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Xiao F, Zeng J, Wang H, Zhu H, Guo Y, Zhang Z, Xiao Y, Hu G, Huang K, Yang Q, Guo H. MGME1 associates with poor prognosis and is vital for cell proliferation in lower-grade glioma. Aging (Albany NY) 2023; 15:3690-3714. [PMID: 37166417 PMCID: PMC10449294 DOI: 10.18632/aging.204705] [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: 02/06/2023] [Accepted: 04/18/2023] [Indexed: 05/12/2023]
Abstract
OBJECTIVE Mitochondrial genome maintenance exonuclease 1 (MGME1) is associated with DNA depletion, deletion, duplication, and rearrangement. However, the function of MGME1 in tumors, especially lower-grade gliomas (LGGs), has not been established. METHODS Pan-cancer analysis was used to define the expression patterns and prognostic value of MGME1 in various cancers. Subsequently, we systematically determined the associations between MGME1 expression and clinicopathological characteristics, prognosis, biological functions, immune characteristics, genomic mutations, and therapeutic responses of LGGs based on their expression patterns. The expression level and specific functions of MGME1 in LGGs was detected by conducting in vitro experiments. RESULTS Abnormally enhanced and high MGME1 expressions were associated with poor prognoses of various tumors, including LGG. Multivariate and univariate Cox regression analyses manifested that MGME1 expression was an independent prognostic biomarker for LGG. The immune-related signatures, infiltration of immune cells, immune checkpoint genes (ICPGs), copy number alteration (CNA), tumor mutation burden (TMB), and treatment responses of LGG patients were associated with the expression of MGME1. The in vitro experiments affirmed that MGME1 was elevated and tightly connected with the cell proliferation and cell cycle in LGG. CONCLUSIONS MGME1 is an independent prognostic biomarker and closely related to the cell proliferation in LGG.
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Affiliation(s)
- Feng Xiao
- Departments of Neurosurgery, The Second Affiliated Hospital of Nanchang University, Nanchang 330006, Jiangxi, China
- Jiangxi Key Laboratory of Neurological Tumors and Cerebrovascular Diseases, Nanchang 330006, Jiangxi, China
- Jiangxi Health Commission Key Laboratory of Neurological Medicine, Nanchang 330006, Jiangxi, China
- Institute of Neuroscience, Nanchang University, Nanchang 330006, Jiangxi, China
| | - Jie Zeng
- Departments of Neurosurgery, The Second Affiliated Hospital of Nanchang University, Nanchang 330006, Jiangxi, China
- Jiangxi Key Laboratory of Neurological Tumors and Cerebrovascular Diseases, Nanchang 330006, Jiangxi, China
- Jiangxi Health Commission Key Laboratory of Neurological Medicine, Nanchang 330006, Jiangxi, China
- Institute of Neuroscience, Nanchang University, Nanchang 330006, Jiangxi, China
| | - Haiyan Wang
- Department of Operation, The Second Affiliated Hospital of Nanchang University, Nanchang 330006, Jiangxi, China
| | - Hong Zhu
- Departments of Neurosurgery, The Second Affiliated Hospital of Nanchang University, Nanchang 330006, Jiangxi, China
- Jiangxi Key Laboratory of Neurological Tumors and Cerebrovascular Diseases, Nanchang 330006, Jiangxi, China
- Jiangxi Health Commission Key Laboratory of Neurological Medicine, Nanchang 330006, Jiangxi, China
- Institute of Neuroscience, Nanchang University, Nanchang 330006, Jiangxi, China
| | - Yun Guo
- Departments of Neurosurgery, The Second Affiliated Hospital of Nanchang University, Nanchang 330006, Jiangxi, China
- Jiangxi Key Laboratory of Neurological Tumors and Cerebrovascular Diseases, Nanchang 330006, Jiangxi, China
- Jiangxi Health Commission Key Laboratory of Neurological Medicine, Nanchang 330006, Jiangxi, China
- Institute of Neuroscience, Nanchang University, Nanchang 330006, Jiangxi, China
| | - Zhe Zhang
- Departments of Neurosurgery, The Second Affiliated Hospital of Nanchang University, Nanchang 330006, Jiangxi, China
