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Teng X, Wang Y, Liu L, Yang H, Wu M, Chen X, Ren Y, Wang Y, Duan E, Dong H, Jiang L, Zhang Y, Zhang W, Chen R, Liu S, Liu X, Tian Y, Chen L, Wang Y, Wan J. Rice Floury Endosperm26 encoding a mitochondrial single-stranded DNA-binding protein is essential for RNA-splicing of mitochondrial genes and endosperm development. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2024:112151. [PMID: 38848768 DOI: 10.1016/j.plantsci.2024.112151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Revised: 04/15/2024] [Accepted: 06/04/2024] [Indexed: 06/09/2024]
Abstract
Endosperm, the major storage organ in cereal grains, determines the grain yield and quality. Mitochondria provide the energy for dry matter accumulation, in the endosperm development. Although mitochondrial single-stranded DNA-binding proteins (mtSSBs) play a canonical role in the maintenance of single-stranded mitochondrial DNA, their molecular functions in RNA processing and endosperm development remain obscure. Here, we report a defective rice endosperm mutant, floury endosperm26 (flo26), which develops abnormal starch grains in the endosperm. Map-based cloning and complementation experiments showed that FLO26 allele encodes a mitochondrial single-stranded DNA-binding protein, named as mtSSB1.1. Loss of function of mtSSB1.1 affects the transcriptional level of many mitochondrially-encoded genes and RNA splicing of nad1, a core component of respiratory chain complex I in mitochondria. As a result, dysfunctional mature nad1 led to dramatically decreased complex I activity, thereby reducing ATP production. Our results reveal that mtSSB1.1 plays an important role in the maintenance of mitochondrial function and endosperm development by stabilizing the splicing of mitochondrial RNA in rice.
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Affiliation(s)
- Xuan Teng
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing 210095, China; Zhongshan Biological Breeding Laboratory, No.50 Zhongling Street, Nanjing 210014, China
| | - Yongfei Wang
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing 210095, China
| | - Linglong Liu
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing 210095, China; Zhongshan Biological Breeding Laboratory, No.50 Zhongling Street, Nanjing 210014, China
| | - Hang Yang
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing 210095, China
| | - Mingming Wu
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing 210095, China
| | - Xiaoli Chen
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing 210095, China
| | - Yulong Ren
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Yunlong Wang
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing 210095, China; Zhongshan Biological Breeding Laboratory, No.50 Zhongling Street, Nanjing 210014, China
| | - Erchao Duan
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing 210095, China; Zhongshan Biological Breeding Laboratory, No.50 Zhongling Street, Nanjing 210014, China
| | - Hui Dong
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing 210095, China; Zhongshan Biological Breeding Laboratory, No.50 Zhongling Street, Nanjing 210014, China
| | - Ling Jiang
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing 210095, China; Zhongshan Biological Breeding Laboratory, No.50 Zhongling Street, Nanjing 210014, China
| | - Yuanyan Zhang
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing 210095, China
| | - Wenwei Zhang
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing 210095, China; Zhongshan Biological Breeding Laboratory, No.50 Zhongling Street, Nanjing 210014, China
| | - Rongbo Chen
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing 210095, China
| | - Shijia Liu
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing 210095, China; Zhongshan Biological Breeding Laboratory, No.50 Zhongling Street, Nanjing 210014, China
| | - Xi Liu
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing 210095, China; Zhongshan Biological Breeding Laboratory, No.50 Zhongling Street, Nanjing 210014, China
| | - Yunlu Tian
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing 210095, China; Zhongshan Biological Breeding Laboratory, No.50 Zhongling Street, Nanjing 210014, China
| | - Liangming Chen
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing 210095, China; Zhongshan Biological Breeding Laboratory, No.50 Zhongling Street, Nanjing 210014, China
| | - Yihua Wang
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing 210095, China; Zhongshan Biological Breeding Laboratory, No.50 Zhongling Street, Nanjing 210014, China.
| | - Jianmin Wan
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing 210095, China; State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China; Zhongshan Biological Breeding Laboratory, No.50 Zhongling Street, Nanjing 210014, China
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Cheng Q, Liu QQ, Lu CA. A state-of-the-science review of using mitochondrial DNA copy number as a biomarker for environmental exposure. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2024; 346:123642. [PMID: 38402934 DOI: 10.1016/j.envpol.2024.123642] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2023] [Revised: 02/06/2024] [Accepted: 02/22/2024] [Indexed: 02/27/2024]
Abstract
Mitochondria are bioenergetic, biosynthetic, and signaling organelles in eukaryotes, and contain their own genomes, mitochondrial DNA (mtDNA), to supply energy to cells by generating ATP via oxidative phosphorylation. Therefore, the threat to mitochondria' integrity and health resulting from environmental exposure could induce adverse health effects in organisms. In this review, we summarized the association between mtDNA copy number (mtDNAcn), and environmental exposures as reported in the literature. We conducted a literature search in the Web of Science using [Mitochondrial DNA copy number] and [Exposure] as two keywords and employed three selection criteria for the final inclusion of 97 papers for review. The consensus of data was that mtDNAcn could be used as a plausible biomarker for cumulative exposures to environmental chemical and physical agents. In order to furtherly expand the application of mtDNAcn in ecological and environmental health research, we suggested a series of algorithms aiming to standardize the calculation of mtDNAcn based on the PCR results in this review. We also discussed the pitfalls of using whole blood/plasma samples for mtDNAcn measurements and regard buccal cells a plausible and practical alternative. Finally, we recognized the importance of better understanding the mechanistic analysis and regulatory mechanism of mtDNAcn, in particular the signals release and regulation pathways. We believe that the development of using mtDNAcn as an exposure biomarker will revolutionize the evaluation of chronic sub-lethal toxicity of chemicals to organisms in ecological and environmental health research that has not yet been implemented.
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Affiliation(s)
- Qing Cheng
- College of Resources and Environment, Southwest University, Chongqing, 400715, People's Republic of China
| | - Qing Qing Liu
- College of Resources and Environment, Southwest University, Chongqing, 400715, People's Republic of China
| | - Chensheng Alex Lu
- College of Resources and Environment, Southwest University, Chongqing, 400715, People's Republic of China; School of Public Health, University of Washington, Seattle, WA, 98195, USA.
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3
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Dadkhah K, Mianji GR, Barzegar A, Farhadi A. Characterization of the mitochondrial Huso huso genome and new aspects of its organization in the presence of tandem repeats in 12S rRNA. BMC Ecol Evol 2023; 23:55. [PMID: 37749487 PMCID: PMC10521412 DOI: 10.1186/s12862-023-02166-2] [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: 10/18/2022] [Accepted: 09/08/2023] [Indexed: 09/27/2023] Open
Abstract
BACKGROUND The sturgeon group has been economically significant worldwide due to caviar production. Sturgeons consist of 27 species in the world. Mitogenome data could be used to infer genetic diversity and investigate the evolutionary history of sturgeons. A limited number of complete mitogenomes in this family were sequenced. Here, we annotated the mitochondrial Huso huso genome, which revealed new aspects of this species. RESULTS In this species, the mitochondrial genome consisted of 13 genes encoding proteins, 22tRNA and 2rRNA, and two non-coding regions that followed other vertebrates. In addition, H. huso had a pseudo-tRNA-Glu between ND6 and Cytb and a 52-nucleotide tandem repeat with two replications in 12S rRNA. This duplication event is probably related to the slipped strand during replication, which could remain in the strand due to mispairing during replication. Furthermore, an 82 bp repeat sequence with three replications was observed in the D-loop control region, which is usually visible in different species. Regulatory elements were also seen in the control region of the mitochondrial genome, which included termination sequences and conserved regulatory blocks. Genomic compounds showed the highest conservation in rRNA and tRNA, while protein-encoded genes and nonencoded regions had the highest divergence. The mitochondrial genome was phylogenetically assayed using 12 protein-encoding genes. CONCLUSIONS In H. huso sequencing, we identified a distinct genome organization relative to other species that have never been reported. In recent years, along with the advancement in sequencing identified more genome rearrangements. However, it is an essential aspect of researching the evolution of the mitochondrial genome that needs to be recognized.
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Affiliation(s)
- Khadijeh Dadkhah
- Laboratory for Molecular Genetics and Animal Biotechnology, Faculty of Animal Sciences and Fisheries, Sari Agricultural Sciences and Natural Resources University, Sari, Iran.
| | - Ghodrat Rahimi Mianji
- Laboratory for Molecular Genetics and Animal Biotechnology, Faculty of Animal Sciences and Fisheries, Sari Agricultural Sciences and Natural Resources University, Sari, Iran
| | - Ali Barzegar
- Department of Basic Sciences, Sari Agricultural Sciences and Natural Resources University, Sari, Iran
| | - Ayoub Farhadi
- Laboratory for Molecular Genetics and Animal Biotechnology, Faculty of Animal Sciences and Fisheries, Sari Agricultural Sciences and Natural Resources University, Sari, Iran
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Irvin EM, Wang H. Single-molecule imaging of genome maintenance proteins encountering specific DNA sequences and structures. DNA Repair (Amst) 2023; 128:103528. [PMID: 37392578 PMCID: PMC10989508 DOI: 10.1016/j.dnarep.2023.103528] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2023] [Revised: 06/08/2023] [Accepted: 06/21/2023] [Indexed: 07/03/2023]
Abstract
DNA repair pathways are tightly regulated processes that recognize specific hallmarks of DNA damage and coordinate lesion repair through discrete mechanisms, all within the context of a three-dimensional chromatin landscape. Dysregulation or malfunction of any one of the protein constituents in these pathways can contribute to aging and a variety of diseases. While the collective action of these many proteins is what drives DNA repair on the organismal scale, it is the interactions between individual proteins and DNA that facilitate each step of these pathways. In much the same way that ensemble biochemical techniques have characterized the various steps of DNA repair pathways, single-molecule imaging (SMI) approaches zoom in further, characterizing the individual protein-DNA interactions that compose each pathway step. SMI techniques offer the high resolving power needed to characterize the molecular structure and functional dynamics of individual biological interactions on the nanoscale. In this review, we highlight how our lab has used SMI techniques - traditional atomic force microscopy (AFM) imaging in air, high-speed AFM (HS-AFM) in liquids, and the DNA tightrope assay - over the past decade to study protein-nucleic acid interactions involved in DNA repair, mitochondrial DNA replication, and telomere maintenance. We discuss how DNA substrates containing specific DNA sequences or structures that emulate DNA repair intermediates or telomeres were generated and validated. For each highlighted project, we discuss novel findings made possible by the spatial and temporal resolution offered by these SMI techniques and unique DNA substrates.
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Affiliation(s)
| | - Hong Wang
- Toxicology Program, North Carolina State University, Raleigh, NC, USA; Physics Department, North Carolina State University, Raleigh, NC, USA; Center for Human Health and the Environment, North Carolina State University, Raleigh, NC, USA.
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5
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Lee Y, Cho CH, Noh C, Yang JH, Park SI, Lee YM, West JA, Bhattacharya D, Jo K, Yoon HS. Origin of minicircular mitochondrial genomes in red algae. Nat Commun 2023; 14:3363. [PMID: 37291154 PMCID: PMC10250338 DOI: 10.1038/s41467-023-39084-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Accepted: 05/30/2023] [Indexed: 06/10/2023] Open
Abstract
Eukaryotic organelle genomes are generally of conserved size and gene content within phylogenetic groups. However, significant variation in genome structure may occur. Here, we report that the Stylonematophyceae red algae contain multipartite circular mitochondrial genomes (i.e., minicircles) which encode one or two genes bounded by a specific cassette and a conserved constant region. These minicircles are visualized using fluorescence microscope and scanning electron microscope, proving the circularity. Mitochondrial gene sets are reduced in these highly divergent mitogenomes. Newly generated chromosome-level nuclear genome assembly of Rhodosorus marinus reveals that most mitochondrial ribosomal subunit genes are transferred to the nuclear genome. Hetero-concatemers that resulted from recombination between minicircles and unique gene inventory that is responsible for mitochondrial genome stability may explain how the transition from typical mitochondrial genome to minicircles occurs. Our results offer inspiration on minicircular organelle genome formation and highlight an extreme case of mitochondrial gene inventory reduction.
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Affiliation(s)
- Yongsung Lee
- Department of Biological Sciences, Sungkyunkwan University, Suwon, 16419, Korea
| | - Chung Hyun Cho
- Department of Biological Sciences, Sungkyunkwan University, Suwon, 16419, Korea
| | - Chanyoung Noh
- Department of Chemistry, Sogang University, Seoul, 04107, Korea
| | - Ji Hyun Yang
- Department of Biological Sciences, Sungkyunkwan University, Suwon, 16419, Korea
| | - Seung In Park
- Department of Biological Sciences, Sungkyunkwan University, Suwon, 16419, Korea
| | - Yu Min Lee
- Department of Biological Sciences, Sungkyunkwan University, Suwon, 16419, Korea
| | - John A West
- School of Biosciences 2, University of Melbourne, Parkville, Victoria, 3010, Australia
| | - Debashish Bhattacharya
- Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, 08901, USA
| | - Kyubong Jo
- Department of Chemistry, Sogang University, Seoul, 04107, Korea.
| | - Hwan Su Yoon
- Department of Biological Sciences, Sungkyunkwan University, Suwon, 16419, Korea.
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6
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Zhang L, Ma J, Shen Z, Wang B, Jiang Q, Ma F, Ju Y, Duan G, Zhang Q, Su X. Low copy numbers for mitochondrial DNA moderates the strength of nuclear-cytoplasmic incompatibility in plants. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2023; 65:739-754. [PMID: 36308719 DOI: 10.1111/jipb.13400] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Accepted: 10/27/2022] [Indexed: 06/16/2023]
Abstract
Plant cells contain only small amounts of mitochondrial DNA (mtDNA), with the genomic information shared among multiple mitochondria. The biological relevance and molecular mechanism underlying this hallmark of plant cells has been unclear. Here, we report that Arabidopsis thaliana plants exhibited significantly reduced growth and mitochondrial dysfunction when the mtDNA copy number was increased to the degree that each mitochondrion possessed DNA. The amounts of mitochondrion-encoded transcripts increased several fold in the presence of elevated mtDNA levels. However, the efficiency of RNA editing decreased with this excess of mitochondrion-encoded transcripts, resulting in impaired assembly of mitochondrial complexes containing mtDNA-encoded subunits, such as respiratory complexes I and IV. These observations indicate the occurrence of nuclear-mitochondrial incompatibility in the cells with increased amounts of mtDNA and provide an initial answer to the fundamental question of why plant cells have much lower mtDNA levels than animal cells. We propose that keeping mtDNA levels low moderates nuclear-mitochondrial incompatibility and that this may be a crucial factor driving plant cells to restrict the copy numbers of mtDNA.
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Affiliation(s)
- Liguang Zhang
- Key Laboratory of Ministry of Education for Cell Proliferation and Differentiation, College of Life Sciences, Peking University, Beijing, 100871, China
| | - Jin Ma
- Key Laboratory of Ministry of Education for Cell Proliferation and Differentiation, College of Life Sciences, Peking University, Beijing, 100871, China
| | - Zhaorui Shen
- Key Laboratory of Ministry of Education for Cell Proliferation and Differentiation, College of Life Sciences, Peking University, Beijing, 100871, China
| | - Bo Wang
- State Key Laboratory of Protein and Plant Gene Research and Biomedical Pioneering Innovation Center (BIOPIC), College of Life Sciences, Peking University, Beijing, 100871, China
| | - Qingling Jiang
- Key Laboratory of Ministry of Education for Cell Proliferation and Differentiation, College of Life Sciences, Peking University, Beijing, 100871, China
| | - Fei Ma
- Key Laboratory of Ministry of Education for Cell Proliferation and Differentiation, College of Life Sciences, Peking University, Beijing, 100871, China
| | - Yan Ju
- Key Laboratory of Ministry of Education for Cell Proliferation and Differentiation, College of Life Sciences, Peking University, Beijing, 100871, China
| | - Guangxing Duan
- Key Laboratory of Ministry of Education for Cell Proliferation and Differentiation, College of Life Sciences, Peking University, Beijing, 100871, China
| | - Quan Zhang
- Key Laboratory of Ministry of Education for Cell Proliferation and Differentiation, College of Life Sciences, Peking University, Beijing, 100871, China
| | - Xiaodong Su
- State Key Laboratory of Protein and Plant Gene Research and Biomedical Pioneering Innovation Center (BIOPIC), College of Life Sciences, Peking University, Beijing, 100871, China
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7
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Al Khatib I, Deng J, Symes A, Kerr M, Zhang H, Huang SYN, Pommier Y, Khan A, Shutt TE. Functional characterization of two variants of mitochondrial topoisomerase TOP1MT that impact regulation of the mitochondrial genome. J Biol Chem 2022; 298:102420. [PMID: 36030054 PMCID: PMC9513266 DOI: 10.1016/j.jbc.2022.102420] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Revised: 08/02/2022] [Accepted: 08/03/2022] [Indexed: 11/21/2022] Open
Abstract
TOP1MT encodes a mitochondrial topoisomerase that is important for mtDNA regulation and is involved in mitochondrial replication, transcription, and translation. Two variants predicted to affect TOP1MT function (V1 - R198C and V2 - V338L) were identified by exome sequencing of a newborn with hypertrophic cardiomyopathy. As no pathogenic TOP1MT variants had been confirmed previously, we characterized these variants for their ability to rescue several TOP1MT functions in KO cells. Consistent with these TOP1MT variants contributing to the patient phenotype, our comprehensive characterization suggests that both variants had impaired activity. Critically, we determined neither variant was able to restore steady state levels of mitochondrial-encoded proteins nor to rescue oxidative phosphorylation when re-expressed in TOP1MT KO cells. However, we found the two variants behaved differently in some respects; while the V1 variant was more efficient in restoring transcript levels, the V2 variant showed better rescue of mtDNA copy number and replication. These findings suggest that the different TOP1MT variants affect distinct TOP1MT functions. Altogether, these findings begin to provide insight into the many roles that TOP1MT plays in the maintenance and expression of the mitochondrial genome and how impairments in this important protein may lead to human pathology.
