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Song MA, Kim JY, Gorr MW, Miller RA, Karpurapu M, Nguyen J, Patel D, Archer KJ, Pabla N, Shields PG, Wold LE, Christman JW, Chung S. Sex-specific lung inflammation and mitochondrial damage in a model of electronic cigarette exposure in asthma. Am J Physiol Lung Cell Mol Physiol 2023; 325:L568-L579. [PMID: 37697923 PMCID: PMC11068405 DOI: 10.1152/ajplung.00033.2023] [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: 01/23/2023] [Revised: 07/14/2023] [Accepted: 08/30/2023] [Indexed: 09/13/2023] Open
Abstract
The prevalence of electronic cigarette (EC) use among adult with asthma has continued to increase over time, in part due to the belief of being less harmful than smoking. However, the extent of their toxicity and the involved mechanisms contributing to the deleterious impact of EC exposure on patients with preexisting asthma have not been delineated. In the present project, we tested the hypothesis that EC use contributes to respiratory damage and worsening inflammation in the lungs of patients with asthma. To define the consequences of EC exposure in established asthma, we used a mouse model with/without preexisting asthma for short-term exposure to EC aerosols. C57/BL6J mice were sensitized and challenged with a DRA (dust mite, ragweed, Aspergillus fumigates, 200 µg/mL) mixture and exposed daily to EC with nicotine (2% nicotine in 30:70 propylene glycol: vegetable glycerin) or filtered air for 2 wk. The mice were evaluated at 24 h after the final EC exposure. After EC exposure in asthmatic mice, lung inflammatory cell infiltration and goblet cell hyperplasia were increased, whereas EC alone did not cause airway inflammation. Our data also show that mitochondrial DNA (mtDNA) content and a key mtDNA regulator, mitochondrial transcription factor A (TFAM), are reduced in asthmatic EC-exposed mice in a sex-dependent manner. Together, these results indicate that TFAM loss in lung epithelium following EC contributes to male-predominant sex pathological differences, including mitochondrial damage, inflammation, and remodeling in asthmatic airways.NEW & NOTEWORTHY Respiratory immunity is dysregulated in preexisting asthma, and further perturbations by EC use could exacerbate asthma severity. However, the extent of their toxicity and the involved mechanisms contributing to the deleterious impact of EC exposure on patients with preexisting asthma have not been delineated. We found that EC has unique biological impacts in lungs and potential sex differences with loss of TFAM, a key mtDNA regulator, in lung epithelial region from our animal EC study.
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Affiliation(s)
- Min-Ae Song
- Division of Environmental Health Sciences, College of Public Health, The Ohio State University, Columbus, Ohio, United States
| | - Ji Young Kim
- Division of Pharmaceutics and Pharmacology, College of Pharmacy and Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio, United States
| | - Matthew W Gorr
- Division of Cardiac Surgery, Department of Surgery, College of Medicine, The Ohio State University, Columbus, Ohio, United States
| | - Roy A Miller
- Division of Cardiac Surgery, Department of Surgery, College of Medicine, The Ohio State University, Columbus, Ohio, United States
| | - Manjula Karpurapu
- Division of Pulmonary, Critical Care and Sleep Medicine, Davis Heart and Lung Research Institute, The Ohio State University, Columbus, Ohio, United States
| | - Jackie Nguyen
- Division of Pulmonary, Critical Care and Sleep Medicine, Davis Heart and Lung Research Institute, The Ohio State University, Columbus, Ohio, United States
| | - Devki Patel
- Division of Environmental Health Sciences, College of Public Health, The Ohio State University, Columbus, Ohio, United States
| | - Kellie J Archer
- Division of Biostatistics, College of Public Health, The Ohio State University, Columbus, Ohio, United States
| | - Navjot Pabla
- Division of Pharmaceutics and Pharmacology, College of Pharmacy and Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio, United States
| | - Peter G Shields
- Comprehensive Cancer Center, The Ohio State University and James Cancer Hospital, Columbus, Ohio, United States
| | - Loren E Wold
- Division of Cardiac Surgery, Department of Surgery, College of Medicine, The Ohio State University, Columbus, Ohio, United States
| | - John W Christman
- Division of Pulmonary, Critical Care and Sleep Medicine, Davis Heart and Lung Research Institute, The Ohio State University, Columbus, Ohio, United States
| | - Sangwoon Chung
- Division of Pulmonary, Critical Care and Sleep Medicine, Davis Heart and Lung Research Institute, The Ohio State University, Columbus, Ohio, United States
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2
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Murakami A, Takeda D, Hirota J, Saito I, Amano-Iga R, Yatagai N, Arimoto S, Kakei Y, Akashi M, Hasegawa T. Relationship of Mitochondrial-Related Protein Expression with the Differentiation, Metastasis, and Poor Prognosis of Oral Squamous Cell Carcinoma. Cancers (Basel) 2023; 15:4071. [PMID: 37627097 PMCID: PMC10452162 DOI: 10.3390/cancers15164071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Revised: 08/09/2023] [Accepted: 08/09/2023] [Indexed: 08/27/2023] Open
Abstract
Mitochondrial dysfunction and respiratory function changes have been consistently associated with the initiation and progression of cancer. The purpose of this study was to retrospectively investigate the expression of mitochondrial tumor-suppressor and DNA-repair proteins in patients with oral squamous cell carcinoma (OSCC) and to evaluate the relationship between their expression and prognosis. We enrolled 197 patients with OSCC who underwent surgical resection between August 2013 and October 2018. Clinical, pathological, and epidemiological data were retrospectively collected from hospital records. The expression of peroxisome proliferator-activated receptor gamma coactivator-1α (PGC-1α), mitochondrial transcription factor A, mitochondrial tumor suppressor gene 1, silent information regulator 3, and 8-hydroxyguanine DNA glycosylase was investigated using immunochemistry. The 3-year disease-specific survival (DSS) rates of patients showing positive expression of all selected proteins were significantly higher than those of patients showing a lack of expression. Multivariate analysis revealed that the expression of PGC-1α (hazard ratio, 4.684) and vascular invasion (hazard ratio, 5.690) can predict the DSS rate (p < 0.001). Low PGC-1α expression and vascular invasion are potential clinically effective predictors of the prognosis of OSCC.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Takumi Hasegawa
- Department of Oral and Maxillofacial Surgery, Kobe University Graduate School of Medicine, Kobe 650-0017, Japan; (A.M.); (D.T.); (S.A.); (Y.K.); (M.A.)
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3
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Lin CC, Wang YP, Sun YK, Chiu CH, Lin MW, Tzeng IS. Mitochondrial replication, transcription, and function in obstructive sleep apnea. Respir Physiol Neurobiol 2023:104066. [PMID: 37080370 DOI: 10.1016/j.resp.2023.104066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Revised: 03/31/2023] [Accepted: 04/17/2023] [Indexed: 04/22/2023]
Abstract
We assessed mitochondrial replication, transcription, and function in the upper airways of obstructive sleep apnea (OSA) patients and the effects of uvulopalatopharyngoplasty. Twenty subjects with mild and 40 with moderate to severe OSA requiring uvulopalatopharyngoplasty were included. Mitochondrial transcription factor A (TFAM) and peroxisome proliferator-activated receptor gamma coactivator 1-alpha (PGC-1α) in uvula specimens were assessed by immunohistochemical staining, and their mRNA and protein expression was examined using reverse-transcription polymerase chain reaction and western blotting, respectively. The mitochondrial to nuclear DNA (Mt/N) ratio in the blood, exhaled breath condensate (EBC), and uvula was measured using quantitative reverse-transcription polymerase chain reaction. TFAM and PGC-1α protein concentrations in the plasma and EBC were determined using enzyme-linked immunosorbent assay. All tested parameters were higher in the OSA group than in the control. Three months later, 21 uvulopalatopharyngoplasty-responsive patients with OSA showed decreased TFAM and PGC-1α concentrations and EBC Mt/N ratio while these remained high in 19 uvulopalatopharyngoplasty-unresponsive patients. The OSA group showed severe inflammation, increased mitochondrial replication and transcription-related signaling, and mitochondrial dysfunction in the uvula. Successful OSA treatment using uvulopalatopharyngoplasty restored the TFAM and PGC-1α levels and EBC Mt/N ratio.
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Affiliation(s)
- Ching-Chi Lin
- Division of Pulmonary Medicine, Department of Internal Medicine, Taipei Tzu Chi Hospital, Buddhist Tzu Chi Medical Foundation, New Taipei City, Taiwan.
| | - Ying-Piao Wang
- Department of Otolaryngology, Mackay Memorial Hospital, Taipei, Taiwan
| | - Yi-Kun Sun
- Division of Pulmonary Medicine, Department of Internal Medicine, Taipei Tzu Chi Hospital, Buddhist Tzu Chi Medical Foundation, New Taipei City, Taiwan
| | - Chung-Hsin Chiu
- Division of Pulmonary Medicine, Department of Internal Medicine, Taipei Tzu Chi Hospital, Buddhist Tzu Chi Medical Foundation, New Taipei City, Taiwan
| | - Mei-Wei Lin
- Division of Pulmonary Medicine, Department of Internal Medicine, Taipei Tzu Chi Hospital, Buddhist Tzu Chi Medical Foundation, New Taipei City, Taiwan
| | - I-Shiang Tzeng
- Department of Research, Taipei Tzu Chi Hospital, Buddhist Tzu Chi Medical Foundation, New Taipei City, Taiwan
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4
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Golubickaite I, Ugenskiene R, Bartnykaite A, Poskiene L, Vegiene A, Padervinskis E, Rudzianskas V, Juozaityte E. Mitochondria-Related TFAM and POLG Gene Variants and Associations with Tumor Characteristics and Patient Survival in Head and Neck Cancer. Genes (Basel) 2023; 14:434. [PMID: 36833361 PMCID: PMC9956916 DOI: 10.3390/genes14020434] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Revised: 02/02/2023] [Accepted: 02/07/2023] [Indexed: 02/11/2023] Open
Abstract
In 2020, 878,348 newly reported cases and 444,347 deaths related to head and neck cancer were reported. These numbers suggest that there is still a need for molecular biomarkers for the diagnosis and prognosis of the disease. In this study, we aimed to analyze mitochondria-related mitochondrial transcription factor A (TFAM) and DNA polymerase γ (POLG) single-nucleotide polymorphisms (SNPs) in the head and neck cancer patient group and evaluate associations between SNPs, disease characteristics, and patient outcomes. Genotyping was performed using TaqMan probes with Real-Time polymerase chain reaction. We found associations between TFAM gene SNPs rs11006129 and rs3900887 and patient survival status. We found that patients with the TFAM rs11006129 CC genotype and non-carriers of the T allele had longer survival times than those with the CT genotype or T-allele carriers. Additionally, patients with the TFAM rs3900887 A allele tended to have shorter survival times than non-carriers of the A allele. Our findings suggest that variants in the TFAM gene may play an important role in head and neck cancer patient survival and could be considered and further evaluated as prognostic biomarkers. However, due to the limited sample size (n = 115), further studies in larger and more diverse cohorts are needed to confirm these findings.