- Jiangxi Key Laboratory of Neurological Tumors and Cerebrovascular Diseases, Nanchang 330006, Jiangxi, China
- Jiangxi Health Commission Key Laboratory of Neurological Medicine, Nanchang 330006, Jiangxi, China
- Institute of Neuroscience, Nanchang University, Nanchang 330006, Jiangxi, China
| | - Yao Xiao
- Departments of Neurosurgery, The Second Affiliated Hospital of Nanchang University, Nanchang 330006, Jiangxi, China
- Jiangxi Key Laboratory of Neurological Tumors and Cerebrovascular Diseases, Nanchang 330006, Jiangxi, China
- Jiangxi Health Commission Key Laboratory of Neurological Medicine, Nanchang 330006, Jiangxi, China
- Institute of Neuroscience, Nanchang University, Nanchang 330006, Jiangxi, China
| | - Guowen Hu
- Departments of Neurosurgery, The Second Affiliated Hospital of Nanchang University, Nanchang 330006, Jiangxi, China
| | - Kai Huang
- Departments of Neurosurgery, The Second Affiliated Hospital of Nanchang University, Nanchang 330006, Jiangxi, China
- Jiangxi Key Laboratory of Neurological Tumors and Cerebrovascular Diseases, Nanchang 330006, Jiangxi, China
- Jiangxi Health Commission Key Laboratory of Neurological Medicine, Nanchang 330006, Jiangxi, China
- Institute of Neuroscience, Nanchang University, Nanchang 330006, Jiangxi, China
| | - Qing Yang
- Department of Respiratory Medicine, The Second Affiliated Hospital of Nanchang University, Nanchang 330030, Jiangxi, China
| | - Hua Guo
- Departments of Neurosurgery, The Second Affiliated Hospital of Nanchang University, Nanchang 330006, Jiangxi, China
- Jiangxi Key Laboratory of Neurological Tumors and Cerebrovascular Diseases, Nanchang 330006, Jiangxi, China
- Jiangxi Health Commission Key Laboratory of Neurological Medicine, Nanchang 330006, Jiangxi, China
- Institute of Neuroscience, Nanchang University, Nanchang 330006, Jiangxi, China
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Urrutia KM, Xu W, Zhao L. The 5′-phosphate enhances the DNA-binding and exonuclease activities of human mitochondrial genome maintenance nuclease 1 (MGME1). J Biol Chem 2022; 298:102306. [PMID: 35934053 PMCID: PMC9460513 DOI: 10.1016/j.jbc.2022.102306] [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: 04/13/2022] [Revised: 07/13/2022] [Accepted: 07/15/2022] [Indexed: 11/15/2022] Open
Abstract
In higher eukaryotes, mitochondria play multiple roles in energy production, signaling, and biosynthesis. Mitochondria possess multiple copies of mitochondrial DNA (mtDNA), which encodes 37 genes that are essential for mitochondrial and cellular function. When mtDNA is challenged by endogenous and exogenous factors, mtDNA undergoes repair, degradation, and compensatory synthesis. mtDNA degradation is an emerging pathway in mtDNA damage response and maintenance. A key factor involved is the human mitochondrial genome maintenance exonuclease 1 (MGME1). Despite previous biochemical and functional studies, controversies exist regarding the polarity of MGME1-mediated DNA cleavage. Also, how DNA sequence may affect the activities of MGME1 remains elusive. Such information is not only fundamental to the understanding of MGME1 but critical for deciphering the mechanism of mtDNA degradation. Herein, we use quantitative assays to examine the effects of substrate structure and sequence on the DNA-binding and enzymatic activities of MGME1. We demonstrate that MGME1 binds to and cleaves from the 5′-end of single-stranded DNA substrates, especially in the presence of 5′-phosphate, which plays an important role in DNA binding and optimal cleavage by MGME1. In addition, MGME1 tolerates certain modifications at the terminal end, such as a 5′-deoxyribosephosphate intermediate formed in base excision repair. We show that MGME1 processes different sequences with varying efficiencies, with dT and dC sequences being the most and least efficiently digested, respectively. Our results provide insights into the enzymatic properties of MGME1 and a rationale for the coordination of MGME1 with the 3′–5′ exonuclease activity of DNA polymerase γ in mtDNA degradation.