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Affiliation(s)
- Iman Al Khatib
- Department of Biochemistry & Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Jingti Deng
- Department of Biochemistry & Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Andrew Symes
- Department of Geomatics Engineering, Schulich School of Engineering, University of Calgary, Calgary, Alberta, Canada
| | | | - Hongliang Zhang
- Laboratory of Molecular Pharmacology, Developmental Therapeutics Branch, Center for Cancer Research, NCI, National Institutes of Health, Bethesda, Maryland, USA
| | - Shar-Yin Naomi Huang
- Laboratory of Molecular Pharmacology, Developmental Therapeutics Branch, Center for Cancer Research, NCI, National Institutes of Health, Bethesda, Maryland, USA
| | - Yves Pommier
- Laboratory of Molecular Pharmacology, Developmental Therapeutics Branch, Center for Cancer Research, NCI, National Institutes of Health, Bethesda, Maryland, USA
| | - Aneal Khan
- Discovery DNA, Calgary, Alberta, Canada; M.A.G.I.C. Clinic Ltd (Metabolics and Genetics in Calgary), Department of Pediatrics, Cumming School of Medicine, Alberta Children's Hospital Research Institute, University of Calgary, Calgary, Alberta, Canada
| | - Timothy E Shutt
- Departments of Biochemistry & Molecular Biology and Medical Genetics, Cumming School of Medicine, Alberta Children's Hospital Research Institute, Hotchkiss Brain Institute, University of Calgary, Calgary, Alberta, Canada.
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8
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Mitochondrial DNA Repair in Neurodegenerative Diseases and Ageing. Int J Mol Sci 2022; 23:ijms231911391. [PMID: 36232693 PMCID: PMC9569545 DOI: 10.3390/ijms231911391] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Revised: 09/20/2022] [Accepted: 09/21/2022] [Indexed: 11/17/2022] Open
Abstract
Mitochondria are the only organelles, along with the nucleus, that have their own DNA. Mitochondrial DNA (mtDNA) is a double-stranded circular molecule of ~16.5 kbp that can exist in multiple copies within the organelle. Both strands are translated and encode for 22 tRNAs, 2 rRNAs, and 13 proteins. mtDNA molecules are anchored to the inner mitochondrial membrane and, in association with proteins, form a structure called nucleoid, which exerts a structural and protective function. Indeed, mitochondria have evolved mechanisms necessary to protect their DNA from chemical and physical lesions such as DNA repair pathways similar to those present in the nucleus. However, there are mitochondria-specific mechanisms such as rapid mtDNA turnover, fission, fusion, and mitophagy. Nevertheless, mtDNA mutations may be abundant in somatic tissue due mainly to the proximity of the mtDNA to the oxidative phosphorylation (OXPHOS) system and, consequently, to the reactive oxygen species (ROS) formed during ATP production. In this review, we summarise the most common types of mtDNA lesions and mitochondria repair mechanisms. The second part of the review focuses on the physiological role of mtDNA damage in ageing and the effect of mtDNA mutations in neurodegenerative disorders such as Alzheimer’s and Parkinson’s disease. Considering the central role of mitochondria in maintaining cellular homeostasis, the analysis of mitochondrial function is a central point for developing personalised medicine.
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Abd Radzak SM, Mohd Khair SZN, Ahmad F, Patar A, Idris Z, Mohamed Yusoff AA. Insights regarding mitochondrial DNA copy number alterations in human cancer (Review). Int J Mol Med 2022; 50:104. [PMID: 35713211 PMCID: PMC9304817 DOI: 10.3892/ijmm.2022.5160] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Accepted: 05/26/2022] [Indexed: 11/25/2022] Open
Abstract
Mitochondria are the critical organelles involved in various cellular functions. Mitochondrial biogenesis is activated by multiple cellular mechanisms which require a synchronous regulation between mitochondrial DNA (mtDNA) and nuclear DNA (nDNA). The mitochondrial DNA copy number (mtDNA-CN) is a proxy indicator for mitochondrial activity, and its alteration reflects mitochondrial biogenesis and function. Despite the precise mechanisms that modulate the amount and composition of mtDNA, which have not been fully elucidated, mtDNA-CN is known to influence numerous cellular pathways that are associated with cancer and as well as multiple other diseases. In addition, the utility of current technology in measuring mtDNA-CN contributes to its extensive assessment of diverse traits and tumorigenesis. The present review provides an overview of mtDNA-CN variations across human cancers and an extensive summary of the existing knowledge on the regulation and machinery of mtDNA-CN. The current information on the advanced methods used for mtDNA-CN assessment is also presented.
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Affiliation(s)
- Siti Muslihah Abd Radzak
- Department of Neurosciences, School of Medical Sciences, Universiti Sains Malaysia, Health Campus, Kubang Kerian, Kelantan 16150, Malaysia
| | - Siti Zulaikha Nashwa Mohd Khair
- Department of Neurosciences, School of Medical Sciences, Universiti Sains Malaysia, Health Campus, Kubang Kerian, Kelantan 16150, Malaysia
| | - Farizan Ahmad
- Department of Neurosciences, School of Medical Sciences, Universiti Sains Malaysia, Health Campus, Kubang Kerian, Kelantan 16150, Malaysia
| | - Azim Patar
- Department of Neurosciences, School of Medical Sciences, Universiti Sains Malaysia, Health Campus, Kubang Kerian, Kelantan 16150, Malaysia
| | - Zamzuri Idris
- Department of Neurosciences, School of Medical Sciences, Universiti Sains Malaysia, Health Campus, Kubang Kerian, Kelantan 16150, Malaysia
| | - Abdul Aziz Mohamed Yusoff
- Department of Neurosciences, School of Medical Sciences, Universiti Sains Malaysia, Health Campus, Kubang Kerian, Kelantan 16150, Malaysia
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10
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Alorda-Clara M, Torrens-Mas M, Morla-Barcelo PM, Roca P, Sastre-Serra J, Pons DG, Oliver J. High Concentrations of Genistein Decrease Cell Viability Depending on Oxidative Stress and Inflammation in Colon Cancer Cell Lines. Int J Mol Sci 2022; 23:ijms23147526. [PMID: 35886874 PMCID: PMC9323408 DOI: 10.3390/ijms23147526] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Revised: 07/01/2022] [Accepted: 07/06/2022] [Indexed: 12/24/2022] Open
Abstract
Genistein could play a crucial role in modulating three closely linked physiological processes altered during cancer: oxidative stress, mitochondrial biogenesis, and inflammation. However, genistein’s role in colorectal cancer remains unclear. We aimed to determine genistein’s effects in two colon cancer cells: HT29 and SW620, primary and metastatic cancer cells, respectively. After genistein treatment for 48 h, cell viability and hydrogen peroxide (H2O2) production were studied. The cell cycle was studied by flow cytometry, mRNA and protein levels were analyzed by RT-qPCR and Western blot, respectively, and finally, cytoskeleton remodeling and NF-κB translocation were determined by confocal microscopy. Genistein 100 µM decreased cell viability and produced G2/M arrest, increased H2O2, and produced filopodia in SW620 cells. In HT29 cells, genistein produced an increase of cell death, H2O2 production, and in the number of stress fibers. In HT29 cells, mitochondrial biogenesis was increased, however, in SW620 cells, it was decreased. Finally, the expression of inflammation-related genes increased in both cell lines, being greater in SW620 cells, where NF-κB translocation to the nucleus was higher. These results indicate that high concentrations of genistein could increase oxidative stress and inflammation in colon cancer cells and, ultimately, decrease cell viability.
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Affiliation(s)
- Marina Alorda-Clara
- Grupo Multidisciplinar de Oncología Traslacional, Institut Universitari d’Investigació en Ciències de la Salut (IUNICS), Universitat de les Illes Balears, E-07122 Palma de Mallorca, Illes Balears, Spain; (M.A.-C.); (M.T.-M.); (P.M.M.-B.); (P.R.); (J.S.-S.); (J.O.)
- Instituto de Investigación Sanitaria Illes Balears (IdISBa), Hospital Universitario Son Espases, Edificio S, E-07120 Palma de Mallorca, Illes Balears, Spain
| | - Margalida Torrens-Mas
- Grupo Multidisciplinar de Oncología Traslacional, Institut Universitari d’Investigació en Ciències de la Salut (IUNICS), Universitat de les Illes Balears, E-07122 Palma de Mallorca, Illes Balears, Spain; (M.A.-C.); (M.T.-M.); (P.M.M.-B.); (P.R.); (J.S.-S.); (J.O.)
- Instituto de Investigación Sanitaria Illes Balears (IdISBa), Hospital Universitario Son Espases, Edificio S, E-07120 Palma de Mallorca, Illes Balears, Spain
- Translational Research in Aging and Longevity (TRIAL) Group, Instituto de Investigación Sanitaria Illes Balears (IdISBa), E-07120 Palma de Mallorca, Illes Balears, Spain
| | - Pere Miquel Morla-Barcelo
- Grupo Multidisciplinar de Oncología Traslacional, Institut Universitari d’Investigació en Ciències de la Salut (IUNICS), Universitat de les Illes Balears, E-07122 Palma de Mallorca, Illes Balears, Spain; (M.A.-C.); (M.T.-M.); (P.M.M.-B.); (P.R.); (J.S.-S.); (J.O.)
| | - Pilar Roca
- Grupo Multidisciplinar de Oncología Traslacional, Institut Universitari d’Investigació en Ciències de la Salut (IUNICS), Universitat de les Illes Balears, E-07122 Palma de Mallorca, Illes Balears, Spain; (M.A.-C.); (M.T.-M.); (P.M.M.-B.); (P.R.); (J.S.-S.); (J.O.)
- Instituto de Investigación Sanitaria Illes Balears (IdISBa), Hospital Universitario Son Espases, Edificio S, E-07120 Palma de Mallorca, Illes Balears, Spain
- Ciber Fisiopatología Obesidad y Nutrición (CB06/03), Instituto Salud Carlos III, E-28029 Madrid, Madrid, Spain
| | - Jorge Sastre-Serra
- Grupo Multidisciplinar de Oncología Traslacional, Institut Universitari d’Investigació en Ciències de la Salut (IUNICS), Universitat de les Illes Balears, E-07122 Palma de Mallorca, Illes Balears, Spain; (M.A.-C.); (M.T.-M.); (P.M.M.-B.); (P.R.); (J.S.-S.); (J.O.)
- Instituto de Investigación Sanitaria Illes Balears (IdISBa), Hospital Universitario Son Espases, Edificio S, E-07120 Palma de Mallorca, Illes Balears, Spain
- Ciber Fisiopatología Obesidad y Nutrición (CB06/03), Instituto Salud Carlos III, E-28029 Madrid, Madrid, Spain
| | - Daniel Gabriel Pons
- Grupo Multidisciplinar de Oncología Traslacional, Institut Universitari d’Investigació en Ciències de la Salut (IUNICS), Universitat de les Illes Balears, E-07122 Palma de Mallorca, Illes Balears, Spain; (M.A.-C.); (M.T.-M.); (P.M.M.-B.); (P.R.); (J.S.-S.); (J.O.)
- Instituto de Investigación Sanitaria Illes Balears (IdISBa), Hospital Universitario Son Espases, Edificio S, E-07120 Palma de Mallorca, Illes Balears, Spain
- Correspondence: ; Tel.: +34-971173149
| | - Jordi Oliver
- Grupo Multidisciplinar de Oncología Traslacional, Institut Universitari d’Investigació en Ciències de la Salut (IUNICS), Universitat de les Illes Balears, E-07122 Palma de Mallorca, Illes Balears, Spain; (M.A.-C.); (M.T.-M.); (P.M.M.-B.); (P.R.); (J.S.-S.); (J.O.)
- Instituto de Investigación Sanitaria Illes Balears (IdISBa), Hospital Universitario Son Espases, Edificio S, E-07120 Palma de Mallorca, Illes Balears, Spain
- Ciber Fisiopatología Obesidad y Nutrición (CB06/03), Instituto Salud Carlos III, E-28029 Madrid, Madrid, Spain
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11
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Liu C, Fu Z, Wu S, Wang X, Zhang S, Chu C, Hong Y, Wu W, Chen S, Jiang Y, Wu Y, Song Y, Liu Y, Guo X. Mitochondrial HSF1 triggers mitochondrial dysfunction and neurodegeneration in Huntington's disease. EMBO Mol Med 2022; 14:e15851. [PMID: 35670111 PMCID: PMC9260212 DOI: 10.15252/emmm.202215851] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Revised: 05/10/2022] [Accepted: 05/10/2022] [Indexed: 12/18/2022] Open
Affiliation(s)
- Chunyue Liu
- State Key Laboratory of Reproductive Medicine Key Laboratory of Human Functional Genomics of Jiangsu Province Department of Neurobiology Interdisciplinary InnoCenter for Organoids School of Basic Medical Sciences Nanjing Medical University Nanjing China
- State Key Laboratory of Reproductive Medicine Interdisciplinary InnoCenter for Organoids Institute for Stem Cell and Neural Regeneration School of Pharmacy Nanjing Medical University Nanjing China
| | - Zixing Fu
- State Key Laboratory of Reproductive Medicine Key Laboratory of Human Functional Genomics of Jiangsu Province Department of Neurobiology Interdisciplinary InnoCenter for Organoids School of Basic Medical Sciences Nanjing Medical University Nanjing China
| | - Shanshan Wu
- State Key Laboratory of Reproductive Medicine Interdisciplinary InnoCenter for Organoids Institute for Stem Cell and Neural Regeneration School of Pharmacy Nanjing Medical University Nanjing China
| | - Xiaosong Wang
- State Key Laboratory of Reproductive Medicine Key Laboratory of Human Functional Genomics of Jiangsu Province Department of Neurobiology Interdisciplinary InnoCenter for Organoids School of Basic Medical Sciences Nanjing Medical University Nanjing China
| | - Shengrong Zhang
- State Key Laboratory of Reproductive Medicine Key Laboratory of Human Functional Genomics of Jiangsu Province Department of Neurobiology Interdisciplinary InnoCenter for Organoids School of Basic Medical Sciences Nanjing Medical University Nanjing China
| | - Chu Chu
- State Key Laboratory of Reproductive Medicine Interdisciplinary InnoCenter for Organoids Institute for Stem Cell and Neural Regeneration School of Pharmacy Nanjing Medical University Nanjing China
| | - Yuan Hong
- State Key Laboratory of Reproductive Medicine Interdisciplinary InnoCenter for Organoids Institute for Stem Cell and Neural Regeneration School of Pharmacy Nanjing Medical University Nanjing China
| | - Wenbo Wu
- State Key Laboratory of Reproductive Medicine Key Laboratory of Human Functional Genomics of Jiangsu Province Department of Neurobiology Interdisciplinary InnoCenter for Organoids School of Basic Medical Sciences Nanjing Medical University Nanjing China
| | - Shengqi Chen
- State Key Laboratory of Reproductive Medicine Key Laboratory of Human Functional Genomics of Jiangsu Province Department of Neurobiology Interdisciplinary InnoCenter for Organoids School of Basic Medical Sciences Nanjing Medical University Nanjing China
| | - Yueqing Jiang
- State Key Laboratory of Reproductive Medicine Key Laboratory of Human Functional Genomics of Jiangsu Province Department of Neurobiology Interdisciplinary InnoCenter for Organoids School of Basic Medical Sciences Nanjing Medical University Nanjing China
| | - Yang Wu
- State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics Key Laboratory of Magnetic Resonance in Biological Systems Wuhan Center for Magnetic Resonance, Innovation Academy for Precision Measurement Science and Technology Chinese Academy of Sciences Wuhan China
| | - Yongbo Song
- Department of Pharmacology Shenyang Pharmaceutical University Shenyang China
| | - Yan Liu
- State Key Laboratory of Reproductive Medicine Interdisciplinary InnoCenter for Organoids Institute for Stem Cell and Neural Regeneration School of Pharmacy Nanjing Medical University Nanjing China
| | - Xing Guo
- State Key Laboratory of Reproductive Medicine Key Laboratory of Human Functional Genomics of Jiangsu Province Department of Neurobiology Interdisciplinary InnoCenter for Organoids School of Basic Medical Sciences Nanjing Medical University Nanjing China
- Department of Endocrinology Sir Run Run Hospital Nanjing Medical University Nanjing Jiangsu China
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12
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Jiang M, Xie X, Zhu X, Jiang S, Milenkovic D, Misic J, Shi Y, Tandukar N, Li X, Atanassov I, Jenninger L, Hoberg E, Albarran-Gutierrez S, Szilagyi Z, Macao B, Siira SJ, Carelli V, Griffith JD, Gustafsson CM, Nicholls TJ, Filipovska A, Larsson NG, Falkenberg M. The mitochondrial single-stranded DNA binding protein is essential for initiation of mtDNA replication. SCIENCE ADVANCES 2021; 7:eabf8631. [PMID: 34215584 PMCID: PMC11057760 DOI: 10.1126/sciadv.abf8631] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Accepted: 05/20/2021] [Indexed: 06/13/2023]
Abstract
We report a role for the mitochondrial single-stranded DNA binding protein (mtSSB) in regulating mitochondrial DNA (mtDNA) replication initiation in mammalian mitochondria. Transcription from the light-strand promoter (LSP) is required both for gene expression and for generating the RNA primers needed for initiation of mtDNA synthesis. In the absence of mtSSB, transcription from LSP is strongly up-regulated, but no replication primers are formed. Using deep sequencing in a mouse knockout model and biochemical reconstitution experiments with pure proteins, we find that mtSSB is necessary to restrict transcription initiation to optimize RNA primer formation at both origins of mtDNA replication. Last, we show that human pathological versions of mtSSB causing severe mitochondrial disease cannot efficiently support primer formation and initiation of mtDNA replication.
