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Chikhirzhina E, Tsimokha A, Tomilin AN, Polyanichko A. Structure and Functions of HMGB3 Protein. Int J Mol Sci 2024; 25:7656. [PMID: 39062899 PMCID: PMC11276821 DOI: 10.3390/ijms25147656] [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: 05/24/2024] [Revised: 07/08/2024] [Accepted: 07/09/2024] [Indexed: 07/28/2024] Open
Abstract
HMGB3 protein belongs to the group of HMGB proteins from the superfamily of nuclear proteins with high electrophoretic mobility. HMGB proteins play an active part in almost all cellular processes associated with DNA-repair, replication, recombination, and transcription-and, additionally, can act as cytokines during infectious processes, inflammatory responses, and injuries. Although the structure and functions of HMGB1 and HMGB2 proteins have been intensively studied for decades, very little attention has been paid to HMGB3 until recently. In this review, we summarize the currently available data on the molecular structure, post-translational modifications, and biological functions of HMGB3, as well as the possible role of the ubiquitin-proteasome system-dependent HMGB3 degradation in tumor development.
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Affiliation(s)
- Elena Chikhirzhina
- Institute of Cytology of the Russian Academy of Sciences, Tikhoretsky Av. 4, 194064 St. Petersburg, Russia; (A.T.); (A.N.T.); (A.P.)
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Huh H, Shen J, Ajjugal Y, Ramachandran A, Patel SS, Lee SH. Sequence-specific dynamic DNA bending explains mitochondrial TFAM's dual role in DNA packaging and transcription initiation. Nat Commun 2024; 15:5446. [PMID: 38937458 PMCID: PMC11211510 DOI: 10.1038/s41467-024-49728-6] [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: 09/06/2023] [Accepted: 06/17/2024] [Indexed: 06/29/2024] Open
Abstract
Mitochondrial transcription factor A (TFAM) employs DNA bending to package mitochondrial DNA (mtDNA) into nucleoids and recruit mitochondrial RNA polymerase (POLRMT) at specific promoter sites, light strand promoter (LSP) and heavy strand promoter (HSP). Herein, we characterize the conformational dynamics of TFAM on promoter and non-promoter sequences using single-molecule fluorescence resonance energy transfer (smFRET) and single-molecule protein-induced fluorescence enhancement (smPIFE) methods. The DNA-TFAM complexes dynamically transition between partially and fully bent DNA conformational states. The bending/unbending transition rates and bending stability are DNA sequence-dependent-LSP forms the most stable fully bent complex and the non-specific sequence the least, which correlates with the lifetimes and affinities of TFAM with these DNA sequences. By quantifying the dynamic nature of the DNA-TFAM complexes, our study provides insights into how TFAM acts as a multifunctional protein through the DNA bending states to achieve sequence specificity and fidelity in mitochondrial transcription while performing mtDNA packaging.
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Affiliation(s)
- Hyun Huh
- Institute for Quantitative Biomedicine, Rutgers University, Piscataway, NJ, 08854, USA
| | - Jiayu Shen
- Graduate School of Biomedical Sciences, Robert Wood Johnson Medical School, Rutgers University, Piscataway, NJ, 08854, USA
- Department of Biochemistry and Molecular Biology, Robert Wood Johnson Medical School, Rutgers University, Piscataway, NJ, 08854, USA
| | - Yogeeshwar Ajjugal
- Department of Biochemistry and Molecular Biology, Robert Wood Johnson Medical School, Rutgers University, Piscataway, NJ, 08854, USA
| | - Aparna Ramachandran
- Department of Biochemistry and Molecular Biology, Robert Wood Johnson Medical School, Rutgers University, Piscataway, NJ, 08854, USA
| | - Smita S Patel
- Department of Biochemistry and Molecular Biology, Robert Wood Johnson Medical School, Rutgers University, Piscataway, NJ, 08854, USA.
| | - Sang-Hyuk Lee
- Institute for Quantitative Biomedicine, Rutgers University, Piscataway, NJ, 08854, USA.
- Department of Physics and Astronomy, Rutgers University, Piscataway, NJ, 08854, USA.
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Zhao W, Hussen AS, Freudenthal BD, Suo Z, Zhao L. Mitochondrial transcription factor A (TFAM) has 5'-deoxyribose phosphate lyase activity in vitro. DNA Repair (Amst) 2024; 137:103666. [PMID: 38492429 PMCID: PMC11056281 DOI: 10.1016/j.dnarep.2024.103666] [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: 11/29/2023] [Revised: 02/16/2024] [Accepted: 03/01/2024] [Indexed: 03/18/2024]
Abstract
Mitochondrial DNA (mtDNA) plays a key role in mitochondrial and cellular functions. mtDNA is maintained by active DNA turnover and base excision repair (BER). In BER, one of the toxic repair intermediates is 5'-deoxyribose phosphate (5'dRp). Human mitochondrial DNA polymerase γ has weak dRp lyase activities, and another known dRp lyase in the nucleus, human DNA polymerase β, can also localize to mitochondria in certain cell and tissue types. Nonetheless, whether additional proteins have the ability to remove 5'dRp in mitochondria remains unknown. Our prior work on the AP lyase activity of mitochondrial transcription factor A (TFAM) has prompted us to examine its ability to remove 5'dRp residues in vitro. TFAM is the primary DNA-packaging factor in human mitochondria and interacts with mitochondrial DNA extensively. Our data demonstrate that TFAM has the dRp lyase activity with different DNA substrates. Under single-turnover conditions, TFAM removes 5'dRp residues at a rate comparable to that of DNA polymerase (pol) β, albeit slower than that of pol λ. Among the three proteins examined, pol λ shows the highest single-turnover rates in dRp lyase reactions. The catalytic effect of TFAM is facilitated by lysine residues of TFAM via Schiff base chemistry, as evidenced by the observation of dRp-lysine adducts in mass spectrometry experiments. The catalytic effect of TFAM observed here is analogous to the AP lyase activity of TFAM reported previously. Together, these results suggest a potential role of TFAM in preventing the accumulation of toxic DNA repair intermediates.
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Affiliation(s)
- Wenxin Zhao
- Department of Chemistry, University of California, Riverside, Riverside, CA 92521, United States
| | - Adil S Hussen
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, KS 66160, United States
| | - Bret D Freudenthal
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, KS 66160, United States; Department of Cancer Biology, University of Kansas Medical Center, Kansas City, KS 66160, United States; University of Kansas Cancer Center, Kansas City, KS 66160, United States
| | - Zucai Suo
- Department of Biomedical Sciences, College of Medicine, Florida State University, Tallahassee, FL 32306, United States
| | - Linlin Zhao
- Department of Chemistry, University of California, Riverside, Riverside, CA 92521, United States; Environmental Toxicology Graduate Program, University of California, Riverside, Riverside, CA 92521, United States.
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4
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Isaac RS, Tullius TW, Hansen KG, Dubocanin D, Couvillion M, Stergachis AB, Churchman LS. Single-nucleoid architecture reveals heterogeneous packaging of mitochondrial DNA. Nat Struct Mol Biol 2024; 31:568-577. [PMID: 38347148 PMCID: PMC11370055 DOI: 10.1038/s41594-024-01225-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Accepted: 01/09/2024] [Indexed: 03/03/2024]
Abstract
Cellular metabolism relies on the regulation and maintenance of mitochondrial DNA (mtDNA). Hundreds to thousands of copies of mtDNA exist in each cell, yet because mitochondria lack histones or other machinery important for nuclear genome compaction, it remains unresolved how mtDNA is packaged into individual nucleoids. In this study, we used long-read single-molecule accessibility mapping to measure the compaction of individual full-length mtDNA molecules at near single-nucleotide resolution. We found that, unlike the nuclear genome, human mtDNA largely undergoes all-or-none global compaction, with most nucleoids existing in an inaccessible, inactive state. Highly accessible mitochondrial nucleoids are co-occupied by transcription and replication components and selectively form a triple-stranded displacement loop structure. In addition, we showed that the primary nucleoid-associated protein TFAM directly modulates the fraction of inaccessible nucleoids both in vivo and in vitro, acting consistently with a nucleation-and-spreading mechanism to coat and compact mitochondrial nucleoids. Together, these findings reveal the primary architecture of mtDNA packaging and regulation in human cells.