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Affiliation(s)
- Kathleen M Urrutia
- Department of Chemistry, University of California, Riverside, Riverside, California, USA
| | - Wenyan Xu
- Department of Chemistry, University of California, Riverside, Riverside, California, USA
| | - Linlin Zhao
- Department of Chemistry, University of California, Riverside, Riverside, California, USA; Environmental Toxicology Graduate Program, University of California, Riverside, Riverside, California, USA.
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3
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Guedouari H, Ould Amer Y, Pichaud N, Hebert-Chatelain E. Characterization of the interactome of c-Src within the mitochondrial matrix by proximity-dependent biotin identification. Mitochondrion 2021; 57:257-269. [PMID: 33412331 DOI: 10.1016/j.mito.2020.12.012] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Revised: 12/09/2020] [Accepted: 12/30/2020] [Indexed: 12/27/2022]
Abstract
C-Src kinase is localized in several subcellular compartments, including mitochondria where it is involved in the regulation of organelle functions and overall metabolism. Surprisingly, the characterization of the intramitochondrial Src interactome has never been fully determined. Using in vitro proximity-dependent biotin identification (BioID) coupled to mass spectrometry, we identified 51 candidate proteins that may interact directly or indirectly with c-Src within the mitochondrial matrix. Pathway analysis suggests that these proteins are involved in a large array of mitochondrial functions such as protein folding and import, mitochondrial organization and transport, oxidative phosphorylation, tricarboxylic acid cycle and metabolism of amino and fatty acids. Among these proteins, we identified 24 tyrosine phosphorylation sites in 17 mitochondrial proteins (AKAP1, VDAC1, VDAC2, VDAC3, LonP1, Hsp90, SLP2, PHB2, MIC60, UBA1, EF-Tu, LRPPRC, ACO2, OAT, ACAT1, ETFβ and ATP5β) as potential substrates for intramitochondrial Src using in silico prediction of tyrosine phospho-sites. Interaction of c-Src with SLP2 and ATP5β was confirmed using coimmunoprecipitation. This study suggests that the intramitochondrial Src could target several proteins and regulate different mitochondrial functions.
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Affiliation(s)
- Hala Guedouari
- Canada Research Chair in Mitochondrial Signaling and Physiopathology, Moncton, NB, Canada; University of Moncton, Dept. of Biology, Moncton, NB, Canada
| | - Yasmine Ould Amer
- Canada Research Chair in Mitochondrial Signaling and Physiopathology, Moncton, NB, Canada; University of Moncton, Dept. of Biology, Moncton, NB, Canada
| | - Nicolas Pichaud
- University of Moncton, Dept. of Chemistry and Biochemistry, Moncton, NB, Canada
| | - Etienne Hebert-Chatelain
- Canada Research Chair in Mitochondrial Signaling and Physiopathology, Moncton, NB, Canada; University of Moncton, Dept. of Biology, Moncton, NB, Canada.
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4
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Baudouin HCM, Pfeiffer L, Ochsenreiter T. A comparison of three approaches for the discovery of novel tripartite attachment complex proteins in Trypanosoma brucei. PLoS Negl Trop Dis 2020; 14:e0008568. [PMID: 32936798 PMCID: PMC7521757 DOI: 10.1371/journal.pntd.0008568] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Revised: 09/28/2020] [Accepted: 07/07/2020] [Indexed: 11/19/2022] Open
Abstract
Trypanosoma brucei is a single celled eukaryotic parasite and the causative agent of human African trypanosomiasis and nagana in cattle. Aside from its medical relevance, T. brucei has also been key to the discovery of several general biological principles including GPI-anchoring, RNA-editing and trans-splicing. The parasite contains a single mitochondrion with a singular genome. Recent studies have identified several molecular components of the mitochondrial genome segregation machinery (tripartite attachment complex, TAC), which connects the basal body of the flagellum to the mitochondrial DNA of T. brucei. The TAC component in closest proximity to the mitochondrial DNA is TAC102. Here we apply and compare three different approaches (proximity labelling, immunoprecipitation and yeast two-hybrid) to identify novel interactors of TAC102 and subsequently verify their localisation. Furthermore, we establish the direct interaction of TAC102 and p166 in the unilateral filaments of the TAC. Trypanosoma brucei belongs to a group of organisms that exist as human, animal and plant parasites. T. brucei (a human and animal parasite) has been developed as a model system to study basic biological as well as disease related questions in this group of organisms. We study how the parasite duplicates and divides its mitochondrial genome, an essential component of its energy generating machinery. The structure involved in dividing the mitochondrial genome into the daughter cells during cell division is called the tripartite attachment complex (TAC). The TAC is likely a unique structure not present in the host and thus might provide a new avenue for drug development. In this manuscript, we compare different techniques that allow the identification of novel components of this structure and verify the localisation of some of them. Furthermore, we also establish the interaction of two previously identified protein components.