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Affiliation(s)
- Min Jiang
- Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang 310024, China
- Department of Mitochondrial Biology, Max Planck Institute for Biology of Ageing, 50931 Cologne, Germany
| | - Xie Xie
- Department of Medical Biochemistry and Cell Biology, University of Gothenburg, PO Box 440, Gothenburg 405 30, Sweden
| | - Xuefeng Zhu
- Department of Medical Biochemistry and Cell Biology, University of Gothenburg, PO Box 440, Gothenburg 405 30, Sweden
| | - Shan Jiang
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm 17177, Sweden
| | - Dusanka Milenkovic
- Department of Mitochondrial Biology, Max Planck Institute for Biology of Ageing, 50931 Cologne, Germany
| | - Jelena Misic
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm 17177, Sweden
| | - Yonghong Shi
- Department of Medical Biochemistry and Cell Biology, University of Gothenburg, PO Box 440, Gothenburg 405 30, Sweden
| | - Nirwan Tandukar
- Lineberger Comprehensive Cancer Center, Department of Microbiology and Immunology, University of North Carolina, Chapel Hill, NC 27514, USA
| | - Xinping Li
- Proteomics Core Facility, Max Planck Institute for Biology of Ageing, 50931 Cologne, Germany
| | - Ilian Atanassov
- Proteomics Core Facility, Max Planck Institute for Biology of Ageing, 50931 Cologne, Germany
| | - Louise Jenninger
- Department of Medical Biochemistry and Cell Biology, University of Gothenburg, PO Box 440, Gothenburg 405 30, Sweden
| | - Emily Hoberg
- Department of Medical Biochemistry and Cell Biology, University of Gothenburg, PO Box 440, Gothenburg 405 30, Sweden
| | - Sara Albarran-Gutierrez
- Department of Mitochondrial Biology, Max Planck Institute for Biology of Ageing, 50931 Cologne, Germany
| | - Zsolt Szilagyi
- Department of Medical Biochemistry and Cell Biology, University of Gothenburg, PO Box 440, Gothenburg 405 30, Sweden
| | - Bertil Macao
- Department of Medical Biochemistry and Cell Biology, University of Gothenburg, PO Box 440, Gothenburg 405 30, Sweden
| | - Stefan J Siira
- Harry Perkins Institute of Medical Research and ARC Centre of Excellence in Synthetic Biology, Nedlands, WA 6009, Australia
- Telethon Kids Institute, Northern Entrance, Perth Children's Hospital, 15 Hospital Avenue, Nedlands, WA, Australia
| | - Valerio Carelli
- Department of Biomedical and Neuromotor Sciences (DIBINEM), University of Bologna, Bologna, Italy
- IRCCS Istituto delle Scienze Neurologiche di Bologna, Programma di Neurogenetica, Bologna, Italy
| | - Jack D Griffith
- Lineberger Comprehensive Cancer Center, Department of Microbiology and Immunology, University of North Carolina, Chapel Hill, NC 27514, USA
| | - Claes M Gustafsson
- Department of Medical Biochemistry and Cell Biology, University of Gothenburg, PO Box 440, Gothenburg 405 30, Sweden
| | - Thomas J Nicholls
- Wellcome Centre for Mitochondrial Research, Biosciences Institute, The Medical School, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Aleksandra Filipovska
- Harry Perkins Institute of Medical Research and ARC Centre of Excellence in Synthetic Biology, Nedlands, WA 6009, Australia
- Telethon Kids Institute, Northern Entrance, Perth Children's Hospital, 15 Hospital Avenue, Nedlands, WA, Australia
| | - Nils-Göran Larsson
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm 17177, Sweden.
| | - Maria Falkenberg
- Department of Medical Biochemistry and Cell Biology, University of Gothenburg, PO Box 440, Gothenburg 405 30, Sweden.
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13
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Silva-Pinheiro P, Pardo-Hernández C, Reyes A, Tilokani L, Mishra A, Cerutti R, Li S, Rozsivalova DH, Valenzuela S, Dogan SA, Peter B, Fernández-Silva P, Trifunovic A, Prudent J, Minczuk M, Bindoff L, Macao B, Zeviani M, Falkenberg M, Viscomi C. DNA polymerase gamma mutations that impair holoenzyme stability cause catalytic subunit depletion. Nucleic Acids Res 2021; 49:5230-5248. [PMID: 33956154 PMCID: PMC8136776 DOI: 10.1093/nar/gkab282] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Revised: 03/29/2021] [Accepted: 04/08/2021] [Indexed: 01/31/2023] Open
Abstract
Mutations in POLG, encoding POLγA, the catalytic subunit of the mitochondrial DNA polymerase, cause a spectrum of disorders characterized by mtDNA instability. However, the molecular pathogenesis of POLG-related diseases is poorly understood and efficient treatments are missing. Here, we generate the PolgA449T/A449T mouse model, which reproduces the A467T change, the most common human recessive mutation of POLG. We show that the mouse A449T mutation impairs DNA binding and mtDNA synthesis activities of POLγ, leading to a stalling phenotype. Most importantly, the A449T mutation also strongly impairs interactions with POLγB, the accessory subunit of the POLγ holoenzyme. This allows the free POLγA to become a substrate for LONP1 protease degradation, leading to dramatically reduced levels of POLγA in A449T mouse tissues. Therefore, in addition to its role as a processivity factor, POLγB acts to stabilize POLγA and to prevent LONP1-dependent degradation. Notably, we validated this mechanism for other disease-associated mutations affecting the interaction between the two POLγ subunits. We suggest that targeting POLγA turnover can be exploited as a target for the development of future therapies.
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Affiliation(s)
- Pedro Silva-Pinheiro
- MRC/University of Cambridge Mitochondrial Biology Unit, Hills Road, CB2 0XY Cambridge, UK
| | - Carlos Pardo-Hernández
- Department of Medical Biochemistry and Cell Biology, University of Gothenburg, Medicinaregatan 9A P.O. Box 440, SE405 30 Gothenburg, Sweden
| | - Aurelio Reyes
- MRC/University of Cambridge Mitochondrial Biology Unit, Hills Road, CB2 0XY Cambridge, UK
| | - Lisa Tilokani
- MRC/University of Cambridge Mitochondrial Biology Unit, Hills Road, CB2 0XY Cambridge, UK
| | - Anup Mishra
- Department of Medical Biochemistry and Cell Biology, University of Gothenburg, Medicinaregatan 9A P.O. Box 440, SE405 30 Gothenburg, Sweden
| | - Raffaele Cerutti
- Department of Neurosciences, University of Padova, via Giustiniani, 2-35128 Padova, Italy
| | - Shuaifeng Li
- Center for Cancer Biology, Life Science of Institution, Zhejiang University, Hangzhou 310058, China
| | - Dieu-Hien Rozsivalova
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD) and Center for Molecular Medicine (CMMC), University of Cologne, Joseph-Stelzmann-Strasse 26, 50931 Cologne, Germany
| | - Sebastian Valenzuela
- Department of Medical Biochemistry and Cell Biology, University of Gothenburg, Medicinaregatan 9A P.O. Box 440, SE405 30 Gothenburg, Sweden
| | - Sukru A Dogan
- Department of Molecular Biology and Genetics, Center for Life Sciences and Technologies, Bogazici University, 34342 Istanbul, Turkey
| | - Bradley Peter
- Department of Medical Biochemistry and Cell Biology, University of Gothenburg, Medicinaregatan 9A P.O. Box 440, SE405 30 Gothenburg, Sweden
| | - Patricio Fernández-Silva
- Biochemistry and Molecular and Cell Biology Department, University of Zaragoza, C/ Pedro Cerbuna s/n 50.009-Zaragoza, and Biocomputation and Complex Systems Physics Institute (BIFI), C/ Mariano Esquillor, 50.018-Zaragoza, Spain
| | - Aleksandra Trifunovic
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD) and Center for Molecular Medicine (CMMC), University of Cologne, Joseph-Stelzmann-Strasse 26, 50931 Cologne, Germany
| | - Julien Prudent
- MRC/University of Cambridge Mitochondrial Biology Unit, Hills Road, CB2 0XY Cambridge, UK
| | - Michal Minczuk
- MRC/University of Cambridge Mitochondrial Biology Unit, Hills Road, CB2 0XY Cambridge, UK
| | - Laurence Bindoff
- Department of Clinical Medicine, University of Bergen, 5007 Bergen, Norway
- Neuro-SysMed, Department of Neurology, Haukeland University Hospital, Jonas Lies vei 65, 5021 Bergen, Norway
| | - Bertil Macao
- Department of Medical Biochemistry and Cell Biology, University of Gothenburg, Medicinaregatan 9A P.O. Box 440, SE405 30 Gothenburg, Sweden
| | - Massimo Zeviani
- Department of Neurosciences, University of Padova, via Giustiniani, 2-35128 Padova, Italy
- Venetian Institute of Molecular Medicine, via Orus 2-35128 Padova, Italy
| | - Maria Falkenberg
- Department of Medical Biochemistry and Cell Biology, University of Gothenburg, Medicinaregatan 9A P.O. Box 440, SE405 30 Gothenburg, Sweden
| | - Carlo Viscomi
- Department of Biomedical Sciences, University of Padova, via Ugo Bassi 58/B-35131 Padova, Italy
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14
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S Mogre S, Brown AI, Koslover EF. Getting around the cell: physical transport in the intracellular world. Phys Biol 2020; 17:061003. [PMID: 32663814 DOI: 10.1088/1478-3975/aba5e5] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Eukaryotic cells face the challenging task of transporting a variety of particles through the complex intracellular milieu in order to deliver, distribute, and mix the many components that support cell function. In this review, we explore the biological objectives and physical mechanisms of intracellular transport. Our focus is on cytoplasmic and intra-organelle transport at the whole-cell scale. We outline several key biological functions that depend on physically transporting components across the cell, including the delivery of secreted proteins, support of cell growth and repair, propagation of intracellular signals, establishment of organelle contacts, and spatial organization of metabolic gradients. We then review the three primary physical modes of transport in eukaryotic cells: diffusive motion, motor-driven transport, and advection by cytoplasmic flow. For each mechanism, we identify the main factors that determine speed and directionality. We also highlight the efficiency of each transport mode in fulfilling various key objectives of transport, such as particle mixing, directed delivery, and rapid target search. Taken together, the interplay of diffusion, molecular motors, and flows supports the intracellular transport needs that underlie a broad variety of biological phenomena.
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Affiliation(s)
- Saurabh S Mogre
- Department of Physics, University of California, San Diego, San Diego, California 92093, United States of America
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15
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Sweet AD, Johnson KP, Cameron SL. Mitochondrial genomes of Columbicola feather lice are highly fragmented, indicating repeated evolution of minicircle-type genomes in parasitic lice. PeerJ 2020; 8:e8759. [PMID: 32231878 PMCID: PMC7098387 DOI: 10.7717/peerj.8759] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Accepted: 02/16/2020] [Indexed: 01/21/2023] Open
Abstract
Most animals have a conserved mitochondrial genome structure composed of a single chromosome. However, some organisms have their mitochondrial genes separated on several smaller circular or linear chromosomes. Highly fragmented circular chromosomes (“minicircles”) are especially prevalent in parasitic lice (Insecta: Phthiraptera), with 16 species known to have between nine and 20 mitochondrial minicircles per genome. All of these species belong to the same clade (mammalian lice), suggesting a single origin of drastic fragmentation. Nevertheless, other work indicates a lesser degree of fragmentation (2–3 chromosomes/genome) is present in some avian feather lice (Ischnocera: Philopteridae). In this study, we tested for minicircles in four species of the feather louse genus Columbicola (Philopteridae). Using whole genome shotgun sequence data, we applied three different bioinformatic approaches for assembling the Columbicola mitochondrial genome. We further confirmed these approaches by assembling the mitochondrial genome of Pediculus humanus from shotgun sequencing reads, a species known to have minicircles. Columbicola spp. genomes are highly fragmented into 15–17 minicircles between ∼1,100 and ∼3,100 bp in length, with 1–4 genes per minicircle. Subsequent annotation of the minicircles indicated that tRNA arrangements of minicircles varied substantially between species. These mitochondrial minicircles for species of Columbicola represent the first feather lice (Philopteridae) for which minicircles have been found in a full mitochondrial genome assembly. Combined with recent phylogenetic studies of parasitic lice, our results provide strong evidence that highly fragmented mitochondrial genomes, which are otherwise rare across the Tree of Life, evolved multiple times within parasitic lice.
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Affiliation(s)
- Andrew D Sweet
- Department of Entomology, Purdue University, West Lafayette, IN, United States of America
| | - Kevin P Johnson
- Illinois Natural History Survey, Prairie Research Institute, University of Illinois, Champaign, IL, United States of America
| | - Stephen L Cameron
- Department of Entomology, Purdue University, West Lafayette, IN, United States of America
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16
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Impact of global structure on diffusive exploration of organelle networks. Sci Rep 2020; 10:4984. [PMID: 32188905 PMCID: PMC7080787 DOI: 10.1038/s41598-020-61598-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Accepted: 02/25/2020] [Indexed: 01/08/2023] Open
Abstract
We investigate diffusive search on planar networks, motivated by tubular organelle networks in cell biology that contain molecules searching for reaction partners and binding sites. Exact calculation of the diffusive mean first-passage time on a spatial network is used to characterize the typical search time as a function of network connectivity. We find that global structural properties — the total edge length and number of loops — are sufficient to largely determine network exploration times for a variety of both synthetic planar networks and organelle morphologies extracted from living cells. For synthetic networks on a lattice, we predict the search time dependence on these global structural parameters by connecting with percolation theory, providing a bridge from irregular real-world networks to a simpler physical model. The dependence of search time on global network structural properties suggests that network architecture can be designed for efficient search without controlling the precise arrangement of connections. Specifically, increasing the number of loops substantially decreases search times, pointing to a potential physical mechanism for regulating reaction rates within organelle network structures.
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17
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Chiaratti MR, Macabelli CH, Augusto Neto JD, Grejo MP, Pandey AK, Perecin F, Collado MD. Maternal transmission of mitochondrial diseases. Genet Mol Biol 2020; 43:e20190095. [PMID: 32141474 PMCID: PMC7197987 DOI: 10.1590/1678-4685-gmb-2019-0095] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Accepted: 11/01/2019] [Indexed: 12/19/2022] Open
Abstract
Given the major role of the mitochondrion in cellular homeostasis, dysfunctions of this organelle may lead to several common diseases in humans. Among these, maternal diseases linked to mitochondrial DNA (mtDNA) mutations are of special interest due to the unclear pattern of mitochondrial inheritance. Multiple copies of mtDNA are present in a cell, each encoding for 37 genes essential for mitochondrial function. In cases of mtDNA mutations, mitochondrial malfunctioning relies on mutation load, as mutant and wild-type molecules may co-exist within the cell. Since the mutation load associated with disease manifestation varies for different mutations and tissues, it is hard to predict the progeny phenotype based on mutation load in the progenitor. In addition, poorly understood mechanisms act in the female germline to prevent the accumulation of deleterious mtDNA in the following generations. In this review, we outline basic aspects of mitochondrial inheritance in mammals and how they may lead to maternally-inherited diseases. Furthermore, we discuss potential therapeutic strategies for these diseases, which may be used in the future to prevent their transmission.