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Affiliation(s)
- R Stefan Isaac
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Thomas W Tullius
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Katja G Hansen
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Danilo Dubocanin
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, WA, USA
| | - Mary Couvillion
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Andrew B Stergachis
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, WA, USA.
- Department of Genome Sciences, University of Washington, Seattle, WA, USA.
| | - L Stirling Churchman
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA.
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Tan BG, Gustafsson CM, Falkenberg M. Mechanisms and regulation of human mitochondrial transcription. Nat Rev Mol Cell Biol 2024; 25:119-132. [PMID: 37783784 DOI: 10.1038/s41580-023-00661-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/21/2023] [Indexed: 10/04/2023]
Abstract
The expression of mitochondrial genes is regulated in response to the metabolic needs of different cell types, but the basic mechanisms underlying this process are still poorly understood. In this Review, we describe how different layers of regulation cooperate to fine tune initiation of both mitochondrial DNA (mtDNA) transcription and replication in human cells. We discuss our current understanding of the molecular mechanisms that drive and regulate transcription initiation from mtDNA promoters, and how the packaging of mtDNA into nucleoids can control the number of mtDNA molecules available for both transcription and replication. Indeed, a unique aspect of the mitochondrial transcription machinery is that it is coupled to mtDNA replication, such that mitochondrial RNA polymerase is additionally required for primer synthesis at mtDNA origins of replication. We discuss how the choice between replication-primer formation and genome-length RNA synthesis is controlled at the main origin of replication (OriH) and how the recent discovery of an additional mitochondrial promoter (LSP2) in humans may change this long-standing model.
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Affiliation(s)
- Benedict G Tan
- Institute for Mitochondrial Diseases and Ageing, Faculty of Medicine and University Hospital Cologne, Cluster of Excellence Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
| | - Claes M Gustafsson
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, University of Gothenburg, Gothenburg, Sweden
| | - Maria Falkenberg
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, University of Gothenburg, Gothenburg, Sweden.
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Wang CM, Liu CM, Jia XZ, Zhao SB, Nie ZY, Lv CT, Jiang Q, Hao YL. Expression of mitochondrial transcription factor A in granulosa cells: implications for oocyte maturation and in vitro fertilization outcomes. J Assist Reprod Genet 2024; 41:363-370. [PMID: 38079076 PMCID: PMC10894778 DOI: 10.1007/s10815-023-03001-9] [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: 09/12/2023] [Accepted: 11/29/2023] [Indexed: 02/27/2024] Open
Abstract
OBJECTIVE In vitro fertilization-embryo transfer (IVF-ET) is a widely used treatment for infertility, with oocyte maturation and quality having a significant impact on oocyte fertilization, embryo development, and fetal growth. Mitochondrial transcription factor A (TFAM) is essential for maintaining the mitochondrial oxidative respiratory chain and supplying energy for oocyte development, fertilization, and embryonic development. In this study, we aimed to examine TFAM expression in women undergoing IVF-ET and assess its impact on the IVF outcomes. METHODS We recruited 85 women who underwent IVF-ET treatment for infertility. On the date of egg collection, granulosa cells were extracted from the clear follicular fluid of the first mature egg using ultrasound-guided needle aspiration. The collected granulosa cells served three purposes: (1) detecting TFAM gene expression in granulosa cells via immunocytochemistry, (2) determining TFAM mRNA expression using reverse transcription-PCR (RT-PCR), and (3) measuring TFAM protein expression through western blotting. RESULT Based on the results, we found that TFAM was localized and expressed in the cytoplasm of granulosa cells, whereas no expression was detected in the nucleus. Granulosa cells exhibited a linear correlation between TFAM mRNA and TFAM protein expression. The study participants were divided into three groups using the ternary method based on relative TFAM mRNA expression thresholds of 33% and 76%: the low-expression group (n = 30), the moderate-expression group (n = 27), and the high-expression group (n = 28). When compared to the other two groups, the moderate expression group exhibited a significantly higher egg utilization rate, 2 pronucleus rate, fertilization rate, and clinical pregnancy rate (P < 0.05). CONCLUSION TFAM was detected in the cytoplasm of human ovarian granulosa cells. Women with moderate TFAM expression demonstrate enhanced outcomes in IVF.
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Affiliation(s)
- Cong-Min Wang
- Department of Reproductive Medicine, The Fourth Hospital of Hebei Medical University, 12 Jiankang Road, Chang 'an District, Shijiazhuang, 050011, China
| | - Chun-Miao Liu
- Department of Obstetrics, The Fourth Hospital of Shijiazhuang, Shijiazhuang, 050011, China
| | - Xin-Zhuan Jia
- Department of Reproductive Medicine, The Fourth Hospital of Hebei Medical University, 12 Jiankang Road, Chang 'an District, Shijiazhuang, 050011, China
| | - Shi-Bin Zhao
- Department of Reproductive Medicine, The Fourth Hospital of Hebei Medical University, 12 Jiankang Road, Chang 'an District, Shijiazhuang, 050011, China
| | - Zhao-Yan Nie
- Department of Reproductive Medicine, The Fourth Hospital of Hebei Medical University, 12 Jiankang Road, Chang 'an District, Shijiazhuang, 050011, China
| | - Cui-Ting Lv
- Department of Reproductive Medicine, The Fourth Hospital of Hebei Medical University, 12 Jiankang Road, Chang 'an District, Shijiazhuang, 050011, China
| | - Qian Jiang
- Department of Reproductive Medicine, The Fourth Hospital of Hebei Medical University, 12 Jiankang Road, Chang 'an District, Shijiazhuang, 050011, China
| | - Ya-Li Hao
- Department of Reproductive Medicine, The Fourth Hospital of Hebei Medical University, 12 Jiankang Road, Chang 'an District, Shijiazhuang, 050011, China.
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Schrott S, Osman C. Two mitochondrial HMG-box proteins, Cim1 and Abf2, antagonistically regulate mtDNA copy number in Saccharomyces cerevisiae. Nucleic Acids Res 2023; 51:11813-11835. [PMID: 37850632 PMCID: PMC10681731 DOI: 10.1093/nar/gkad849] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Revised: 08/21/2023] [Accepted: 09/24/2023] [Indexed: 10/19/2023] Open
Abstract
The mitochondrial genome, mtDNA, is present in multiple copies in cells and encodes essential subunits of oxidative phosphorylation complexes. mtDNA levels have to change in response to metabolic demands and copy number alterations are implicated in various diseases. The mitochondrial HMG-box proteins Abf2 in yeast and TFAM in mammals are critical for mtDNA maintenance and packaging and have been linked to mtDNA copy number control. Here, we discover the previously unrecognized mitochondrial HMG-box protein Cim1 (copy number influence on mtDNA) in Saccharomyces cerevisiae, which exhibits metabolic state dependent mtDNA association. Surprisingly, in contrast to Abf2's supportive role in mtDNA maintenance, Cim1 negatively regulates mtDNA copy number. Cells lacking Cim1 display increased mtDNA levels and enhanced mitochondrial function, while Cim1 overexpression results in mtDNA loss. Intriguingly, Cim1 deletion alleviates mtDNA maintenance defects associated with loss of Abf2, while defects caused by Cim1 overexpression are mitigated by simultaneous overexpression of Abf2. Moreover, we find that the conserved LON protease Pim1 is essential to maintain low Cim1 levels, thereby preventing its accumulation and concomitant repressive effects on mtDNA. We propose a model in which the protein ratio of antagonistically acting Cim1 and Abf2 determines mtDNA copy number.