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Affiliation(s)
- Ieva Golubickaite
- Department of Genetics and Molecular Medicine, Lithuanian University of Health Sciences, 44307 Kaunas, Lithuania
| | - Rasa Ugenskiene
- Department of Genetics and Molecular Medicine, Lithuanian University of Health Sciences, 44307 Kaunas, Lithuania
- Institute of Oncology, Lithuanian University of Health Sciences, 44307 Kaunas, Lithuania
| | - Agne Bartnykaite
- Institute of Oncology, Lithuanian University of Health Sciences, 44307 Kaunas, Lithuania
| | - Lina Poskiene
- Department of Pathological Anatomy, Lithuanian University of Health Sciences, 44307 Kaunas, Lithuania
| | - Aurelija Vegiene
- Department of Otorhinolaryngology, Lithuanian University of Health Sciences, 44307 Kaunas, Lithuania
| | - Evaldas Padervinskis
- Department of Otorhinolaryngology, Lithuanian University of Health Sciences, 44307 Kaunas, Lithuania
| | - Viktoras Rudzianskas
- Institute of Oncology, Lithuanian University of Health Sciences, 44307 Kaunas, Lithuania
| | - Elona Juozaityte
- Institute of Oncology, Lithuanian University of Health Sciences, 44307 Kaunas, Lithuania
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5
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Oliveira VCD, Roballo KCS, Mariano Junior CG, Ambrósio CE. Gene Editing Technologies Targeting TFAM and Its Relation to Mitochondrial Diseases. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2023; 1429:173-189. [PMID: 37486522 DOI: 10.1007/978-3-031-33325-5_10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/25/2023]
Abstract
Mitochondria are organelles present in the cytoplasm of eukaryotic cells; they play a key role in adenosine triphosphate (ATP) synthesis and oxidative phosphorylation. Mitochondria have their own DNA, mitochondrial DNA (mtDNA), keeping the function of the mitochondria. Mitochondrial transcription factor A (TFAM) is a member of the HMGB subfamily that binds to mtDNA promoters is and considered essential in mtDNA replication and transcription. More recently, TFAM has been shown to play a central role in the maintenance and regulation of mitochondrial copy number, inflammatory response, expression regulation, and mitochondrial genome activity. Gene editing tools such as the CRISPR-Cas 9 technique, TALENs, and other gene editing tools have been used to investigate the role of TFAM in mitochondrial mechanics and biogenesis as well as its correlation to mitochondrial disorders. Thus this chapter brings a summary of mitochondria function, dysfunction, the importance of TFAM in the maintenance of mitochondria, and state of the art of gene editing tools involving TFAM and mtDNA.
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Affiliation(s)
- Vanessa Cristina de Oliveira
- Department of Veterinary Medicine, Faculty of Animal Science and Food Engineering, University of São Paulo, Pirassununga, SP, Brazil.
| | - Kelly Cristine Santos Roballo
- Biomedical Affairs and Research, Edward Via College of Osteopathic Medicine, Blacksburg, VA, USA
- Department of Biomedical Sciences and Pathobiology, Virginia Maryland College of Veterinary Medicine, Virginia Tech, Blacksburg, VA, USA
| | - Clesio Gomes Mariano Junior
- Department of Veterinary Medicine, Faculty of Animal Science and Food Engineering, University of São Paulo, Pirassununga, SP, Brazil
| | - Carlos Eduardo Ambrósio
- Department of Veterinary Medicine, Faculty of Animal Science and Food Engineering, University of São Paulo, Pirassununga, SP, Brazil
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6
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Targeting Mitochondria as a Therapeutic Approach for Parkinson's Disease. Cell Mol Neurobiol 2022; 43:1499-1518. [PMID: 35951210 DOI: 10.1007/s10571-022-01265-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Accepted: 07/21/2022] [Indexed: 11/03/2022]
Abstract
Neurodegeneration is among the most critical challenges that involve modern societies and annually influences millions of patients worldwide. While the pathophysiology of Parkinson's disease (PD) is complicated, the role of mitochondrial is demonstrated. The in vitro and in vivo models and genome-wide association studies in human cases proved that specific genes, including PINK1, Parkin, DJ-1, SNCA, and LRRK2, linked mitochondrial dysfunction with PD. Also, mitochondrial DNA (mtDNA) plays an essential role in the pathophysiology of PD. Targeting mitochondria as a therapeutic approach to inhibit or slow down PD formation and progression seems to be an exciting issue. The current review summarized known mutations associated with both mitochondrial dysfunction and PD. The significance of mtDNA in Parkinson's disease pathogenesis and potential PD therapeutic approaches targeting mitochondrial dysfunction was then discussed.
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7
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Shin J, Hong SG, Choi SY, Rath ME, Saredy J, Jovin DG, Sayoc J, Park HS, Eguchi S, Rizzo V, Scalia R, Wang H, Houser SR, Park JY. Flow-induced endothelial mitochondrial remodeling mitigates mitochondrial reactive oxygen species production and promotes mitochondrial DNA integrity in a p53-dependent manner. Redox Biol 2022; 50:102252. [PMID: 35121402 PMCID: PMC8818582 DOI: 10.1016/j.redox.2022.102252] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Revised: 01/25/2022] [Accepted: 01/26/2022] [Indexed: 12/12/2022] Open
Abstract
Tumor suppressor p53 plays a pivotal role in orchestrating mitochondrial remodeling by regulating their content, fusion/fission processes, and intracellular signaling molecules that are associated with mitophagy and apoptosis pathways. In order to determine a molecular mechanism underlying flow-mediated mitochondrial remodeling in endothelial cells, we examined, herein, the role of p53 on mitochondrial adaptations to physiological flow and its relevance to vascular function using endothelial cell-specific p53 deficient mice. We observed no changes in aerobic capacity, basal blood pressure, or endothelial mitochondrial phenotypes in the endothelial p53 mull animals. However, after 7 weeks of voluntary wheel running exercise, blood pressure reduction and endothelial mitochondrial remodeling (biogenesis, elongation, and mtDNA replication) were substantially blunted in endothelial p53 null animals compared to the wild-type, subjected to angiotensin II-induced hypertension. In addition, endothelial mtDNA lesions were significantly reduced following voluntary running exercise in wild-type mice, but not in the endothelial p53 null mice. Moreover, in vitro studies demonstrated that unidirectional laminar flow exposure significantly increased key putative regulators for mitochondrial remodeling and reduced mitochondrial reactive oxygen species generation and mtDNA damage in a p53-dependent manner. Mechanistically, unidirectional laminar flow instigated translocalization of p53 into the mitochondrial matrix where it binds to mitochondrial transcription factor A, TFAM, resulting in improving mtDNA integrity. Taken together, our findings suggest that p53 plays an integral role in mitochondrial remodeling under physiological flow condition and the flow-induced p53-TFAM axis may be a novel molecular intersection for enhancing mitochondrial homeostasis in endothelial cells.
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8
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Golubickaite I, Ugenskiene R, Cepaite J, Ziliene E, Inciura A, Poskiene L, Juozaityte E. Mitochondria-related TFAM gene variants and their effects on patients with cervical cancer. Biomed Rep 2021; 15:106. [PMID: 34765190 PMCID: PMC8576402 DOI: 10.3892/br.2021.1482] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Accepted: 10/13/2021] [Indexed: 12/26/2022] Open
Abstract
Cervical cancer is the fourth most common type of cancer in women worldwide, with high incidence and mortality rates, particularly in developing countries. There are human papillomavirus vaccines and cytological screening programs available; however, there are no molecular markers that would aid the prognosis of the course of the disease or prediction of the outcomes of the patients. The aim of the present study was to investigate the associations between single nucleotide polymorphisms (SNPs) of the mitochondrial transcription factor A (TFAM) gene (rs11006132, rs11006129, rs1937, rs16912174, rs16912202 and rs3900887), and the clinical parameters and tumor phenotype of patients with cervical cancer. DNA isolated from patients with cervical cancer (n=172) was used for genotyping using Real-Time PCR using TaqMan probes. It was revealed that the TFAM rs3900887 TT and AT genotypes were associated with a lower risk of developing larger tumors. The results showed an association between the rs3900887 SNP and tumor phenotype, indicating TFAM rs3900887 as a potential biomarker for tumor size in cervical cancer.
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Affiliation(s)
- Ieva Golubickaite
- Department of Genetics and Molecular Medicine, Lithuanian University of Health Sciences, 44307 Kaunas, Lithuania
| | - Rasa Ugenskiene
- Department of Genetics and Molecular Medicine, Lithuanian University of Health Sciences, 44307 Kaunas, Lithuania.,Institute of Oncology, Lithuanian University of Health Sciences, 44307 Kaunas, Lithuania
| | - Juste Cepaite
- Institute of Oncology, Lithuanian University of Health Sciences, 44307 Kaunas, Lithuania
| | - Egle Ziliene
- Institute of Oncology, Lithuanian University of Health Sciences, 44307 Kaunas, Lithuania
| | - Arturas Inciura
- Institute of Oncology, Lithuanian University of Health Sciences, 44307 Kaunas, Lithuania
| | - Lina Poskiene
- Department of Pathological Anatomy, Lithuanian University of Health Sciences, 44307 Kaunas, Lithuania
| | - Elona Juozaityte
- Institute of Oncology, Lithuanian University of Health Sciences, 44307 Kaunas, Lithuania
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9
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HBD1 protein with a tandem repeat of two HMG-box domains is a DNA clip to organize chloroplast nucleoids in Chlamydomonas reinhardtii. Proc Natl Acad Sci U S A 2021; 118:2021053118. [PMID: 33975946 PMCID: PMC8157925 DOI: 10.1073/pnas.2021053118] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Compaction of bulky DNA is a universal issue for all DNA-based life forms. Chloroplast nucleoids (chloroplast DNA-protein complexes) are critical for chloroplast DNA maintenance and transcription, thereby supporting photosynthesis, but their detailed structure remains enigmatic. Our proteomic analysis of chloroplast nucleoids of the green alga Chlamydomonas reinhardtii identified a protein (HBD1) with a tandem repeat of two DNA-binding high mobility group box (HMG-box) domains, which is structurally similar to major mitochondrial nucleoid proteins transcription factor A, mitochondrial (TFAM), and ARS binding factor 2 protein (Abf2p). Disruption of the HBD1 gene by CRISPR-Cas9-mediated genome editing resulted in the scattering of chloroplast nucleoids. This phenotype was complemented when intact HBD1 was reintroduced, whereas a truncated HBD1 with a single HMG-box domain failed to complement the phenotype. Furthermore, ectopic expression of HBD1 in the mitochondria of yeast Δabf2 mutant successfully complemented the defects, suggesting functional similarity between HBD1 and Abf2p. Furthermore, in vitro assays of HBD1, including the electrophoretic mobility shift assay and DNA origami/atomic force microscopy, showed that HBD1 is capable of introducing U-turns and cross-strand bridges, indicating that proteins with two HMG-box domains would function as DNA clips to compact DNA in both chloroplast and mitochondrial nucleoids.
