciences, University of Alberta, Edmonton, Alberta T6G 2E9, Canada
| | - Rebecca D Taylor
- From the Department of Biological Sciences, University of Alberta, Edmonton, Alberta T6G 2E9, Canada
| | - Nancy E Go
- From the Department of Biological Sciences, University of Alberta, Edmonton, Alberta T6G 2E9, Canada
| | - Annie Wong
- From the Department of Biological Sciences, University of Alberta, Edmonton, Alberta T6G 2E9, Canada
| | - E Laura Sherman
- From the Department of Biological Sciences, University of Alberta, Edmonton, Alberta T6G 2E9, Canada
| | - Frank E Nargang
- From the Department of Biological Sciences, University of Alberta, Edmonton, Alberta T6G 2E9, Canada
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Abstract
Almost 20 years ago, the discovery that mitochondrial release of cytochrome c initiates a cascade that leads to cell death brought about a wholesale change in how cell biologists think of mitochondria. Formerly viewed as sites of biosynthesis and bioenergy production, these double membrane organelles could now be thought of as regulators of signal transduction. Within a few years, multiple other mitochondria-centric signaling mechanisms have been proposed, including release of reactive oxygen species and the scaffolding of signaling complexes on the outer mitochondrial membrane. It has also been shown that mitochondrial dysfunction causes induction of stress responses, bolstering the idea that mitochondria communicate their fitness to the rest of the cell. In the past decade, multiple new modes of mitochondrial signaling have been discovered. These include the release of metabolites, mitochondrial motility and dynamics, and interaction with other organelles such as endoplasmic reticulum in regulating signaling. Collectively these studies have established that mitochondria-dependent signaling has diverse physiological and pathophysiological outcomes. This review is a brief account of recent work in mitochondria-dependent signaling in the historical framework of the early studies.
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Affiliation(s)
- Navdeep S Chandel
- Section of Pulmonary and Critical Care Medicine, Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA.
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35
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Highly divergent mitochondrion-related organelles in anaerobic parasitic protozoa. Biochimie 2014; 100:3-17. [DOI: 10.1016/j.biochi.2013.11.018] [Citation(s) in RCA: 103] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2013] [Accepted: 11/24/2013] [Indexed: 11/20/2022]
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36
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Yuan Y, Li M, Hong N, Hong Y. Correlative light and electron microscopic analyses of mitochondrial distribution in blastomeres of early fish embryos. FASEB J 2014; 28:577-585. [DOI: 10.1096/fj.13-233635] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/30/2023]
Affiliation(s)
- Yongming Yuan
- Department of Biological SciencesNational University of SingaporeSingaporeSingapore
| | - Mingyou Li
- Department of Biological SciencesNational University of SingaporeSingaporeSingapore
- College of Fisheries and Life ScienceShanghai Ocean UniversityShanghaiChina
| | - Ni Hong
- Department of Biological SciencesNational University of SingaporeSingaporeSingapore
| | - Yunhan Hong
- Department of Biological SciencesNational University of SingaporeSingaporeSingapore
- College of Fisheries and Life ScienceShanghai Ocean UniversityShanghaiChina
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37
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The role of Djp1 in import of the mitochondrial protein Mim1 demonstrates specificity between a cochaperone and its substrate protein. Mol Cell Biol 2013; 33:4083-94. [PMID: 23959800 DOI: 10.1128/mcb.00227-13] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A special group of mitochondrial outer membrane proteins spans the membrane once, exposing soluble domains to both sides of the membrane. These proteins are synthesized in the cytosol and then inserted into the membrane by an unknown mechanism. To identify proteins that are involved in the biogenesis of the single-span model protein Mim1, we performed a high-throughput screen in yeast. Two interesting candidates were the cytosolic cochaperone Djp1 and the mitochondrial import receptor Tom70. Our results indeed demonstrate a direct interaction of newly synthesized Mim1 molecules with Tom70. We further observed lower steady-state levels of Mim1 in mitochondria from djp1Δ and tom70 tom71Δ cells and massive mislocalization of overexpressed GFP-Mim1 to the endoplasmic reticulum in the absence of Djp1. Importantly, these phenotypes were observed specifically for the deletion of DJP1 and were not detected in mutant cells lacking any of the other cytosolic cochaperones of the Hsp40 family. Furthermore, the djp1Δ tom70Δ tom71Δ triple deletion resulted in a severe synthetic sick/lethal growth phenotype. Taking our results together, we identified Tom70 and Djp1 as crucial players in the biogenesis of Mim1. Moreover, the involvement of Djp1 provides a unique case of specificity between a cochaperone and its substrate protein.
