1
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Song Y, Wang W, Wang B, Shi Q. The Protective Mechanism of TFAM on Mitochondrial DNA and its Role in Neurodegenerative Diseases. Mol Neurobiol 2024; 61:4381-4390. [PMID: 38087167 DOI: 10.1007/s12035-023-03841-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Accepted: 11/28/2023] [Indexed: 07/11/2024]
Abstract
Mitochondrial transcription factor A (TFAM) is a mitochondrial protein encoded by nuclear genes and transported from the cytoplasm to the mitochondria. TFAM is essential for the maintenance, expression, and delivery of mitochondrial DNA (mtDNA) and can regulate the replication and transcription of mtDNA. TFAM is associated with the formation of mtDNA nucleomimetic structures, mtDNA repair, and mtDNA stability. However, the mechanism by which TFAM protects mtDNA is still being studied. This review provides a summary of the protective mechanism of TFAM on mtDNA including the discrete regulatory effects of TFAM acetylation and phosphorylation on mtDNA, the regulation of Ca2+ levels by TFAM to activate transcription in mitochondria, and the increased binding of TFAM to mtDNA damage hot spots. This review also discusses the association between TFAM and some neurodegenerative diseases.
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Affiliation(s)
- Ying Song
- Department of Pharmacology, Zhejiang University of Technology, Hangzhou, Zhejiang, 310014, People's Republic of China.
- Hangzhou King's Bio-Pharmaceutical Technology Co., Ltd., Hangzhou, 310007, Zhejiang, China.
| | - Wenjun Wang
- Department of Pharmacology, Zhejiang University of Technology, Hangzhou, Zhejiang, 310014, People's Republic of China
| | - Beibei Wang
- Department of Pharmacology, Zhejiang University of Technology, Hangzhou, Zhejiang, 310014, People's Republic of China
| | - Qiwen Shi
- Department of Pharmacology, Zhejiang University of Technology, Hangzhou, Zhejiang, 310014, People's Republic of China
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2
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González-Arzola K, Díaz-Quintana A. Mitochondrial Factors in the Cell Nucleus. Int J Mol Sci 2023; 24:13656. [PMID: 37686461 PMCID: PMC10563088 DOI: 10.3390/ijms241713656] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Revised: 08/31/2023] [Accepted: 08/31/2023] [Indexed: 09/10/2023] Open
Abstract
The origin of eukaryotic organisms involved the integration of mitochondria into the ancestor cell, with a massive gene transfer from the original proteobacterium to the host nucleus. Thus, mitochondrial performance relies on a mosaic of nuclear gene products from a variety of genomes. The concerted regulation of their synthesis is necessary for metabolic housekeeping and stress response. This governance involves crosstalk between mitochondrial, cytoplasmic, and nuclear factors. While anterograde and retrograde regulation preserve mitochondrial homeostasis, the mitochondria can modulate a wide set of nuclear genes in response to an extensive variety of conditions, whose response mechanisms often merge. In this review, we summarise how mitochondrial metabolites and proteins-encoded either in the nucleus or in the organelle-target the cell nucleus and exert different actions modulating gene expression and the chromatin state, or even causing DNA fragmentation in response to common stress conditions, such as hypoxia, oxidative stress, unfolded protein stress, and DNA damage.
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Affiliation(s)
- Katiuska González-Arzola
- Centro Andaluz de Biología Molecular y Medicina Regenerativa—CABIMER, Consejo Superior de Investigaciones Científicas—Universidad de Sevilla—Universidad Pablo de Olavide, 41092 Seville, Spain
- Departamento de Bioquímica Vegetal y Biología Molecular, Universidad de Sevilla, 41012 Seville, Spain
| | - Antonio Díaz-Quintana
- Departamento de Bioquímica Vegetal y Biología Molecular, Universidad de Sevilla, 41012 Seville, Spain
- Instituto de Investigaciones Químicas—cicCartuja, Universidad de Sevilla—C.S.I.C, 41092 Seville, Spain
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3
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Kozhukhar N, Alexeyev MF. 35 Years of TFAM Research: Old Protein, New Puzzles. BIOLOGY 2023; 12:823. [PMID: 37372108 DOI: 10.3390/biology12060823] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Revised: 05/29/2023] [Accepted: 06/03/2023] [Indexed: 06/29/2023]
Abstract
Transcription Factor A Mitochondrial (TFAM), through its contributions to mtDNA maintenance and expression, is essential for cellular bioenergetics and, therefore, for the very survival of cells. Thirty-five years of research on TFAM structure and function generated a considerable body of experimental evidence, some of which remains to be fully reconciled. Recent advancements allowed an unprecedented glimpse into the structure of TFAM complexed with promoter DNA and TFAM within the open promoter complexes. These novel insights, however, raise new questions about the function of this remarkable protein. In our review, we compile the available literature on TFAM structure and function and provide some critical analysis of the available data.