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10
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Borsche M, Pereira SL, Klein C, Grünewald A. Mitochondria and Parkinson's Disease: Clinical, Molecular, and Translational Aspects. JOURNAL OF PARKINSONS DISEASE 2021; 11:45-60. [PMID: 33074190 PMCID: PMC7990451 DOI: 10.3233/jpd-201981] [Citation(s) in RCA: 92] [Impact Index Per Article: 30.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Mitochondrial dysfunction represents a well-established player in the pathogenesis of both monogenic and idiopathic Parkinson’s disease (PD). Initially originating from the observation that mitochondrial toxins cause PD, findings from genetic PD supported a contribution of mitochondrial dysfunction to the disease. Here, proteins encoded by the autosomal recessively inherited PD genes Parkin, PTEN-induced kinase 1 (PINK1), and DJ-1 are involved in mitochondrial pathways. Additional evidence for mitochondrial dysfunction stems from models of autosomal-dominant PD due to mutations in alpha-synuclein (SNCA) and leucine-rich repeat kinase 2 (LRRK2). Moreover, patients harboring alterations in mitochondrial polymerase gamma (POLG) often exhibit signs of parkinsonism. While some molecular studies suggest that mitochondrial dysfunction is a primary event in PD, others speculate that it is the result of impaired mitochondrial clearance. Most recent research even implicated damage-associated molecular patterns released from non-degraded mitochondria in neuroinflammatory processes in PD. Here, we summarize the manifold literature dealing with mitochondria in the context of PD. Moreover, in light of recent advances in the field of personalized medicine, patient stratification according to the degree of mitochondrial impairment followed by mitochondrial enhancement therapy may hold potential for at least a subset of genetic and idiopathic PD cases. Thus, in the second part of this review, we discuss therapeutic approaches targeting mitochondrial dysfunction with the aim to prevent or delay neurodegeneration in PD.
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Affiliation(s)
- Max Borsche
- Institute of Neurogenetics, University of Lübeck, Lübeck, Germany.,Department of Neurology, University of Lübeck, Lübeck, Germany
| | - Sandro L Pereira
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Christine Klein
- Institute of Neurogenetics, University of Lübeck, Lübeck, Germany
| | - Anne Grünewald
- Institute of Neurogenetics, University of Lübeck, Lübeck, Germany.,Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
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11
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de Lima MA, Morotti F, Bayeux BM, de Rezende RG, Botigelli RC, De Bem THC, Fontes PK, Nogueira MFG, Meirelles FV, Baruselli PS, da Silveira JC, Perecin F, Seneda MM. Ovarian follicular dynamics, progesterone concentrations, pregnancy rates and transcriptional patterns in Bos indicus females with a high or low antral follicle count. Sci Rep 2020; 10:19557. [PMID: 33177637 PMCID: PMC7658257 DOI: 10.1038/s41598-020-76601-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Accepted: 09/02/2020] [Indexed: 11/22/2022] Open
Abstract
We evaluated the effect of the antral follicle count (AFC) on ovarian follicular dynamics, pregnancy rates, progesterone concentrations, and transcriptional patterns of genes in Nelore cattle (Bos taurus indicus) after a timed artificial insemination (TAI) programme. Cows were separated based on the AFC, and those with a high AFC showed a larger (P < 0.0001) ovarian diameter and area than those with a very low AFC. Females with a very low AFC exhibited a larger (P < 0.01) diameter of the dominant follicle at TAI (13.6 ± 0.3 vs. 12.2 ± 0.4 mm) and a tendency (P = 0.06) to have different serum progesterone concentrations (2.9 ± 0.3 vs. 2.1 ± 0.3 ng/mL; on day 18, considering day 0 as the beginning of the synchronization protocol) than those with a high AFC. The pregnancy rate was higher (P ≤ 0.05) in animals with a very low (57.9%) and low (53.1%) AFC than in those with a high AFC (45.2%). The expression of genes related to intercellular communication, meiotic control, epigenetic modulation, cell division, follicular growth, cell maintenance, steroidogenesis and cellular stress response was assessed on day 5. In females with a low AFC, 8 and 21 genes in oocytes and cumulus cells, respectively, were upregulated (P < 0.05), while 3 and 6 genes in oocytes and cumulus cells, respectively, were downregulated. The results described here will help elucidate the differences in ovarian physiology and the reproductive success of Bos indicus females with a low or high AFC.
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Affiliation(s)
| | - Fábio Morotti
- Animal Reproduction and Biotechnology Laboratory, State University of Londrina-UEL, Londrina, PR, Brazil.
- Laboratório de Reprodução Animal, DCV, CCA, UEL, Cx. Postal: 10.011, Londrina, PR, Cep: 86057-970, Brazil.
| | | | | | | | | | | | | | | | | | | | - Felipe Perecin
- Department of Veterinary Medicine, FZEA/USP, Pirassununga, SP, Brazil
| | - Marcelo Marcondes Seneda
- Animal Reproduction and Biotechnology Laboratory, State University of Londrina-UEL, Londrina, PR, Brazil
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12
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Zhu Y, Xu J, Hu W, Wang F, Zhou Y, Xu W, Gong W, Shao L. TFAM depletion overcomes hepatocellular carcinoma resistance to doxorubicin and sorafenib through AMPK activation and mitochondrial dysfunction. Gene 2020; 753:144807. [PMID: 32461017 DOI: 10.1016/j.gene.2020.144807] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Revised: 05/06/2020] [Accepted: 05/21/2020] [Indexed: 02/06/2023]
Abstract
Mitochondrial transcription factor A (TFAM), which is required for mitochondrial DNA (mtDNA) transcription, has been linked to metabolic changes that contribute to tumorigenesis and chemoresistance. In this work, we investigated the expression pattern and role of TFAM in hepatocellular carcinoma (HCC). TFAM expression level is similar in 18 out of 20 paired normal liver and HCC tissues with only 2 HCC tissues showing 1.8-fold increase in TFAM. Similar phenomenon was observed in HCC cell lines compared to normal liver lines. Interestingly, TFAM expression is upregulated in resistant HCC cells regardless of the differential TFAM expression level in their parental lines and mechanism of resistance. TFAM depletion led to inhibition of growth and survival but not migration, and sensitization to doxorubicin and sorafenib treatment, through AMPK activation, reduction of nucleoside triphosphates and mitochondrial respiration in HCC cells. In addition, we demonstrated that resistant HCC cell lines were more sensitive to TFAM inhibition than parental lines, and this might be due to the increased mitochondrial biogenesis in resistant HCC cell lines. Our work reveals the preferential role of TFAM in HCC cell response to standard of care drugs, which suggests a potential sensitizing therapeutic target for HCC treatment.
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Affiliation(s)
- Ying Zhu
- Department of Gastroenterology, Shenzhen Hospital of Southern Medical University, Shenzhen, Guangdong, China
| | - Jianguo Xu
- Department of Liver Disease Center, Shenzhen Hospital of Southern Medical University, Shenzhen, Guangdong, China
| | - Wei Hu
- Department of Gastroenterology, Shenzhen Hospital of Southern Medical University, Shenzhen, Guangdong, China
| | - Fang Wang
- Department of Gastroenterology, Shenzhen Hospital of Southern Medical University, Shenzhen, Guangdong, China
| | - Yan Zhou
- Information Management Section, Bethune International Peace Hospital, Shijiazhuang City, Hebei Province, China
| | - Wen Xu
- Department of Gastroenterology, Shenzhen Hospital of Southern Medical University, Shenzhen, Guangdong, China
| | - Wei Gong
- Department of Gastroenterology, Shenzhen Hospital of Southern Medical University, Shenzhen, Guangdong, China.
| | - Lichun Shao
- Department of Gastroenterology, The Air Force Hospital From Northern Theatre of PLA, Shenyang, Liaoning, China.
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13
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Hunt RJ, Granat L, McElroy GS, Ranganathan R, Chandel NS, Bateman JM. Mitochondrial stress causes neuronal dysfunction via an ATF4-dependent increase in L-2-hydroxyglutarate. J Cell Biol 2019; 218:4007-4016. [PMID: 31645461 PMCID: PMC6891100 DOI: 10.1083/jcb.201904148] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Revised: 08/19/2019] [Accepted: 09/11/2019] [Indexed: 12/16/2022] Open
Abstract
Mitochondrial stress contributes to a range of neurological diseases. Mitonuclear signaling pathways triggered by mitochondrial stress remodel cellular physiology and metabolism. How these signaling mechanisms contribute to neuronal dysfunction and disease is poorly understood. We find that mitochondrial stress in neurons activates the transcription factor ATF4 as part of the endoplasmic reticulum unfolded protein response (UPR) in Drosophila We show that ATF4 activation reprograms nuclear gene expression and contributes to neuronal dysfunction. Mitochondrial stress causes an ATF4-dependent increase in the level of the metabolite L-2-hydroxyglutarate (L-2-HG) in the Drosophila brain. Reducing L-2-HG levels directly, by overexpressing L-2-HG dehydrogenase, improves neurological function. Modulation of L-2-HG levels by mitochondrial stress signaling therefore regulates neuronal function.