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38
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Novel TPR-containing subunit of TOM complex functions as cytosolic receptor for Entamoeba mitosomal transport. Sci Rep 2013; 3:1129. [PMID: 23350036 PMCID: PMC3553487 DOI: 10.1038/srep01129] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2012] [Accepted: 12/27/2012] [Indexed: 11/24/2022] Open
Abstract
Under anaerobic environments, the mitochondria have undergone remarkable reduction and transformation into highly reduced structures, referred as mitochondrion-related organelles (MROs), which include mitosomes and hydrogenosomes. In agreement with the concept of reductive evolution, mitosomes of Entamoeba histolytica lack most of the components of the TOM (translocase of the outer mitochondrial membrane) complex, which is required for the targeting and membrane translocation of preproteins into the canonical aerobic mitochondria. Here we showed, in E. histolytica mitosomes, the presence of a 600-kDa TOM complex composed of Tom40, a conserved pore-forming subunit, and Tom60, a novel lineage-specific receptor protein. Tom60, containing multiple tetratricopeptide repeats, is localized to the mitosomal outer membrane and the cytosol, and serves as a receptor of both mitosomal matrix and membrane preproteins. Our data indicate that Entamoeba has invented a novel lineage-specific shuttle receptor of the TOM complex as a consequence of adaptation to an anaerobic environment.
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Pusnik M, Mani J, Schmidt O, Niemann M, Oeljeklaus S, Schnarwiler F, Warscheid B, Lithgow T, Meisinger C, Schneider A. An essential novel component of the noncanonical mitochondrial outer membrane protein import system of trypanosomatids. Mol Biol Cell 2012; 23:3420-8. [PMID: 22787278 PMCID: PMC3431924 DOI: 10.1091/mbc.e12-02-0107] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
The mitochondrial outer membrane protein Tom40 is the general entry gate for imported proteins in essentially all eukaryotes. Trypanosomatids lack Tom40, however, and use instead a protein termed the archaic translocase of the outer mitochondrial membrane (ATOM). Here we report the discovery of pATOM36, a novel essential component of the trypanosomal outer membrane protein import system that interacts with ATOM. pATOM36 is not related to known Tom proteins from other organisms and mediates the import of matrix proteins. However, there is a group of precursor proteins whose import is independent of pATOM36. Domain-swapping experiments indicate that the N-terminal presequence-containing domain of the substrate proteins at least in part determines the dependence on pATOM36. Secondary structure profiling suggests that pATOM36 is composed largely of α-helices and its assembly into the outer membrane is independent of the sorting and assembly machinery complex. Taken together, these results show that pATOM36 is a novel component associated with the ATOM complex that promotes the import of a subpopulation of proteins into the mitochondrial matrix.