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Affiliation(s)
- Hélène Clémentine Margareta Baudouin
- Institute of Cell Biology, University of Bern, Bern, Switzerland
- Graduate School for Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland
| | - Laura Pfeiffer
- Institute of Cell Biology, University of Bern, Bern, Switzerland
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5
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Linden A, Deckers M, Parfentev I, Pflanz R, Homberg B, Neumann P, Ficner R, Rehling P, Urlaub H. A Cross-linking Mass Spectrometry Approach Defines Protein Interactions in Yeast Mitochondria. Mol Cell Proteomics 2020; 19:1161-1178. [PMID: 32332106 PMCID: PMC7338081 DOI: 10.1074/mcp.ra120.002028] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Revised: 04/24/2020] [Indexed: 12/13/2022] Open
Abstract
Protein cross-linking and the analysis of cross-linked peptides by mass spectrometry is currently receiving much attention. Not only is this approach applied to isolated complexes to provide information about spatial arrangements of proteins, but it is also increasingly applied to entire cells and their organelles. As in quantitative proteomics, the application of isotopic labeling further makes it possible to monitor quantitative changes in the protein-protein interactions between different states of a system. Here, we cross-linked mitochondria from Saccharomyces cerevisiae grown on either glycerol- or glucose-containing medium to monitor protein-protein interactions under non-fermentative and fermentative conditions. We investigated qualitatively the protein-protein interactions of the 400 most abundant proteins applying stringent data-filtering criteria, i.e. a minimum of two cross-linked peptide spectrum matches and a cut-off in the spectrum scoring of the used search engine. The cross-linker BS3 proved to be equally suited for connecting proteins in all compartments of mitochondria when compared with its water-insoluble but membrane-permeable derivative DSS. We also applied quantitative cross-linking to mitochondria of both the growth conditions using stable-isotope labeled BS3. Significant differences of cross-linked proteins under glycerol and glucose conditions were detected, however, mainly because of the different copy numbers of these proteins in mitochondria under both the conditions. Results obtained from the glycerol condition indicate that the internal NADH:ubiquinone oxidoreductase Ndi1 is part of an electron transport chain supercomplex. We have also detected several hitherto uncharacterized proteins and identified their interaction partners. Among those, Min8 was found to be associated with cytochrome c oxidase. BN-PAGE analyses of min8Δ mitochondria suggest that Min8 promotes the incorporation of Cox12 into cytochrome c oxidase.
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Affiliation(s)
- Andreas Linden
- Bioanalytical Mass Spectrometry Group, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany; Institute of Clinical Chemistry, University Medical Center Göttingen, Göttingen, Germany
| | - Markus Deckers
- Department of Cellular Biochemistry, University Medical Center Göttingen, Göttingen, Germany
| | - Iwan Parfentev
- Bioanalytical Mass Spectrometry Group, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Ralf Pflanz
- Bioanalytical Mass Spectrometry Group, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Bettina Homberg
- Department of Cellular Biochemistry, University Medical Center Göttingen, Göttingen, Germany
| | - Piotr Neumann
- Department of Molecular Structural Biology, Institute for Microbiology and Genetics, Göttingen Center for Molecular Biosciences, Georg-August-University Göttingen, Göttingen, Germany
| | - Ralf Ficner
- Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells" (MBExC), University of Göttingen, Göttingen, Germany; Department of Molecular Structural Biology, Institute for Microbiology and Genetics, Göttingen Center for Molecular Biosciences, Georg-August-University Göttingen, Göttingen, Germany
| | - Peter Rehling
- Department of Cellular Biochemistry, University Medical Center Göttingen, Göttingen, Germany; Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells" (MBExC), University of Göttingen, Göttingen, Germany; Max Planck Institute for Biophysical Chemistry, Göttingen, Germany.
| | - Henning Urlaub
- Bioanalytical Mass Spectrometry Group, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany; Institute of Clinical Chemistry, University Medical Center Göttingen, Göttingen, Germany.