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Affiliation(s)
- Marcos R Chiaratti
- Universidade Federal de São Carlos, Departamento de Genética e Evolução, Laboratório de Genética e Biotecnologia, São Carlos, SP, Brazil
| | - Carolina H Macabelli
- Universidade Federal de São Carlos, Departamento de Genética e Evolução, Laboratório de Genética e Biotecnologia, São Carlos, SP, Brazil
| | - José Djaci Augusto Neto
- Universidade Federal de São Carlos, Departamento de Genética e Evolução, Laboratório de Genética e Biotecnologia, São Carlos, SP, Brazil
| | - Mateus Priolo Grejo
- Universidade Federal de São Carlos, Departamento de Genética e Evolução, Laboratório de Genética e Biotecnologia, São Carlos, SP, Brazil
| | - Anand Kumar Pandey
- Lala Lajpat Rai University of Veterinary and Animal Sciences, Hisar, Haryana, India
| | - Felipe Perecin
- Universidade de São Paulo, Faculdade de Zootecnia e Engenharia de Alimentos, Departamento de Medicina Veterinária, Laboratório de Morfofisiologia Molecular e Desenvolvimento, Pirassununga, SP, Brazil
| | - Maite Del Collado
- Universidade de São Paulo, Faculdade de Zootecnia e Engenharia de Alimentos, Departamento de Medicina Veterinária, Laboratório de Morfofisiologia Molecular e Desenvolvimento, Pirassununga, SP, Brazil
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18
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Intramitochondrial Src kinase links mitochondrial dysfunctions and aggressiveness of breast cancer cells. Cell Death Dis 2019; 10:940. [PMID: 31819039 PMCID: PMC6901437 DOI: 10.1038/s41419-019-2134-8] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Revised: 10/09/2019] [Accepted: 11/06/2019] [Indexed: 12/13/2022]
Abstract
High levels and activity of Src kinase are common among breast cancer subtypes, and several inhibitors of the kinase are currently tested in clinical trials. Alterations in mitochondrial activity is also observed among the different types of breast cancer. Src kinase is localized in several subcellular compartments, including mitochondria where it targets several proteins to modulate the activity of the organelle. Although the subcellular localization of other oncogenes modulates the potency of known treatments, nothing is known about the specific role of intra-mitochondrial Src (mtSrc) in breast cancer. The aim of this work was to determine whether mtSrc kinase has specific impact on breast cancer cells. We first observed that activity of mtSrc is higher in breast cancer cells of the triple negative subtype. Over-expression of Src specifically targeted to mitochondria reduced mtDNA levels, mitochondrial membrane potential and cellular respiration. These alterations of mitochondrial functions led to lower cellular viability, shorter cell cycle and increased invasive capacity. Proteomic analyses revealed that mtSrc targets the mitochondrial single-stranded DNA-binding protein, a regulator of mtDNA replication. Our findings suggest that mtSrc promotes aggressiveness of breast cancer cells via phosphorylation of mitochondrial single-stranded DNA-binding protein leading to reduced mtDNA levels and mitochondrial activity. This study highlights the importance of considering the subcellular localization of Src kinase in the development of potent therapy for breast cancer.
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19
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Holt IJ. The mitochondrial R-loop. Nucleic Acids Res 2019; 47:5480-5489. [PMID: 31045202 PMCID: PMC6582354 DOI: 10.1093/nar/gkz277] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Revised: 03/11/2019] [Accepted: 04/29/2019] [Indexed: 12/18/2022] Open
Abstract
The DNA in mitochondria contributes essential components of the organelle’s energy producing machinery that is essential for life. In 1971, many mitochondrial DNA molecules were found to have a third strand of DNA that maps to a region containing critical regulatory elements for transcription and replication. Forty-five years later, a third strand of RNA in the same region has been reported. This mitochondrial R-loop is present on thousands of copies of mitochondrial DNA per cell making it potentially the most abundant R-loop in nature. Here, I assess the discovery of the mitochondrial R-loop, discuss why it remained unrecognized for almost half a century and propose for it central roles in the replication, organization and expression of mitochondrial DNA, which if compromised can lead to disease states.
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Affiliation(s)
- Ian J Holt
- Biodonostia Health Research Institute, 20014 San Sebastián, Spain & IKERBASQUE, Basque Foundation for Science, 48013 Bilbao, Spain.,Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, Royal Free Campus, London, NW3 2PF, UK.,CIBERNED (Center for Networked Biomedical Research on Neurodegenerative Diseases, Ministry of Economy and Competitiveness, Institute Carlos III), Madrid, Spain
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20
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Ježek P, Dlasková A. Dynamic of mitochondrial network, cristae, and mitochondrial nucleoids in pancreatic β-cells. Mitochondrion 2019; 49:245-258. [DOI: 10.1016/j.mito.2019.06.007] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Revised: 06/21/2019] [Accepted: 06/24/2019] [Indexed: 12/17/2022]
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21
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Hensen F, Potter A, van Esveld SL, Tarrés-Solé A, Chakraborty A, Solà M, Spelbrink JN. Mitochondrial RNA granules are critically dependent on mtDNA replication factors Twinkle and mtSSB. Nucleic Acids Res 2019; 47:3680-3698. [PMID: 30715486 PMCID: PMC6468249 DOI: 10.1093/nar/gkz047] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Revised: 01/16/2019] [Accepted: 01/24/2019] [Indexed: 01/13/2023] Open
Abstract
Newly synthesized mitochondrial RNA is concentrated in structures juxtaposed to nucleoids, called RNA granules, that have been implicated in mitochondrial RNA processing and ribosome biogenesis. Here we show that two classical mtDNA replication factors, the mtDNA helicase Twinkle and single-stranded DNA-binding protein mtSSB, contribute to RNA metabolism in mitochondria and to RNA granule biology. Twinkle colocalizes with both mitochondrial RNA granules and nucleoids, and it can serve as bait to greatly enrich established RNA granule proteins, such as G-rich sequence factor 1, GRSF1. Likewise, mtSSB also is not restricted to the nucleoids, and repression of either mtSSB or Twinkle alters mtRNA metabolism. Short-term Twinkle depletion greatly diminishes RNA granules but does not inhibit RNA synthesis or processing. Either mtSSB or GRSF1 depletion results in RNA processing defects, accumulation of mtRNA breakdown products as well as increased levels of dsRNA and RNA:DNA hybrids. In particular, the processing and degradation defects become more pronounced with both proteins depleted. These findings suggest that Twinkle is essential for RNA organization in granules, and that mtSSB is involved in the recently proposed GRSF1-mtRNA degradosome pathway, a route suggested to be particularly aimed at degradation of G-quadruplex prone long non-coding mtRNAs.
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Affiliation(s)
- Fenna Hensen
- Radboud Center for Mitochondrial Medicine, Department of Paediatrics, Radboudumc, Nijmegen, The Netherlands
| | - Alisa Potter
- Radboud Center for Mitochondrial Medicine, Department of Paediatrics, Radboudumc, Nijmegen, The Netherlands
| | - Selma L van Esveld
- Radboud Center for Mitochondrial Medicine & Center for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, Radboudumc, Nijmegen, The Netherlands
| | - Aleix Tarrés-Solé
- Structural MitoLab, Department of Structural Biology, "Maria de Maeztu" Unit of Excellence, Molecular Biology Institute Barcelona (IBMB-CSIC), Barcelona 08028, Spain
| | - Arka Chakraborty
- Structural MitoLab, Department of Structural Biology, "Maria de Maeztu" Unit of Excellence, Molecular Biology Institute Barcelona (IBMB-CSIC), Barcelona 08028, Spain
| | - Maria Solà
- Structural MitoLab, Department of Structural Biology, "Maria de Maeztu" Unit of Excellence, Molecular Biology Institute Barcelona (IBMB-CSIC), Barcelona 08028, Spain
| | - Johannes N Spelbrink
- Radboud Center for Mitochondrial Medicine, Department of Paediatrics, Radboudumc, Nijmegen, The Netherlands
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22
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Gustafson MA, McCormick EM, Perera L, Longley MJ, Bai R, Kong J, Dulik M, Shen L, Goldstein AC, McCormack SE, Laskin BL, Leroy BP, Ortiz-Gonzalez XR, Ellington MG, Copeland WC, Falk MJ. Mitochondrial single-stranded DNA binding protein novel de novo SSBP1 mutation in a child with single large-scale mtDNA deletion (SLSMD) clinically manifesting as Pearson, Kearns-Sayre, and Leigh syndromes. PLoS One 2019; 14:e0221829. [PMID: 31479473 PMCID: PMC6719858 DOI: 10.1371/journal.pone.0221829] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2019] [Accepted: 08/15/2019] [Indexed: 12/04/2022] Open
Abstract
Mitochondrial DNA (mtDNA) genome integrity is essential for proper mitochondrial respiratory chain function to generate cellular energy. Nuclear genes encode several proteins that function at the mtDNA replication fork, including mitochondrial single-stranded DNA-binding protein (SSBP1), which is a tetrameric protein that binds and protects single-stranded mtDNA (ssDNA). Recently, two studies have reported pathogenic variants in SSBP1 associated with hearing loss, optic atrophy, and retinal degeneration. Here, we report a 14-year-old Chinese boy with severe and progressive mitochondrial disease manifestations across the full Pearson, Kearns-Sayre, and Leigh syndromes spectrum, including infantile anemia and bone marrow failure, growth failure, ptosis, ophthalmoplegia, ataxia, severe retinal dystrophy of the rod-cone type, sensorineural hearing loss, chronic kidney disease, multiple endocrine deficiencies, and metabolic strokes. mtDNA genome sequencing identified a single large-scale 5 kilobase mtDNA deletion (m.8629_14068del5440), present at 68% and 16% heteroplasmy in the proband's fibroblast cell line and blood, respectively, suggestive of a mtDNA maintenance defect. On trio whole exome blood sequencing, the proband was found to harbor a novel de novo heterozygous mutation c.79G>A (p.E27K) in SSBP1. Size exclusion chromatography of p.E27K SSBP1 revealed it remains a stable tetramer. However, differential scanning fluorimetry demonstrated p.E27K SSBP1 relative to wild type had modestly decreased thermostability. Functional assays also revealed p.E27K SSBP1 had altered DNA binding. Molecular modeling of SSBP1 tetramers with varying combinations of mutant subunits predicted general changes in surface accessible charges, strength of inter-subunit interactions, and protein dynamics. Overall, the observed changes in protein dynamics and DNA binding behavior suggest that p.E27K SSBP1 can interfere with DNA replication and precipitate the introduction of large-scale mtDNA deletions. Thus, a single large-scale mtDNA deletion (SLSMD) with manifestations across the clinical spectrum of Pearson, Kearns-Sayre, and Leigh syndromes may result from a nuclear gene disorder disrupting mitochondrial DNA replication.
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Affiliation(s)
- Margaret A. Gustafson
- Genome Integrity and Structural Biology Laboratory, NIEHS, NIH, Research Triangle Park, NC, United States of America
| | - Elizabeth M. McCormick
- Mitochondrial Medicine Frontier Program, Division of Human Genetics, Department of Pediatrics, Children’s Hospital of Philadelphia, Philadelphia, PA, United States of America
| | - Lalith Perera
- Genome Integrity and Structural Biology Laboratory, NIEHS, NIH, Research Triangle Park, NC, United States of America
| | - Matthew J. Longley
- Genome Integrity and Structural Biology Laboratory, NIEHS, NIH, Research Triangle Park, NC, United States of America
| | - Renkui Bai
- GeneDx, Gaithersburg, MD, United States of America
| | - Jianping Kong
- Mitochondrial Medicine Frontier Program, Division of Human Genetics, Department of Pediatrics, Children’s Hospital of Philadelphia, Philadelphia, PA, United States of America
| | - Matthew Dulik
- Mitochondrial Medicine Frontier Program, Division of Human Genetics, Department of Pediatrics, Children’s Hospital of Philadelphia, Philadelphia, PA, United States of America
- Department of Pathology and Laboratory Medicine, Children’s Hospital of Philadelphia, Philadelphia, PA, United States of America
| | - Lishuang Shen
- Center for Personalized Medicine, Department of Pathology & Laboratory Medicine, Children’s Hospital Los Angeles, Los Angeles, CA, United States of America
| | - Amy C. Goldstein
- Mitochondrial Medicine Frontier Program, Division of Human Genetics, Department of Pediatrics, Children’s Hospital of Philadelphia, Philadelphia, PA, United States of America
- Department of Pediatrics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, United States of America
| | - Shana E. McCormack
- Mitochondrial Medicine Frontier Program, Division of Human Genetics, Department of Pediatrics, Children’s Hospital of Philadelphia, Philadelphia, PA, United States of America
- Department of Pediatrics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, United States of America
- Division of Endocrinology and Diabetes, Children's Hospital of Philadelphia, Philadelphia, PA, United States of America
| | - Benjamin L. Laskin
- Department of Pediatrics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, United States of America
- Division of Nephrology, Children's Hospital of Philadelphia, Philadelphia, PA, United States of America
| | - Bart P. Leroy
- Center for Medical Genetics Ghent, Ghent University and Ghent University Hospital, Ghent, Belgium
- Department of Ophthalmology, Ghent University Hospital, Ghent, Belgium
- Division of Ophthalmology, Children's Hospital of Philadelphia, Philadelphia, PA, United States of America
| | - Xilma R. Ortiz-Gonzalez
- Division of Neurology, Children's Hospital of Philadelphia, Philadelphia, PA, United States of America
| | - Meredith G. Ellington
- Genome Integrity and Structural Biology Laboratory, NIEHS, NIH, Research Triangle Park, NC, United States of America
| | - William C. Copeland
- Genome Integrity and Structural Biology Laboratory, NIEHS, NIH, Research Triangle Park, NC, United States of America
| | - Marni J. Falk
- Mitochondrial Medicine Frontier Program, Division of Human Genetics, Department of Pediatrics, Children’s Hospital of Philadelphia, Philadelphia, PA, United States of America
- Department of Pediatrics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, United States of America
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23
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Kaur P, Longley MJ, Pan H, Wang H, Copeland WC. Single-molecule DREEM imaging reveals DNA wrapping around human mitochondrial single-stranded DNA binding protein. Nucleic Acids Res 2019; 46:11287-11302. [PMID: 30256971 PMCID: PMC6265486 DOI: 10.1093/nar/gky875] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Accepted: 09/18/2018] [Indexed: 01/01/2023] Open
Abstract
Improper maintenance of the mitochondrial genome progressively disrupts cellular respiration and causes severe metabolic disorders commonly termed mitochondrial diseases. Mitochondrial single-stranded DNA binding protein (mtSSB) is an essential component of the mtDNA replication machinery. We utilized single-molecule methods to examine the modes by which human mtSSB binds DNA to help define protein interactions at the mtDNA replication fork. Direct visualization of individual mtSSB molecules by atomic force microscopy (AFM) revealed a random distribution of mtSSB tetramers bound to extended regions of single-stranded DNA (ssDNA), strongly suggesting non-cooperative binding by mtSSB. Selective binding to ssDNA was confirmed by AFM imaging of individual mtSSB tetramers bound to gapped plasmid DNA substrates bearing defined single-stranded regions. Shortening of the contour length of gapped DNA upon binding mtSSB was attributed to DNA wrapping around mtSSB. Tracing the DNA path in mtSSB–ssDNA complexes with Dual-Resonance-frequency-Enhanced Electrostatic force Microscopy established a predominant binding mode with one DNA strand winding once around each mtSSB tetramer at physiological salt conditions. Single-molecule imaging suggests mtSSB may not saturate or fully protect single-stranded replication intermediates during mtDNA synthesis, leaving the mitochondrial genome vulnerable to chemical mutagenesis, deletions driven by primer relocation or other actions consistent with clinically observed deletion biases.
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Affiliation(s)
- Parminder Kaur
- Physics Department, North Carolina State University, Raleigh, North Carolina, NC 27695, USA.,Center for Human Health and the Environment, North Carolina State University, Raleigh, North Carolina, NC 27695, USA
| | - Matthew J Longley
- Genome Integrity and Structural Biology Laboratory, NIEHS, NIH, Research Triangle Park, NC 27709, USA
| | - Hai Pan
- Physics Department, North Carolina State University, Raleigh, North Carolina, NC 27695, USA
| | - Hong Wang
- Physics Department, North Carolina State University, Raleigh, North Carolina, NC 27695, USA.,Center for Human Health and the Environment, North Carolina State University, Raleigh, North Carolina, NC 27695, USA
| | - William C Copeland
- Genome Integrity and Structural Biology Laboratory, NIEHS, NIH, Research Triangle Park, NC 27709, USA
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24
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Chu Q, Ding Y, Cai W, Liu L, Zhang H, Song J. Marek's Disease Virus Infection Induced Mitochondria Changes in Chickens. Int J Mol Sci 2019; 20:ijms20133150. [PMID: 31252692 PMCID: PMC6651546 DOI: 10.3390/ijms20133150] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2019] [Revised: 06/24/2019] [Accepted: 06/26/2019] [Indexed: 11/16/2022] Open
Abstract
Mitochondria are crucial cellular organelles in eukaryotes and participate in many cell processes including immune response, growth development, and tumorigenesis. Marek’s disease (MD), caused by an avian alpha-herpesvirus Marek’s disease virus (MDV), is characterized with lymphomas and immunosuppression. In this research, we hypothesize that mitochondria may play roles in response to MDV infection. To test it, mitochondrial DNA (mtDNA) abundance and gene expression in immune organs were examined in two well-defined and highly inbred lines of chickens, the MD-susceptible line 72 and the MD-resistant line 63. We found that mitochondrial DNA contents decreased significantly at the transformation phase in spleen of the MD-susceptible line 72 birds in contrast to the MD-resistant line 63. The mtDNA-genes and the nucleus-genes relevant to mtDNA maintenance and transcription, however, were significantly up-regulated. Interestingly, we found that POLG2 might play a potential role that led to the imbalance of mtDNA copy number and gene expression alteration. MDV infection induced imbalance of mitochondrial contents and gene expression, demonstrating the indispensability of mitochondria in virus-induced cell transformation and subsequent lymphoma formation, such as MD development in chicken. This is the first report on relationship between virus infection and mitochondria in chicken, which provides important insights into the understanding on pathogenesis and tumorigenesis due to viral infection.