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Affiliation(s)
- Natalya Kozhukhar
- Department of Physiology and Cell Biology, University of South Alabama, Mobile, AL 36688, USA
| | - Mikhail F Alexeyev
- Department of Physiology and Cell Biology, University of South Alabama, Mobile, AL 36688, USA
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4
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Seike H, Ishimori K, Watanabe A, Kiryu M, Hatakeyama S, Tanaka S, Yoshihara R. Two high-mobility group domains of MHG1 are necessary to maintain mtDNA in Neurospora crassa. Fungal Biol 2022; 126:826-833. [PMID: 36517150 DOI: 10.1016/j.funbio.2022.11.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Revised: 10/13/2022] [Accepted: 11/08/2022] [Indexed: 11/15/2022]
Abstract
The mhg1 (NCU02695/ada-23) gene encodes the mitochondrial high-mobility group box (HMG-box or HMGB) protein in Neurospora crassa. The mhg1 KO strain (mhg1KO) has mitochondrial DNA (mtDNA) instability and a short lifespan; however, the function of MHG1 remains unclear. To investigate the role of this protein in the maintenance of mtDNA, domain deleted MHG1 proteins were expressed in the mhg1KO strain, and their effects were analyzed. We identified two putative HMG-domains, HMGBI and HMGBII. Although deletion of the HMG-box did not abolish MHG1's mitochondrial localization, the mhg1KO phenotype of a severe growth defect and a high sensitivity to mutagens could not be restored by introduction of HMG-box deleted mhg1 gene into the KO strain. It was indicated that recombinant full-length MHG1, i.e., mitochondrial targeting sequence (MTS) containing protein, did not exhibit explicit DNA binding, whereas the MHG1 protein truncated for the MTS sequence did in vitro by an electrophoretic mobility shift assay. Furthermore, recombinant MHG1 protein lacking MTS and HMG-domains, either HMGBI or HMGBII, had DNA affinity and an altered band shift pattern compared with MTS-truncated MHG1 protein. These results suggest that cleavage of MTS and appropriate DNA binding via HMG-domains are indispensable for maintaining mtDNA in N. crassa.
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Affiliation(s)
- Hayami Seike
- Department of Regulatory Biology, Faculty of Science, Saitama University, Shimo-Ohkubo 255, Sakura-ku, Saitama, Saitama, 338-8570, Japan
| | - Keisuke Ishimori
- Department of Regulatory Biology, Faculty of Science, Saitama University, Shimo-Ohkubo 255, Sakura-ku, Saitama, Saitama, 338-8570, Japan
| | - Asagi Watanabe
- Department of Regulatory Biology, Faculty of Science, Saitama University, Shimo-Ohkubo 255, Sakura-ku, Saitama, Saitama, 338-8570, Japan
| | - Mao Kiryu
- Department of Regulatory Biology, Faculty of Science, Saitama University, Shimo-Ohkubo 255, Sakura-ku, Saitama, Saitama, 338-8570, Japan
| | - Shin Hatakeyama
- Department of Regulatory Biology, Faculty of Science, Saitama University, Shimo-Ohkubo 255, Sakura-ku, Saitama, Saitama, 338-8570, Japan
| | - Shuuitsu Tanaka
- Department of Regulatory Biology, Faculty of Science, Saitama University, Shimo-Ohkubo 255, Sakura-ku, Saitama, Saitama, 338-8570, Japan
| | - Ryouhei Yoshihara
- Department of Regulatory Biology, Faculty of Science, Saitama University, Shimo-Ohkubo 255, Sakura-ku, Saitama, Saitama, 338-8570, Japan.
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5
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Zhu S, Xu N, Han Y, Ye X, Yang L, Zuo J, Liu W. MTERF3 contributes to MPP+-induced mitochondrial dysfunction in SH-SY5Y cells. Acta Biochim Biophys Sin (Shanghai) 2022; 54:1113-1121. [PMID: 35904214 PMCID: PMC9828133 DOI: 10.3724/abbs.2022098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Accepted: 01/18/2022] [Indexed: 11/25/2022] Open
Abstract
Parkinson's disease (PD) is a neurodegenerative disorder causing severe social and economic burdens. The origin of PD has been usually attributed to mitochondrial dysfunction. To this end, mitochondrial transcription regulators become attractive subjects for understanding PD pathogenesis. Previously, we found that the expression of mitochondrial transcription termination factor 3 (MTERF3) was reduced in MPP+-induced mice model of PD. In the present study, we probe the function of MTERF3 and its role in MPP+-induced cellular model of PD. Initially, we observe that MTERF3 expression is also reduced in MPP+-induced cellular model of PD, which can be mainly attributed to the increase of MTERF3 degradation. Next, we examine the effect of MTERF3 knockdown and overexpression on the replication, transcription, and translation of mitochondrial DNA (mtDNA). We show that knockdown and overexpression of MTERF3 have opposite effects on mtDNA transcript level but similar effects on mtDNA expression level, in line with MTERF3's dual roles in mtDNA transcription and translation. In addition, we examine the effect of MTERF3 knockdown and overexpression on mitochondrial function with and without MPP+ treatment, and find that MTERF3 seems to play a generally protective role in MPP+-induced mitochondrial dysfunction. Together, this work suggests a regulatory role of MTERF3 in MPP+-induced cellular model of PD and may provide clues in designing novel therapeutics against PD.