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Affiliation(s)
- Rachel J Hunt
- Maurice Wohl Clinical Neuroscience Institute, King's College London, London, UK
| | - Lucy Granat
- Maurice Wohl Clinical Neuroscience Institute, King's College London, London, UK
| | - Gregory S McElroy
- Department of Medicine and Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL
| | - Ramya Ranganathan
- Maurice Wohl Clinical Neuroscience Institute, King's College London, London, UK
| | - Navdeep S Chandel
- Department of Medicine and Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL
| | - Joseph M Bateman
- Maurice Wohl Clinical Neuroscience Institute, King's College London, London, UK
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14
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de Oliveira VC, Moreira GSA, Bressan FF, Gomes Mariano Junior C, Roballo KCS, Charpentier M, Concordet JP, Meirelles FV, Ambrósio CE. Edition of TFAM gene by CRISPR/Cas9 technology in bovine model. PLoS One 2019; 14:e0213376. [PMID: 30845180 PMCID: PMC6405117 DOI: 10.1371/journal.pone.0213376] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2018] [Accepted: 02/19/2019] [Indexed: 11/24/2022] Open
Abstract
The mitochondrial transcription factor A (TFAM) is a mitochondrial DNA (mtDNA) binding protein essential for the initiation of transcription and genome maintenance. Recently it was demonstrated that the primary role of TFAM is to maintain the integrity of mtDNA and that it is a key regulator of mtDNA copy number. It was also shown that TFAM plays a central role in the mtDNA stress-mediated inflammatory response. In our study, we proposed to evaluate the possibility of editing the TFAM gene by CRISPR/Cas9 technology in bovine fibroblasts, as TFAM regulates the replication specificity of mtDNA. We further attempted to maintain these cells in culture post edition in a medium supplemented with uridine and pyruvate to mimic Rho zero cells that are capable of surviving without mtDNA, because it is known that the TFAM gene is lethal in knockout mice and chicken. Moreover, we evaluated the effects of TFAM modification on mtDNA copy number. The CRISPR gRNA was designed to target exon 1 of the bovine TFAM gene and subsequently cloned. Fibroblasts were transfected with Cas9 and control plasmids. After 24 h of transfection, cells were analyzed by flow cytometry to evaluate the efficiency of transfection. The site directed-mutation frequency was assessed by T7 endonuclease assay, and cell clones were analyzed for mtDNA copy number by Sanger DNA sequencing. We achieved transfection efficiency of 51.3%. We selected 23 successfully transformed clones for further analysis, and seven of these exhibited directed mutations at the CRISPR/Cas9 targeted site. Moreover, we also found a decrease in mtDNA copy number in the gene edited clones compared to that in the controls. These TFAM gene mutant cells were viable in culture when supplemented with uridine and pyruvate. We conclude that this CRISPR/Cas9 design was efficient, resulting in seven heterozygous mutant clones and opening up the possibility to use these mutant cell lines as a model system to elucidate the role of TFAM in the maintenance of mtDNA integrity.
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Affiliation(s)
- Vanessa Cristina de Oliveira
- Department of Veterinary Medicine, Faculty of Animal Science and Food Engineering, University of São Paulo, Pirassununga, São Paulo, Brazil
| | - Gabriel Sassarão Alves Moreira
- Department of Veterinary Medicine, Faculty of Animal Science and Food Engineering, University of São Paulo, Pirassununga, São Paulo, Brazil
| | - Fabiana Fernandes Bressan
- Department of Veterinary Medicine, Faculty of Animal Science and Food Engineering, University of São Paulo, Pirassununga, São Paulo, Brazil
| | - Clésio Gomes Mariano Junior
- Department of Veterinary Medicine, Faculty of Animal Science and Food Engineering, University of São Paulo, Pirassununga, São Paulo, Brazil
| | - Kelly Cristine Santos Roballo
- Department of Veterinary Medicine, Faculty of Animal Science and Food Engineering, University of São Paulo, Pirassununga, São Paulo, Brazil
| | - Marine Charpentier
- Laboratoire Structure et Instabilité des Génomes, Museum National d’Histoire Naturelle, INSERM U1154, CNRS UMR7196, Paris, France
| | - Jean-Paul Concordet
- Laboratoire Structure et Instabilité des Génomes, Museum National d’Histoire Naturelle, INSERM U1154, CNRS UMR7196, Paris, France
| | - Flávio Vieira Meirelles
- Department of Veterinary Medicine, Faculty of Animal Science and Food Engineering, University of São Paulo, Pirassununga, São Paulo, Brazil
| | - Carlos Eduardo Ambrósio
- Department of Veterinary Medicine, Faculty of Animal Science and Food Engineering, University of São Paulo, Pirassununga, São Paulo, Brazil
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15
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Bajwa E, Pointer CB, Klegeris A. The Role of Mitochondrial Damage-Associated Molecular Patterns in Chronic Neuroinflammation. Mediators Inflamm 2019; 2019:4050796. [PMID: 31065234 PMCID: PMC6466851 DOI: 10.1155/2019/4050796] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2018] [Revised: 03/01/2019] [Accepted: 03/06/2019] [Indexed: 01/05/2023] Open
Abstract
Mitochondrial dysfunction has been established as a common feature of neurodegenerative disorders that contributes to disease pathology by causing impaired cellular energy production. Mitochondrial molecules released into the extracellular space following neuronal damage or death may also play a role in these diseases by acting as signaling molecules called damage-associated molecular patterns (DAMPs). Mitochondrial DAMPs have been shown to initiate proinflammatory immune responses from nonneuronal glial cells, including microglia and astrocytes; thereby, they have the potential to contribute to the chronic neuroinflammation present in these disorders accelerating the degeneration of neurons. In this review, we highlight the mitochondrial DAMPs cytochrome c (CytC), mitochondrial transcription factor A (TFAM), and cardiolipin and explore their potential role in the central nervous system disorders including Alzheimer's disease and Parkinson's disease, which are characterized by neurodegeneration and chronic neuroinflammation.
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Affiliation(s)
- Ekta Bajwa
- Department of Biology, University of British Columbia Okanagan Campus, Kelowna, BC, Canada
| | - Caitlin B. Pointer
- Department of Biology, University of British Columbia Okanagan Campus, Kelowna, BC, Canada
| | - Andis Klegeris
- Department of Biology, University of British Columbia Okanagan Campus, Kelowna, BC, Canada
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16
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Araujo LF, Siena ADD, Plaça JR, Brotto DB, Barros II, Muys BR, Biagi CAO, Peronni KC, Sousa JF, Molfetta GA, West LC, West AP, Leopoldino AM, Espreafico EM, Silva WA. Mitochondrial transcription factor A (TFAM) shapes metabolic and invasion gene signatures in melanoma. Sci Rep 2018; 8:14190. [PMID: 30242167 PMCID: PMC6155108 DOI: 10.1038/s41598-018-31170-6] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2017] [Accepted: 07/27/2018] [Indexed: 12/27/2022] Open
Abstract
Mitochondria are central key players in cell metabolism, and mitochondrial DNA (mtDNA) instability has been linked to metabolic changes that contribute to tumorigenesis and to increased expression of pro-tumorigenic genes. Here, we use melanoma cell lines and metastatic melanoma tumors to evaluate the effect of mtDNA alterations and the expression of the mtDNA packaging factor, TFAM, on energetic metabolism and pro-tumorigenic nuclear gene expression changes. We report a positive correlation between mtDNA copy number, glucose consumption, and ATP production in melanoma cell lines. Gene expression analysis reveals a down-regulation of glycolytic enzymes in cell lines and an up-regulation of amino acid metabolism enzymes in melanoma tumors, suggesting that TFAM may shift melanoma fuel utilization from glycolysis towards amino acid metabolism, especially glutamine. Indeed, proliferation assays reveal that TFAM-down melanoma cell lines display a growth arrest in glutamine-free media, emphasizing that these cells rely more on glutamine metabolism than glycolysis. Finally, our data indicate that TFAM correlates to VEGF expression and may contribute to tumorigenesis by triggering a more invasive gene expression signature. Our findings contribute to the understanding of how TFAM affects melanoma cell metabolism, and they provide new insight into the mechanisms by which TFAM and mtDNA copy number influence melanoma tumorigenesis.
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Affiliation(s)
- L F Araujo
- Department of Genetics-Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil
- National institute of Science and Technology in Stem Cell and Cell Therapy, Center for Cell-based Therapy-CEPID/FAPESP, Ribeirão Preto, Brazil
- Medical Genomics Laboratory, CIPE, AC Camargo Cancer Center, São Paulo, Brazil
| | - A D D Siena
- Department of Genetics-Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil
- National institute of Science and Technology in Stem Cell and Cell Therapy, Center for Cell-based Therapy-CEPID/FAPESP, Ribeirão Preto, Brazil
| | - J R Plaça
- National institute of Science and Technology in Stem Cell and Cell Therapy, Center for Cell-based Therapy-CEPID/FAPESP, Ribeirão Preto, Brazil
| | - D B Brotto
- Department of Genetics-Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil
- National institute of Science and Technology in Stem Cell and Cell Therapy, Center for Cell-based Therapy-CEPID/FAPESP, Ribeirão Preto, Brazil
| | - I I Barros
- Department of Genetics-Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil
- National institute of Science and Technology in Stem Cell and Cell Therapy, Center for Cell-based Therapy-CEPID/FAPESP, Ribeirão Preto, Brazil
| | - B R Muys
- Department of Genetics-Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil
- National institute of Science and Technology in Stem Cell and Cell Therapy, Center for Cell-based Therapy-CEPID/FAPESP, Ribeirão Preto, Brazil
| | - C A O Biagi
- Department of Genetics-Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil
- National institute of Science and Technology in Stem Cell and Cell Therapy, Center for Cell-based Therapy-CEPID/FAPESP, Ribeirão Preto, Brazil
| | - K C Peronni
- National institute of Science and Technology in Stem Cell and Cell Therapy, Center for Cell-based Therapy-CEPID/FAPESP, Ribeirão Preto, Brazil
| | - J F Sousa
- Department of Genetics-Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil
- National institute of Science and Technology in Stem Cell and Cell Therapy, Center for Cell-based Therapy-CEPID/FAPESP, Ribeirão Preto, Brazil
| | - G A Molfetta
- Department of Genetics-Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil
- National institute of Science and Technology in Stem Cell and Cell Therapy, Center for Cell-based Therapy-CEPID/FAPESP, Ribeirão Preto, Brazil
| | - L C West
- Microbial Pathogenesis & Immunology, Health Science Center, Texas A&M University, College Station, USA
| | - A P West
- Microbial Pathogenesis & Immunology, Health Science Center, Texas A&M University, College Station, USA
| | - A M Leopoldino
- Department of Clinical Analysis-Toxicology and Food Sciences, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Ribeirão Preto, Brazil
| | - E M Espreafico
- Department of Cellular and Molecular Biology-Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil
| | - W A Silva
- Department of Genetics-Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil.
- National institute of Science and Technology in Stem Cell and Cell Therapy, Center for Cell-based Therapy-CEPID/FAPESP, Ribeirão Preto, Brazil.
- Center for Integrative System Biology-CISBi-NAP/USP, University of São Paulo, Ribeirão Preto, Brazil.
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17
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van der Ende M, Grefte S, Plas R, Meijerink J, Witkamp RF, Keijer J, van Norren K. Mitochondrial dynamics in cancer-induced cachexia. Biochim Biophys Acta Rev Cancer 2018; 1870:137-150. [PMID: 30059724 DOI: 10.1016/j.bbcan.2018.07.008] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Revised: 07/25/2018] [Accepted: 07/26/2018] [Indexed: 12/25/2022]
Abstract
Cancer-induced cachexia has a negative impact on quality of life and adversely affects therapeutic outcomes and survival rates. It is characterized by, often severe, loss of muscle, with or without loss of fat mass. Insight in the pathophysiology of this complex metabolic syndrome and direct treatment options are still limited, which creates a research demand. Results from recent studies point towards a significant involvement of muscle mitochondrial networks. However, data are scattered and a comprehensive overview is lacking. This paper aims to fill existing knowledge gaps by integrating published data sets on muscle protein or gene expression from cancer-induced cachexia animal models. To this end, a database was compiled from 94 research papers, comprising 11 different rodent models. This was combined with four genome-wide transcriptome datasets of cancer-induced cachexia rodent models. Analysis showed that the expression of genes involved in mitochondrial fusion, fission, ATP production and mitochondrial density is decreased, while that of genes involved ROS detoxification and mitophagy is increased. Our results underline the relevance of including post-translational modifications of key proteins involved in mitochondrial functioning in future studies on cancer-induced cachexia.