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Affiliation(s)
- Mascha Pusnik
- Department of Chemistry and Biochemistry, University of Bern, CH-3012 Bern, Switzerland
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40
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Rath E, Haller D. Mitochondria at the interface between danger signaling and metabolism: role of unfolded protein responses in chronic inflammation. Inflamm Bowel Dis 2012; 18:1364-77. [PMID: 22183876 DOI: 10.1002/ibd.21944] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/05/2011] [Accepted: 10/19/2011] [Indexed: 12/16/2022]
Abstract
Inflammatory bowel diseases (IBDs), like many other chronic diseases, feature multiple cellular stress responses including endoplasmic reticulum (ER) unfolded protein response (UPR). Maintaining protein homeostasis is indispensable for cell survival and, consequently, distinct signaling pathways have evolved to transmit organelle stress. While the ER UPR, aiming to restore ER homeostasis after challenges to ER function, has been extensively studied in the context of chronic diseases, only recently the related mitochondrial UPR (mtUPR), induced by disturbances of mitochondrial proteostasis, has drawn some attention. ER and mitochondria are in close contact and interact physically and functionally. Accumulating data have placed mitochondria at the center of diverse cellular functions and suggest mitochondria as integrators of signaling pathways such as autophagy and inflammation. Consequently, it is likely that mitochondrial stress and ER stress cannot be regarded separately and that mitochondrial stress, as well as ER stress, participates in the pathology of IBD. Protein homeostasis is particularly sensitive toward infections, oxidative stress, and energy deficiency. Thus, environmental disturbances impacting organelle function lead to the concerted activation of distinct UPRs. The metabolic status might therefore serve as an innate mechanism to sense the epithelial environment, including luminal-derived and host-derived factors. This review highlights mtUPR and its interrelation with ER UPR, focuses on recent studies identifying mitochondria as integrators of cellular danger signaling, and, furthermore, illustrates the importance ER UPR and mitochondrial dysfunction in IBD.
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Affiliation(s)
- Eva Rath
- Technische Universität München, Chair for Biofunctionality, ZIEL, Research Center for Nutrition and Food Science, CDD, Center for Diet and Disease, Freising-Weihenstephan, Germany
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Rao S, Schmidt O, Harbauer AB, Schönfisch B, Guiard B, Pfanner N, Meisinger C. Biogenesis of the preprotein translocase of the outer mitochondrial membrane: protein kinase A phosphorylates the precursor of Tom40 and impairs its import. Mol Biol Cell 2012; 23:1618-27. [PMID: 22419819 PMCID: PMC3338429 DOI: 10.1091/mbc.e11-11-0933] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
The translocase of the outer mitochondrial membrane (TOM) is essential for the import of proteins into mitochondria. Cytosolic protein kinase A phosphorylates the precursor of the channel-forming protein Tom40 and inhibits its import into mitochondria, thus regulating the biogenesis of the protein entry gate of mitochondria. The preprotein translocase of the outer mitochondrial membrane (TOM) functions as the main entry gate for the import of nuclear-encoded proteins into mitochondria. The major subunits of the TOM complex are the three receptors Tom20, Tom22, and Tom70 and the central channel-forming protein Tom40. Cytosolic kinases have been shown to regulate the biogenesis and activity of the Tom receptors. Casein kinase 2 stimulates the biogenesis of Tom22 and Tom20, whereas protein kinase A (PKA) impairs the receptor function of Tom70. Here we report that PKA exerts an inhibitory effect on the biogenesis of the β-barrel protein Tom40. Tom40 is synthesized as precursor on cytosolic ribosomes and subsequently imported into mitochondria. We show that PKA phosphorylates the precursor of Tom40. The phosphorylated Tom40 precursor is impaired in import into mitochondria, whereas the nonphosphorylated precursor is efficiently imported. We conclude that PKA plays a dual role in the regulation of the TOM complex. Phosphorylation by PKA not only impairs the receptor activity of Tom70, but it also inhibits the biogenesis of the channel protein Tom40.