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6
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Yan T, Liu F, Gao J, Lu H, Cai J, Zhao X, Sun Y. Multilevel regulation of RUVBL2 expression predicts poor prognosis in hepatocellular carcinoma. Cancer Cell Int 2019; 19:249. [PMID: 31572066 PMCID: PMC6764127 DOI: 10.1186/s12935-019-0974-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Accepted: 09/23/2019] [Indexed: 12/24/2022] Open
Abstract
Background Hepatocellular carcinoma (HCC) is the second-most lethal cancer worldwide with a complex pathogenesis. RuvB-like 2 (RUVBL2) was previously found to contribute to hepatocarcinogenesis. However, its expression, regulation and clinical significance have not been systematically evaluated in a large number of clinical samples. Methods Here, we performed a comprehensive analysis of RUVBL2 based on multiple datasets from 371 liver cancer patients of The Cancer Genome Atlas (TCGA) and on immunohistochemical staining in 153 subjects. In addition, the aberrant signaling pathways caused by RUVBL2 overexpression were investigated. Results We demonstrated that promoter hypomethylation, copy number gain, MYC amplification and CTNNB1 mutation were all responsible for RUVBL2 overexpression in HCC. High levels of RUVBL2 mRNA were associated with shorter recurrence-free survival time (RFS) but not overall survival time (OS). Furthermore, RUVBL2 protein was overexpressed in the nucleus and cytoplasm of HCC samples. Univariate and multivariate survival analyses showed that strong nuclear and cytoplasmic staining of RUVBL2 independently predicted worse OS and RFS with a 2.03-fold and a 1.71-fold increase in the hazard ratio, respectively. High levels of RUVBL2 promoted carcinogenesis through the heat shock protein 90 (HSP90)-Cell Division Cycle 37 (CDC37), AKT serine/threonine kinase (AKT) and mitogen-activated protein kinase (ERK/MAPK) pathways. Conclusion The deregulation of RUVBL2 in HCC is influenced at the genomic, epigenetic and transcriptional levels. Our findings highlight the potential roles of RUVBL2 as a promising prognostic marker as well as a therapeutic target for HCC.
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Affiliation(s)
- Tao Yan
- 1Department of Anesthesiology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Science & Peking Union Medical College, Beijing, 100021 China
| | - Fang Liu
- 2State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, 17 Panjiayuan Nanli, Chaoyang District, Beijing, 100021 China
| | - Jiajia Gao
- 2State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, 17 Panjiayuan Nanli, Chaoyang District, Beijing, 100021 China
| | - Haizhen Lu
- 3Department of Pathology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Science & Peking Union Medical College, Beijing, 100021 China
| | - Jianqiang Cai
- 4Department of Hepatobiliary Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Science & Peking Union Medical College, Beijing, 100021 China
| | - Xiaohang Zhao
- 2State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, 17 Panjiayuan Nanli, Chaoyang District, Beijing, 100021 China
| | - Yulin Sun
- 2State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, 17 Panjiayuan Nanli, Chaoyang District, Beijing, 100021 China
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Helicase-like transcription factor (Hltf) gene-deletion promotes oxidative phosphorylation (OXPHOS) in colorectal tumors of AOM/DSS-treated mice. PLoS One 2019; 14:e0221751. [PMID: 31461471 PMCID: PMC6713344 DOI: 10.1371/journal.pone.0221751] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Accepted: 08/14/2019] [Indexed: 12/20/2022] Open
Abstract
The helicase-like transcription factor (HLTF) gene-a tumor suppressor in human colorectal cancer (CRC)-is regulated by alternative splicing and promoter hypermethylation. In this study, we used the AOM/DSS-induced mouse model to show Hltf-deletion caused poor survival concomitant with increased tumor multiplicity, and dramatically shifted the topographic distribution of lesions into the rectum. Differential isoform expression analysis revealed both the truncated isoform that lacks a DNA-repair domain and the full length isoform capable of DNA damage repair are present during adenocarcinoma formation in controls. iPathwayGuide identified 51 dynamically regulated genes of 10,967 total genes with measured expression. Oxidative Phosphorylation (Kegg: 00190), the top biological pathway perturbed by Hltf-deletion, resulted from increased transcription of Atp5e, Cox7c, Uqcr11, Ndufa4 and Ndufb6 genes, concomitant with increased endogenous levels of ATP (p = 0.0062). Upregulation of gene expression, as validated with qRT-PCR, accompanied a stable mtDNA/nDNA ratio. This is the first study to show Hltf-deletion in an inflammation-associated CRC model elevates mitochondrial bioenergetics.