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Affiliation(s)
| | | | - Yanyan Han
- />Department of Cellular and Genetic MedicineSchool of Basic Medical SciencesFudan UniversityShanghai200032China
| | - Xiaofei Ye
- />Department of Cellular and Genetic MedicineSchool of Basic Medical SciencesFudan UniversityShanghai200032China
| | - Ling Yang
- />Department of Cellular and Genetic MedicineSchool of Basic Medical SciencesFudan UniversityShanghai200032China
| | - Ji Zuo
- />Department of Cellular and Genetic MedicineSchool of Basic Medical SciencesFudan UniversityShanghai200032China
| | - Wen Liu
- />Department of Cellular and Genetic MedicineSchool of Basic Medical SciencesFudan UniversityShanghai200032China
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6
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Kozhukhar N, Spadafora D, Rodriguez YAR, Alexeyev MF. A Method for In Situ Reverse Genetic Analysis of Proteins Involved mtDNA Replication. Cells 2022; 11:2168. [PMID: 35883613 PMCID: PMC9316749 DOI: 10.3390/cells11142168] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Revised: 06/29/2022] [Accepted: 07/10/2022] [Indexed: 02/01/2023] Open
Abstract
The unavailability of tractable reverse genetic analysis approaches represents an obstacle to a better understanding of mitochondrial DNA replication. Here, we used CRISPR-Cas9 mediated gene editing to establish the conditional viability of knockouts in the key proteins involved in mtDNA replication. This observation prompted us to develop a set of tools for reverse genetic analysis in situ, which we called the GeneSwap approach. The technique was validated by identifying 730 amino acid (aa) substitutions in the mature human TFAM that are conditionally permissive for mtDNA replication. We established that HMG domains of TFAM are functionally independent, which opens opportunities for engineering chimeric TFAMs with customized properties for studies on mtDNA replication, mitochondrial transcription, and respiratory chain function. Finally, we present evidence that the HMG2 domain plays the leading role in TFAM species-specificity, thus indicating a potential pathway for TFAM-mtDNA evolutionary co-adaptations.
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Affiliation(s)
| | | | | | - Mikhail F. Alexeyev
- Department of Physiology and Cell Biology, University of South Alabama, Mobile, AL 36688, USA; (N.K.); (D.S.); (Y.A.R.R.)
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7
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Autophagy modulation in resveratrol protective effects on steroidogenesis in high-fat diet-fed mice and H 2O 2-challenged TM3 cells. Mol Biol Rep 2022; 49:2973-2983. [PMID: 35000049 DOI: 10.1007/s11033-022-07120-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2021] [Accepted: 01/04/2022] [Indexed: 10/19/2022]
Abstract
BACKGROUND Autophagy dysregulation and oxidative stress play critical pathophysiological roles in developing obesity-related metabolic health disorders. This study aims to investigate how autophagy modulation is related to resveratrol (RSV) antioxidant activities and preventive effects on steroidogenesis decline associated with a high-fat diet (HFD) and oxidative damage. METHODS AND RESULTS Eight-week-old C57BL/6 J male mice were fed with HFD with or without supplement RSV (400 mg/kg/day) by gavage for 16 weeks. The control group was fed with a standard diet with no RSV or the same amount of RSV. Mouse Leydig cell line TM3 cell was used for in vitro studies. Oxidative stress was induced in TM3 cells with H2O2, followed by RSV treatment plus autophagy activator rapamycin or autophagy inhibitor 3-methyladenine, respectively. RSV supplement could upregulate proteins level of StAR and mitochondrial proteins COX4 and mtTFA, indicating the amelioration of steroidogenesis decline and mitochondrial dysfunction caused by HFD. Antioxidants such as GPx4 and SOD2 were improved by RSV as well. The observation of autophagosomes and the changes in expressions of LC3II/I, Beclin1, and Atg7 indicated that RSV could reverse the autophagy defect associated with HFD. 3-methyladenine inhibition of autophagy partially abolished RSV protection on mitochondrial function and steroidogenesis in H2O2-challenged TM3 cells. However, the combination use of rapamycin and RSV did not improve protection on Leydig cells against oxidative damage. CONCLUSIONS The stimulation of autophagy by RSV is closely linked to its antioxidant actions and positive impact on steroidogenesis in HFD mice. The findings suggest RSV is protective against obesity-related Leydig cell impairment.
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8
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Chiang S, Braidy N, Maleki S, Lal S, Richardson DR, Huang MLH. Mechanisms of impaired mitochondrial homeostasis and NAD + metabolism in a model of mitochondrial heart disease exhibiting redox active iron accumulation. Redox Biol 2021; 46:102038. [PMID: 34416478 PMCID: PMC8379503 DOI: 10.1016/j.redox.2021.102038] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 05/22/2021] [Accepted: 06/05/2021] [Indexed: 01/18/2023] Open
Abstract
Due to the high redox activity of the mitochondrion, this organelle can suffer oxidative stress. To manage energy demands while minimizing redox stress, mitochondrial homeostasis is maintained by the dynamic processes of mitochondrial biogenesis, mitochondrial network dynamics (fusion/fission), and mitochondrial clearance by mitophagy. Friedreich's ataxia (FA) is a mitochondrial disease resulting in a fatal hypertrophic cardiomyopathy due to the deficiency of the mitochondrial protein, frataxin. Our previous studies identified defective mitochondrial iron metabolism and oxidative stress potentiating cardiac pathology in FA. However, how these factors alter mitochondrial homeostasis remains uncharacterized in FA cardiomyopathy. This investigation examined the muscle creatine kinase conditional frataxin knockout mouse, which closely mimics FA cardiomyopathy, to dissect the mechanisms of dysfunctional mitochondrial homeostasis. Dysfunction of key mitochondrial homeostatic mechanisms were elucidated in the knockout hearts relative to wild-type littermates, namely: (1) mitochondrial proliferation with condensed cristae; (2) impaired NAD+ metabolism due to perturbations in Sirt1 activity and NAD+ salvage; (3) increased mitochondrial biogenesis, fusion and fission; and (4) mitochondrial accumulation of Pink1/Parkin with increased autophagic/mitophagic flux. Immunohistochemistry of FA patients' heart confirmed significantly enhanced expression of markers of mitochondrial biogenesis, fusion/fission and autophagy. These novel findings demonstrate cardiac frataxin-deficiency results in significant changes to metabolic mechanisms critical for mitochondrial homeostasis. This mechanistic dissection provides critical insight, offering the potential for maintaining mitochondrial homeostasis in FA and potentially other cardio-degenerative diseases by implementing innovative treatments targeting mitochondrial homeostasis and NAD+ metabolism.