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Affiliation(s)
- Simon Schrott
- Faculty of Biology, Ludwig-Maximilians-Universität München, Großhaderner Str. 2, Planegg-Martinsried 82152, Germany
| | - Christof Osman
- Faculty of Biology, Ludwig-Maximilians-Universität München, Großhaderner Str. 2, Planegg-Martinsried 82152, Germany
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Ma X, Xin D, She R, Liu D, Ge J, Mei Z. Novel insight into cGAS-STING pathway in ischemic stroke: from pre- to post-disease. Front Immunol 2023; 14:1275408. [PMID: 37915571 PMCID: PMC10616885 DOI: 10.3389/fimmu.2023.1275408] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Accepted: 10/04/2023] [Indexed: 11/03/2023] Open
Abstract
Ischemic stroke, a primary cause of disability and the second leading cause of mortality, has emerged as an urgent public health issue. Growing evidence suggests that the Cyclic GMP-AMP synthase (cGAS)- Stimulator of interferon genes (STING) pathway, a component of innate immunity, is closely associated with microglia activation, neuroinflammation, and regulated cell death in ischemic stroke. However, the mechanisms underlying this pathway remain inadequately understood. This article comprehensively reviews the existing literature on the cGAS-STING pathway and its multifaceted relationship with ischemic stroke. Initially, it examines how various risk factors and pre-disease mechanisms such as metabolic dysfunction and senescence (e.g., hypertension, hyperglycemia, hyperlipidemia) affect the cGAS-STING pathway in relation to ischemic stroke. Subsequently, we explore in depth the potential pathophysiological relationship between this pathway and oxidative stress, endoplasmic reticulum stress, neuroinflammation as well as regulated cell death including ferroptosis and PANoptosis following cerebral ischemia injury. Finally, it suggests that intervention targeting the cGAS-STING pathway may serve as promising therapeutic strategies for addressing neuroinflammation associated with ischemic stroke. Taken together, this review concludes that targeting the microglia cGAS-STING pathway may shed light on the exploration of new therapeutic strategies against ischemic stroke.
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Affiliation(s)
- Xiaoqi Ma
- Key Laboratory of Hunan Province for Integrated Traditional Chinese and Western Medicine on Prevention and Treatment of Cardio-Cerebral Diseases, College of Integrated Traditional Chinese and Western Medicine, Hunan University of Chinese Medicine, Changsha, Hunan, China
| | - Dan Xin
- Institute of Pharmacy, Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Ruining She
- Key Laboratory of Hunan Province for Integrated Traditional Chinese and Western Medicine on Prevention and Treatment of Cardio-Cerebral Diseases, College of Integrated Traditional Chinese and Western Medicine, Hunan University of Chinese Medicine, Changsha, Hunan, China
| | - Danhong Liu
- Key Laboratory of Hunan Province for Integrated Traditional Chinese and Western Medicine on Prevention and Treatment of Cardio-Cerebral Diseases, College of Integrated Traditional Chinese and Western Medicine, Hunan University of Chinese Medicine, Changsha, Hunan, China
| | - Jinwen Ge
- Hunan Academy of Chinese Medicine, Hunan University of Chinese Medicine, Changsha, China
| | - Zhigang Mei
- Key Laboratory of Hunan Province for Integrated Traditional Chinese and Western Medicine on Prevention and Treatment of Cardio-Cerebral Diseases, College of Integrated Traditional Chinese and Western Medicine, Hunan University of Chinese Medicine, Changsha, Hunan, China
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Alexeyev M. TFAM in mtDNA Homeostasis: Open Questions. DNA 2023; 3:134-136. [PMID: 37771599 PMCID: PMC10538575 DOI: 10.3390/dna3030011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/30/2023]
Abstract
Transcription factor A, mitochondrial (TFAM) is a key player in mitochondrial DNA (mtDNA) transcription and replication [...]
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Affiliation(s)
- Mikhail Alexeyev
- Department of Physiology and Cell Biology, University of South Alabama, Mobile, AL 36688, USA
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Lin Y, Yang B, Huang Y, Zhang Y, Jiang Y, Ma L, Shen YQ. Mitochondrial DNA-targeted therapy: A novel approach to combat cancer. CELL INSIGHT 2023; 2:100113. [PMID: 37554301 PMCID: PMC10404627 DOI: 10.1016/j.cellin.2023.100113] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Revised: 07/14/2023] [Accepted: 07/16/2023] [Indexed: 08/10/2023]
Abstract
Mitochondrial DNA (mtDNA) encodes proteins and RNAs that are essential for mitochondrial function and cellular homeostasis, and participates in important processes of cellular bioenergetics and metabolism. Alterations in mtDNA are associated with various diseases, especially cancers, and are considered as biomarkers for some types of tumors. Moreover, mtDNA alterations have been found to affect the proliferation, progression and metastasis of cancer cells, as well as their interactions with the immune system and the tumor microenvironment (TME). The important role of mtDNA in cancer development makes it a significant target for cancer treatment. In recent years, many novel therapeutic methods targeting mtDNA have emerged. In this study, we first discussed how cancerogenesis is triggered by mtDNA mutations, including alterations in gene copy number, aberrant gene expression and epigenetic modifications. Then, we described in detail the mechanisms underlying the interactions between mtDNA and the extramitochondrial environment, which are crucial for understanding the efficacy and safety of mtDNA-targeted therapy. Next, we provided a comprehensive overview of the recent progress in cancer therapy strategies that target mtDNA. We classified them into two categories based on their mechanisms of action: indirect and direct targeting strategies. Indirect targeting strategies aimed to induce mtDNA damage and dysfunction by modulating pathways that are involved in mtDNA stability and integrity, while direct targeting strategies utilized molecules that can selectively bind to or cleave mtDNA to achieve the therapeutic efficacy. This study highlights the importance of mtDNA-targeted therapy in cancer treatment, and will provide insights for future research and development of targeted drugs and therapeutic strategies.