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8
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Zhao L. Mitochondrial DNA degradation: A quality control measure for mitochondrial genome maintenance and stress response. Enzymes 2019; 45:311-341. [PMID: 31627882 DOI: 10.1016/bs.enz.2019.08.004] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Mitochondria play a central role in bioenergetics, and fulfill a plethora of functions in cell signaling, programmed cell death, and biosynthesis of key protein cofactors. Mitochondria harbor their own genomic DNA, which encodes protein subunits of the electron transport chain and a full set of transfer and ribosomal RNAs. Mitochondrial DNA (mtDNA) is essential for cellular and organismal functions, and defects in mitochondrial genome maintenance have been implicated in common human diseases and mitochondrial disorders. mtDNA repair and degradation are known pathways to cope with mtDNA damage; however, molecular factors involved in this process have remained unclear. Such knowledge is fundamental to the understanding of mitochondrial genomic maintenance and pathology, because mtDNA degradation may contribute to the etiology of mtDNA depletion syndromes and to the activation of the innate immune response by fragmented mtDNA. This article reviews the current literature regarding the importance of mitochondrial DNA degradation in mtDNA maintenance and stress response, and the recent progress in uncovering molecular factors involved in mtDNA degradation. These factors include key components of the mtDNA replication machinery, such as DNA polymerase γ, helicase Twinkle, and exonuclease MGME1, as well as a major DNA-packaging protein, mitochondrial transcription factor A (TFAM).
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Affiliation(s)
- Linlin Zhao
- Department of Chemistry, University of California, Riverside, Riverside, CA, United States.
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9
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Mice lacking the mitochondrial exonuclease MGME1 accumulate mtDNA deletions without developing progeria. Nat Commun 2018; 9:1202. [PMID: 29572490 PMCID: PMC5865154 DOI: 10.1038/s41467-018-03552-x] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Accepted: 02/21/2018] [Indexed: 12/17/2022] Open
Abstract
Replication of mammalian mitochondrial DNA (mtDNA) is an essential process that requires high fidelity and control at multiple levels to ensure proper mitochondrial function. Mutations in the mitochondrial genome maintenance exonuclease 1 (MGME1) gene were recently reported in mitochondrial disease patients. Here, to study disease pathophysiology, we generated Mgme1 knockout mice and report that homozygous knockouts develop depletion and multiple deletions of mtDNA. The mtDNA replication stalling phenotypes vary dramatically in different tissues of Mgme1 knockout mice. Mice with MGME1 deficiency accumulate a long linear subgenomic mtDNA species, similar to the one found in mtDNA mutator mice, but do not develop progeria. This finding resolves a long-standing debate by showing that point mutations of mtDNA are the main cause of progeria in mtDNA mutator mice. We also propose a role for MGME1 in the regulation of replication and transcription termination at the end of the control region of mtDNA. It has been debated whether premature ageing in mitochondrial DNA mutator mice is driven by point mutations or deletions of mtDNA. Matic et al generate Mgme1 knockout mice and show here that these mice have tissue-specific replication stalling and accumulate deleted mtDNA, without developing progeria.