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Affiliation(s)
- Miranda van der Ende
- Division of Human Nutrition, Wageningen University and Research, Wageningen, Netherlands; Human and Animal Physiology, Wageningen University and Research, Wageningen, Netherlands
| | - Sander Grefte
- Human and Animal Physiology, Wageningen University and Research, Wageningen, Netherlands
| | - Rogier Plas
- Division of Human Nutrition, Wageningen University and Research, Wageningen, Netherlands
| | - Jocelijn Meijerink
- Division of Human Nutrition, Wageningen University and Research, Wageningen, Netherlands
| | - Renger F Witkamp
- Division of Human Nutrition, Wageningen University and Research, Wageningen, Netherlands
| | - Jaap Keijer
- Human and Animal Physiology, Wageningen University and Research, Wageningen, Netherlands
| | - Klaske van Norren
- Division of Human Nutrition, Wageningen University and Research, Wageningen, Netherlands.
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18
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Friedland W, Schmitt E, Kundrát P, Baiocco G, Ottolenghi A. Track-structure simulations of energy deposition patterns to mitochondria and damage to their DNA. Int J Radiat Biol 2018; 95:3-11. [PMID: 29584515 DOI: 10.1080/09553002.2018.1450532] [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] [Indexed: 10/17/2022]
Abstract
PURPOSE Mitochondria have been implicated in initiating and/or amplifying the biological effects of ionizing radiation not mediated via damage to nuclear DNA. To help elucidate the underlying mechanisms, energy deposition patterns to mitochondria and radiation damage to their DNA have been modelled. METHODS Track-structure simulations have been performed with PARTRAC biophysical tool for 60Co γ-rays and 5 MeV α-particles. Energy deposition to the cell's mitochondria has been analyzed. A model of mitochondrial DNA reflecting experimental information on its structure has been developed and used to assess its radiation-induced damage. RESULTS Energy deposition to mitochondria is highly inhomogeneous, especially at low doses. Although a dose-dependent fraction of mitochondria sees no energy deposition at all, the hit ones receive rather high amounts of energy. Nevertheless, only little damage to mitochondrial DNA occurs, even at large doses. CONCLUSION Mitochondrial DNA does not represent a critical target for radiation effects. Likely, the key role of mitochondria in radiation-induced biological effects arises from the communication between mitochondria and/or with the nucleus. Through this signaling, initial modifications in a few heavily hit mitochondria seem to be amplified to a massive long-term effect manifested in the whole cell or even tissue.
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Affiliation(s)
- Werner Friedland
- a Institute of Radiation Protection, Helmholtz Zentrum München - German Research Center for Environmental Health , Neuherberg , Germany
| | - Elke Schmitt
- a Institute of Radiation Protection, Helmholtz Zentrum München - German Research Center for Environmental Health , Neuherberg , Germany
| | - Pavel Kundrát
- a Institute of Radiation Protection, Helmholtz Zentrum München - German Research Center for Environmental Health , Neuherberg , Germany
| | - Giorgio Baiocco
- b Department of Physics , University of Pavia , Pavia , Italy
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19
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Sandmann A, Sticht H. Probing the role of intercalating protein sidechains for kink formation in DNA. PLoS One 2018; 13:e0192605. [PMID: 29432448 PMCID: PMC5809078 DOI: 10.1371/journal.pone.0192605] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2017] [Accepted: 01/28/2018] [Indexed: 11/18/2022] Open
Abstract
Protein binding can induce DNA kinks, which are for example important to enhance the specificity of the interaction and to facilitate the assembly of multi protein complexes. The respective proteins frequently exhibit amino acid sidechains that intercalate between the DNA base steps at the site of the kink. However, on a molecular level there is only little information available about the role of individual sidechains for kink formation. To unravel structural principles of protein-induced DNA kinking we have performed molecular dynamics (MD) simulations of five complexes that varied in their architecture, function, and identity of intercalated residues. Simulations were performed for the DNA complexes of wildtype proteins (Sac7d, Sox-4, CcpA, TFAM, TBP) and for mutants, in which the intercalating residues were individually or combined replaced by alanine. The work revealed that for systems with multiple intercalated residues, not all of them are necessarily required for kink formation. In some complexes (Sox-4, TBP), one of the residues proved to be essential for kink formation, whereas the second residue has only a very small effect on the magnitude of the kink. In other systems (e.g. Sac7d) each of the intercalated residues proved to be individually capable of conferring a strong kink suggesting a partially redundant role of the intercalating residues. Mutation of the key residues responsible for kinking either resulted in stable complexes with reduced kink angles or caused conformational instability as evidenced by a shift of the kink to an adjacent base step. Thus, MD simulations can help to identify the role of individual inserted residues for kinking, which is not readily apparent from an inspection of the static structures. This information might be helpful for understanding protein-DNA interactions in more detail and for designing proteins with altered DNA binding properties in the future.
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Affiliation(s)
- Achim Sandmann
- Bioinformatik, Institut für Biochemie, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Heinrich Sticht
- Bioinformatik, Institut für Biochemie, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
- * E-mail:
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20
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Zank DC, Bueno M, Mora AL, Rojas M. Idiopathic Pulmonary Fibrosis: Aging, Mitochondrial Dysfunction, and Cellular Bioenergetics. Front Med (Lausanne) 2018; 5:10. [PMID: 29459894 PMCID: PMC5807592 DOI: 10.3389/fmed.2018.00010] [Citation(s) in RCA: 102] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2017] [Accepted: 01/15/2018] [Indexed: 12/12/2022] Open
Abstract
At present, the etiology of idiopathic pulmonary fibrosis (IPF) remains elusive. Over the past two decades, however, researchers have identified and described the underlying processes that result in metabolic dysregulation, metabolic reprogramming, and mitochondrial dysfunction observed in the cells of IPF lungs. Metabolic changes and mitochondrial dysfunction in IPF include decreased efficiency of electron transport chain function with increasing production of reactive oxygen species, decreased mitochondrial biogenesis, and impaired mitochondrial macroautophagy, a key pathway for the removal of dysfunctional mitochondria. Metabolic changes in IPF have potential impact on lung cell function, differentiation, and activation of fibrotic responses. These alterations result in activation of TGF-β and predispose to the development of pulmonary fibrosis. IPF is a disease of the aged, and many of these same bioenergetic changes are present to a lesser extent with normal aging, raising the possibility that these anticipated alterations in metabolic processes play important roles in creating susceptibility to the development of IPF. This review explores what is known regarding the cellular metabolic and mitochondrial changes that are found in IPF, and examines this body of literature to identify future research direction and potential points of intervention in the pathogenesis of IPF.
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Affiliation(s)
- Daniel C Zank
- Division of Pulmonary, Allergy and Critical Care Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States
| | - Marta Bueno
- Division of Pulmonary, Allergy and Critical Care Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States.,Vascular Medicine Institute, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States
| | - Ana L Mora
- Division of Pulmonary, Allergy and Critical Care Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States.,Vascular Medicine Institute, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States
| | - Mauricio Rojas
- Division of Pulmonary, Allergy and Critical Care Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States.,McGowan Institute of Regenerative Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States.,Dorothy P. & Richard P. Simmons Center for Interstitial Lung Disease, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States
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21
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Singh KK, Choudhury AR, Tiwari HK. Numtogenesis as a mechanism for development of cancer. Semin Cancer Biol 2017; 47:101-109. [PMID: 28511886 DOI: 10.1016/j.semcancer.2017.05.003] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2016] [Revised: 04/20/2017] [Accepted: 10/14/2016] [Indexed: 01/10/2023]
Abstract
Transfer of genetic material from cytoplasmic organelles to the nucleus, an ongoing process, has implications in evolution, aging, and human pathologies such as cancer. The transferred mitochondrial DNA (mtDNA) fragments in the nuclear genome are called nuclear mtDNA or NUMTs. We have named the process numtogenesis, defining the term as the transfer of mtDNA into the nuclear genome, or, less specifically, the transfer of mitochondria or mitochondrial components into the nucleus. There is increasing evidence of the involvement of NUMTs in human biology and pathology. Although information pertaining to NUMTs and numtogenesis is sparse, the role of this aspect of mitochondrial biology to human cancers is apparent. In this review, we present available knowledge about the origin and mechanisms of numtogenesis, with special emphasis on the role of NUMTs in human malignancies. We describe studies undertaken in our laboratory and in others and discuss the influence of NUMTs in tumor initiation and progression and in survival of cancer patients. We describe suppressors of numtogenesis and evolutionary conserved mechanisms underlying numtogenesis in cancer. An understanding the emerging field of numtogenesis should allow comprehension of this process in various malignancies and other diseases and, more generally, in human health.
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Affiliation(s)
- Keshav K Singh
- Departments of Genetics, Birmingham, AL, 35294, USA; Departments of Pathology, Birmingham, AL, 35294, USA; Departments of Environmental Health, Center for Free Radical Biology, Birmingham, AL, 35294, USA; Center for Aging, Birmingham, AL, 35294, USA; UAB Comprehensive Cancer Center, University of Alabama at Birmingham, AL, 35294, USA; Birmingham Veterans Affairs Medical Center, AL, 35294, USA.