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Affiliation(s)
- Shannon Chiang
- Molecular Pharmacology and Pathology Program, Department of Pathology, University of Sydney, NSW, 2006, Australia
| | - Nady Braidy
- Centre for Healthy Brain Ageing, University of New South Wales, NSW, 2052, Australia
| | - Sanaz Maleki
- Department of Pathology, University of Sydney, NSW, 2006, Australia
| | - Sean Lal
- School of Medical Sciences, University of Sydney, NSW, 2006, Australia; Division of Cardiology, Royal Prince Alfred Hospital, Sydney, NSW, 2050, Australia
| | - Des R Richardson
- Molecular Pharmacology and Pathology Program, Department of Pathology, University of Sydney, NSW, 2006, Australia; Department of Pathology and Biological Responses, Nagoya University Graduate School of Medicine, Nagoya 466-8550, Japan; Centre for Cancer Cell Biology and Drug Discovery, Griffith Institute for Drug Discovery, Griffith University, Nathan, Brisbane, Queensland, Australia.
| | - Michael L-H Huang
- Molecular Pharmacology and Pathology Program, Department of Pathology, University of Sydney, NSW, 2006, Australia; School of Medical Sciences, University of Sydney, NSW, 2006, Australia.
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9
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Maletzko A, Key J, Wittig I, Gispert S, Koepf G, Canet-Pons J, Torres-Odio S, West AP, Auburger G. Increased presence of nuclear DNAJA3 and upregulation of cytosolic STAT1 and of nucleic acid sensors trigger innate immunity in the ClpP-null mouse. Neurogenetics 2021; 22:297-312. [PMID: 34345994 PMCID: PMC8426249 DOI: 10.1007/s10048-021-00657-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Accepted: 07/08/2021] [Indexed: 11/29/2022]
Abstract
Mitochondrial dysfunction may activate innate immunity, e.g. upon abnormal handling of mitochondrial DNA in TFAM mutants or in altered mitophagy. Recent reports showed that also deletion of mitochondrial matrix peptidase ClpP in mice triggers transcriptional upregulation of inflammatory factors. Here, we studied ClpP-null mouse brain at two ages and mouse embryonal fibroblasts, to identify which signaling pathways are responsible, employing mass spectrometry, subcellular fractionation, immunoblots, and reverse transcriptase polymerase chain reaction. Several mitochondrial unfolded protein response factors showed accumulation and altered migration in blue-native gels, prominently the co-chaperone DNAJA3. Its mitochondrial dysregulation increased also its extra-mitochondrial abundance in the nucleus, a relevant observation given that DNAJA3 modulates innate immunity. Similar observations were made for STAT1, a putative DNAJA3 interactor. Elevated expression was observed not only for the transcription factors Stat1/2, but also for two interferon-stimulated genes (Ifi44, Gbp3). Inflammatory responses were strongest for the RLR pattern recognition receptors (Ddx58, Ifih1, Oasl2, Trim25) and several cytosolic nucleic acid sensors (Ifit1, Ifit3, Oas1b, Ifi204, Mnda). The consistent dysregulation of these factors from an early age might influence also human Perrault syndrome, where ClpP loss-of-function leads to early infertility and deafness, with subsequent widespread neurodegeneration.
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Affiliation(s)
- Antonia Maletzko
- Experimental Neurology, Medical School, Goethe University, 60590, Frankfurt, Germany
| | - Jana Key
- Experimental Neurology, Medical School, Goethe University, 60590, Frankfurt, Germany.,Faculty of Biosciences, Goethe University, Altenhöferallee 1, 60438, Frankfurt, Germany
| | - Ilka Wittig
- Functional Proteomics, Faculty of Medicine, Goethe University, 60590, Frankfurt, Germany
| | - Suzana Gispert
- Experimental Neurology, Medical School, Goethe University, 60590, Frankfurt, Germany
| | - Gabriele Koepf
- Experimental Neurology, Medical School, Goethe University, 60590, Frankfurt, Germany
| | - Júlia Canet-Pons
- Experimental Neurology, Medical School, Goethe University, 60590, Frankfurt, Germany
| | - Sylvia Torres-Odio
- Experimental Neurology, Medical School, Goethe University, 60590, Frankfurt, Germany.,Department of Microbial Pathogenesis and Immunology, College of Medicine, Texas A&M, University Health Science Center, Bryan, TX, 77807, USA
| | - A Phillip West
- Department of Microbial Pathogenesis and Immunology, College of Medicine, Texas A&M, University Health Science Center, Bryan, TX, 77807, USA
| | - Georg Auburger
- Experimental Neurology, Medical School, Goethe University, 60590, Frankfurt, Germany.