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Affiliation(s)
- Yumeng Lin
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Research Unit of Oral Carcinogenesis and Management, Chinese Academy of Medical Sciences, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan 610041, PR China
| | - Bowen Yang
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Research Unit of Oral Carcinogenesis and Management, Chinese Academy of Medical Sciences, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan 610041, PR China
| | - Yibo Huang
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Research Unit of Oral Carcinogenesis and Management, Chinese Academy of Medical Sciences, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan 610041, PR China
| | - You Zhang
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Research Unit of Oral Carcinogenesis and Management, Chinese Academy of Medical Sciences, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan 610041, PR China
| | - Yu Jiang
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Research Unit of Oral Carcinogenesis and Management, Chinese Academy of Medical Sciences, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan 610041, PR China
| | - Longyun Ma
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Research Unit of Oral Carcinogenesis and Management, Chinese Academy of Medical Sciences, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan 610041, PR China
| | - Ying-Qiang Shen
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Research Unit of Oral Carcinogenesis and Management, Chinese Academy of Medical Sciences, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan 610041, PR China
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Tarrés-Solé A, Battistini F, Gerhold JM, Piétrement O, Martínez-García B, Ruiz-López E, Lyonnais S, Bernadó P, Roca J, Orozco M, Le Cam E, Sedman J, Solà M. Structural analysis of the Candida albicans mitochondrial DNA maintenance factor Gcf1p reveals a dynamic DNA-bridging mechanism. Nucleic Acids Res 2023; 51:5864-5882. [PMID: 37207342 PMCID: PMC10287934 DOI: 10.1093/nar/gkad397] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 04/01/2023] [Accepted: 05/03/2023] [Indexed: 05/21/2023] Open
Abstract
The compaction of mitochondrial DNA (mtDNA) is regulated by architectural HMG-box proteins whose limited cross-species similarity suggests diverse underlying mechanisms. Viability of Candida albicans, a human antibiotic-resistant mucosal pathogen, is compromised by altering mtDNA regulators. Among them, there is the mtDNA maintenance factor Gcf1p, which differs in sequence and structure from its human and Saccharomyces cerevisiae counterparts, TFAM and Abf2p. Our crystallographic, biophysical, biochemical and computational analysis showed that Gcf1p forms dynamic protein/DNA multimers by a combined action of an N-terminal unstructured tail and a long helix. Furthermore, an HMG-box domain canonically binds the minor groove and dramatically bends the DNA while, unprecedentedly, a second HMG-box binds the major groove without imposing distortions. This architectural protein thus uses its multiple domains to bridge co-aligned DNA segments without altering the DNA topology, revealing a new mechanism of mtDNA condensation.
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Affiliation(s)
- Aleix Tarrés-Solé
- Structural MitoLab, Molecular Biology Institute Barcelona (IBMB-CSIC), Barcelona Science Park, Barcelona 08028, Spain
| | - Federica Battistini
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona 08028, Spain
- Department of Biochemistry, University of Barcelona, Barcelona 08028, Spain
| | - Joachim M Gerhold
- Institute of Molecular and Cell Biology, University of Tartu, Tartu 51010, Estonia
| | - Olivier Piétrement
- Genome Integrity and Cancer UMR 9019 CNRS, Université Paris Saclay, Gustave Roussy Campus, 114 rue Edouard Vaillant 94805VillejuifCedex, France
| | | | - Elena Ruiz-López
- Structural MitoLab, Molecular Biology Institute Barcelona (IBMB-CSIC), Barcelona Science Park, Barcelona 08028, Spain
| | - Sébastien Lyonnais
- Structural MitoLab, Molecular Biology Institute Barcelona (IBMB-CSIC), Barcelona Science Park, Barcelona 08028, Spain
| | - Pau Bernadó
- Centre de Biologie Structurale (CBS), Inserm, CNRS and Université de Montpellier, France, Sébastien Lyonnais, UAR 3725 CNRS, Université de Montpellier, 34000 Montpellier, France
| | - Joaquim Roca
- Molecular Biology Institute Barcelona (IBMB-CSIC), Barcelona 08028, Spain
| | - Modesto Orozco
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona 08028, Spain
- Department of Biochemistry, University of Barcelona, Barcelona 08028, Spain
| | - Eric Le Cam
- Genome Integrity and Cancer UMR 9019 CNRS, Université Paris Saclay, Gustave Roussy Campus, 114 rue Edouard Vaillant 94805VillejuifCedex, France
| | - Juhan Sedman
- Institute of Molecular and Cell Biology, University of Tartu, Tartu 51010, Estonia
| | - Maria Solà
- Structural MitoLab, Molecular Biology Institute Barcelona (IBMB-CSIC), Barcelona Science Park, Barcelona 08028, Spain
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12
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Kozhukhar N, Alexeyev MF. 35 Years of TFAM Research: Old Protein, New Puzzles. BIOLOGY 2023; 12:823. [PMID: 37372108 DOI: 10.3390/biology12060823] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Revised: 05/29/2023] [Accepted: 06/03/2023] [Indexed: 06/29/2023]
Abstract
Transcription Factor A Mitochondrial (TFAM), through its contributions to mtDNA maintenance and expression, is essential for cellular bioenergetics and, therefore, for the very survival of cells. Thirty-five years of research on TFAM structure and function generated a considerable body of experimental evidence, some of which remains to be fully reconciled. Recent advancements allowed an unprecedented glimpse into the structure of TFAM complexed with promoter DNA and TFAM within the open promoter complexes. These novel insights, however, raise new questions about the function of this remarkable protein. In our review, we compile the available literature on TFAM structure and function and provide some critical analysis of the available data.
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Affiliation(s)
- Natalya Kozhukhar
- Department of Physiology and Cell Biology, University of South Alabama, Mobile, AL 36688, USA
| | - Mikhail F Alexeyev
- Department of Physiology and Cell Biology, University of South Alabama, Mobile, AL 36688, USA
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Kozhukhar N, Alexeyev MF. The C-Terminal Tail of Mitochondrial Transcription Factor A Is Dispensable for Mitochondrial DNA Replication and Transcription In Situ. Int J Mol Sci 2023; 24:9430. [PMID: 37298383 PMCID: PMC10253692 DOI: 10.3390/ijms24119430] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Revised: 05/04/2023] [Accepted: 05/26/2023] [Indexed: 06/12/2023] Open
Abstract
Mitochondrial transcription factor A (TFAM) is one of the widely studied but still incompletely understood mitochondrial protein, which plays a crucial role in the maintenance and transcription of mitochondrial DNA (mtDNA). The available experimental evidence is often contradictory in assigning the same function to various TFAM domains, partly owing to the limitations of those experimental systems. Recently, we developed the GeneSwap approach, which enables in situ reverse genetic analysis of mtDNA replication and transcription and is devoid of many of the limitations of the previously used techniques. Here, we utilized this approach to analyze the contributions of the TFAM C-terminal (tail) domain to mtDNA transcription and replication. We determined, at a single amino acid (aa) resolution, the TFAM tail requirements for in situ mtDNA replication in murine cells and established that tail-less TFAM supports both mtDNA replication and transcription. Unexpectedly, in cells expressing either C-terminally truncated murine TFAM or DNA-bending human TFAM mutant L6, HSP1 transcription was impaired to a greater extent than LSP transcription. Our findings are incompatible with the prevailing model of mtDNA transcription and thus suggest the need for further refinement.
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Affiliation(s)
| | - Mikhail F. Alexeyev
- Department of Physiology and Cell Biology, University of South Alabama, Mobile, AL 36688, USA
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14
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Zhao W, Xu W, Tang J, Kaushik S, Chang CEA, Zhao L. Key Amino Acid Residues of Mitochondrial Transcription Factor A Synergize with Abasic (AP) Site Dynamics To Facilitate AP-Lyase Reactions. ACS Chem Biol 2023; 18:1168-1179. [PMID: 36930463 PMCID: PMC10198963 DOI: 10.1021/acschembio.3c00047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/18/2023]
Abstract
Human mitochondrial DNA (mtDNA) encodes 37 essential genes and plays a critical role in mitochondrial and cellular functions. mtDNA is susceptible to damage by endogenous and exogenous chemicals. Damaged mtDNA molecules are counteracted by the redundancy, repair, and degradation of mtDNA. In response to difficult-to-repair or excessive amounts of DNA lesions, mtDNA degradation is a crucial mitochondrial genome maintenance mechanism. Nevertheless, the molecular basis of mtDNA degradation remains incompletely understood. Recently, mitochondrial transcription factor A (TFAM) has emerged as a factor in degrading damaged mtDNA containing abasic (AP) sites. TFAM has AP-lyase activity, which cleaves DNA at AP sites. Human TFAM and its homologs contain a higher abundance of Glu than that of the proteome. To decipher the role of Glu in TFAM-catalyzed AP-DNA cleavage, we constructed TFAM variants and used biochemical assays, kinetic simulations, and molecular dynamics (MD) simulations to probe the functional importance of E187 near a key residue K186. Our previous studies showed that K186 is a primary residue to cleave AP-DNA via Schiff base chemistry. Here, we demonstrate that E187 facilitates β-elimination, key to AP-DNA strand scission. MD simulations showed that extrahelical confirmation of the AP lesion and the flexibility of E187 in TFAM-DNA complexes facilitate AP-lyase reactions. Together, highly abundant Lys and Glu residues in TFAM promote AP-DNA strand scission, supporting the role of TFAM in AP-DNA turnover and implying the breadth of this process across different species.