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Affiliation(s)
- Qin Chu
- Institute of Animal Husbandry and Veterinary Medicine, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100094, China
- Department of Animal and Avian Sciences, University of Maryland, College Park, MD 20740, USA
| | - Yi Ding
- Department of Animal and Avian Sciences, University of Maryland, College Park, MD 20740, USA
| | - Wentao Cai
- Department of Animal and Avian Sciences, University of Maryland, College Park, MD 20740, USA
| | - Lei Liu
- Department of Animal and Avian Sciences, University of Maryland, College Park, MD 20740, USA
| | - Huanmin Zhang
- USDA, Agriculture Research Service, Avian Disease and Oncology Laboratory, East Lansing, MI 48823, USA
| | - Jiuzhou Song
- Department of Animal and Avian Sciences, University of Maryland, College Park, MD 20740, USA.
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25
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Kullar PJ, Gomez-Duran A, Gammage PA, Garone C, Minczuk M, Golder Z, Wilson J, Montoya J, Häkli S, Kärppä M, Horvath R, Majamaa K, Chinnery PF. Heterozygous SSBP1 start loss mutation co-segregates with hearing loss and the m.1555A>G mtDNA variant in a large multigenerational family. Brain 2019; 141:55-62. [PMID: 29182774 PMCID: PMC5837410 DOI: 10.1093/brain/awx295] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2017] [Accepted: 09/25/2017] [Indexed: 11/30/2022] Open
Abstract
The m.1555A>G mtDNA variant causes maternally inherited deafness, but the reasons for the highly variable clinical penetrance are not known. Exome sequencing identified a heterozygous start loss mutation in SSBP1, encoding the single stranded binding protein 1 (SSBP1), segregating with hearing loss in a multi-generational family transmitting m.1555A>G, associated with mtDNA depletion and multiple deletions in skeletal muscle. The SSBP1 mutation reduced steady state SSBP1 levels leading to a perturbation of mtDNA metabolism, likely compounding the intra-mitochondrial translation defect due to m.1555A>G in a tissue-specific manner. This family demonstrates the importance of rare trans-acting genetic nuclear modifiers in the clinical expression of mtDNA disease.
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Affiliation(s)
- Peter J Kullar
- MRC-Mitochondrial Biology Unit, University of Cambridge, CB2 0XY, UK.,Department of Clinical Neurosciences, University of Cambridge, Cambridge, CB2 0QQ, UK
| | - Aurora Gomez-Duran
- MRC-Mitochondrial Biology Unit, University of Cambridge, CB2 0XY, UK.,Department of Clinical Neurosciences, University of Cambridge, Cambridge, CB2 0QQ, UK
| | - Payam A Gammage
- MRC-Mitochondrial Biology Unit, University of Cambridge, CB2 0XY, UK
| | - Caterina Garone
- MRC-Mitochondrial Biology Unit, University of Cambridge, CB2 0XY, UK
| | - Michal Minczuk
- MRC-Mitochondrial Biology Unit, University of Cambridge, CB2 0XY, UK
| | - Zoe Golder
- MRC-Mitochondrial Biology Unit, University of Cambridge, CB2 0XY, UK.,Department of Clinical Neurosciences, University of Cambridge, Cambridge, CB2 0QQ, UK
| | - Janet Wilson
- Institute of Health and Society, Newcastle University, Baddiley-Clark Building, Richardson Road, Newcastle upon Tyne, NE2 4AX, UK
| | - Julio Montoya
- Universidad de Zaragoza-CIBER de Enfermedades Raras (CIBERER)-Instituto de Investigación Sanitaria de Aragón, Spain
| | - Sanna Häkli
- Research Unit of Clinical Neuroscience, University of Oulu, Oulu, Finland and Medical Research Center Oulu, Oulu University Hospital and University of Oulu, Oulu, Finland
| | - Mikko Kärppä
- Research Unit of Clinical Neuroscience, University of Oulu, Oulu, Finland and Medical Research Center Oulu, Oulu University Hospital and University of Oulu, Oulu, Finland
| | - Rita Horvath
- Institute of Genetic Medicine, Newcastle University, UK
| | - Kari Majamaa
- Research Unit of Clinical Neuroscience, University of Oulu, Oulu, Finland and Medical Research Center Oulu, Oulu University Hospital and University of Oulu, Oulu, Finland
| | - Patrick F Chinnery
- MRC-Mitochondrial Biology Unit, University of Cambridge, CB2 0XY, UK.,Department of Clinical Neurosciences, University of Cambridge, Cambridge, CB2 0QQ, UK
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26
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Mitochondrial Nucleoids: Superresolution microscopy analysis. Int J Biochem Cell Biol 2018; 106:21-25. [PMID: 30391784 DOI: 10.1016/j.biocel.2018.10.012] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Revised: 10/11/2018] [Accepted: 10/15/2018] [Indexed: 11/23/2022]
Abstract
The mitochondrion owns an autonomous genome. Double-stranded circular mitochondrial DNA (mtDNA) is organized in complexes with a packing/stabilizing transcription factor TFAM, having multiple roles, and proteins of gene expression machinery in structures called nucleoids. From hundreds to thousands nucleoids exist distributed in the matrix of mitochondrial reticulum network. A single mtDNA molecule contained within the single nucleoid is a currently preferred but questioned model. Nevertheless, mtDNA replication should lead transiently to its doubling within a nucleoid. However, nucleoid division has not yet been documented in detail. A 3D superresolution microscopy is required to resolve nucleoid biology occurring in ∼100 nm space, having an advantage over electron microscopy tomography in resolving the particular protein components. We discuss stochastic vs. stimulated emission depletion microscopy yielding wide vs. narrow nucleoid size distribution, respectively. Nucleoid clustering into spheroids fragmented from the continuous mitochondrial network, likewise possible nucleoid attachment to the inner membrane is reviewed.
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27
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Tian HP, Sun YH, He L, Yi YF, Gao X, Xu DL. Single-Stranded DNA-Binding Protein 1 Abrogates Cardiac Fibroblast Proliferation and Collagen Expression Induced by Angiotensin II. Int Heart J 2018; 59:1398-1408. [PMID: 30369577 DOI: 10.1536/ihj.17-650] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Angiotensin II (Ang II), an effective component of renin-angiotensin system, plays a pivotal role in cardiac fibrosis, which may further contribute to heart failure. Single-stranded DNA-binding protein 1 (SSBP1), a DNA damage response protein, regulates both mitochondrial function and extracellular matrix remodeling. In this study, we aim to investigate the role of SSBP1 in cardiac fibrosis that is induced by Ang II. We infused C57BL/6J mice with vehicle or Ang II and valsartan using implanted osmotic mini-pumps. Moreover, heart function was examined by echocardiography and cardiac fibrosis was analyzed via picrosirus red staining. The expression of COL1A1, COL3A1, SSBP1, p53, Nox1, and Nox4 was analyzed via qRT-PCR and/or immunoblots. The SSBP1 expression was manipulated via SSBP1 shRNA and pcDNA3.1/SSBP1 plasmids, while the p53 expression was enhanced via AdCMV-p53 infection. The exposure to Ang II increased the mouse heart weight, systolic blood pressure, interventricular septal thickness diastolic (IVSTD) and left ventricular end posterior wall dimension diastolic (LVPWD), which were counteracted by valsartan. While cardiac fibrosis was induced with Ang II treatment, it was relieved using valsartan. Furthermore, Ang II treatment caused mitochondrial dysfunction, oxidative stress, and down-regulated SSBP1 expression. The knockdown of SSBP1 increased cardiac fibroblast proliferation, collagen expression, and decreased p53 expression, which was impeded via SSBP1 overexpression. Moreover, the forced expression of p53 abated the fibroblast proliferation and collagen expression that was induced by Ang II. To summarize, SSBP1 was down-regulated by Ang II and implicated in cardiac fibroblast proliferation and collagen expression partly via the p53 protein.
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Affiliation(s)
- Hai-Ping Tian
- Department of Cardiology, Nanfang Hospital, Southern Medical University.,Department of Cardiology, Affiliated Hospital of Inner Mongolia Medical University
| | - Yan-Hong Sun
- Department of Physiology, Inner Mongolia Medical University
| | - Lan He
- Department of Respiratory Diseases, Affiliated Hospital of Inner Mongolia Medical University
| | - Ya-Fang Yi
- Department of Cardiology, Affiliated Hospital of Inner Mongolia Medical University
| | - Xiang Gao
- Department of Cardiology, Affiliated Hospital of Inner Mongolia Medical University
| | - Ding-Li Xu
- Department of Cardiology, Nanfang Hospital, Southern Medical University
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28
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Sharma N, Chakravarthy S, Longley MJ, Copeland WC, Prakash A. The C-terminal tail of the NEIL1 DNA glycosylase interacts with the human mitochondrial single-stranded DNA binding protein. DNA Repair (Amst) 2018; 65:11-19. [PMID: 29522991 PMCID: PMC5911420 DOI: 10.1016/j.dnarep.2018.02.012] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2017] [Revised: 02/27/2018] [Accepted: 02/28/2018] [Indexed: 12/11/2022]
Abstract
The 16.5 kb mitochondrial genome is subjected to damage from reactive oxygen species (ROS) generated in the cell during normal cellular metabolism and external sources such as ionizing radiation and ultraviolet light. ROS cause harmful damage to DNA bases that could result in mutagenesis and various diseases, if not properly repaired. The base excision repair (BER) pathway is the primary pathway involved in maintaining the integrity of mtDNA. Several enzymes that partake in BER within the nucleus have also been identified in the mitochondria. The nei-like (NEIL) DNA glycosylases initiate BER by excising oxidized pyrimidine bases and others such as the ring-opened formamidopyrimidine and the hydantoin lesions. During BER, the NEIL enzymes interact with proteins that are involved with DNA replication and transcription. In the current manuscript, we detected NEIL1 in purified mitochondrial extracts from human cells and showed that NEIL1 interacts with the human mitochondrial single-stranded DNA binding protein (mtSSB) via its C-terminal tail using protein painting, far-western analysis, and gel-filtration chromatography. Finally, we scrutinized the NEIL1-mtSSB interaction in the presence and absence of a partial-duplex DNA substrate using a combination of multi-angle light scattering (MALS) and small-angle X-ray scattering (SAXS). The data indicate that NEIL1 and homotetrameric mtSSB form a larger ternary complex in presence of DNA, however, the tetrameric form of mtSSB gets disrupted by NEIL1 in the absence of DNA as revealed by the formation of a smaller NEIL1-mtSSBmonomer complex.
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Affiliation(s)
- Nidhi Sharma
- University of South Alabama, Mitchell Cancer Institute, 1660 Springhill Avenue, Mobile, AL 36604, United States
| | - Srinivas Chakravarthy
- Illinois Institute of Technology, Advanced Photon Source, Bldg. 435B/Sector 18, 9700 S. Cass Avenue, Argonne, IL 60439-4860, United States
| | - Matthew J Longley
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, 111 T.W. Alexander Drive, Research Triangle Park, NC 27709, United States
| | - William C Copeland
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, 111 T.W. Alexander Drive, Research Triangle Park, NC 27709, United States
| | - Aishwarya Prakash
- University of South Alabama, Mitchell Cancer Institute, 1660 Springhill Avenue, Mobile, AL 36604, United States.
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29
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Nuclear genes involved in mitochondrial diseases caused by instability of mitochondrial DNA. J Appl Genet 2018; 59:43-57. [PMID: 29344903 PMCID: PMC5799321 DOI: 10.1007/s13353-017-0424-3] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2017] [Accepted: 12/20/2017] [Indexed: 02/07/2023]
Abstract
Mitochondrial diseases are defined by a respiratory chain dysfunction and in most of the cases manifest as multisystem disorders with predominant expression in muscles and nerves and may be caused by mutations in mitochondrial (mtDNA) or nuclear (nDNA) genomes. Most of the proteins involved in respiratory chain function are nuclear encoded, although 13 subunits of respiratory chain complexes (together with 2 rRNAs and 22 tRNAs necessary for their translation) encoded by mtDNA are essential for cell function. nDNA encodes not only respiratory chain subunits but also all the proteins responsible for mtDNA maintenance, especially those involved in replication, as well as other proteins necessary for the transcription and copy number control of this multicopy genome. Mutations in these genes can cause secondary instability of the mitochondrial genome in the form of depletion (decreased number of mtDNA molecules in the cell), vast multiple deletions or accumulation of point mutations which in turn leads to mitochondrial diseases inherited in a Mendelian fashion. The list of genes involved in mitochondrial DNA maintenance is long, and still incomplete.
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30
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Herbers E, Kekäläinen NJ, Hangas A, Pohjoismäki JL, Goffart S. Tissue specific differences in mitochondrial DNA maintenance and expression. Mitochondrion 2018; 44:85-92. [PMID: 29339192 DOI: 10.1016/j.mito.2018.01.004] [Citation(s) in RCA: 79] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2017] [Revised: 01/05/2018] [Accepted: 01/11/2018] [Indexed: 01/17/2023]
Abstract
The different cell types of multicellular organisms have specialized physiological requirements, affecting also their mitochondrial energy production and metabolism. The genome of mitochondria is essential for mitochondrial oxidative phosphorylation (OXHPOS) and thus plays a central role in many human mitochondrial pathologies. Disorders affecting mitochondrial DNA (mtDNA) maintenance are typically resulting in a tissue-specific pattern of mtDNA deletions and rearrangements. Despite this role in disease as well as a biomarker of mitochondrial biogenesis, the tissue-specific parameters of mitochondrial DNA maintenance have been virtually unexplored. In the presented study, we investigated mtDNA replication, topology, gene expression and damage in six different tissues of adult mice and sought to correlate these with the levels of known protein factors involved in mtDNA replication and transcription. Our results show that while liver and kidney cells replicate their mtDNA using the asynchronous mechanism known from cultured cells, tissues with high OXPHOS activity, such as heart, brain, skeletal muscle and brown fat, employ a strand-coupled replication mode, combined with increased levels of recombination. The strand-coupled replication mode correlated also with mtDNA damage levels, indicating that the replication mechanism represents a tissue-specific strategy to deal with intrinsic oxidative stress. While the preferred replication mode did not correlate with mtDNA transcription or the levels of most known mtDNA maintenance proteins, mtSSB was most abundant in tissues using strand-asynchronous mechanism. Although mitochondrial transcripts were most abundant in tissues with high metabolic rate, the mtDNA copy number per tissue mass was remarkably similar in all tissues. We propose that the tissue-specific features of mtDNA maintenance are primarily driven by the intrinsic reactive oxygen species exposure, mediated by DNA repair factors, whose identity remains to be elucidated.
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Affiliation(s)
- Elena Herbers
- Department of Environmental and Biological Sciences, University of Eastern Finland, P.O. Box 111, FI 80101, Joensuu, Finland
| | - Nina J Kekäläinen
- Department of Environmental and Biological Sciences, University of Eastern Finland, P.O. Box 111, FI 80101, Joensuu, Finland
| | - Anu Hangas
- Department of Environmental and Biological Sciences, University of Eastern Finland, P.O. Box 111, FI 80101, Joensuu, Finland
| | - Jaakko L Pohjoismäki
- Department of Environmental and Biological Sciences, University of Eastern Finland, P.O. Box 111, FI 80101, Joensuu, Finland
| | - Steffi Goffart
- Department of Environmental and Biological Sciences, University of Eastern Finland, P.O. Box 111, FI 80101, Joensuu, Finland.
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Li Q, Qu F, Li R, He X, Zhai Y, Chen W, Zheng Y. A functional polymorphism of SSBP1 gene predicts prognosis and response to chemotherapy in resected gastric cancer patients. Oncotarget 2017; 8:110861-110876. [PMID: 29340022 PMCID: PMC5762290 DOI: 10.18632/oncotarget.22864] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2017] [Accepted: 11/03/2017] [Indexed: 12/17/2022] Open
Abstract
Growing evidence has indicated that single-stranded DNA-binding proteins 1 (SSBP1) is involved in tumor initiation and progression. However, effects of single nucleotide polymorphisms (SNPs) in SSBP1 gene on gastric cancer (GC) prognosis are still unknown. In present study, two functional SNPs from SSBP1 were selected and genotyped in a large cohorts of 1030 resected GC patients (326 in the training set, 704 in the validation set) to explore the association of SNPs with patients’ survival. The rs6976500 G allele (CG/GG) genotypes were found significantly associated with both worse overall survival (OS) and recurrence-free survival (RFS) in the training and the independent validation set when compared to C allele genotype, which reaching a more robust statistical significance in the pooled analysis. Furthermore, integration of rs6976500 genotypes and TNM stage significantly improved the prognosis prediction models based on TNM stage alone. In addition, only carriers with at least one G allele of rs6976500 gained significant survival benefit from FOLFOX-based ACT. Mechanistically, SNP rs6976500 G allele genotype could significantly decrease promoter transcriptional activity and markedly reduce expression level of SSBP1 compared with the C allele genotype in GC cells. This was further substantiated by immunohistochemical assay in 70 GC tissue samples. Our study presents the first evidence that SNP rs6976500 G allele genotypes might contribute to GC prognosis by attenuating SSBP1 promoter activity and gene expression, and provides the guidance in refining therapeutic decisions of GC patients. Further exploration on its function is needed to clarify the exact biological mechanism behind.