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10
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Basu U, Bostwick AM, Das K, Dittenhafer-Reed KE, Patel SS. Structure, mechanism, and regulation of mitochondrial DNA transcription initiation. J Biol Chem 2020; 295:18406-18425. [PMID: 33127643 PMCID: PMC7939475 DOI: 10.1074/jbc.rev120.011202] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2020] [Revised: 10/29/2020] [Indexed: 12/14/2022] Open
Abstract
Mitochondria are specialized compartments that produce requisite ATP to fuel cellular functions and serve as centers of metabolite processing, cellular signaling, and apoptosis. To accomplish these roles, mitochondria rely on the genetic information in their small genome (mitochondrial DNA) and the nucleus. A growing appreciation for mitochondria's role in a myriad of human diseases, including inherited genetic disorders, degenerative diseases, inflammation, and cancer, has fueled the study of biochemical mechanisms that control mitochondrial function. The mitochondrial transcriptional machinery is different from nuclear machinery. The in vitro re-constituted transcriptional complexes of Saccharomyces cerevisiae (yeast) and humans, aided with high-resolution structures and biochemical characterizations, have provided a deeper understanding of the mechanism and regulation of mitochondrial DNA transcription. In this review, we will discuss recent advances in the structure and mechanism of mitochondrial transcription initiation. We will follow up with recent discoveries and formative findings regarding the regulatory events that control mitochondrial DNA transcription, focusing on those involved in cross-talk between the mitochondria and nucleus.
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Affiliation(s)
- Urmimala Basu
- Department of Biochemistry and Molecular Biology, Rutgers Robert Wood Johnson Medical School, Piscataway, New Jersey, USA; Graduate School of Biomedical Sciences, Rutgers Robert Wood Johnson Medical School, Piscataway, New Jersey, USA
| | | | - Kalyan Das
- Department of Microbiology, Immunology, and Transplantation, Rega Institute for Medical Research, KU Leuven, Leuven, Belgium
| | | | - Smita S Patel
- Department of Biochemistry and Molecular Biology, Rutgers Robert Wood Johnson Medical School, Piscataway, New Jersey, USA.
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11
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Zhao Y, Wu D, Jiang D, Zhang X, Wu T, Cui J, Qian M, Zhao J, Oesterreich S, Sun W, Finkel T, Li G. A sequential methodology for the rapid identification and characterization of breast cancer-associated functional SNPs. Nat Commun 2020; 11:3340. [PMID: 32620845 PMCID: PMC7334201 DOI: 10.1038/s41467-020-17159-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Accepted: 06/11/2020] [Indexed: 12/24/2022] Open
Abstract
GWAS cannot identify functional SNPs (fSNP) from disease-associated SNPs in linkage disequilibrium (LD). Here, we report developing three sequential methodologies including Reel-seq (Regulatory element-sequencing) to identify fSNPs in a high-throughput fashion, SDCP-MS (SNP-specific DNA competition pulldown-mass spectrometry) to identify fSNP-bound proteins and AIDP-Wb (allele-imbalanced DNA pulldown-Western blot) to detect allele-specific protein:fSNP binding. We first apply Reel-seq to screen a library containing 4316 breast cancer-associated SNPs and identify 521 candidate fSNPs. As proof of principle, we verify candidate fSNPs on three well-characterized loci: FGFR2, MAP3K1 and BABAM1. Next, using SDCP-MS and AIDP-Wb, we rapidly identify multiple regulatory factors that specifically bind in an allele-imbalanced manner to the fSNPs on the FGFR2 locus. We finally demonstrate that the factors identified by SDCP-MS can regulate risk gene expression. These data suggest that the sequential application of Reel-seq, SDCP-MS, and AIDP-Wb can greatly help to translate large sets of GWAS data into biologically relevant information.
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Affiliation(s)
- Yihan Zhao
- Aging Institute, University of Pittsburgh, Pittsburgh, PA, 15219, USA
- School of Life Sciences, East China Normal University, Shanghai, China
| | - Di Wu
- Adams School of Dentistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Danli Jiang
- Aging Institute, University of Pittsburgh, Pittsburgh, PA, 15219, USA
| | - Xiaoyu Zhang
- Aging Institute, University of Pittsburgh, Pittsburgh, PA, 15219, USA
| | - Ting Wu
- Aging Institute, University of Pittsburgh, Pittsburgh, PA, 15219, USA
- Department of Medicine, Xiangya School of Medicine, Central South University, Changsha, China
| | - Jing Cui
- Department of Medicine, Brigham and Women's Hospital, Boston, MA, 02115, USA
| | - Min Qian
- School of Life Sciences, East China Normal University, Shanghai, China
| | - Jean Zhao
- Department of Chemical Biology, DFCI, Boston, MA, 02115, USA
| | - Steffi Oesterreich
- Department of Pharmacology & Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15261, USA
- Women's Cancer Research Center, Magee-Women's Research Institute, University of Pittsburgh Cancer Institute, 204 Craft Avenue, Pittsburgh, PA, 15213, USA
| | - Wei Sun
- Department of Medicine, Division of Cardiology, University of Pittsburgh Medical Center, Pittsburgh, PA, 15219, USA
| | - Toren Finkel
- Aging Institute, University of Pittsburgh, Pittsburgh, PA, 15219, USA
- Department of Medicine, Division of Cardiology, University of Pittsburgh Medical Center, Pittsburgh, PA, 15219, USA
| | - Gang Li
- Aging Institute, University of Pittsburgh, Pittsburgh, PA, 15219, USA.