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Affiliation(s)
- Sanjana Rao
- Institut für Biochemie und Molekularbiologie, Zentrum für Biochemie und Molekulare Zellforschung, Universität Freiburg, 79104 Freiburg, Germany
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42
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Faou P, Hoogenraad NJ. Tom34: A cytosolic cochaperone of the Hsp90/Hsp70 protein complex involved in mitochondrial protein import. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2012; 1823:348-57. [DOI: 10.1016/j.bbamcr.2011.12.001] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2011] [Revised: 11/17/2011] [Accepted: 12/02/2011] [Indexed: 10/14/2022]
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43
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Becker T, Wenz LS, Krüger V, Lehmann W, Müller JM, Goroncy L, Zufall N, Lithgow T, Guiard B, Chacinska A, Wagner R, Meisinger C, Pfanner N. The mitochondrial import protein Mim1 promotes biogenesis of multispanning outer membrane proteins. ACTA ACUST UNITED AC 2011; 194:387-95. [PMID: 21825073 PMCID: PMC3153637 DOI: 10.1083/jcb.201102044] [Citation(s) in RCA: 103] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The Mim1 complex imports α-helical mitochondrial outer membrane proteins with multiple transmembrane segments. The mitochondrial outer membrane contains translocase complexes for the import of precursor proteins. The translocase of the outer membrane complex functions as a general preprotein entry gate, whereas the sorting and assembly machinery complex mediates membrane insertion of β-barrel proteins of the outer membrane. Several α-helical outer membrane proteins are known to carry multiple transmembrane segments; however, only limited information is available on the biogenesis of these proteins. We report that mitochondria lacking the mitochondrial import protein 1 (Mim1) are impaired in the biogenesis of multispanning outer membrane proteins, whereas overexpression of Mim1 stimulates their import. The Mim1 complex cooperates with the receptor Tom70 in binding of precursor proteins and promotes their insertion and assembly into the outer membrane. We conclude that the Mim1 complex plays a central role in the import of α-helical outer membrane proteins with multiple transmembrane segments.
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Affiliation(s)
- Thomas Becker
- Institute for Biochemistry and Molecular Biology, Centre for Biochemistry and Molecular Cell Research, Freiburg, Germany
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44
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Reusens B, Theys N, Remacle C. Alteration of mitochondrial function in adult rat offspring of malnourished dams. World J Diabetes 2011; 2:149-57. [PMID: 21954419 PMCID: PMC3180527 DOI: 10.4239/wjd.v2.i9.149] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/02/2011] [Revised: 08/16/2011] [Accepted: 08/21/2011] [Indexed: 02/05/2023] Open
Abstract
Under-nutrition as well as over-nutrition during pregnancy has been associated with the development of adult diseases such as diabetes and obesity. Both epigenetic modifications and programming of the mitochondrial function have been recently proposed to explain how altered intrauterine metabolic environment may produce such a phenotype. This review aims to report data reported in several animal models of fetal malnutrition due to maternal low protein or low calorie diet, high fat diet as well as reduction in placental blood flow. We focus our overview on the β cell. We highlight that, notwithstanding early nutritional events, mitochondrial dysfunctions resulting from different alteration by diet or gender are programmed. This may explain the higher propensity to develop obesity and diabetes in later life.
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Affiliation(s)
- Brigitte Reusens
- Brigitte Reusens, Nicolas Theys, Claude Remacle, Laboratory of Cell Biology, Institute of Life Science, Université Catholique de Louvain, 1348 Louvain-la-Neuve, Belgium
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45
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Understanding mitochondrial complex I assembly in health and disease. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2011; 1817:851-62. [PMID: 21924235 DOI: 10.1016/j.bbabio.2011.08.010] [Citation(s) in RCA: 306] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2011] [Revised: 08/17/2011] [Accepted: 08/27/2011] [Indexed: 12/12/2022]
Abstract
Complex I (NADH:ubiquinone oxidoreductase) is the largest multimeric enzyme complex of the mitochondrial respiratory chain, which is responsible for electron transport and the generation of a proton gradient across the mitochondrial inner membrane to drive ATP production. Eukaryotic complex I consists of 14 conserved subunits, which are homologous to the bacterial subunits, and more than 26 accessory subunits. In mammals, complex I consists of 45 subunits, which must be assembled correctly to form the properly functioning mature complex. Complex I dysfunction is the most common oxidative phosphorylation (OXPHOS) disorder in humans and defects in the complex I assembly process are often observed. This assembly process has been difficult to characterize because of its large size, the lack of a high resolution structure for complex I, and its dual control by nuclear and mitochondrial DNA. However, in recent years, some of the atomic structure of the complex has been resolved and new insights into complex I assembly have been generated. Furthermore, a number of proteins have been identified as assembly factors for complex I biogenesis and many patients carrying mutations in genes associated with complex I deficiency and mitochondrial diseases have been discovered. Here, we review the current knowledge of the eukaryotic complex I assembly process and new insights from the identification of novel assembly factors. This article is part of a Special Issue entitled: Biogenesis/Assembly of Respiratory Enzyme Complexes.