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Affiliation(s)
- Qiuchen Li
- Department of Gastroenterology, First Affiliated Hospital of the Medical College, Shihezi University, Shihezi, Xinjiang, 832008, China
| | - Falin Qu
- Department of General Surgery, Tangdu Hospital, The Fourth Military Medical University, Xi'an, Shaanxi, 710038, China
| | - Renli Li
- Department of General Surgery, The Fourth Hospital of Chinese PLA, Xining, Qinghai, 810007, China
| | - Xianli He
- Department of General Surgery, Tangdu Hospital, The Fourth Military Medical University, Xi'an, Shaanxi, 710038, China
| | - Yulong Zhai
- Department of General Surgery, Tangdu Hospital, The Fourth Military Medical University, Xi'an, Shaanxi, 710038, China
| | - Weigang Chen
- Department of Gastroenterology, First Affiliated Hospital of the Medical College, Shihezi University, Shihezi, Xinjiang, 832008, China
| | - Yong Zheng
- Department of Gastroenterology, First Affiliated Hospital of the Medical College, Shihezi University, Shihezi, Xinjiang, 832008, China
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32
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Špaček T, Pavluch V, Alán L, Capková N, Engstová H, Dlasková A, Berková Z, Saudek F, Ježek P. Nkx6.1 decline accompanies mitochondrial DNA reduction but subtle nucleoid size decrease in pancreatic islet β-cells of diabetic Goto Kakizaki rats. Sci Rep 2017; 7:15674. [PMID: 29142323 PMCID: PMC5688109 DOI: 10.1038/s41598-017-15958-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2017] [Accepted: 11/04/2017] [Indexed: 01/12/2023] Open
Abstract
Hypertrophic pancreatic islets (PI) of Goto Kakizaki (GK) diabetic rats contain a lower number of β-cells vs. non-diabetic Wistar rat PI. Remaining β-cells contain reduced mitochondrial (mt) DNA per nucleus (copy number), probably due to declining mtDNA replication machinery, decreased mt biogenesis or enhanced mitophagy. We confirmed mtDNA copy number decrease down to <30% in PI of one-year-old GK rats. Studying relations to mt nucleoids sizes, we employed 3D superresolution fluorescent photoactivable localization microscopy (FPALM) with lentivirally transduced Eos conjugate of mt single-stranded-DNA-binding protein (mtSSB) or transcription factor TFAM; or by 3D immunocytochemistry. mtSSB (binding transcription or replication nucleoids) contoured "nucleoids" which were smaller by 25% (less diameters >150 nm) in GK β-cells. Eos-TFAM-visualized nucleoids, composed of 72% localized TFAM, were smaller by 10% (immunochemically by 3%). A theoretical ~70% decrease in cell nucleoid number (spatial density) was not observed, rejecting model of single mtDNA per nucleoid. The β-cell maintenance factor Nkx6.1 mRNA and protein were declining with age (>12-fold, 10 months) and decreasing with fasting hyperglycemia in GK rats, probably predetermining the impaired mtDNA replication (copy number decrease), while spatial expansion of mtDNA kept nucleoids with only smaller sizes than those containing much higher mtDNA in non-diabetic β-cells.
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Affiliation(s)
- Tomáš Špaček
- Department of Mitochondrial Physiology, No.75, Institute of Physiology, Academy of Sciences of the Czech Republic, Prague, Czech Republic
| | - Vojtěch Pavluch
- Department of Mitochondrial Physiology, No.75, Institute of Physiology, Academy of Sciences of the Czech Republic, Prague, Czech Republic
| | - Lukáš Alán
- Department of Mitochondrial Physiology, No.75, Institute of Physiology, Academy of Sciences of the Czech Republic, Prague, Czech Republic
| | - Nikola Capková
- Department of Mitochondrial Physiology, No.75, Institute of Physiology, Academy of Sciences of the Czech Republic, Prague, Czech Republic
| | - Hana Engstová
- Department of Mitochondrial Physiology, No.75, Institute of Physiology, Academy of Sciences of the Czech Republic, Prague, Czech Republic
| | - Andrea Dlasková
- Department of Mitochondrial Physiology, No.75, Institute of Physiology, Academy of Sciences of the Czech Republic, Prague, Czech Republic
| | - Zuzana Berková
- Institute of Clinical and Experimental Medicine, Prague, Czech Republic
| | - František Saudek
- Institute of Clinical and Experimental Medicine, Prague, Czech Republic
| | - Petr Ježek
- Department of Mitochondrial Physiology, No.75, Institute of Physiology, Academy of Sciences of the Czech Republic, Prague, Czech Republic.
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Morin JA, Cerrón F, Jarillo J, Beltran-Heredia E, Ciesielski GL, Arias-Gonzalez JR, Kaguni LS, Cao FJ, Ibarra B. DNA synthesis determines the binding mode of the human mitochondrial single-stranded DNA-binding protein. Nucleic Acids Res 2017; 45:7237-7248. [PMID: 28486639 PMCID: PMC5499585 DOI: 10.1093/nar/gkx395] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Accepted: 04/27/2017] [Indexed: 12/02/2022] Open
Abstract
Single-stranded DNA-binding proteins (SSBs) play a key role in genome maintenance, binding and organizing single-stranded DNA (ssDNA) intermediates. Multimeric SSBs, such as the human mitochondrial SSB (HmtSSB), present multiple sites to interact with ssDNA, which has been shown in vitro to enable them to bind a variable number of single-stranded nucleotides depending on the salt and protein concentration. It has long been suggested that different binding modes might be used selectively for different functions. To study this possibility, we used optical tweezers to determine and compare the structure and energetics of long, individual HmtSSB–DNA complexes assembled on preformed ssDNA and on ssDNA generated gradually during ‘in situ’ DNA synthesis. We show that HmtSSB binds to preformed ssDNA in two major modes, depending on salt and protein concentration. However, when protein binding was coupled to strand-displacement DNA synthesis, only one of the two binding modes was observed under all experimental conditions. Our results reveal a key role for the gradual generation of ssDNA in modulating the binding mode of a multimeric SSB protein and consequently, in generating the appropriate nucleoprotein structure for DNA synthetic reactions required for genome maintenance.
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Affiliation(s)
- José A Morin
- Instituto Madrileño de Estudios Avanzados en Nanociencia, IMDEA Nanociencia, 28049 Madrid, Spain
| | - Fernando Cerrón
- Instituto Madrileño de Estudios Avanzados en Nanociencia, IMDEA Nanociencia, 28049 Madrid, Spain
| | - Javier Jarillo
- Departamento Física Atómica, Molecular y Nuclear, Universidad Complutense, 28040 Madrid, Spain
| | - Elena Beltran-Heredia
- Departamento Física Atómica, Molecular y Nuclear, Universidad Complutense, 28040 Madrid, Spain
| | - Grzegorz L Ciesielski
- Institute of Biosciences and Medical Technology, University of Tampere, 33520 Tampere, Finland.,Department of Biochemistry and Molecular Biology and Center for Mitochondrial Science and Medicine, Michigan State University, East Lansing, MI 48823, USA
| | - J Ricardo Arias-Gonzalez
- Instituto Madrileño de Estudios Avanzados en Nanociencia, IMDEA Nanociencia, 28049 Madrid, Spain.,Instituto Madrileño de Estudios Avanzados en Nanociencia (IMDEA Nanociencia) and CNB-CSIC-IMDEA Nanociencia Associated Unit 'Unidad de Nanobiotecnología', 28049 Madrid, Spain
| | - Laurie S Kaguni
- Institute of Biosciences and Medical Technology, University of Tampere, 33520 Tampere, Finland.,Department of Biochemistry and Molecular Biology and Center for Mitochondrial Science and Medicine, Michigan State University, East Lansing, MI 48823, USA
| | - Francisco J Cao
- Departamento Física Atómica, Molecular y Nuclear, Universidad Complutense, 28040 Madrid, Spain
| | - Borja Ibarra
- Instituto Madrileño de Estudios Avanzados en Nanociencia, IMDEA Nanociencia, 28049 Madrid, Spain.,Instituto Madrileño de Estudios Avanzados en Nanociencia (IMDEA Nanociencia) and CNB-CSIC-IMDEA Nanociencia Associated Unit 'Unidad de Nanobiotecnología', 28049 Madrid, Spain
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34
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Dalla Rosa I, Zhang H, Khiati S, Wu X, Pommier Y. Transcription profiling suggests that mitochondrial topoisomerase IB acts as a topological barrier and regulator of mitochondrial DNA transcription. J Biol Chem 2017; 292:20162-20172. [PMID: 29021209 DOI: 10.1074/jbc.m117.815241] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Revised: 10/01/2017] [Indexed: 11/06/2022] Open
Abstract
Mitochondrial DNA (mtDNA) is essential for cell viability because it encodes subunits of the respiratory chain complexes. Mitochondrial topoisomerase IB (TOP1MT) facilitates mtDNA replication by removing DNA topological tensions produced during mtDNA transcription, but it appears to be dispensable. To test whether cells lacking TOP1MT have aberrant mtDNA transcription, we performed mitochondrial transcriptome profiling. To that end, we designed and implemented a customized tiling array, which enabled genome-wide, strand-specific, and simultaneous detection of all mitochondrial transcripts. Our technique revealed that Top1mt KO mouse cells process the mitochondrial transcripts normally but that protein-coding mitochondrial transcripts are elevated. Moreover, we found discrete long noncoding RNAs produced by H-strand transcription and encompassing the noncoding regulatory region of mtDNA in human and murine cells and tissues. Of note, these noncoding RNAs were strongly up-regulated in the absence of TOP1MT. In contrast, 7S DNA, produced by mtDNA replication, was reduced in the Top1mt KO cells. We propose that the long noncoding RNA species in the D-loop region are generated by the extension of H-strand transcripts beyond their canonical stop site and that TOP1MT acts as a topological barrier and regulator for mtDNA transcription and D-loop formation.
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Affiliation(s)
- Ilaria Dalla Rosa
- Laboratory of Molecular Pharmacology, Developmental Therapeutics Branch, Center for Cancer Research, NCI, National Institutes of Health, Bethesda, Maryland 20892
| | - Hongliang Zhang
- Laboratory of Molecular Pharmacology, Developmental Therapeutics Branch, Center for Cancer Research, NCI, National Institutes of Health, Bethesda, Maryland 20892
| | - Salim Khiati
- Laboratory of Molecular Pharmacology, Developmental Therapeutics Branch, Center for Cancer Research, NCI, National Institutes of Health, Bethesda, Maryland 20892
| | - Xiaolin Wu
- Laboratory of Molecular Technology, NCI-Frederick, National Institutes of Health, Frederick, Maryland 21702
| | - Yves Pommier
- Laboratory of Molecular Pharmacology, Developmental Therapeutics Branch, Center for Cancer Research, NCI, National Institutes of Health, Bethesda, Maryland 20892.
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35
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Live imaging reveals the dynamics and regulation of mitochondrial nucleoids during the cell cycle in Fucci2-HeLa cells. Sci Rep 2017; 7:11257. [PMID: 28900194 PMCID: PMC5595809 DOI: 10.1038/s41598-017-10843-8] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2017] [Accepted: 08/15/2017] [Indexed: 12/24/2022] Open
Abstract
Mitochondrial DNA (mtDNA) is organized in nucleoprotein complexes called mitochondrial nucleoids (mt-nucleoids), which are critical units of mtDNA replication and transmission. In humans, several hundreds of mt-nucleoids exist in a cell. However, how numerous mt-nucleoids are maintained during the cell cycle remains elusive, because cell cycle synchronization procedures affect mtDNA replication. Here, we analyzed regulation of the maintenance of mt-nucleoids in the cell cycle, using a fluorescent cell cycle indicator, Fucci2. Live imaging of mt-nucleoids with higher temporal resolution showed frequent attachment and detachment of mt-nucleoids throughout the cell cycle. TFAM, an mtDNA packaging protein, was involved in the regulation of this dynamic process, which was important for maintaining proper mt-nucleoid number. Both an increase in mt-nucleoid number and activation of mtDNA replication occurred during S phase. To increase mt-nucleoid number, mtDNA replication, but not nuclear DNA replication, was necessary. We propose that these dynamic and regulatory processes in the cell cycle maintain several hundred mt-nucleoids in proliferating cells.
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36
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Qian Y, Johnson KA. The human mitochondrial single-stranded DNA-binding protein displays distinct kinetics and thermodynamics of DNA binding and exchange. J Biol Chem 2017; 292:13068-13084. [PMID: 28615444 DOI: 10.1074/jbc.m117.791392] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2017] [Revised: 06/08/2017] [Indexed: 11/06/2022] Open
Abstract
The human mitochondrial ssDNA-binding protein (mtSSB) is a homotetrameric protein, involved in mtDNA replication and maintenance. Although mtSSB is structurally similar to SSB from Escherichia coli (EcoSSB), it lacks the C-terminal disordered domain, and little is known about the biophysics of mtSSB-ssDNA interactions. Here, we characterized the kinetics and thermodynamics of mtSSB binding to ssDNA by equilibrium titrations and stopped-flow kinetic measurements. We show that the mtSSB tetramer can bind to ssDNA in two distinct binding modes: (SSB)30 and (SSB)60, defined by DNA binding site sizes of 30 and 60 nucleotides, respectively. We found that the binding mode is modulated by magnesium ion and NaCl concentration, but unlike EcoSSB, the mtSSB does not show negative intersubunit cooperativity. Global fitting of both the equilibrium and kinetic data afforded estimates for the rate and equilibrium constants governing the formation of (SSB)60 and (SSB)30 complexes and for the transitions between the two binding modes. We found that the mtSSB tetramer binds to ssDNA with a rate constant near the diffusion limit (2 × 109 m-1 s-1) and that longer DNA (≥60 nucleotides) rapidly wraps around all four monomers, as revealed by FRET assays. We also show that the mtSSB tetramer can directly transfer from one ssDNA molecule to another via an intermediate with two DNA molecules bound to the mtSSB. In conclusion, our results indicate that human mtSSB shares many physicochemical properties with EcoSSB and that the differences may be explained by the lack of an acidic, disordered C-terminal tail in human mtSSB protein.
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Affiliation(s)
- Yufeng Qian
- Institute for Cellular and Molecular Biology and Department of Molecular Biosciences, University of Texas, Austin, Texas 78712
| | - Kenneth A Johnson
- Institute for Cellular and Molecular Biology and Department of Molecular Biosciences, University of Texas, Austin, Texas 78712.
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37
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Wang Y, Hu L, Zhang X, Zhao H, Xu H, Wei Y, Jiang H, Xie C, Zhou Y, Zhou F. Downregulation of Mitochondrial Single Stranded DNA Binding Protein (SSBP1) Induces Mitochondrial Dysfunction and Increases the Radiosensitivity in Non-Small Cell Lung Cancer Cells. J Cancer 2017. [PMID: 28638454 PMCID: PMC5479245 DOI: 10.7150/jca.18170] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Radiotherapy is one of the major therapeutic strategies for human non-small cell lung cancer (NSCLC), but intrinsic radioresistance of cancer cells makes a further improvement of radiotherapy for NSCLC challenging. Mitochondrial function is frequently dysregulated in cancer cells for adaptation to the changes of tumor microenvironment after exposure to radiation. Therefore, targeting mitochondrial biogenesis and bioenergetics is an attractive strategy to sensitize cancer cells to radiation therapy. In this study, we found that downregulation of single-strand DNA-binding protein 1 (SSBP1) in H1299 cells was associated with inducing mitochondrial dysfunction and increasing radiosensitivity to ionizing radiation. Mechanistically, SSBP1 loss induced mitochondrial dysfunction via decreasing mitochondrial DNA copy number and ATP generation, enhancing the mitochondrial-derived ROS accumulation and downregulating key glycolytic enzymes expression. SSBP1 knockdown increased the radiosensitivity of H1299 cells by inducing increased apoptosis, prolonged G2/M phase arrest and defective homologous recombination repair of DNA double-strand breaks. Our findings identified SSBP1 as a radioresistance-related protein, providing potential novel mitochondrial target for sensitizing NSCLC to radiotherapy.