- Department of Medicine, Division of Cardiology, University of Pittsburgh Medical Center, Pittsburgh, PA, 15219, USA.
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12
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Fan Y, Yang Q, Yang Y, Gao Z, Ma Y, Zhang L, Liang W, Ding G. Sirt6 Suppresses High Glucose-Induced Mitochondrial Dysfunction and Apoptosis in Podocytes through AMPK Activation. Int J Biol Sci 2019; 15:701-713. [PMID: 30745856 PMCID: PMC6367578 DOI: 10.7150/ijbs.29323] [Citation(s) in RCA: 104] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2018] [Accepted: 12/21/2018] [Indexed: 12/11/2022] Open
Abstract
Previous studies have shown that mitochondrial dysfunction plays an important role in high- glucose(HG)-induced podocyte injury and thus contributes to the progression of diabetic nephropathy(DN). The histone deacetylase Sirtuin6 (Sirt6) has been revealed to have an essential role in the regulation of mitochondrial function in skeletal muscle and cardiomyocytes. However, its specific role in mitochondrial homeostasis in podocytes is undetermined. Here, we aimeds to explore the physiological function of Sirt6 in podocyte mitochondria and apoptosis under HG conditions and explore the possible mechanism. Herein, we observed that Sirt6-WT-1 colocalization was suppressed in the glomeruli of patients with DN. In addition, diabetic mice exhibited reduced Sirt6 expression and AMP kinase (AMPK) dephosphorylation accompanied by mitochondrial morphological abnormalities. In vitro, podocytes exposed to HG presented with mitochondrial morphological alterations and podocyte apoptosis accompanied by Sirt6 and p-AMPK downregulation. In addition, HG promoted a decrease in mitochondrial number and an increase in mitochondrial superoxide production as well as a decreased mitochondrial membrane potential. ROS production was also increased in HG-treated podocytes. Conversely, all these mitochondrial defects induced by HG were significantly alleviated by Sirt6 plasmid transfection. Sirt6 overexpression simultaneously alleviated HG-induced podocyte apoptosis and oxidative stress, as well as increased AMPK phosphorylation. Increased levels of H3K9ac and H3K56ac induced by HG were attenuated in podocytes transfected with Sirt6 plasmids. Therefore, these results elucidated that Sirt6 protects mitochondria of podocytes and exerts anti-apoptotic effects via activating AMPK pathway. The present findings provide key insights into the pivotal role of mitochondria regulation by SIRT6 in its protective effects on podocytes.
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Affiliation(s)
- Yanqin Fan
- Division of Nephrology, Renmin Hospital of Wuhan University, Wuhan, Hubei, China
| | - Qian Yang
- Division of Nephrology, Renmin Hospital of Wuhan University, Wuhan, Hubei, China
| | - Yingjie Yang
- Division of Nephrology, Renmin Hospital of Wuhan University, Wuhan, Hubei, China
| | - Zhao Gao
- Division of Nephrology, Renmin Hospital of Wuhan University, Wuhan, Hubei, China
| | - Yiqiong Ma
- Division of Nephrology, Renmin Hospital of Wuhan University, Wuhan, Hubei, China
| | - Lu Zhang
- Division of Nephrology, Renmin Hospital of Wuhan University, Wuhan, Hubei, China
| | - Wei Liang
- Division of Nephrology, Renmin Hospital of Wuhan University, Wuhan, Hubei, China
| | - Guohua Ding
- Division of Nephrology, Renmin Hospital of Wuhan University, Wuhan, Hubei, China
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13
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Lee WR, Na H, Lee SW, Lim WJ, Kim N, Lee JE, Kang C. Transcriptomic analysis of mitochondrial TFAM depletion changing cell morphology and proliferation. Sci Rep 2017; 7:17841. [PMID: 29259235 PMCID: PMC5736646 DOI: 10.1038/s41598-017-18064-9] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Accepted: 12/05/2017] [Indexed: 12/27/2022] Open
Abstract
Human mitochondrial transcription factor A (TFAM) has been implicated in promoting tumor growth and invasion. TFAM activates mitochondrial DNA (mtDNA) transcription, and affects nuclear gene expression through mitochondrial retrograde signaling. In this study, we investigated the effects of TFAM depletion on the morphology and transcriptome of MKN45 gastric cancer cells. Morphology alteration became visible at 12 h after TFAM knockdown: the proportion of growth-arrested polygonal cells versus oval-shaped cells increased, reaching a half-maximum at 24 h and a near-maximum at 36 h. TFAM knockdown upregulated four genes and downregulated six genes by more than threefold at 24 h and similarly at 48 h. Among them, the knockdown of CFAP65 (cilia and flagella associated protein 65) or PCK1 (cytoplasmic phosphoenolpyruvate carboxykinase) rescued the effects of TFAM depletion on cell morphology and proliferation. PCK1 was found to act downstream of CFAP65 in calcium-mediated retrograde signaling. Furthermore, mtDNA depletion by 2',3'-dideoxycytidine was sufficient for induction of CFAP65 and PCK1 expression and inhibition of cell proliferation, but oxidative phosphorylation blockade or mitochondrial membrane potential depolarization was not. Thus, the TFAM-mtDNA-calcium-CFAP65-PCK1 axis participates in mitochondrial retrograde signaling, affecting tumor cell differentiation and proliferation.