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Affiliation(s)
- Wenxin Zhao
- Department of Chemistry, University of California, Riverside, Riverside, California, 92521, United States
| | - Wenyan Xu
- Department of Chemistry, University of California, Riverside, Riverside, California, 92521, United States
| | - Jin Tang
- Department of Chemistry, University of California, Riverside, Riverside, California, 92521, United States
| | - Shivansh Kaushik
- Department of Chemistry, University of California, Riverside, Riverside, California, 92521, United States
| | - Chia-En A. Chang
- Department of Chemistry, University of California, Riverside, Riverside, California, 92521, United States
- Environmental Toxicology Graduate Program, University of California, Riverside, Riverside, California, 92521, United States
| | - Linlin Zhao
- Department of Chemistry, University of California, Riverside, Riverside, California, 92521, United States
- Environmental Toxicology Graduate Program, University of California, Riverside, Riverside, California, 92521, United States
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15
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Rubalcava-Gracia D, García-Villegas R, Larsson NG. No role for nuclear transcription regulators in mammalian mitochondria? Mol Cell 2023; 83:832-842. [PMID: 36182692 DOI: 10.1016/j.molcel.2022.09.010] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 08/17/2022] [Accepted: 09/08/2022] [Indexed: 10/14/2022]
Abstract
Although the mammalian mtDNA transcription machinery is simple and resembles bacteriophage systems, there are many reports that nuclear transcription regulators, as exemplified by MEF2D, MOF, PGC-1α, and hormone receptors, are imported into mammalian mitochondria and directly interact with the mtDNA transcription machinery. However, the supporting experimental evidence for this concept is open to alternate interpretations, and a main issue is the difficulty in distinguishing indirect regulation of mtDNA transcription, caused by altered nuclear gene expression, from direct intramitochondrial effects. We provide a critical discussion and experimental guidelines to stringently assess roles of intramitochondrial factors implicated in direct regulation of mammalian mtDNA transcription.
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Affiliation(s)
- Diana Rubalcava-Gracia
- Division of Molecular Metabolism, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Rodolfo García-Villegas
- Division of Molecular Metabolism, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Nils-Göran Larsson
- Division of Molecular Metabolism, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden.
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16
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Martucci M, Debar L, van den Wildenberg S, Farge G. How to Quantify DNA Compaction by TFAM with Acoustic Force Spectroscopy and Total Internal Reflection Fluorescence Microscopy. Methods Mol Biol 2023; 2615:121-137. [PMID: 36807789 DOI: 10.1007/978-1-0716-2922-2_10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/23/2023]
Abstract
Mitochondrial transcription factor A (TFAM) plays a key role in the organization and compaction of the mitochondrial genome. However, there are only a few simple and accessible methods available to observe and quantify TFAM-dependent DNA compaction. Acoustic Force Spectroscopy (AFS) is a straightforward single-molecule force spectroscopy technique. It allows one to track many individual protein-DNA complexes in parallel and to quantify their mechanical properties. Total internal reflection fluorescence (TIRF) microscopy is a high-throughput single-molecule technique that permits the real-time visualization of the dynamics of TFAM on DNA, parameters inaccessible with classical biochemistry tools. Here we describe, in detail, how to set up, perform, and analyze AFS and TIRF measurements to study DNA compaction by TFAM.
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Affiliation(s)
- Martial Martucci
- Université Clermont Auvergne, CNRS, Laboratoire de Physique de Clermont, Clermont-Ferrand, France
| | - Louis Debar
- Université Clermont Auvergne, CNRS, Laboratoire de Physique de Clermont, Clermont-Ferrand, France
| | - Siet van den Wildenberg
- Université Clermont Auvergne, CNRS, Laboratoire de Physique de Clermont, Clermont-Ferrand, France.,Université Clermont Auvergne, CNRS, IRD, Université Jean Monnet Saint Etienne, LMV, Clermont-Ferrand, France
| | - Geraldine Farge
- Université Clermont Auvergne, CNRS, Laboratoire de Physique de Clermont, Clermont-Ferrand, France.
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17
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Xu W, Tang J, Zhao L. DNA-protein cross-links between abasic DNA damage and mitochondrial transcription factor A (TFAM). Nucleic Acids Res 2022; 51:41-53. [PMID: 36583367 PMCID: PMC9841407 DOI: 10.1093/nar/gkac1214] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Revised: 11/25/2022] [Accepted: 12/07/2022] [Indexed: 12/31/2022] Open
Abstract
In higher eukaryotic cells, mitochondria are essential organelles for energy production, metabolism, and signaling. Mitochondrial DNA (mtDNA) encodes 13 protein subunits for oxidative phosphorylation and a set of tRNAs and rRNAs. mtDNA damage, sourced from endogenous chemicals and environmental factors, contributes to mitochondrial genomic instability, which has been associated with various mitochondrial diseases. DNA-protein cross-links (DPCs) are deleterious DNA lesions that threaten genomic integrity. Although much has been learned about the formation and repair of DPCs in the nucleus, little is known about DPCs in mitochondria. Here, we present in vitro and in cellulo data to demonstrate the formation of DPCs between a prevalent abasic (AP) DNA lesion and a DNA-packaging protein, mitochondrial transcription factor A (TFAM). TFAM cleaves AP-DNA and forms DPCs and single-strand breaks (SSB). Lys residues of TFAM are critical for the formation of TFAM-DPC and a reactive 3'-phospho-α,β-unsaturated aldehyde (3'pUA) residue on SSB. The 3'pUA residue reacts with two Cys of TFAM and contributes to the stable TFAM-DPC formation. Glutathione reacts with 3'pUA and competes with TFAM-DPC formation, corroborating our cellular experiments showing the accumulation of TFAM-DPCs under limiting glutathione. Our data point to the involvement of TFAM in AP-DNA turnover and fill a knowledge gap regarding the protein factors in processing damaged mtDNA.