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Affiliation(s)
- You Wang
- Hubei Key Laboratory of Tumor Biological Behavior, Hubei Cancer Clinical Study Center, Zhongnan Hospital of Wuhan University, Wuhan, China.,Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Liu Hu
- Hubei Key Laboratory of Tumor Biological Behavior, Hubei Cancer Clinical Study Center, Zhongnan Hospital of Wuhan University, Wuhan, China.,Department of Radiation Oncology, Hubei Cancer Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Ximei Zhang
- Hubei Key Laboratory of Tumor Biological Behavior, Hubei Cancer Clinical Study Center, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Hong Zhao
- Hubei Key Laboratory of Tumor Biological Behavior, Hubei Cancer Clinical Study Center, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Hui Xu
- Hubei Key Laboratory of Tumor Biological Behavior, Hubei Cancer Clinical Study Center, Zhongnan Hospital of Wuhan University, Wuhan, China.,Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Yuehua Wei
- Hubei Key Laboratory of Tumor Biological Behavior, Hubei Cancer Clinical Study Center, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Huangang Jiang
- Hubei Key Laboratory of Tumor Biological Behavior, Hubei Cancer Clinical Study Center, Zhongnan Hospital of Wuhan University, Wuhan, China.,Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Conghua Xie
- Hubei Key Laboratory of Tumor Biological Behavior, Hubei Cancer Clinical Study Center, Zhongnan Hospital of Wuhan University, Wuhan, China.,Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Yunfeng Zhou
- Hubei Key Laboratory of Tumor Biological Behavior, Hubei Cancer Clinical Study Center, Zhongnan Hospital of Wuhan University, Wuhan, China.,Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Fuxiang Zhou
- Hubei Key Laboratory of Tumor Biological Behavior, Hubei Cancer Clinical Study Center, Zhongnan Hospital of Wuhan University, Wuhan, China.,Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, Wuhan, China
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38
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Pokrzywinski KL, Biel TG, Kryndushkin D, Rao VA. Therapeutic Targeting of the Mitochondria Initiates Excessive Superoxide Production and Mitochondrial Depolarization Causing Decreased mtDNA Integrity. PLoS One 2016; 11:e0168283. [PMID: 28030582 PMCID: PMC5193408 DOI: 10.1371/journal.pone.0168283] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2016] [Accepted: 11/29/2016] [Indexed: 01/01/2023] Open
Abstract
Mitochondrial dysregulation is closely associated with excessive reactive oxygen species (ROS) production. Altered redox homeostasis has been implicated in the onset of several diseases including cancer. Mitochondrial DNA (mtDNA) and proteins are particularly sensitive to ROS as they are in close proximity to the respiratory chain (RC). Mitoquinone (MitoQ), a mitochondria-targeted redox agent, selectively damages breast cancer cells possibly through damage induced via enhanced ROS production. However, the effects of MitoQ and other triphenylphosphonium (TPP+) conjugated agents on cancer mitochondrial homeostasis remain unknown. The primary objective of this study was to determine the impact of mitochondria-targeted agent [(MTAs) conjugated to TPP+: mitoTEMPOL, mitoquinone and mitochromanol-acetate] on mitochondrial physiology and mtDNA integrity in breast (MDA-MB-231) and lung (H23) cancer cells. The integrity of the mtDNA was assessed by quantifying the degree of mtDNA fragmentation and copy number, as well as by measuring mitochondrial proteins essential to mtDNA stability and maintenance (TFAM, SSBP1, TWINKLE, POLG and POLRMT). Mitochondrial status was evaluated by measuring superoxide production, mitochondrial membrane depolarization, oxygen consumption, extracellular acidification and mRNA or protein levels of the RC complexes along with TCA cycle activity. In this study, we demonstrated that all investigated MTAs impair mitochondrial health and decrease mtDNA integrity in MDA-MB-231 and H23 cells. However, differences in the degree of mitochondrial damage and mtDNA degradation suggest unique properties among each MTA that may be cell line, dose and time dependent. Collectively, our study indicates the potential for TPP+ conjugated molecules to impair breast and lung cancer cells by targeting mitochondrial homeostasis.
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Affiliation(s)
- Kaytee L. Pokrzywinski
- Laboratory of Applied Biochemistry, Division of Biotechnology Research and Review III, Office of Biotechnology Products, Center for Drug Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, Maryland, United States of America
| | - Thomas G. Biel
- Laboratory of Applied Biochemistry, Division of Biotechnology Research and Review III, Office of Biotechnology Products, Center for Drug Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, Maryland, United States of America
| | - Dmitry Kryndushkin
- Laboratory of Applied Biochemistry, Division of Biotechnology Research and Review III, Office of Biotechnology Products, Center for Drug Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, Maryland, United States of America
| | - V. Ashutosh Rao
- Laboratory of Applied Biochemistry, Division of Biotechnology Research and Review III, Office of Biotechnology Products, Center for Drug Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, Maryland, United States of America
- * E-mail:
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39
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Abstract
Recent advances in the field of mitochondrial DNA (mtDNA) replication highlight the diversity of both the mechanisms utilized and the structural and functional organization of the proteins at mtDNA replication fork, despite the relative simplicity of the animal mtDNA genome. DNA polymerase γ, mtDNA helicase and mitochondrial single-stranded DNA-binding protein-the key replisome proteins, have evolved distinct structural features and biochemical properties. These appear to be correlated with mtDNA genomic features in different metazoan taxa and with their modes of DNA replication, although substantial integrative research is warranted to establish firmly these links. To date, several modes of mtDNA replication have been described for animals: rolling circle, theta, strand-displacement, and RITOLS/bootlace. Resolution of a continuing controversy relevant to mtDNA replication in mammals/vertebrates will have a direct impact on the mechanistic interpretation of mtDNA-related human diseases. Here we review these subjects, integrating earlier and recent data to provide a perspective on the major challenges for future research.
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Affiliation(s)
- G L Ciesielski
- Institute of Biosciences and Medical Technology, University of Tampere, Tampere, Finland; Michigan State University, East Lansing, MI, United States
| | - M T Oliveira
- Faculdade de Ciências Agrárias e Veterinárias, Universidade Estadual Paulista "Júlio de Mesquita Filho", Jaboticabal, SP, Brazil
| | - L S Kaguni
- Institute of Biosciences and Medical Technology, University of Tampere, Tampere, Finland; Michigan State University, East Lansing, MI, United States.
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40
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Alán L, Špaček T, Ježek P. Delaunay algorithm and principal component analysis for 3D visualization of mitochondrial DNA nucleoids by Biplane FPALM/dSTORM. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2016; 45:443-61. [PMID: 26846371 DOI: 10.1007/s00249-016-1114-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2015] [Revised: 12/21/2015] [Accepted: 01/12/2016] [Indexed: 12/16/2022]
Abstract
Data segmentation and object rendering is required for localization super-resolution microscopy, fluorescent photoactivation localization microscopy (FPALM), and direct stochastic optical reconstruction microscopy (dSTORM). We developed and validated methods for segmenting objects based on Delaunay triangulation in 3D space, followed by facet culling. We applied them to visualize mitochondrial nucleoids, which confine DNA in complexes with mitochondrial (mt) transcription factor A (TFAM) and gene expression machinery proteins, such as mt single-stranded-DNA-binding protein (mtSSB). Eos2-conjugated TFAM visualized nucleoids in HepG2 cells, which was compared with dSTORM 3D-immunocytochemistry of TFAM, mtSSB, or DNA. The localized fluorophores of FPALM/dSTORM data were segmented using Delaunay triangulation into polyhedron models and by principal component analysis (PCA) into general PCA ellipsoids. The PCA ellipsoids were normalized to the smoothed volume of polyhedrons or by the net unsmoothed Delaunay volume and remodeled into rotational ellipsoids to obtain models, termed DVRE. The most frequent size of ellipsoid nucleoid model imaged via TFAM was 35 × 45 × 95 nm; or 35 × 45 × 75 nm for mtDNA cores; and 25 × 45 × 100 nm for nucleoids imaged via mtSSB. Nucleoids encompassed different point density and wide size ranges, speculatively due to different activity stemming from different TFAM/mtDNA stoichiometry/density. Considering twofold lower axial vs. lateral resolution, only bulky DVRE models with an aspect ratio >3 and tilted toward the xy-plane were considered as two proximal nucleoids, suspicious occurring after division following mtDNA replication. The existence of proximal nucleoids in mtDNA-dSTORM 3D images of mtDNA "doubling"-supported possible direct observations of mt nucleoid division after mtDNA replication.
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Affiliation(s)
- Lukáš Alán
- Department of Membrane Transport Biophysics, No. 75, Institute of Physiology, Academy of Sciences of the Czech Republic, Vídeňská 1083, 14220, Prague 4, Czech Republic
| | - Tomáš Špaček
- Department of Membrane Transport Biophysics, No. 75, Institute of Physiology, Academy of Sciences of the Czech Republic, Vídeňská 1083, 14220, Prague 4, Czech Republic
| | - Petr Ježek
- Department of Membrane Transport Biophysics, No. 75, Institute of Physiology, Academy of Sciences of the Czech Republic, Vídeňská 1083, 14220, Prague 4, Czech Republic.
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Ciesielski GL, Bermek O, Rosado-Ruiz FA, Hovde SL, Neitzke OJ, Griffith JD, Kaguni LS. Mitochondrial Single-stranded DNA-binding Proteins Stimulate the Activity of DNA Polymerase γ by Organization of the Template DNA. J Biol Chem 2015; 290:28697-707. [PMID: 26446790 DOI: 10.1074/jbc.m115.673707] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2015] [Indexed: 11/06/2022] Open
Abstract
The activity of the mitochondrial replicase, DNA polymerase γ (Pol γ) is stimulated by another key component of the mitochondrial replisome, the mitochondrial single-stranded DNA-binding protein (mtSSB). We have performed a comparative analysis of the human and Drosophila Pols γ with their cognate mtSSBs, evaluating their functional relationships using a combined approach of biochemical assays and electron microscopy. We found that increasing concentrations of both mtSSBs led to the elimination of template secondary structure and gradual opening of the template DNA, through a series of visually similar template species. The stimulatory effect of mtSSB on Pol γ on these ssDNA templates is not species-specific. We observed that human mtSSB can be substituted by its Drosophila homologue, and vice versa, finding that a lower concentration of insect mtSSB promotes efficient stimulation of either Pol. Notably, distinct phases of the stimulation by both mtSSBs are distinguishable, and they are characterized by a similar organization of the template DNA for both Pols γ. We conclude that organization of the template DNA is the major factor contributing to the stimulation of Pol γ activity. Additionally, we observed that human Pol γ preferentially utilizes compacted templates, whereas the insect enzyme achieves its maximal activity on open templates, emphasizing the relative importance of template DNA organization in modulating Pol γ activity and the variation among systems.
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Affiliation(s)
- Grzegorz L Ciesielski
- From the Institute of Biosciences and Medical Technology, University of Tampere, 33520 Tampere, Finland, the Department of Biochemistry and Molecular Biology and Center for Mitochondrial Science and Medicine, Michigan State University, East Lansing, Michigan 48823, and
| | - Oya Bermek
- the Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina 27514
| | - Fernando A Rosado-Ruiz
- the Department of Biochemistry and Molecular Biology and Center for Mitochondrial Science and Medicine, Michigan State University, East Lansing, Michigan 48823, and
| | - Stacy L Hovde
- the Department of Biochemistry and Molecular Biology and Center for Mitochondrial Science and Medicine, Michigan State University, East Lansing, Michigan 48823, and
| | - Orrin J Neitzke
- the Department of Biochemistry and Molecular Biology and Center for Mitochondrial Science and Medicine, Michigan State University, East Lansing, Michigan 48823, and
| | - Jack D Griffith
- the Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina 27514
| | - Laurie S Kaguni
- From the Institute of Biosciences and Medical Technology, University of Tampere, 33520 Tampere, Finland, the Department of Biochemistry and Molecular Biology and Center for Mitochondrial Science and Medicine, Michigan State University, East Lansing, Michigan 48823, and
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42
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Ren L, Wang Z, An L, Zhang Z, Tan K, Miao K, Tao L, Cheng L, Zhang Z, Yang M, Wu Z, Tian J. Dynamic comparisons of high-resolution expression profiles highlighting mitochondria-related genes between in vivo and in vitro fertilized early mouse embryos. Hum Reprod 2015; 30:2892-911. [PMID: 26385791 DOI: 10.1093/humrep/dev228] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2015] [Accepted: 08/24/2015] [Indexed: 12/11/2022] Open
Abstract
STUDY QUESTION Does in vitro fertilization (IVF) induce comprehensive and consistent changes in gene expression associated with mitochondrial biogenesis and function in mouse embryos from the pre- to post-implantation stage? SUMMARY ANSWER IVF-induced consistent mitochondrial dysfunction in early mouse embryos by altering the expression of a number of mitochondria-related genes. WHAT IS KNOWN ALREADY Although IVF is generally safe and successful for the treatment of human infertility, there is increasing evidence that those conceived by IVF suffer increased health risks. The mitochondrion is a multifunctional organelle that plays a crucial role in early development. We hypothesized that mitochondrial dysfunction is associated with increased IVF-induced embryonic defects and risks in offspring. STUDY DESIGN, SIZE, DURATION After either IVF and development (IVO groups as control) or IVF and culture (IVF groups), blastocysts were collected and transferred to pseudo-pregnant recipient mice. Both IVO and IVF embryos were sampled at E3.5, E7.5 and E10.5, and the expression profiles of mitochondria-related genes from the pre- to post-implantation stage were compared. PARTICIPANTS/MATERIALS, SETTING, METHODS ICR mice (5- to 6-week-old males and 8- to 9-week-old females) were used to generate IVO and IVF blastocysts. Embryo day (E) 3.5 blastocysts were transferred to pseudo-pregnant recipient mice. Both IVO and IVF embryos were sampled at E3.5, E7.5 and E10.5 for generating transcriptome data. Mitochondria-related genes were filtered for dynamic functional profiling. Mitochondrial dysfunctions indicated by bioinformatic analysis were further validated using cytological and molecular detection, morphometric and phenotypic analysis and integrated analysis with other high-throughput data. MAIN RESULTS AND THE ROLE OF CHANCE A total of 806, 795 and 753 mitochondria-related genes were significantly (P < 0.05) dysregulated in IVF embryos at E3.5, E7.5 and E10.5, respectively. Dynamic functional profiling, together with cytological and molecular investigations, indicated that IVF-induced mitochondrial dysfunctions mainly included: (i) inhibited mitochondrial biogenesis and impaired maintenance of DNA methylation of mitochondria-related genes during the post-implantation stage; (ii) dysregulated glutathione/glutathione peroxidase (GSH/Gpx) system and increased mitochondria-mediated apoptosis; (iii) disturbed mitochondrial β-oxidation, oxidative phosphorylation and amino acid metabolism; and (iv) disrupted mitochondrial transmembrane transport and membrane organization. We also demonstrated that some mitochondrial dysfunctions in IVF embryos, including impaired mitochondrial biogenesis, dysregulated GSH homeostasis and reactive oxygen species-induced apoptosis, can be rescued by treatment with melatonin, a mitochondria-targeted antioxidant, during in vitro culture. LIMITATIONS, REASONS FOR CAUTION Findings in mouse embryos and fetuses may not be fully transferable to humans. Further studies are needed to confirm these findings and to determine their clinical significance better. WIDER IMPLICATIONS OF THE FINDINGS The present study provides a new insight in understanding the mechanism of IVF-induced aberrations during embryonic development and the increased health risks in the offspring. In addition, we highlighted the possibility of improving existing IVF systems by modulating mitochondrial functions.
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Affiliation(s)
- Likun Ren
- Ministry of Agriculture Key Laboratory of Animal Genetics, Breeding and Reproduction, National Engineering Laboratory for Animal Breeding, College of Animal Sciences and Technology, China Agricultural University, Haidian District, Beijing 100193, China
| | - Zhuqing Wang
- Ministry of Agriculture Key Laboratory of Animal Genetics, Breeding and Reproduction, National Engineering Laboratory for Animal Breeding, College of Animal Sciences and Technology, China Agricultural University, Haidian District, Beijing 100193, China
| | - Lei An
- Ministry of Agriculture Key Laboratory of Animal Genetics, Breeding and Reproduction, National Engineering Laboratory for Animal Breeding, College of Animal Sciences and Technology, China Agricultural University, Haidian District, Beijing 100193, China
| | - Zhennan Zhang
- Ministry of Agriculture Key Laboratory of Animal Genetics, Breeding and Reproduction, National Engineering Laboratory for Animal Breeding, College of Animal Sciences and Technology, China Agricultural University, Haidian District, Beijing 100193, China
| | - Kun Tan
- Ministry of Agriculture Key Laboratory of Animal Genetics, Breeding and Reproduction, National Engineering Laboratory for Animal Breeding, College of Animal Sciences and Technology, China Agricultural University, Haidian District, Beijing 100193, China
| | - Kai Miao
- Ministry of Agriculture Key Laboratory of Animal Genetics, Breeding and Reproduction, National Engineering Laboratory for Animal Breeding, College of Animal Sciences and Technology, China Agricultural University, Haidian District, Beijing 100193, China
| | - Li Tao
- Ministry of Agriculture Key Laboratory of Animal Genetics, Breeding and Reproduction, National Engineering Laboratory for Animal Breeding, College of Animal Sciences and Technology, China Agricultural University, Haidian District, Beijing 100193, China
| | - Linghua Cheng
- Ministry of Agriculture Key Laboratory of Animal Genetics, Breeding and Reproduction, National Engineering Laboratory for Animal Breeding, College of Animal Sciences and Technology, China Agricultural University, Haidian District, Beijing 100193, China
| | - Zhenni Zhang
- Ministry of Agriculture Key Laboratory of Animal Genetics, Breeding and Reproduction, National Engineering Laboratory for Animal Breeding, College of Animal Sciences and Technology, China Agricultural University, Haidian District, Beijing 100193, China
| | - Mingyao Yang
- Ministry of Agriculture Key Laboratory of Animal Genetics, Breeding and Reproduction, National Engineering Laboratory for Animal Breeding, College of Animal Sciences and Technology, China Agricultural University, Haidian District, Beijing 100193, China
| | - Zhonghong Wu
- Ministry of Agriculture Key Laboratory of Animal Genetics, Breeding and Reproduction, National Engineering Laboratory for Animal Breeding, College of Animal Sciences and Technology, China Agricultural University, Haidian District, Beijing 100193, China
| | - Jianhui Tian
- Ministry of Agriculture Key Laboratory of Animal Genetics, Breeding and Reproduction, National Engineering Laboratory for Animal Breeding, College of Animal Sciences and Technology, China Agricultural University, Haidian District, Beijing 100193, China
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Olejár T, Pajuelo-Reguera D, Alán L, Dlasková A, Ježek P. Coupled aggregation of mitochondrial single-strand DNA-binding protein tagged with Eos fluorescent protein visualizes synchronized activity of mitochondrial nucleoids. Mol Med Rep 2015; 12:5185-90. [PMID: 26239383 DOI: 10.3892/mmr.2015.4085] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2014] [Accepted: 06/05/2015] [Indexed: 11/05/2022] Open
Abstract
Oligomer aggregation of green-to-red photoconvertible fluorescent protein Eos (EosFP) is a natural feature of the wild‑type variant. The aim of the present study was to follow up mitochondrial nucleoid behavior under natural conditions of living cells transfected with mitochondrial single‑strand DNA‑binding protein (mtSSB) conjugated with EosFP. HEPG2 and SH‑SY5Y cells were subjected to lentiviral transfection and subsequently immunostained with anti‑DNA, anti‑transcription factor A, mitochondrial (TFAM) or anti‑translocase of the inner membrane 23 antibodies. Fluorescent microscopy, conventional confocal microscopy, superresolution biplane fluorescence photo-activation localization microscopy and direct stochastic optical reconstruction microscopy were used for imaging. In the two cell types, apparent couples of equally‑sized mtSSB‑EosFP‑visualized dots were observed. During the time course of the ongoing transfection procedure, however, a small limited number of large aggregates of mtSSB‑EosFP‑tagged protein started to form in the cells, which exhibited a great co‑localization with the noted coupled positions. Antibody staining and 3D immunocytochemistry confirmed that nucleoid components such as TFAM and DNA were co‑localized with these aggregates. Furthermore, the observed reduction of the mtDNA copy number in mtSSB‑EosFP‑transfected cells suggested a possible impairment of nucleoid function. In conclusion, the present study demonstrated that coupled nucleoids are synchronized by mtSSB‑EosFP overexpression and visualized through their equal binding capacity to mtSSB‑EosFP‑tagged protein. This observation suggested parallel replication and transcription activity of nucleoid couples native from a parental one. Preserved coupling in late stages of artificial EosFP‑mediated aggregation of tagged proteins suggested a rational manner of mitochondrial branching that may be cell-type specifically dependent on hierarchical nucleoid replication.