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Affiliation(s)
- Woo Rin Lee
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, 34141, Korea
- Center for Bioanalysis, Korea Research Institute of Standards and Science, Daejeon, 34113, Korea
| | - Heeju Na
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, 34141, Korea
| | - Seon Woo Lee
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, 34141, Korea
| | - Won-Jun Lim
- Genome Editing Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, 34141, Korea
- Department of Bioinformatics, KRIBB School of Bioscience, Korea University of Science and Technology, Daejeon, 34141, Korea
| | - Namshin Kim
- Genome Editing Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, 34141, Korea
- Department of Bioinformatics, KRIBB School of Bioscience, Korea University of Science and Technology, Daejeon, 34141, Korea
| | - J Eugene Lee
- Center for Bioanalysis, Korea Research Institute of Standards and Science, Daejeon, 34113, Korea.
| | - Changwon Kang
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, 34141, Korea.
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14
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Zhang HH, Liu J, Qin GJ, Li XL, Du PJ, Hao X, Zhao D, Tian T, Wu J, Yun M, Bai YH. Melanocortin 4 Receptor Activation Attenuates Mitochondrial Dysfunction in Skeletal Muscle of Diabetic Rats. J Cell Biochem 2017; 118:4072-4079. [PMID: 28409883 DOI: 10.1002/jcb.26062] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2017] [Accepted: 04/13/2017] [Indexed: 12/25/2022]
Abstract
A previous study has confirmed that the central melanocortin system was able to mediate skeletal muscle AMP-activated protein kinase (AMPK) activation in mice fed a high-fat diet, while activation of the AMPK signaling pathway significantly induced mitochondrial biogenesis. Our hypothesis was that melanocortin 4 receptor (MC4R) was involved in the development of skeletal muscle injury in diabetic rats. In this study, we treated diabetic rats intracerebroventricularly with MC4R agonist R027-3225 or antagonist SHU9119, respectively. Then, we measured the production of reactive oxygen species (ROS), the levels of malondialdehyde (MDA) and glutathione (GSH), the mitochondrial DNA (mtDNA) content and mitochondrial biogenesis, and the protein levels of p-AMPK, AMPK, peroxisome proliferator-activated receptor-gamma coactivator 1α (PGC-1α), sirtuin 1 (SIRT1), and manganese superoxide dismutase (MnSOD) in the skeletal muscle of diabetic rats. The results showed that there was significant skeletal muscle injury in the diabetic rats along with serious oxidative stress and decreased mitochondrial biogenesis. Treatment with R027-3225 reduced oxidative stress and induced mitochondrial biogenesis in skeletal muscle, and also activated the AMPK-SIRT1-PGC-1α signaling pathway. However, diabetic rats injected with MC4R antagonist SHU9119 showed an aggravated oxidative stress and mitochondrial dysfunction in skeletal muscle. In conclusion, our results revealed that MC4R activation was able to attenuate oxidative stress and mitochondrial dysfunction in skeletal muscle induced by diabetes partially through activating the AMPK-SIRT1-PGC-1α signaling pathway. J. Cell. Biochem. 118: 4072-4079, 2017. © 2017 Wiley Periodicals, Inc.
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Affiliation(s)
- Hao-Hao Zhang
- Division of Endocrinology, Department of Internal Medicine, First Affiliated Hospital of Zhengzhou University, 40 Daxue Road, Zhengzhou 450052, China
| | - Jiao Liu
- Division of Endocrinology, Department of Internal Medicine, First Affiliated Hospital of Zhengzhou University, 40 Daxue Road, Zhengzhou 450052, China
| | - Gui-Jun Qin
- Division of Endocrinology, Department of Internal Medicine, First Affiliated Hospital of Zhengzhou University, 40 Daxue Road, Zhengzhou 450052, China
| | - Xia-Lian Li
- Division of Endocrinology, Department of Internal Medicine, First Affiliated Hospital of Zhengzhou University, 40 Daxue Road, Zhengzhou 450052, China
| | - Pei-Jie Du
- Division of Endocrinology, Department of Internal Medicine, First Affiliated Hospital of Zhengzhou University, 40 Daxue Road, Zhengzhou 450052, China
| | - Xiao Hao
- Division of Endocrinology, Department of Internal Medicine, First Affiliated Hospital of Zhengzhou University, 40 Daxue Road, Zhengzhou 450052, China
| | - Di Zhao
- Division of Endocrinology, Department of Internal Medicine, First Affiliated Hospital of Zhengzhou University, 40 Daxue Road, Zhengzhou 450052, China
| | - Tian Tian
- Department of Neurology, First Affiliated Hospital of Zhengzhou University, 40 Daxue Road, Zhengzhou 450052, China
| | - Jing Wu
- Department of Pediatrics, First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China
| | - Meng Yun
- Department of MRI, First Affiliated Hospital of Zhengzhou University, 40 Daxue Road, Zhengzhou 450052, China
| | - Yan-Hui Bai
- Department of Ophthalmology, First Affiliated Hospital of Zhengzhou University, 40 Daxue Road, Zhengzhou 450052, China
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15
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Regulatory cis- and trans-elements of mitochondrial D-loop-driven reporter genes in budding tunicates. Mitochondrion 2017; 35:59-69. [PMID: 28526334 DOI: 10.1016/j.mito.2017.05.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2016] [Revised: 01/13/2017] [Accepted: 05/12/2017] [Indexed: 11/22/2022]
Abstract
To unveil the underlying mechanism of mitochondrial gene regulation associated with ageing and budding in the tunicate Polyandrocarpa misakiensis, mitochondrial non-coding-region (NCR)-containing reporter genes were constructed. PmNCR2.3K/GFP was expressed spatiotemporally in a pattern quite similar to mitochondrial 16SrRNA. The reporter gene expression was sensitive to high dose of rifampicin similar to mitochondrial genes, suggesting that the transcription indeed occurs in mitochondria. However, the gene expression also occurred in vivo in the cell nucleus and in vitro in the nuclear extracts. Mitochondrial transcription factor A (PmTFAM) enhanced reporter gene expression, depending on the NCR length. A budding-specific polypeptide TC14-3 is an epigenetic histone methylation inducer. It heavily enhanced reporter gene expression that was interfered by histone methylation inhibitors and PmTFAM RNAi. Our results indicate for the first time that the nuclear histone methylation is involved in mitochondrial gene activity via TFAM gene regulation.