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10
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Liu X, Salokas K, Tamene F, Jiu Y, Weldatsadik RG, Öhman T, Varjosalo M. An AP-MS- and BioID-compatible MAC-tag enables comprehensive mapping of protein interactions and subcellular localizations. Nat Commun 2018; 9:1188. [PMID: 29568061 PMCID: PMC5864832 DOI: 10.1038/s41467-018-03523-2] [Citation(s) in RCA: 154] [Impact Index Per Article: 25.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Accepted: 02/21/2018] [Indexed: 11/09/2022] Open
Abstract
Protein-protein interactions govern almost all cellular functions. These complex networks of stable and transient associations can be mapped by affinity purification mass spectrometry (AP-MS) and complementary proximity-based labeling methods such as BioID. To exploit the advantages of both strategies, we here design and optimize an integrated approach combining AP-MS and BioID in a single construct, which we term MAC-tag. We systematically apply the MAC-tag approach to 18 subcellular and 3 sub-organelle localization markers, generating a molecular context database, which can be used to define a protein’s molecular location. In addition, we show that combining the AP-MS and BioID results makes it possible to obtain interaction distances within a protein complex. Taken together, our integrated strategy enables the comprehensive mapping of the physical and functional interactions of proteins, defining their molecular context and improving our understanding of the cellular interactome. AP-MS and BioID provide complementary insights into cellular protein interaction networks. To facilitate their combined use, the authors here present an AP-MS- and BioID-compatible affinity tag, enabling efficient determination of cellular protein locations and interaction distances.
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Affiliation(s)
- Xiaonan Liu
- Institute of Biotechnology, University of Helsinki, Helsinki, 00014, Finland.,Helsinki Institute of Life Science, University of Helsinki, Helsinki, 00014, Finland
| | - Kari Salokas
- Institute of Biotechnology, University of Helsinki, Helsinki, 00014, Finland.,Helsinki Institute of Life Science, University of Helsinki, Helsinki, 00014, Finland
| | - Fitsum Tamene
- Institute of Biotechnology, University of Helsinki, Helsinki, 00014, Finland.,Helsinki Institute of Life Science, University of Helsinki, Helsinki, 00014, Finland.,Proteomics Unit, University of Helsinki, Helsinki, 00014, Finland
| | - Yaming Jiu
- Institute of Biotechnology, University of Helsinki, Helsinki, 00014, Finland.,Helsinki Institute of Life Science, University of Helsinki, Helsinki, 00014, Finland
| | - Rigbe G Weldatsadik
- Institute of Biotechnology, University of Helsinki, Helsinki, 00014, Finland.,Helsinki Institute of Life Science, University of Helsinki, Helsinki, 00014, Finland.,Proteomics Unit, University of Helsinki, Helsinki, 00014, Finland
| | - Tiina Öhman
- Institute of Biotechnology, University of Helsinki, Helsinki, 00014, Finland.,Helsinki Institute of Life Science, University of Helsinki, Helsinki, 00014, Finland.,Proteomics Unit, University of Helsinki, Helsinki, 00014, Finland
| | - Markku Varjosalo
- Institute of Biotechnology, University of Helsinki, Helsinki, 00014, Finland. .,Helsinki Institute of Life Science, University of Helsinki, Helsinki, 00014, Finland. .,Proteomics Unit, University of Helsinki, Helsinki, 00014, Finland.
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Moss CF, Dalla Rosa I, Hunt LE, Yasukawa T, Young R, Jones AWE, Reddy K, Desai R, Virtue S, Elgar G, Voshol P, Taylor MS, Holt IJ, Reijns MAM, Spinazzola A. Aberrant ribonucleotide incorporation and multiple deletions in mitochondrial DNA of the murine MPV17 disease model. Nucleic Acids Res 2018; 45:12808-12815. [PMID: 29106596 PMCID: PMC5728394 DOI: 10.1093/nar/gkx1009] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2017] [Accepted: 10/17/2017] [Indexed: 12/24/2022] Open
Abstract
All DNA polymerases misincorporate ribonucleotides despite their preference for deoxyribonucleotides, and analysis of cultured cells indicates that mammalian mitochondrial DNA (mtDNA) tolerates such replication errors. However, it is not clear to what extent misincorporation occurs in tissues, or whether this plays a role in human disease. Here, we show that mtDNA of solid tissues contains many more embedded ribonucleotides than that of cultured cells, consistent with the high ratio of ribonucleotide to deoxynucleotide triphosphates in tissues, and that riboadenosines account for three-quarters of them. The pattern of embedded ribonucleotides changes in a mouse model of Mpv17 deficiency, which displays a marked increase in rGMPs in mtDNA. However, while the mitochondrial dGTP is low in the Mpv17−/− liver, the brain shows no change in the overall dGTP pool, leading us to suggest that Mpv17 determines the local concentration or quality of dGTP. Embedded rGMPs are expected to distort the mtDNA and impede its replication, and elevated rGMP incorporation is associated with early-onset mtDNA depletion in liver and late-onset multiple deletions in brain of Mpv17−/− mice. These findings suggest aberrant ribonucleotide incorporation is a primary mtDNA abnormality that can result in pathology.