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Affiliation(s)
- Wenyan Xu
- Department of Chemistry, University of California, Riverside, Riverside, CA 92521, USA
| | - Jin Tang
- Department of Chemistry, University of California, Riverside, Riverside, CA 92521, USA
| | - Linlin Zhao
- To whom correspondence should be addressed. Tel: +1 951 827 9081;
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18
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Seike H, Ishimori K, Watanabe A, Kiryu M, Hatakeyama S, Tanaka S, Yoshihara R. Two high-mobility group domains of MHG1 are necessary to maintain mtDNA in Neurospora crassa. Fungal Biol 2022; 126:826-833. [PMID: 36517150 DOI: 10.1016/j.funbio.2022.11.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Revised: 10/13/2022] [Accepted: 11/08/2022] [Indexed: 11/15/2022]
Abstract
The mhg1 (NCU02695/ada-23) gene encodes the mitochondrial high-mobility group box (HMG-box or HMGB) protein in Neurospora crassa. The mhg1 KO strain (mhg1KO) has mitochondrial DNA (mtDNA) instability and a short lifespan; however, the function of MHG1 remains unclear. To investigate the role of this protein in the maintenance of mtDNA, domain deleted MHG1 proteins were expressed in the mhg1KO strain, and their effects were analyzed. We identified two putative HMG-domains, HMGBI and HMGBII. Although deletion of the HMG-box did not abolish MHG1's mitochondrial localization, the mhg1KO phenotype of a severe growth defect and a high sensitivity to mutagens could not be restored by introduction of HMG-box deleted mhg1 gene into the KO strain. It was indicated that recombinant full-length MHG1, i.e., mitochondrial targeting sequence (MTS) containing protein, did not exhibit explicit DNA binding, whereas the MHG1 protein truncated for the MTS sequence did in vitro by an electrophoretic mobility shift assay. Furthermore, recombinant MHG1 protein lacking MTS and HMG-domains, either HMGBI or HMGBII, had DNA affinity and an altered band shift pattern compared with MTS-truncated MHG1 protein. These results suggest that cleavage of MTS and appropriate DNA binding via HMG-domains are indispensable for maintaining mtDNA in N. crassa.
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Affiliation(s)
- Hayami Seike
- Department of Regulatory Biology, Faculty of Science, Saitama University, Shimo-Ohkubo 255, Sakura-ku, Saitama, Saitama, 338-8570, Japan
| | - Keisuke Ishimori
- Department of Regulatory Biology, Faculty of Science, Saitama University, Shimo-Ohkubo 255, Sakura-ku, Saitama, Saitama, 338-8570, Japan
| | - Asagi Watanabe
- Department of Regulatory Biology, Faculty of Science, Saitama University, Shimo-Ohkubo 255, Sakura-ku, Saitama, Saitama, 338-8570, Japan
| | - Mao Kiryu
- Department of Regulatory Biology, Faculty of Science, Saitama University, Shimo-Ohkubo 255, Sakura-ku, Saitama, Saitama, 338-8570, Japan
| | - Shin Hatakeyama
- Department of Regulatory Biology, Faculty of Science, Saitama University, Shimo-Ohkubo 255, Sakura-ku, Saitama, Saitama, 338-8570, Japan
| | - Shuuitsu Tanaka
- Department of Regulatory Biology, Faculty of Science, Saitama University, Shimo-Ohkubo 255, Sakura-ku, Saitama, Saitama, 338-8570, Japan
| | - Ryouhei Yoshihara
- Department of Regulatory Biology, Faculty of Science, Saitama University, Shimo-Ohkubo 255, Sakura-ku, Saitama, Saitama, 338-8570, Japan.
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19
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Feric M, Sarfallah A, Dar F, Temiakov D, Pappu RV, Misteli T. Mesoscale structure-function relationships in mitochondrial transcriptional condensates. Proc Natl Acad Sci U S A 2022; 119:e2207303119. [PMID: 36191226 PMCID: PMC9565167 DOI: 10.1073/pnas.2207303119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Accepted: 09/09/2022] [Indexed: 12/14/2022] Open
Abstract
In live cells, phase separation is thought to organize macromolecules into membraneless structures known as biomolecular condensates. Here, we reconstituted transcription in condensates from purified mitochondrial components using optimized in vitro reaction conditions to probe the structure-function relationships of biomolecular condensates. We find that the core components of the mt-transcription machinery form multiphasic, viscoelastic condensates in vitro. Strikingly, the rates of condensate-mediated transcription are substantially lower than in solution. The condensate-mediated decrease in transcriptional rates is associated with the formation of vesicle-like structures that are driven by the production and accumulation of RNA during transcription. The generation of RNA alters the global phase behavior and organization of transcription components within condensates. Coarse-grained simulations of mesoscale structures at equilibrium show that the components stably assemble into multiphasic condensates and that the vesicles formed in vitro are the result of dynamical arrest. Overall, our findings illustrate the complex phase behavior of transcribing, multicomponent condensates, and they highlight the intimate, bidirectional interplay of structure and function in transcriptional condensates.
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Affiliation(s)
- Marina Feric
- National Cancer Institute, NIH, Bethesda, MD 20892
- National Institute of General Medical Sciences, NIH, Bethesda, MD 20892
| | - Azadeh Sarfallah
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, PA 19107
| | - Furqan Dar
- Department of Physics, Washington University in St. Louis, St. Louis, MO 63130
- Department of Biomedical Engineering, Center for Biomolecular Condensates, Washington University in St. Louis, St. Louis, MO 63130
| | - Dmitry Temiakov
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, PA 19107
| | - Rohit V. Pappu
- Department of Biomedical Engineering, Center for Biomolecular Condensates, Washington University in St. Louis, St. Louis, MO 63130
| | - Tom Misteli
- National Cancer Institute, NIH, Bethesda, MD 20892
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20
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Wang W, Sun H, Ma X, Zhu T, Zhang H. Circ_0002476 regulates cell growth, invasion, and mtDNA damage in non-small cell lung cancer by targeting miR-1182/TFAM axis. Thorac Cancer 2022; 13:2867-2878. [PMID: 36056804 PMCID: PMC9575079 DOI: 10.1111/1759-7714.14631] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Revised: 08/15/2022] [Accepted: 08/16/2022] [Indexed: 11/30/2022] Open
Abstract
BACKGROUND Many circular RNAs (circRNAs) have been identified as potential targets for cancer therapy. However, the role of circ_0002476 in non-small cell lung cancer (NSCLC) progression has not been explored. METHODS The expression levels of circ_0002476, microRNA (miR)-1182, and mitochondrial transcription factor A (TFAM) were detected by quantitative real-time polymerase chain reaction. Cell functions were measured by cell counting kit 8 assay, EdU assay, colony formation assay, flow cytometry and transwell assay. Mitochondrial DNA (mtDNA) damage was assessed by measuring mtDNA copy number and transcript levels of ND1 and ATP6. Protein expression was examined by western blot. The interaction between miR-1182 and circ_0002476 or TFAM was detected by dual-luciferase reporter assay and RNA pull-down assay. Animal experiments were performed to explore circ_0002476 role in vivo. Exosomes (Exs) were extracted and identified by transmission electron microscopy and nanoparticle tracking analysis. RESULTS Circ_0002476 was overexpressed in NSCLC tissues and cells. Circ_0002476 knockdown suppressed NSCLC cell proliferation and invasion, while promoted apoptosis and mtDNA damage. Circ_0002476 could sponge miR-1182, and miR-1182 inhibitor reversed the influence induced by circ_0002476 knockdown. Moreover, TFAM was targeted by miR-1182, and miR-1182 hindered NSCLC cell progression by regulating TFAM. Additionally, circ_0002476 silencing could reduce NSCLC tumor growth by miR-1182/TFAM. Further analyzed showed that Exs were involved in the transport of circ_0002476 between cells. CONCLUSION Taken together, our findings suggested that circ_0002476 might be a potential molecular target for NSCLC treatment.