| | | | - Hemant K Tiwari
- Department of Biostatistics, University of Alabama at Birmingham, Birmingham, AL, 35294, USA
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22
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Mitochondrial transcription factor A (TFAM) rs1937 and AP endonuclease 1 (APE1) rs1130409 alleles are associated with reduced cognitive performance. Neurosci Lett 2017; 645:46-52. [DOI: 10.1016/j.neulet.2017.02.062] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2016] [Revised: 02/15/2017] [Accepted: 02/22/2017] [Indexed: 12/13/2022]
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23
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Gao W, Wu MH, Wang N, Ying MZ, Zhang YY, Hua J, Chuan L, Wang YJ. Mitochondrial transcription factor A contributes to cisplatin resistance in patients with estrogen receptor-positive breast cancer. Mol Med Rep 2016; 14:5304-5310. [DOI: 10.3892/mmr.2016.5881] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2015] [Accepted: 09/19/2016] [Indexed: 11/05/2022] Open
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24
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Grünewald A, Rygiel KA, Hepplewhite PD, Morris CM, Picard M, Turnbull DM. Mitochondrial DNA Depletion in Respiratory Chain-Deficient Parkinson Disease Neurons. Ann Neurol 2016; 79:366-78. [PMID: 26605748 PMCID: PMC4819690 DOI: 10.1002/ana.24571] [Citation(s) in RCA: 174] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2015] [Accepted: 11/24/2015] [Indexed: 12/11/2022]
Abstract
Objective To determine the extent of respiratory chain abnormalities and investigate the contribution of mtDNA to the loss of respiratory chain complexes (CI–IV) in the substantia nigra (SN) of idiopathic Parkinson disease (IPD) patients at the single‐neuron level. Methods Multiple‐label immunofluorescence was applied to postmortem sections of 10 IPD patients and 10 controls to quantify the abundance of CI–IV subunits (NDUFB8 or NDUFA13, SDHA, UQCRC2, and COXI) and mitochondrial transcription factors (TFAM and TFB2M) relative to mitochondrial mass (porin and GRP75) in dopaminergic neurons. To assess the involvement of mtDNA in respiratory chain deficiency in IPD, SN neurons, isolated with laser‐capture microdissection, were assayed for mtDNA deletions, copy number, and presence of transcription/replication‐associated 7S DNA employing a triplex real‐time polymerase chain reaction (PCR) assay. Results Whereas mitochondrial mass was unchanged in single SN neurons from IPD patients, we observed a significant reduction in the abundances of CI and II subunits. At the single‐cell level, CI and II deficiencies were correlated in patients. The CI deficiency concomitantly occurred with low abundances of the mtDNA transcription factors TFAM and TFB2M, which also initiate transcription‐primed mtDNA replication. Consistent with this, real‐time PCR analysis revealed fewer transcription/replication‐associated mtDNA molecules and an overall reduction in mtDNA copy number in patients. This effect was more pronounced in single IPD neurons with severe CI deficiency. Interpretation Respiratory chain dysfunction in IPD neurons not only involves CI, but also extends to CII. These deficiencies are possibly a consequence of the interplay between nDNA and mtDNA‐encoded factors mechanistically connected via TFAM. ANN NEUROL 2016;79:366–378
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Affiliation(s)
- Anne Grünewald
- Wellcome Trust Centre for Mitochondrial Research and Medical Research Council/Biotechnology and Biological Sciences Research Council Centre for Ageing and Vitality, Institute of Neurosciences, Newcastle University, Newcastle upon Tyne, United Kingdom.,Institute of Neurogenetics, University of Lübeck, Lübeck, Germany.,Molecular and Functional Neurobiology Group, Luxembourg Center for Systems Biomedicine, University of Luxembourg, Campus Belval, Belvaux, Luxembourg
| | - Karolina A Rygiel
- Wellcome Trust Centre for Mitochondrial Research and Medical Research Council/Biotechnology and Biological Sciences Research Council Centre for Ageing and Vitality, Institute of Neurosciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Philippa D Hepplewhite
- Wellcome Trust Centre for Mitochondrial Research and Medical Research Council/Biotechnology and Biological Sciences Research Council Centre for Ageing and Vitality, Institute of Neurosciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Christopher M Morris
- Newcastle Brain Tissue Resource, Campus for Ageing and Vitality, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Martin Picard
- Division of Behavioral Medicine, Department of Psychiatry and Department of Neurology, College of Physicians and Surgeons, Columbia University, Columbia University Medical Center, New York, NY
| | - Doug M Turnbull
- Wellcome Trust Centre for Mitochondrial Research and Medical Research Council/Biotechnology and Biological Sciences Research Council Centre for Ageing and Vitality, Institute of Neurosciences, Newcastle University, Newcastle upon Tyne, United Kingdom
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25
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Traverso JJ, Manoranjan VS, Bishop AR, Rasmussen KØ, Voulgarakis NK. Allostery through protein-induced DNA bubbles. Sci Rep 2015; 5:9037. [PMID: 25762409 PMCID: PMC4356955 DOI: 10.1038/srep09037] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2014] [Accepted: 02/13/2015] [Indexed: 01/03/2023] Open
Abstract
Allostery through DNA is increasingly recognized as an important modulator of DNA functions. Here, we show that the coalescence of protein-induced DNA bubbles can mediate allosteric interactions that drive protein aggregation. We propose that such allostery may regulate DNA's flexibility and the assembly of the transcription machinery. Mitochondrial transcription factor A (TFAM), a dual-function protein involved in mitochondrial DNA (mtDNA) packaging and transcription initiation, is an ideal candidate to test such a hypothesis owing to its ability to locally unwind the double helix. Numerical simulations demonstrate that the coalescence of TFAM-induced bubbles can explain experimentally observed TFAM oligomerization. The resulting melted DNA segment, approximately 10 base pairs long, around the joints of the oligomers act as flexible hinges, which explains the efficiency of TFAM in compacting DNA. Since mitochondrial polymerase (mitoRNAP) is involved in melting the transcription bubble, TFAM may use the same allosteric interaction to both recruit mitoRNAP and initiate transcription.
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Affiliation(s)
- Joseph J Traverso
- 1] Department of Mathematics, Washington State University, Richland, WA 99354, USA [2] Department of Mechanical Engineering, Washington State University, Richland, WA 99354, USA
| | | | - A R Bishop
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - Kim Ø Rasmussen
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
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26
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Abstract
Understanding regulation of mitochondrial DNA (mtDNA) expression is of considerable interest given that mitochondrial dysfunction is important in human pathology and aging. Similar to the situation in bacteria, there is no compartmentalization between transcription and translation in mitochondria; hence, both processes are likely to have a direct molecular crosstalk. Accumulating evidence suggests that there are important mechanisms for regulation of mammalian mtDNA expression at the posttranscriptional level. Regulation of mRNA maturation, mRNA stability, translational coordination, ribosomal biogenesis, and translation itself all form the basis for controlling oxidative phosphorylation capacity. Consequently, a wide variety of inherited human mitochondrial diseases are caused by mutations of nuclear genes regulating various aspects of mitochondrial translation. Furthermore, mutations of mtDNA, associated with human disease and aging, often affect tRNA genes critical for mitochondrial translation. Recent advances in molecular understanding of mitochondrial translation regulation will most likely provide novel avenues for modulating mitochondrial function for treating human disease.
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Affiliation(s)
- B Martin Hällberg
- Department of Cell and Molecular Biology, Karolinska Institutet, 171 77 Stockholm, Sweden; Röntgen-Ångström-Cluster, Karolinska Institutet Outstation, Centre for Structural Systems Biology, DESY Campus, 22603 Hamburg, Germany; European Molecular Biology Laboratory, Hamburg Unit, 22603 Hamburg, Germany.
| | - Nils-Göran Larsson
- Department of Mitochondrial Biology, Max Planck Institute for Biology of Ageing, 509 31 Cologne, Germany; Department of Laboratory Medicine, Karolinska Institutet, 171 77 Stockholm, Sweden.
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27
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Abstract
Heart failure has become a huge public health problem. The treatment options for heart failure, however, are considerably limited. The significant disparity between the scope of a prominent health problem and the restricted means of therapy propagates heart failure epidemics. Delineating novel mechanisms of heart failure is imperative. Emerging evidence suggests that epigenetic regulation may take part in the pathogenesis of heart failure. Epigenetic regulation involves DNA and histone modifications that lead to changes in DNA-based transcriptional programs without altering the DNA sequence. Although more and more mechanisms are being discovered, the best understood epigenetic modifications are achieved through covalent biochemical reactions including histone acetylation, histone methylation and DNA methylation. Connecting environmental stimuli with genomic programs, epigenetic regulation remains important in maintaining homeostases and the pathogeneses of diseases. This review summarizes the most recent developments regarding individual epigenetic modifications and their implications in the pathogenesis of heart failure. Understanding this strategically important mechanism is potentially the key for developing powerful interventions in the future.
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Affiliation(s)
- Dian J Cao
- Department of Internal Medicine, Cardiology Division, UT Southwestern Medical Center, Dallas VA Medical Center, 4500 S Lancaster Rd, Dallas, TX 75216, USA
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28
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Sharoyko VV, Abels M, Sun J, Nicholas LM, Mollet IG, Stamenkovic JA, Göhring I, Malmgren S, Storm P, Fadista J, Spégel P, Metodiev MD, Larsson NG, Eliasson L, Wierup N, Mulder H. Loss of TFB1M results in mitochondrial dysfunction that leads to impaired insulin secretion and diabetes. Hum Mol Genet 2014; 23:5733-49. [PMID: 24916378 DOI: 10.1093/hmg/ddu288] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
We have previously identified transcription factor B1 mitochondrial (TFB1M) as a type 2 diabetes (T2D) risk gene, using human and mouse genetics. To further understand the function of TFB1M and how it is associated with T2D, we created a β-cell-specific knockout of Tfb1m, which gradually developed diabetes. Prior to the onset of diabetes, β-Tfb1m(-/-) mice exhibited retarded glucose clearance owing to impaired insulin secretion. β-Tfb1m(-/-) islets released less insulin in response to fuels, contained less insulin and secretory granules and displayed reduced β-cell mass. Moreover, mitochondria in Tfb1m-deficient β-cells were more abundant with disrupted architecture. TFB1M is known to control mitochondrial protein translation by adenine dimethylation of 12S ribosomal RNA (rRNA). Here, we found that the levels of TFB1M and mitochondrial-encoded proteins, mitochondrial 12S rRNA methylation, ATP production and oxygen consumption were reduced in β-Tfb1m(-/-) islets. Furthermore, the levels of reactive oxygen species (ROS) in response to cellular stress were increased whereas induction of defense mechanisms was attenuated. We also show increased apoptosis and necrosis as well as infiltration of macrophages and CD4(+) cells in the islets. Taken together, our findings demonstrate that Tfb1m-deficiency in β-cells caused mitochondrial dysfunction and subsequently diabetes owing to combined loss of β-cell function and mass. These observations reflect pathogenetic processes in human islets: using RNA sequencing, we found that the TFB1M risk variant exhibited a negative gene-dosage effect on islet TFB1M mRNA levels, as well as insulin secretion. Our findings highlight the role of mitochondrial dysfunction in impairments of β-cell function and mass, the hallmarks of T2D.