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Affiliation(s)
- Tomáš Olejár
- Department of Membrane Transport Biophysics, Institute of Physiology, The Czech Academy of Sciences, Prague 14220, Czech Republic
| | - David Pajuelo-Reguera
- Department of Membrane Transport Biophysics, Institute of Physiology, The Czech Academy of Sciences, Prague 14220, Czech Republic
| | - Lukáš Alán
- Department of Membrane Transport Biophysics, Institute of Physiology, The Czech Academy of Sciences, Prague 14220, Czech Republic
| | - Andrea Dlasková
- Department of Membrane Transport Biophysics, Institute of Physiology, The Czech Academy of Sciences, Prague 14220, Czech Republic
| | - Petr Ježek
- Department of Membrane Transport Biophysics, Institute of Physiology, The Czech Academy of Sciences, Prague 14220, Czech Republic
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Miralles Fusté J, Shi Y, Wanrooij S, Zhu X, Jemt E, Persson Ö, Sabouri N, Gustafsson CM, Falkenberg M. In vivo occupancy of mitochondrial single-stranded DNA binding protein supports the strand displacement mode of DNA replication. PLoS Genet 2014; 10:e1004832. [PMID: 25474639 PMCID: PMC4256270 DOI: 10.1371/journal.pgen.1004832] [Citation(s) in RCA: 100] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2014] [Accepted: 10/15/2014] [Indexed: 01/10/2023] Open
Abstract
Mitochondrial DNA (mtDNA) encodes for proteins required for oxidative phosphorylation, and mutations affecting the genome have been linked to a number of diseases as well as the natural ageing process in mammals. Human mtDNA is replicated by a molecular machinery that is distinct from the nuclear replisome, but there is still no consensus on the exact mode of mtDNA replication. We here demonstrate that the mitochondrial single-stranded DNA binding protein (mtSSB) directs origin specific initiation of mtDNA replication. MtSSB covers the parental heavy strand, which is displaced during mtDNA replication. MtSSB blocks primer synthesis on the displaced strand and restricts initiation of light-strand mtDNA synthesis to the specific origin of light-strand DNA synthesis (OriL). The in vivo occupancy profile of mtSSB displays a distinct pattern, with the highest levels of mtSSB close to the mitochondrial control region and with a gradual decline towards OriL. The pattern correlates with the replication products expected for the strand displacement mode of mtDNA synthesis, lending strong in vivo support for this debated model for mitochondrial DNA replication. Mitochondria are cytoplasmatic organelles that produce most of the adenosine triphosphate (ATP) used by the cell as a source of chemical energy. A subset of proteins required for ATP production is encoded by a distinct mitochondrial DNA genome (mtDNA). Proper maintenance of mtDNA is essential, since mutations or depletion of this circular molecule may lead to a number of different diseases and also contribute to normal ageing. We are interested in the molecular mechanisms that ensure correct replication and propagation of mtDNA. Even if many of the responsible enzymes have been identified, there is still a debate within our scientific field regarding the exact mode of mtDNA replication. We have here used a combination of in vitro biochemistry and in vivo protein-DNA interaction characterization to address this question. Our findings demonstrate that the mitochondrial single-stranded DNA-binding protein (mtSSB) restricts initiation of mtDNA replication to a specific origin of replication. By characterizing how mtSSB interacts with the two strands of mtDNA in vivo, we are able to directly demonstrate the relevance of one proposed mode of mitochondrial DNA replication and at the same time seriously question the validity of other, alternative modes that have been proposed over the years.
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Affiliation(s)
- Javier Miralles Fusté
- Department of Medical Biochemistry and Cell Biology, University of Gothenburg, Gothenburg, Sweden
| | - Yonghong Shi
- Department of Medical Biochemistry and Cell Biology, University of Gothenburg, Gothenburg, Sweden
| | - Sjoerd Wanrooij
- Department of Medical Biochemistry and Biophysics, Umeå University, Umeå, Sweden
| | - Xuefeng Zhu
- Department of Medical Biochemistry and Cell Biology, University of Gothenburg, Gothenburg, Sweden
| | - Elisabeth Jemt
- Department of Medical Biochemistry and Cell Biology, University of Gothenburg, Gothenburg, Sweden
| | - Örjan Persson
- Department of Medical Biochemistry and Cell Biology, University of Gothenburg, Gothenburg, Sweden
| | - Nasim Sabouri
- Department of Medical Biochemistry and Biophysics, Umeå University, Umeå, Sweden
| | - Claes M. Gustafsson
- Department of Medical Biochemistry and Cell Biology, University of Gothenburg, Gothenburg, Sweden
| | - Maria Falkenberg
- Department of Medical Biochemistry and Cell Biology, University of Gothenburg, Gothenburg, Sweden
- * E-mail:
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45
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Holt IJ, Jacobs HT. Unique features of DNA replication in mitochondria: a functional and evolutionary perspective. Bioessays 2014; 36:1024-31. [PMID: 25220172 DOI: 10.1002/bies.201400052] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Last year, we reported a new mechanism of DNA replication in mammals. It occurs inside mitochondria and entails the use of processed transcripts, termed bootlaces, which hybridize with the displaced parental strand as the replication fork advances. Here we discuss possible reasons why such an unusual mechanism of DNA replication might have evolved. The bootlace mechanism can minimize the occurrence and impact of single-strand breaks that would otherwise threaten genome stability. Furthermore, by providing an implicit mismatch recognition system, it should limit the occurrence of replication-dependent deletions and insertions, and defend against invading elements. Such a mechanism may also limit attempts to manipulate the mammalian mitochondrial genome.
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Affiliation(s)
- Ian J Holt
- MRC National Institute for Medical Research, London, UK
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46
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Lee SK, Zhao MH, Zheng Z, Kwon JW, Liang S, Kim SH, Kim NH, Cui XS. Polymerase subunit gamma 2 affects porcine oocyte maturation and subsequent embryonic development. Theriogenology 2014; 83:121-30. [PMID: 25308052 DOI: 10.1016/j.theriogenology.2014.08.019] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2014] [Revised: 07/16/2014] [Accepted: 08/31/2014] [Indexed: 01/30/2023]
Abstract
Deoxyribonucleic acid polymerase subunit gamma (POLG) is an enzyme encoded by the mitochondrial Polg gene. Polymerase (DNA directed), gamma 2, accessory subunit, also known as POLG2, is involved in mitochondrial replication. In the present study, we examined the role of Polg2 in the maturation of porcine oocytes. After Polg2 knockdown, the mitochondrial DNA copy number was significantly (P < 0.05) lower than that in the control group. However, there was no decrease in mitochondrial membrane potential. The decrease in mitochondrial DNA copy number led to reductions in adenosine-5'-triphosphate content (P < 0.05) and the maturation rate (P < 0.05) of oocytes. Furthermore, in the Polg2-knockdown group, maturation-promoting factor activity was decreased (P < 0.05) and the percentage of oocytes displaying abnormal actin filaments and microtubules was significantly increased (P < 0.05). This likely led to the reduced development rate and number of cells per blastocyst in this group (P < 0.05). In conclusion, Polg2 seems to be critical for mitochondrial replication and regulation of adenosine-5'-triphosphate content and affects porcine oocyte maturation and subsequent embryonic development.
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Affiliation(s)
- Seul-Ki Lee
- Department of Animal Sciences, Chungbuk National University, Cheongju, South Korea; Brain Korea 21 Center for Bio-Resource Development, Cheongju, South Korea
| | - Ming-Hui Zhao
- Department of Animal Sciences, Chungbuk National University, Cheongju, South Korea; Brain Korea 21 Center for Bio-Resource Development, Cheongju, South Korea
| | - Zhong Zheng
- Department of Animal Sciences, Chungbuk National University, Cheongju, South Korea; Brain Korea 21 Center for Bio-Resource Development, Cheongju, South Korea
| | - Jung-Woo Kwon
- Department of Animal Sciences, Chungbuk National University, Cheongju, South Korea; Brain Korea 21 Center for Bio-Resource Development, Cheongju, South Korea
| | - Shuang Liang
- Department of Animal Sciences, Chungbuk National University, Cheongju, South Korea; Brain Korea 21 Center for Bio-Resource Development, Cheongju, South Korea
| | - Seon-Hyang Kim
- Department of Animal Sciences, Chungbuk National University, Cheongju, South Korea; Brain Korea 21 Center for Bio-Resource Development, Cheongju, South Korea
| | - Nam-Hyung Kim
- Department of Animal Sciences, Chungbuk National University, Cheongju, South Korea; Brain Korea 21 Center for Bio-Resource Development, Cheongju, South Korea
| | - Xiang-Shun Cui
- Department of Animal Sciences, Chungbuk National University, Cheongju, South Korea; Brain Korea 21 Center for Bio-Resource Development, Cheongju, South Korea.
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47
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In D-loop: 40 years of mitochondrial 7S DNA. Exp Gerontol 2014; 56:175-81. [PMID: 24709344 DOI: 10.1016/j.exger.2014.03.027] [Citation(s) in RCA: 172] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2013] [Revised: 03/27/2014] [Accepted: 03/28/2014] [Indexed: 11/23/2022]
Abstract
Given the tiny size of the mammalian mitochondrial genome, at only 16.5 kb, it is often surprising how little we know about some of its molecular features, and the molecular mechanisms governing its maintenance. One such conundrum is the biogenesis and function of the mitochondrial displacement loop (D-loop). The mitochondrial D-loop is a triple-stranded region found in the major non-coding region (NCR) of many mitochondrial genomes, and is formed by stable incorporation of a third, short DNA strand known as 7S DNA. In this article we review the current affairs regarding the main features of the D-loop structure, the diverse frequency of D-loops in the mtDNAs of various species and tissues, and also the mechanisms of its synthesis and turnover. This is followed by an account of the possible functions of the mitochondrial D-loop that have been proposed over the last four decades. In the last section, we discuss the potential links of the D-loop with mammalian ageing.
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Behrouzi B, Kenigsberg S, Alladin N, Swanson S, Zicherman J, Hong SH, Moskovtsev SI, Librach CL. Evaluation of potential protein biomarkers in patients with high sperm DNA damage. Syst Biol Reprod Med 2013; 59:153-63. [PMID: 23634713 DOI: 10.3109/19396368.2013.775396] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The laboratory evaluation of male infertility remains an essential area of research as 40-60% of infertility cases are attributable to male-related factors. Current sperm analysis methods add only partial information on sperm quality and fertility outcomes. The specific underlying cause of infertility in most cases is unknown, while a proportion of male infertility could be caused by molecular factors such as the absence or abnormal expression of some essential sperm proteins. The objective of this study was to screen for associations between sperm protein profiles and sperm concentration, motility, and DNA fragmentation index in patients undergoing fertility evaluation in a clinical setting. Based on those parameters, semen samples were categorized as either normal or abnormal. We screened 34 semen samples with various abnormal parameters and compared them to 24 normal control samples by using one dimensional (1-D) gel electrophoresis and mass-spectrometry. In this study, we anticipated to establish a normal sperm parameter profile which would be compared to abnormal sperm samples and reveal candidate proteins. Our preliminary results indicate that no normal uniform profile could be established, which affirms the complexity of male fertility and confirms the limitations of standard semen analysis. Four main protein groups were identified in correlation with abnormal DNA fragmentation and/or motility. The first group included sperm nuclear proteins such as the SPANX (sperm protein associated with the nucleus on the X chromosome) isoforms and several types of histones. The second group contained mitochondria-related functions and oxidative stress proteins including Mitochondrial Ferritin, Mitochondrial Single-Stranded DNA Binding Protein, and several isoforms of Peroxiredoxins. Two other protein groups were related to sperm motility such as microtubule-based flagellum and spindle microtubule as well as proteins related to the ubiquitin-proteasome pathway. Further research is required in order to characterize these potential biomarkers of male fertility potential.
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49
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Kasashima K, Nagao Y, Endo H. Dynamic regulation of mitochondrial genome maintenance in germ cells. Reprod Med Biol 2013; 13:11-20. [PMID: 24482608 PMCID: PMC3890057 DOI: 10.1007/s12522-013-0162-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2013] [Accepted: 07/04/2013] [Indexed: 12/11/2022] Open
Abstract
Mitochondria play a crucial role in the development and function of germ cells. Mitochondria contain a maternally inherited genome that should be transmitted to offspring without reactive oxygen species‐induced damage during germ line development. Germ cells are also involved in the mitochondrial DNA (mtDNA) bottleneck; thus, the appropriate regulation of mtDNA in these cells is very important for this characteristic transmission. In this review, we focused on unique regulation of the mitochondrial genome in animal germ cells; paternal elimination and the mtDNA bottleneck in females. We also summarized the mitochondrial nucleoid factors involved in various mtDNA regulation pathways. Among them, mitochondrial transcription factor A (TFAM), which has pleiotropic and essential roles in mtDNA maintenance, appears to have putative roles in germ cell regulation.
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Affiliation(s)
- Katsumi Kasashima
- Department of Biochemistry, Jichi Medical University, 3311-1 Yakushiji, Shimotsuke, Tochigi 329-0498 Japan
| | - Yasumitsu Nagao
- Center for Experimental Medicine, Jichi Medical University, Shimotsuke, Tochigi 329-0498 Japan
| | - Hitoshi Endo
- Department of Biochemistry, Jichi Medical University, 3311-1 Yakushiji, Shimotsuke, Tochigi 329-0498 Japan
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50
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Szczesny RJ, Hejnowicz MS, Steczkiewicz K, Muszewska A, Borowski LS, Ginalski K, Dziembowski A. Identification of a novel human mitochondrial endo-/exonuclease Ddk1/c20orf72 necessary for maintenance of proper 7S DNA levels. Nucleic Acids Res 2013; 41:3144-61. [PMID: 23358826 PMCID: PMC3597694 DOI: 10.1093/nar/gkt029] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Although the human mitochondrial genome has been investigated for several decades, the proteins responsible for its replication and expression, especially nucleolytic enzymes, are poorly described. Here, we characterized a novel putative PD-(D/E)XK nuclease encoded by the human C20orf72 gene named Ddk1 for its predicted catalytic residues. We show that Ddk1 is a mitochondrially localized metal-dependent DNase lacking detectable ribonuclease activity. Ddk1 degrades DNA mainly in a 3'-5' direction with a strong preference for single-stranded DNA. Interestingly, Ddk1 requires free ends for its activity and does not degrade circular substrates. In addition, when a chimeric RNA-DNA substrate is provided, Ddk1 can slide over the RNA fragment and digest DNA endonucleolytically. Although the levels of the mitochondrial DNA are unchanged on RNAi-mediated depletion of Ddk1, the mitochondrial single-stranded DNA molecule (7S DNA) accumulates. On the other hand, overexperssion of Ddk1 decreases the levels of 7S DNA, suggesting an important role of the protein in 7S DNA regulation. We propose a structural model of Ddk1 and discuss its similarity to other PD-(D/E)XK superfamily members.
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Affiliation(s)
- Roman J Szczesny
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Pawinskiego 5a, 02-106 Warsaw, Poland
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