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Affiliation(s)
- Weijie Wang
- Department of Thoracic Surgery, The Affiliated Xiangshan Hospital of Wenzhou Medial University, Ningbo, China
| | - Haiting Sun
- Department of Thoracic Surgery, The Affiliated Xiangshan Hospital of Wenzhou Medial University, Ningbo, China
| | - Xuan Ma
- Department of Thoracic Surgery, The Affiliated Xiangshan Hospital of Wenzhou Medial University, Ningbo, China
| | - Ting Zhu
- Department of Thoracic Surgery, The Affiliated Xiangshan Hospital of Wenzhou Medial University, Ningbo, China
| | - Haina Zhang
- Department of Thoracic Surgery, The Affiliated Xiangshan Hospital of Wenzhou Medial University, Ningbo, China
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21
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Sharma N, Thompson MK, Arrington JF, Terry DM, Chakravarthy S, Prevelige PE, Prakash A. Novel interaction interfaces mediate the interaction between the NEIL1 DNA glycosylase and mitochondrial transcription factor A. Front Cell Dev Biol 2022; 10:893806. [PMID: 35938152 PMCID: PMC9354671 DOI: 10.3389/fcell.2022.893806] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Accepted: 07/01/2022] [Indexed: 02/01/2023] Open
Abstract
The maintenance of human mitochondrial DNA (mtDNA) is critical for proper cellular function as damage to mtDNA, if left unrepaired, can lead to a diverse array of pathologies. Of the pathways identified to participate in DNA repair within the mitochondria, base excision repair (BER) is the most extensively studied. Protein-protein interactions drive the step-by-step coordination required for the successful completion of this pathway and are important for crosstalk with other mitochondrial factors involved in genome maintenance. Human NEIL1 is one of seven DNA glycosylases that initiates BER in both the nuclear and mitochondrial compartments. In the current work, we scrutinized the interaction between NEIL1 and mitochondrial transcription factor A (TFAM), a protein that is essential for various aspects of mtDNA metabolism. We note, for the first time, that both the N- and C- terminal domains of NEIL1 interact with TFAM revealing a unique NEIL1 protein-binding interface. The interaction between the two proteins, as observed biochemically, appears to be transient and is most apparent at concentrations of low salt. The presence of DNA (or RNA) also positively influences the interaction between the two proteins, and molar mass estimates indicate that duplex DNA is required for complex formation at higher salt concentrations. Hydrogen deuterium exchange mass spectrometry data reveal that both proteins exchange less deuterium upon DNA binding, indicative of an interaction, and the addition of NEIL1 to the TFAM-DNA complex alters the interaction landscape. The transcriptional activity of TFAM appears to be independent of NEIL1 expression under normal cellular conditions, however, in the presence of DNA damage, we observe a significant reduction in the mRNA expression of TFAM-transcribed mitochondrial genes in the absence of NEIL1. Overall, our data indicate that the interaction between NEIL1 and TFAM can be modulated by local environment such as salt concentrations, protein availability, the presence of nucleic acids, as well as the presence of DNA damage.
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Affiliation(s)
- Nidhi Sharma
- Department of Biochemistry and Molecular Biology, Mitchell Cancer Institute, University of South Alabama, Mobile, AL, United States
| | - Marlo K. Thompson
- Department of Biochemistry and Molecular Biology, Mitchell Cancer Institute, University of South Alabama, Mobile, AL, United States
| | - Jennifer F. Arrington
- Department of Biochemistry and Molecular Biology, Mitchell Cancer Institute, University of South Alabama, Mobile, AL, United States
| | - Dava M. Terry
- Department of Biochemistry and Molecular Biology, Mitchell Cancer Institute, University of South Alabama, Mobile, AL, United States
| | - Srinivas Chakravarthy
- Advanced Photon Source, Illinois Institute of Technology, Chicago, IL, United States
| | - Peter E. Prevelige
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Aishwarya Prakash
- Department of Biochemistry and Molecular Biology, Mitchell Cancer Institute, University of South Alabama, Mobile, AL, United States
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22
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Zhu X, Xie X, Das H, Tan BG, Shi Y, Al-Behadili A, Peter B, Motori E, Valenzuela S, Posse V, Gustafsson CM, Hällberg BM, Falkenberg M. Non-coding 7S RNA inhibits transcription via mitochondrial RNA polymerase dimerization. Cell 2022; 185:2309-2323.e24. [PMID: 35662414 DOI: 10.1016/j.cell.2022.05.006] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 04/05/2022] [Accepted: 05/05/2022] [Indexed: 12/19/2022]
Abstract
The mitochondrial genome encodes 13 components of the oxidative phosphorylation system, and altered mitochondrial transcription drives various human pathologies. A polyadenylated, non-coding RNA molecule known as 7S RNA is transcribed from a region immediately downstream of the light strand promoter in mammalian cells, and its levels change rapidly in response to physiological conditions. Here, we report that 7S RNA has a regulatory function, as it controls levels of mitochondrial transcription both in vitro and in cultured human cells. Using cryo-EM, we show that POLRMT dimerization is induced by interactions with 7S RNA. The resulting POLRMT dimer interface sequesters domains necessary for promoter recognition and unwinding, thereby preventing transcription initiation. We propose that the non-coding 7S RNA molecule is a component of a negative feedback loop that regulates mitochondrial transcription in mammalian cells.
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Affiliation(s)
- Xuefeng Zhu
- Department of Medical Biochemistry and Cell Biology, University of Gothenburg, PO Box 440, 405 30 Gothenburg, Sweden
| | - Xie Xie
- Department of Medical Biochemistry and Cell Biology, University of Gothenburg, PO Box 440, 405 30 Gothenburg, Sweden
| | - Hrishikesh Das
- Department of Cell and Molecular Biology, Karolinska Institutet, 171 77 Stockholm, Sweden
| | - Benedict G Tan
- Department of Medical Biochemistry and Cell Biology, University of Gothenburg, PO Box 440, 405 30 Gothenburg, Sweden
| | - Yonghong Shi
- Department of Medical Biochemistry and Cell Biology, University of Gothenburg, PO Box 440, 405 30 Gothenburg, Sweden
| | - Ali Al-Behadili
- Department of Medical Biochemistry and Cell Biology, University of Gothenburg, PO Box 440, 405 30 Gothenburg, Sweden
| | - Bradley Peter
- Department of Medical Biochemistry and Cell Biology, University of Gothenburg, PO Box 440, 405 30 Gothenburg, Sweden
| | - Elisa Motori
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), 50931 Cologne, Germany; Institute of Biochemistry, University of Cologne, Zülpicher Str. 47, 50674 Cologne, Germany
| | - Sebastian Valenzuela
- Department of Medical Biochemistry and Cell Biology, University of Gothenburg, PO Box 440, 405 30 Gothenburg, Sweden
| | - Viktor Posse
- Department of Medical Biochemistry and Cell Biology, University of Gothenburg, PO Box 440, 405 30 Gothenburg, Sweden
| | - Claes M Gustafsson
- Department of Medical Biochemistry and Cell Biology, University of Gothenburg, PO Box 440, 405 30 Gothenburg, Sweden
| | - B Martin Hällberg
- Department of Cell and Molecular Biology, Karolinska Institutet, 171 77 Stockholm, Sweden.
| | - Maria Falkenberg
- Department of Medical Biochemistry and Cell Biology, University of Gothenburg, PO Box 440, 405 30 Gothenburg, Sweden.
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23
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Mehmedović M, Martucci M, Spåhr H, Ishak L, Mishra A, Sanchez-Sandoval ME, Pardo-Hernández C, Peter B, van den Wildenberg SM, Falkenberg M, Farge G. Disease causing mutation (P178L) in mitochondrial transcription factor A results in impaired mitochondrial transcription initiation. Biochim Biophys Acta Mol Basis Dis 2022; 1868:166467. [PMID: 35716868 DOI: 10.1016/j.bbadis.2022.166467] [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: 03/13/2022] [Revised: 05/31/2022] [Accepted: 06/09/2022] [Indexed: 10/18/2022]
Abstract
Mitochondrial transcription factor A (TFAM) is essential for the maintenance, expression, and packaging of mitochondrial DNA (mtDNA). Recently, a pathogenic homozygous variant in TFAM (P178L) has been associated with a severe mtDNA depletion syndrome leading to neonatal liver failure and early death. We have performed a biochemical characterization of the TFAM variant P178L in order to understand the molecular basis for the pathogenicity of this mutation. We observe no effects on DNA binding, and compaction of DNA is only mildly affected by the P178L amino acid change. Instead, the mutation severely impairs mtDNA transcription initiation at the mitochondrial heavy and light strand promoters. Molecular modeling suggests that the P178L mutation affects promoter sequence recognition and the interaction between TFAM and the tether helix of POLRMT, thus explaining transcription initiation deficiency.