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Affiliation(s)
| | | | - Jiangming Sun
- Department of Clinical Sciences in Malmö, Unit of Molecular Metabolism
| | - Lisa M Nicholas
- Department of Clinical Sciences in Malmö, Unit of Molecular Metabolism
| | | | | | - Isabel Göhring
- Department of Clinical Sciences in Malmö, Unit of Molecular Metabolism
| | - Siri Malmgren
- Department of Clinical Sciences in Malmö, Unit of Molecular Metabolism
| | - Petter Storm
- Unit of Diabetes and Endocrinology, Lund University Diabetes Centre, Clinical Research Centre, Skåne University Hospital, 205 02 Malmö, Sweden and
| | - João Fadista
- Unit of Diabetes and Endocrinology, Lund University Diabetes Centre, Clinical Research Centre, Skåne University Hospital, 205 02 Malmö, Sweden and
| | - Peter Spégel
- Department of Clinical Sciences in Malmö, Unit of Molecular Metabolism
| | - Metodi D Metodiev
- Max Planck Institute for Biology of Ageing, D-50931 Cologne, Germany
| | | | | | | | - Hindrik Mulder
- Department of Clinical Sciences in Malmö, Unit of Molecular Metabolism,
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29
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Upregulation of TFAM and mitochondria copy number in human lymphoblastoid cells. Mitochondrion 2014; 15:52-8. [PMID: 24462998 DOI: 10.1016/j.mito.2014.01.002] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2013] [Revised: 01/10/2014] [Accepted: 01/15/2014] [Indexed: 12/12/2022]
Abstract
Mitochondria are central to several physiological and pathological conditions in humans. In the present study, we performed copy number analysis of nuclear encoded mitochondrial genes, in peripheral blood mononuclear cells (PBMCs) and its representative lymphoblastoid cells (LCLs). We have observed hyper diploid copies of mitochondrial transcription factor A (TFAM) gene in the LCLs along with increased mtDNA copy number, mitochondrial mass, intracellular ROS and mitochondrial membrane potential, suggesting elevated mitochondrial biogenesis in LCLs. Gene expression analysis confirmed TFAM over-expression in LCLs when compared to PBMC. Based on our observation, we suggest that increased copy number of TFAM gene upregulates its expression, increases mtDNA copy numbers and protects it from oxidative stress induced damage in the transformed LCLs.
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30
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Posse V, Hoberg E, Dierckx A, Shahzad S, Koolmeister C, Larsson NG, Wilhelmsson LM, Hällberg BM, Gustafsson CM. The amino terminal extension of mammalian mitochondrial RNA polymerase ensures promoter specific transcription initiation. Nucleic Acids Res 2014; 42:3638-47. [PMID: 24445803 PMCID: PMC3973307 DOI: 10.1093/nar/gkt1397] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Mammalian mitochondrial transcription is executed by a single subunit mitochondrial RNA polymerase (Polrmt) and its two accessory factors, mitochondrial transcription factors A and B2 (Tfam and Tfb2m). Polrmt is structurally related to single-subunit phage RNA polymerases, but it also contains a unique N-terminal extension (NTE) of unknown function. We here demonstrate that the NTE functions together with Tfam to ensure promoter-specific transcription. When the NTE is deleted, Polrmt can initiate transcription in the absence of Tfam, both from promoters and non-specific DNA sequences. Additionally, when in presence of Tfam and a mitochondrial promoter, the NTE-deleted mutant has an even higher transcription activity than wild-type polymerase, indicating that the NTE functions as an inhibitory domain. Our studies lead to a model according to which Tfam specifically recruits wild-type Polrmt to promoter sequences, relieving the inhibitory effect of the NTE, as a first step in transcription initiation. In the second step, Tfb2m is recruited into the complex and transcription is initiated.
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Affiliation(s)
- Viktor Posse
- Department of Medical Biochemistry and Cell Biology, University of Gothenburg, PO Box 440, Gothenburg, Sweden, Department of Chemical and Biological Engineering/Physical Chemistry, Chalmers University of Technology, S-41296 Gothenburg, Sweden, Department of Cell and Molecular Biology, Karolinska Institutet, S-171 77 Stockholm, Sweden, Department of Laboratory Medicine, Karolinska Institutet, SE-17177 Stockholm, Sweden, Max Planck Institute for Biology of Ageing, Gleueler Str. 50 a D-50931 Cologne, Germany, Centre for Structural Systems Biology, DESY-Campus, D-22603 Hamburg, Germany and European Molecular Biology Laboratory, Hamburg Unit, 22603 Hamburg, Germany
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31
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Sobek S, Boege F. DNA topoisomerases in mtDNA maintenance and ageing. Exp Gerontol 2014; 56:135-41. [PMID: 24440386 DOI: 10.1016/j.exger.2014.01.009] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2013] [Revised: 01/03/2014] [Accepted: 01/06/2014] [Indexed: 11/26/2022]
Abstract
DNA topoisomerases pass DNA strands through each other, a function essential for all DNA metabolic processes that create supercoils or entanglements of DNA. Topoisomerases play an ambivalent role in nuclear genome maintenance: Deficiency compromises gene transcription, replication and chromosome segregation, while the inherent DNA-cleavage activity of the enzymes endangers DNA integrity. Indeed, many DNA-damaging agents act through enhancing topoisomerase DNA cleavage. Mitochondrial DNA (mtDNA) clearly requires topoisomerase activity for transcription and replication, because it is a closed, double-stranded DNA molecule. Three topoisomerases have so far been found in mammalian mitochondria (I, IIβ, IIIα), but their precise role in mtDNA metabolism, mitochondrial maintenance and respiratory function remains mostly unclear. It is a reasonable surmise that these enzymes exhibit similar ambiguity with respect to genome maintenance and gene transcription as their nuclear counterparts. Here, we review what is known about the physiological roles of mitochondrial topoisomerases and draft three scenarios of how these enzymes possibly contribute to ageing-related mtDNA attrition and respiratory chain dysfunction. These scenarios are: mtDNA attrition by exogenously stimulated topoisomerase DNA cleavage, unbalancing of mitochondrial and nuclear transcription by direct effects on mitochondrial transcription, and contributions to enhanced mtDNA entanglement and recombination.
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Affiliation(s)
- Stefan Sobek
- Institute of Clinical Chemistry and Laboratory Diagnostics, Heinrich Heine University, Med. Faculty, Düsseldorf, Germany
| | - Fritz Boege
- Institute of Clinical Chemistry and Laboratory Diagnostics, Heinrich Heine University, Med. Faculty, Düsseldorf, Germany.
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32
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Yakubovskaya E, Guja KE, Eng ET, Choi WS, Mejia E, Beglov D, Lukin M, Kozakov D, Garcia-Diaz M. Organization of the human mitochondrial transcription initiation complex. Nucleic Acids Res 2014; 42:4100-12. [PMID: 24413562 PMCID: PMC3973321 DOI: 10.1093/nar/gkt1360] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
Initiation of transcription in human mitochondria involves two factors, TFAM and TFB2M, in addition to the mitochondrial RNA polymerase, POLRMT. We have investigated the organization of the human mitochondrial transcription initiation complex on the light-strand promoter (LSP) through solution X-ray scattering, electron microscopy (EM) and biochemical studies. Our EM results demonstrate a compact organization of the initiation complex, suggesting that protein–protein interactions might help mediate initiation. We demonstrate that, in the absence of DNA, only POLRMT and TFAM form a stable interaction, albeit one with low affinity. This is consistent with the expected transient nature of the interactions necessary for initiation and implies that the promoter DNA acts as a scaffold that enables formation of the full initiation complex. Docking of known crystal structures into our EM maps results in a model for transcriptional initiation that strongly correlates with new and existing biochemical observations. Our results reveal the organization of TFAM, POLRMT and TFB2M around the LSP and represent the first structural characterization of the entire mitochondrial transcriptional initiation complex.
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Affiliation(s)
- Elena Yakubovskaya
- Department of Pharmacological Sciences, Stony Brook University, Stony Brook, NY 11794, Cryo-Electron Microscopy Facility, New York Structural Biology Center, New York, NY 10027 and Department of Biomedical Engineering, Boston University, Boston, MA 02215, USA
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33
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Hypothalamic–Pituitary–Thyroid Axis Hormones Stimulate Mitochondrial Function and Biogenesis in Human Hair Follicles. J Invest Dermatol 2014; 134:33-42. [DOI: 10.1038/jid.2013.286] [Citation(s) in RCA: 65] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2012] [Revised: 04/29/2013] [Accepted: 05/31/2013] [Indexed: 12/22/2022]
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34
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Sobek S, Dalla Rosa I, Pommier Y, Bornholz B, Kalfalah F, Zhang H, Wiesner RJ, von Kleist-Retzow JC, Hillebrand F, Schaal H, Mielke C, Christensen MO, Boege F. Negative regulation of mitochondrial transcription by mitochondrial topoisomerase I. Nucleic Acids Res 2013; 41:9848-57. [PMID: 23982517 PMCID: PMC3834834 DOI: 10.1093/nar/gkt768] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Mitochondrial topoisomerase I is a genetically distinct mitochondria-dedicated enzyme with a crucial but so far unknown role in the homeostasis of mitochondrial DNA metabolism. Here, we present data suggesting a negative regulatory function in mitochondrial transcription or transcript stability. Deficiency or depletion of mitochondrial topoisomerase I increased mitochondrial transcripts, whereas overexpression lowered mitochondrial transcripts, depleted respiratory complexes I, III and IV, decreased cell respiration and raised superoxide levels. Acute depletion of mitochondrial topoisomerase I triggered neither a nuclear mito-biogenic stress response nor compensatory topoisomerase IIβ upregulation, suggesting the concomitant increase in mitochondrial transcripts was due to release of a local inhibitory effect. Mitochondrial topoisomerase I was co-immunoprecipitated with mitochondrial RNA polymerase. It selectively accumulated and rapidly exchanged at a subset of nucleoids distinguished by the presence of newly synthesized RNA and/or mitochondrial RNA polymerase. The inactive Y559F-mutant behaved similarly without affecting mitochondrial transcripts. In conclusion, mitochondrial topoisomerase I dampens mitochondrial transcription and thereby alters respiratory capacity. The mechanism involves selective association of the active enzyme with transcriptionally active nucleoids and a direct interaction with mitochondrial RNA polymerase. The inhibitory role of topoisomerase I in mitochondrial transcription is strikingly different from the stimulatory role of topoisomerase I in nuclear transcription.
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Affiliation(s)
- Stefan Sobek
- Institute of Clinical Chemistry and Laboratory Diagnostics, Heinrich-Heine-University, Med. Faculty, D-40225 Düsseldorf, Germany, Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA, Center for Physiology and Pathophysiology, Institute of Vegetative Physiology, University of Köln, D-50931 Köln, Germany, Center for Molecular Medicine Cologne, University of Köln, D-50931 Köln, Germany, Cologne Excellence Cluster on Cellular Stress Responses in Aging-associated Diseases, University of Köln, D-50931 Köln, Germany, Department of Pediatrics, Med. Faculty, University of Köln, D-50931 Köln, Germany and Center for Microbiology and Virology, Institute of Virology, Heinrich-Heine-University, Med. Faculty, D-40225 Düsseldorf, Germany
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35
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Kukat C, Larsson NG. mtDNA makes a U-turn for the mitochondrial nucleoid. Trends Cell Biol 2013; 23:457-63. [PMID: 23721879 DOI: 10.1016/j.tcb.2013.04.009] [Citation(s) in RCA: 89] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2013] [Revised: 04/17/2013] [Accepted: 04/22/2013] [Indexed: 11/29/2022]
Abstract
Mitochondria contain mtDNA derived from the ancestral endosymbiont genome. Important subunits of the oxidative phosphorylation system, which supplies cells with the energy currency ATP, are encoded by mtDNA. A naked mtDNA molecule is longer than a typical mitochondrion and is therefore compacted in vivo to form a nucleoprotein complex, denoted the mitochondrial nucleoid. Mitochondrial transcription factor A (TFAM) is the main factor packaging mtDNA into nucleoids and is also essential for mtDNA transcription initiation. The crystal structure of TFAM shows that it bends mtDNA in a sharp U-turn, which likely provides the structural basis for its dual functions. Super-resolution imaging studies have revealed that the nucleoid has an average diameter of ∼100nm and frequently contains a single copy of mtDNA. In this review the structure of the mitochondrial nucleoid and its possible regulatory roles in mtDNA expression will be discussed.