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16
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Cai X, Bao L, Ren J, Li Y, Zhang Z. Grape seed procyanidin B2 protects podocytes from high glucose-induced mitochondrial dysfunction and apoptosis via the AMPK-SIRT1-PGC-1α axis in vitro. Food Funct 2016; 7:805-15. [PMID: 26650960 DOI: 10.1039/c5fo01062d] [Citation(s) in RCA: 70] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Grape seed procyanidin B2 (GSPB2) was reported to have protective effects on diabetic nephropathy (DN) as a strong antioxidant. Our previous studies demonstrated that GSPB2 was effective in ameliorating podocyte injury in rats with DN. However, little is known about the benefits of GSPB2 in protecting against podocyte apoptosis and its molecular mechanisms in vitro. In the present study, we investigated whether GSPB2 could protect podocytes from high glucose-induced apoptosis and explored the possible mechanism. Cell viability and apoptosis were detected by 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) and flow cytometry, respectively. The intracellular reactive oxygen species (ROS) level was measured using a dichlorofluorescein diacetate (DCFH-DA) fluorescent probe. Real-time reverse transcription-PCR was used to determine the gene expression of nuclear respiratory factor 1 (NRF-1) and mitochondrial transcription factor A (TFAM), and quantitative real-time PCR was used to detect mitochondrial DNA (mtDNA) copy number. Western blots were carried out for the related protein expression in podocytes. Our results showed that GSPB2 significantly inhibited high glucose-induced podocyte apoptosis and increased the expression of nephrin and podocalyxin. GSPB2 treatment also suppressed intracellular ROS production and oxidative stress. The mRNA expressions of NRF-1, TFAM and mtDNA copy number were markedly increased, and mitochondrial swelling was effectively reduced in podocytes cultured under high glucose after GSPB2 treatment. The AMPK-SIRT1-PGC-1α axis was also activated by GSPB2 intervention. In conclusion, GSPB2 protected podocytes from high glucose-induced mitochondrial dysfunction and apoptosis via the AMPK-SIRT1-PGC-1α axis in vitro, suggesting a potential role of GSPB2 in the treatment of DN.
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Affiliation(s)
- Xiaxia Cai
- Department of Nutrition and Food Hygiene, School of Public Health, Peking University, Beijing, P. R. China.
| | - Lei Bao
- Department of Clinical Nutrition, Peking University International Hospital, Beijing, P. R. China
| | - Jinwei Ren
- Department of Nutrition and Food Hygiene, School of Public Health, Peking University, Beijing, P. R. China.
| | - Yong Li
- Department of Nutrition and Food Hygiene, School of Public Health, Peking University, Beijing, P. R. China.
| | - Zhaofeng Zhang
- Department of Nutrition and Food Hygiene, School of Public Health, Peking University, Beijing, P. R. China.
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Lionaki E, Gkikas I, Tavernarakis N. Differential Protein Distribution between the Nucleus and Mitochondria: Implications in Aging. Front Genet 2016; 7:162. [PMID: 27695477 PMCID: PMC5025450 DOI: 10.3389/fgene.2016.00162] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2016] [Accepted: 09/01/2016] [Indexed: 01/05/2023] Open
Abstract
The coordination of nuclear and mitochondrial genomes plays a pivotal role in maintenance of mitochondrial biogenesis and functionality during stress and aging. Environmental and cellular inputs signal to nucleus and/or mitochondria to trigger interorganellar compensatory responses. Loss of this tightly orchestrated coordination results in loss of cellular homeostasis and underlies various pathologies and age-related diseases. Several signaling cascades that govern interorganellar communication have been revealed up to now, and have been classified as part of the anterograde (nucleus to mitochondria) or retrograde (mitochondrial to nucleus) response. Many of these molecular pathways rely on the dual distribution of nuclear or mitochondrial components under basal or stress conditions. These dually localized components usually engage in specific tasks in their primary organelle of function, whilst upon cellular stimuli, they appear in the other organelle where they engage in the same or a different task, triggering a compensatory stress response. In this review, we focus on protein factors distributed between the nucleus and mitochondria and activated to exert their functions upon basal or stress conditions. We further discuss implications of bi-organellar targeting in the context of aging.
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Affiliation(s)
- Eirini Lionaki
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas Heraklion, Greece
| | - Ilias Gkikas
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas Heraklion, Greece
| | - Nektarios Tavernarakis
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-HellasHeraklion, Greece; Department of Basic Sciences, Faculty of Medicine, University of CreteHeraklion, Greece
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