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46
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Nanoscale distribution of mitochondrial import receptor Tom20 is adjusted to cellular conditions and exhibits an inner-cellular gradient. Proc Natl Acad Sci U S A 2011; 108:13546-51. [PMID: 21799113 DOI: 10.1073/pnas.1107553108] [Citation(s) in RCA: 109] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
The translocase of the mitochondrial outer membrane (TOM) complex is the main import pore for nuclear-encoded proteins into mitochondria, yet little is known about its spatial distribution within the outer membrane. Super-resolution stimulated emission depletion microscopy was used to determine quantitatively the nanoscale distribution of Tom20, a subunit of the TOM complex, in more than 1,000 cells. We demonstrate that Tom20 is located in clusters whose nanoscale distribution is finely adjusted to the cellular growth conditions as well as to the specific position of a cell within a microcolony. The density of the clusters correlates to the mitochondrial membrane potential. The distributions of clusters of Tom20 and of Tom22 follow an inner-cellular gradient from the perinuclear to the peripheral mitochondria. We conclude that the nanoscale distribution of the TOM complex is finely adjusted to the cellular conditions, resulting in distribution gradients both within single cells and between adjacent cells.
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47
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Takano T, Kohara M, Kasama Y, Nishimura T, Saito M, Kai C, Tsukiyama-Kohara K. Translocase of outer mitochondrial membrane 70 expression is induced by hepatitis C virus and is related to the apoptotic response. J Med Virol 2011; 83:801-9. [DOI: 10.1002/jmv.22046] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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48
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Danne JC, Waller RF. Analysis of dinoflagellate mitochondrial protein sorting signals indicates a highly stable protein targeting system across eukaryotic diversity. J Mol Biol 2011; 408:643-53. [PMID: 21376056 DOI: 10.1016/j.jmb.2011.02.057] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2010] [Revised: 02/21/2011] [Accepted: 02/24/2011] [Indexed: 11/17/2022]
Abstract
Protein targeting into mitochondria from the cytoplasm is fundamental to the cell biology of all eukaryotes. Our understanding of this process is heavily biased towards "model" organisms, such as animals and fungi, and it is less clear how conserved this process is throughout diverse eukaryotes. In this study, we have surveyed mitochondrial protein sorting signals from a representative of the dinoflagellate algae. Dinoflagellates are a phylum belonging to the group Alveolata, which also includes apicomplexan parasites and ciliates. We generated 46 mitochondrial gene sequences from the dinoflagellate Karlodinium micrum and analysed these for mitochondrial sorting signals. Most of the sequences contain predicted N-terminal peptide extensions that conform to mitochondrial targeting peptides from animals and fungi in terms of length, amino acid composition, and propensity to form amphipathic α-helices. The remainder lack predicted mitochondrial targeting peptides and represent carrier proteins of the inner mitochondrial membrane that have internal targeting signals in model eukaryotes. We tested for functional conservation of the dinoflagellate mitochondrial sorting signals by expressing K. micrum mitochondrial proteins in the fungus Saccharomyces cerevisiae. Both the N-terminal and internal targeting signals were sufficiently conserved to operate in this distantly related system. This study indicates that the character of mitochondrial sorting signals was well established prior to the radiation of major eukaryotic lineages and has shown remarkable conservation during long periods of evolution.
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Affiliation(s)
- Jillian C Danne
- School of Botany, University of Melbourne, Victoria 3010, Australia
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49
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Dukanovic J, Rapaport D. Multiple pathways in the integration of proteins into the mitochondrial outer membrane. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2011; 1808:971-80. [DOI: 10.1016/j.bbamem.2010.06.021] [Citation(s) in RCA: 92] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2010] [Revised: 06/22/2010] [Accepted: 06/23/2010] [Indexed: 11/25/2022]
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50
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Gebert N, Ryan MT, Pfanner N, Wiedemann N, Stojanovski D. Mitochondrial protein import machineries and lipids: A functional connection. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2011; 1808:1002-11. [DOI: 10.1016/j.bbamem.2010.08.003] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2010] [Revised: 08/02/2010] [Accepted: 08/02/2010] [Indexed: 01/01/2023]
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