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Affiliation(s)
- Christian Kukat
- Department of Mitochondrial Biology, Max Planck Institute for Biology of Ageing, Joseph-Stelzmann-Strasse 9b, 50931 Cologne, Germany
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36
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Harmel J, Ruzzenente B, Terzioglu M, Spåhr H, Falkenberg M, Larsson NG. The leucine-rich pentatricopeptide repeat-containing protein (LRPPRC) does not activate transcription in mammalian mitochondria. J Biol Chem 2013; 288:15510-9. [PMID: 23599432 PMCID: PMC3668712 DOI: 10.1074/jbc.m113.471649] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
Regulation of mtDNA expression is critical for controlling oxidative phosphorylation capacity and has been reported to occur at several different levels in mammalian mitochondria. LRPPRC (leucine-rich pentatricopeptide repeat-containing protein) has a key role in this regulation and acts at the post-transcriptional level to stabilize mitochondrial mRNAs, to promote mitochondrial mRNA polyadenylation, and to coordinate mitochondrial translation. However, recent studies have suggested that LRPPRC may have an additional intramitochondrial role by directly interacting with the mitochondrial RNA polymerase POLRMT to stimulate mtDNA transcription. In this study, we have further examined the intramitochondrial roles for LRPPRC by creating bacterial artificial chromosome transgenic mice with moderately increased LRPPRC expression and heterozygous Lrpprc knock-out mice with moderately decreased LRPPRC expression. Variation of LRPPRC levels in mice in vivo, occurring within a predicted normal physiological range, strongly affected the levels of an unprocessed mitochondrial precursor transcript (ND5-cytochrome b) but had no effect on steady-state levels of mitochondrial transcripts or de novo transcription of mtDNA. We further assessed the role of LRPPRC in mitochondrial transcription by performing size exclusion chromatography and immunoprecipitation experiments in human cell lines and mice, but we found no interaction between LRPPRC and POLRMT. Furthermore, addition of purified LRPPRC to a recombinant human in vitro transcription system did not activate mtDNA transcription. On the basis of these data, we conclude that LRPPRC does not directly regulate mtDNA transcription but rather acts as a post-transcriptional regulator of mammalian mtDNA expression.
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Affiliation(s)
- Julia Harmel
- Department of Mitochondrial Biology, Max Planck Institute for Biology of Ageing, D-50931 Cologne, Germany
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37
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Wredenberg A, Lagouge M, Bratic A, Metodiev MD, Spåhr H, Mourier A, Freyer C, Ruzzenente B, Tain L, Grönke S, Baggio F, Kukat C, Kremmer E, Wibom R, Polosa PL, Habermann B, Partridge L, Park CB, Larsson NG. MTERF3 regulates mitochondrial ribosome biogenesis in invertebrates and mammals. PLoS Genet 2013; 9:e1003178. [PMID: 23300484 PMCID: PMC3536695 DOI: 10.1371/journal.pgen.1003178] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2012] [Accepted: 10/31/2012] [Indexed: 11/18/2022] Open
Abstract
Regulation of mitochondrial DNA (mtDNA) expression is critical for the control of oxidative phosphorylation in response to physiological demand, and this regulation is often impaired in disease and aging. We have previously shown that mitochondrial transcription termination factor 3 (MTERF3) is a key regulator that represses mtDNA transcription in the mouse, but its molecular mode of action has remained elusive. Based on the hypothesis that key regulatory mechanisms for mtDNA expression are conserved in metazoans, we analyzed Mterf3 knockout and knockdown flies. We demonstrate here that decreased expression of MTERF3 not only leads to activation of mtDNA transcription, but also impairs assembly of the large mitochondrial ribosomal subunit. This novel function of MTERF3 in mitochondrial ribosomal biogenesis is conserved in the mouse, thus we identify a novel and unexpected role for MTERF3 in coordinating the crosstalk between transcription and translation for the regulation of mammalian mtDNA gene expression.
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Affiliation(s)
- Anna Wredenberg
- Max-Planck Institute for Biology of Ageing, Köln, Germany
- Department Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Marie Lagouge
- Max-Planck Institute for Biology of Ageing, Köln, Germany
| | - Ana Bratic
- Max-Planck Institute for Biology of Ageing, Köln, Germany
- Department Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden
| | | | - Henrik Spåhr
- Max-Planck Institute for Biology of Ageing, Köln, Germany
| | - Arnaud Mourier
- Max-Planck Institute for Biology of Ageing, Köln, Germany
| | - Christoph Freyer
- Max-Planck Institute for Biology of Ageing, Köln, Germany
- Department Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden
| | | | - Luke Tain
- Max-Planck Institute for Biology of Ageing, Köln, Germany
| | | | | | | | - Elisabeth Kremmer
- Helmholtz Center, Institute for Molecular Immunology, Munich, Germany
| | - Rolf Wibom
- Department Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Paola Loguercio Polosa
- Department of Biosciences, Biotechnologies, and Pharmacological Sciences, University of Bari Aldo Moro, Bari, Italy
| | | | | | - Chan Bae Park
- Institute for Medical Sciences, Ajou University School of Medicine, Suwon, Korea
- Mitochondria Hub Regulation Center, Dong-A University College of Medicine, Busan, Republic of Korea
- * E-mail: (CBP); (N-GL)
| | - Nils-Göran Larsson
- Max-Planck Institute for Biology of Ageing, Köln, Germany
- Department Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden
- * E-mail: (CBP); (N-GL)
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38
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Voos W, Ward LA, Truscott KN. The role of AAA+ proteases in mitochondrial protein biogenesis, homeostasis and activity control. Subcell Biochem 2013; 66:223-263. [PMID: 23479443 DOI: 10.1007/978-94-007-5940-4_9] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Mitochondria are specialised organelles that are structurally and functionally integrated into cells in the vast majority of eukaryotes. They are the site of numerous enzymatic reactions, some of which are essential for life. The double lipid membrane of the mitochondrion, that spatially defines the organelle and is necessary for some functions, also creates a physical but semi-permeable barrier to the rest of the cell. Thus to ensure the biogenesis, regulation and maintenance of a functional population of proteins, an autonomous protein handling network within mitochondria is required. This includes resident mitochondrial protein translocation machinery, processing peptidases, molecular chaperones and proteases. This review highlights the contribution of proteases of the AAA+ superfamily to protein quality and activity control within the mitochondrion. Here they are responsible for the degradation of unfolded, unassembled and oxidatively damaged proteins as well as the activity control of some enzymes. Since most knowledge about these proteases has been gained from studies in the eukaryotic microorganism Saccharomyces cerevisiae, much of the discussion here centres on their role in this organism. However, reference is made to mitochondrial AAA+ proteases in other organisms, particularly in cases where they play a unique role such as the mitochondrial unfolded protein response. As these proteases influence mitochondrial function in both health and disease in humans, an understanding of their regulation and diverse activities is necessary.
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Affiliation(s)
- Wolfgang Voos
- Institut für Biochemie und Molekularbiologie (IBMB), Universität Bonn, Nussallee 11, 53115, Bonn, Germany,
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39
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Lee S, Sterky FH, Mourier A, Terzioglu M, Cullheim S, Olson L, Larsson NG. Mitofusin 2 is necessary for striatal axonal projections of midbrain dopamine neurons. Hum Mol Genet 2012; 21:4827-35. [PMID: 22914740 DOI: 10.1093/hmg/dds352] [Citation(s) in RCA: 132] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Mitochondrial dysfunction is implicated in aging and degenerative disorders such as Parkinson's disease (PD). Continuous fission and fusion of mitochondria shapes their morphology and is essential to maintain oxidative phosphorylation. Loss-of-function mutations in PTEN-induced kinase1 (PINK1) or Parkin cause a recessive form of PD and have been linked to altered regulation of mitochondrial dynamics. More specifically, the E3 ubiquitin ligase Parkin has been shown to directly regulate the levels of mitofusin 1 (Mfn1) and Mfn2, two homologous outer membrane large GTPases that govern mitochondrial fusion, but it is not known whether this is of relevance for disease pathophysiology. Here, we address the importance of Mfn1 and Mfn2 in midbrain dopamine (DA) neurons in vivo by characterizing mice with DA neuron-specific knockout of Mfn1 or Mfn2. We find that Mfn1 is dispensable for DA neuron survival and motor function. In contrast, Mfn2 DA neuron-specific knockouts develop a fatal phenotype with reduced weight, locomotor disturbances and death by 7 weeks of age. Mfn2 knockout DA neurons have spherical and enlarged mitochondria with abnormal cristae and impaired respiratory chain function. Parkin does not translocate to these defective mitochondria. Surprisingly, Mfn2 DA neuron-specific knockout mice have normal numbers of midbrain DA neurons, whereas there is a severe loss of DA nerve terminals in the striatum, accompanied by depletion of striatal DA levels. These results show that Mfn2, but not Mfn1, is required for axonal projections of DA neurons in vivo.
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Affiliation(s)
- Seungmin Lee
- Department of Laboratory Medicine, and 2Department of Neuroscience, Karolinska Institutet, Retzius väg 8, Stockholm, Sweden
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Abstract
It is well known that remnants of partial or whole copies of mitochondrial DNA, known as Nuclear MiTochondrial sequences (NUMTs), are found in nuclear genomes. Since whole genome sequences have become available, many bioinformatics studies have identified putative NUMTs and from those attempted to infer the factors involved in NUMT creation. These studies conclude that NUMTs represent randomly chosen regions of the mitochondrial genome. There is less consensus regarding the nuclear insertion sites of NUMTs - previous studies have discussed the possible role of retrotransposons, but some recent ones have reported no correlation or even anti-correlation between NUMT sites and retrotransposons. These studies have generally defined NUMT sites using BLAST with default parameters. We analyze a redefined set of human NUMTs, computed with a carefully considered protocol. We discover that the inferred insertion points of NUMTs have a strong tendency to have high-predicted DNA curvature, occur in experimentally defined open chromatin regions and often occur immediately adjacent to A + T oligomers. We also show clear evidence that their flanking regions are indeed rich in retrotransposons. Finally we show that parts of the mitochondrial genome D-loop are under-represented as a source of NUMTs in primate evolution.
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Affiliation(s)
- Junko Tsuji
- Department of Computational Biology, Graduate School of Frontier Science, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8561, Japan
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