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Affiliation(s)
| | - Ilaria Dalla Rosa
- MRC Laboratory, Mill Hill, London NW7 1AA, UK.,Department of Clinical Neurosciences, Institute of Neurology, Royal Free Campus, University College London NW3 2PF, UK
| | - Lilian E Hunt
- Advanced Sequencing Facility, Francis Crick Institute, London NW1 1AT, UK
| | | | - Robert Young
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, The University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Aleck W E Jones
- MRC Laboratory, Mill Hill, London NW7 1AA, UK.,Department of Clinical Neurosciences, Institute of Neurology, Royal Free Campus, University College London NW3 2PF, UK
| | - Kaalak Reddy
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, The University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Radha Desai
- MRC Laboratory, Mill Hill, London NW7 1AA, UK
| | - Sam Virtue
- MRC Metabolic Diseases Unit, Wellcome Trust-MRC Institute of Metabolic Science, Cambridge CB2 0QQ, UK
| | - Greg Elgar
- Advanced Sequencing Facility, Francis Crick Institute, London NW1 1AT, UK
| | - Peter Voshol
- MRC Metabolic Diseases Unit, Wellcome Trust-MRC Institute of Metabolic Science, Cambridge CB2 0QQ, UK
| | - Martin S Taylor
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, The University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Ian J Holt
- MRC Laboratory, Mill Hill, London NW7 1AA, UK.,Department of Clinical Neurosciences, Institute of Neurology, Royal Free Campus, University College London NW3 2PF, UK.,Biodonostia Health Research Institute, 20014 San Sebastián, Spain and IKERBASQUE, Basque Foundation for Science, 48013 Bilbao, Spain
| | - Martin A M Reijns
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, The University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Antonella Spinazzola
- MRC Laboratory, Mill Hill, London NW7 1AA, UK.,Department of Clinical Neurosciences, Institute of Neurology, Royal Free Campus, University College London NW3 2PF, UK.,MRC Centre for Neuromuscular Diseases, UCL Institute of Neurology and National Hospital for Neurology and Neurosurgery, Queen Square, London WC1N 3BG, UK
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Mitochondrial Nucleoid: Shield and Switch of the Mitochondrial Genome. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2017; 2017:8060949. [PMID: 28680532 PMCID: PMC5478868 DOI: 10.1155/2017/8060949] [Citation(s) in RCA: 81] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/18/2017] [Revised: 03/06/2017] [Accepted: 04/03/2017] [Indexed: 11/18/2022]
Abstract
Mitochondria preserve very complex and distinctively unique machinery to maintain and express the content of mitochondrial DNA (mtDNA). Similar to chromosomes, mtDNA is packaged into discrete mtDNA-protein complexes referred to as a nucleoid. In addition to its role as a mtDNA shield, over 50 nucleoid-associated proteins play roles in mtDNA maintenance and gene expression through either temporary or permanent association with mtDNA or other nucleoid-associated proteins. The number of mtDNA(s) contained within a single nucleoid is a fundamental question but remains a somewhat controversial issue. Disturbance in nucleoid components and mutations in mtDNA were identified as significant in various diseases, including carcinogenesis. Significant interest in the nucleoid structure and its regulation has been stimulated in relation to mitochondrial diseases, which encompass diseases in multicellular organisms and are associated with accumulation of numerous mutations in mtDNA. In this review, mitochondrial nucleoid structure, nucleoid-associated proteins, and their regulatory roles in mitochondrial metabolism are briefly addressed to provide an overview of the emerging research field involving mitochondrial biology.
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