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Affiliation(s)
- Majda Mehmedović
- Department of Medical Biochemistry and Cell Biology, University of Gothenburg, P.O. Box 440, SE-405 30 Gothenburg, Sweden
| | - Martial Martucci
- Université Clermont Auvergne, CNRS, Laboratoire de Physique de Clermont, F-63000 Clermont-Ferrand, France
| | - Henrik Spåhr
- Department of Mitochondrial Biology, Max Planck Institute for Biology of Ageing, 50931 Cologne, Germany; Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm 17177, Sweden; Max Planck Institute for Biology of Ageing - Karolinska Institutet Laboratory, Karolinska Institutet, Stockholm 17177, Sweden
| | - Layal Ishak
- Department of Medical Biochemistry and Cell Biology, University of Gothenburg, P.O. Box 440, SE-405 30 Gothenburg, Sweden
| | - Anup Mishra
- Department of Medical Biochemistry and Cell Biology, University of Gothenburg, P.O. Box 440, SE-405 30 Gothenburg, Sweden
| | - Maria Eugenia Sanchez-Sandoval
- Department of Medical Biochemistry and Cell Biology, University of Gothenburg, P.O. Box 440, SE-405 30 Gothenburg, Sweden
| | - Carlos Pardo-Hernández
- Department of Medical Biochemistry and Cell Biology, University of Gothenburg, P.O. Box 440, SE-405 30 Gothenburg, Sweden
| | - Bradley Peter
- Department of Medical Biochemistry and Cell Biology, University of Gothenburg, P.O. Box 440, SE-405 30 Gothenburg, Sweden
| | - Siet M van den Wildenberg
- Université Clermont Auvergne, CNRS, Laboratoire de Physique de Clermont, F-63000 Clermont-Ferrand, France; Université Clermont Auvergne, CNRS, IRD, Université Jean Monnet Saint Etienne, LMV, F-63000 Clermont-Ferrand, France
| | - Maria Falkenberg
- Department of Medical Biochemistry and Cell Biology, University of Gothenburg, P.O. Box 440, SE-405 30 Gothenburg, Sweden.
| | - Geraldine Farge
- Université Clermont Auvergne, CNRS, Laboratoire de Physique de Clermont, F-63000 Clermont-Ferrand, France.
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24
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Rajendran A, Krishnamurthy K, Park S, Nakata E, Kwon Y, Morii T. Topologically‐Interlocked Minicircles as Probes of DNA Topology and DNA‐Protein Interactions. Chemistry 2022; 28:e202200108. [DOI: 10.1002/chem.202200108] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Indexed: 12/30/2022]
Affiliation(s)
| | | | - Seojeong Park
- College of Pharmacy Ewha Womans University Seoul 120-750 Republic of Korea
| | - Eiji Nakata
- Institute of Advanced Energy Kyoto University Uji Kyoto, 611–0011 Japan
| | - Youngjoo Kwon
- College of Pharmacy Ewha Womans University Seoul 120-750 Republic of Korea
| | - Takashi Morii
- Institute of Advanced Energy Kyoto University Uji Kyoto, 611–0011 Japan
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25
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Miranda M, Bonekamp NA, Kühl I. Starting the engine of the powerhouse: mitochondrial transcription and beyond. Biol Chem 2022; 403:779-805. [PMID: 35355496 DOI: 10.1515/hsz-2021-0416] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Accepted: 03/09/2022] [Indexed: 12/25/2022]
Abstract
Mitochondria are central hubs for cellular metabolism, coordinating a variety of metabolic reactions crucial for human health. Mitochondria provide most of the cellular energy via their oxidative phosphorylation (OXPHOS) system, which requires the coordinated expression of genes encoded by both the nuclear (nDNA) and mitochondrial genomes (mtDNA). Transcription of mtDNA is not only essential for the biogenesis of the OXPHOS system, but also generates RNA primers necessary to initiate mtDNA replication. Like the prokaryotic system, mitochondria have no membrane-based compartmentalization to separate the different steps of mtDNA maintenance and expression and depend entirely on nDNA-encoded factors imported into the organelle. Our understanding of mitochondrial transcription in mammalian cells has largely progressed, but the mechanisms regulating mtDNA gene expression are still poorly understood despite their profound importance for human disease. Here, we review mechanisms of mitochondrial gene expression with a focus on the recent findings in the field of mammalian mtDNA transcription and disease phenotypes caused by defects in proteins involved in this process.
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Affiliation(s)
- Maria Miranda
- Department of Mitochondrial Biology, Max Planck Institute for Biology of Ageing, Cologne, D-50931, Germany
| | - Nina A Bonekamp
- Department of Neuroanatomy, Mannheim Center for Translational Neurosciences (MCTN), Medical Faculty Mannheim, Heidelberg University, Mannheim, D-68167, Germany
| | - Inge Kühl
- Department of Cell Biology, Institute of Integrative Biology of the Cell (I2BC), UMR9198, CEA, CNRS, Université Paris-Saclay, Gif-sur-Yvette, F-91190, France
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26
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Zamudio-Ochoa A, Morozov YI, Sarfallah A, Anikin M, Temiakov D. OUP accepted manuscript. Nucleic Acids Res 2022; 50:2765-2781. [PMID: 35191499 PMCID: PMC8934621 DOI: 10.1093/nar/gkac103] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Revised: 01/27/2022] [Accepted: 02/03/2022] [Indexed: 11/13/2022] Open
Abstract
Recognition of mammalian mitochondrial promoters requires the concerted action of mitochondrial RNA polymerase (mtRNAP) and transcription initiation factors TFAM and TFB2M. In this work, we found that transcript slippage results in heterogeneity of the human mitochondrial transcripts in vivo and in vitro. This allowed us to correctly interpret the RNAseq data, identify the bona fide transcription start sites (TSS), and assign mitochondrial promoters for > 50% of mammalian species and some other vertebrates. The divergent structure of the mammalian promoters reveals previously unappreciated aspects of mtDNA evolution. The correct assignment of TSS also enabled us to establish the precise register of the DNA in the initiation complex and permitted investigation of the sequence-specific protein-DNA interactions. We determined the molecular basis of promoter recognition by mtRNAP and TFB2M, which cooperatively recognize bases near TSS in a species-specific manner. Our findings reveal a role of mitochondrial transcription machinery in mitonuclear coevolution and speciation.
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Affiliation(s)
- Angelica Zamudio-Ochoa
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, 1020 Locust Street, Philadelphia, PA 19107, USA
| | - Yaroslav I Morozov
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, 1020 Locust Street, Philadelphia, PA 19107, USA
| | - Azadeh Sarfallah
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, 1020 Locust Street, Philadelphia, PA 19107, USA
| | - Michael Anikin
- Department of Cell Biology and Neuroscience, Rowan University, School of Osteopathic Medicine, 42 E Laurel Rd, Stratford, NJ 08084, USA
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27
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Choi WS, Garcia-Diaz M. A minimal motif for sequence recognition by mitochondrial transcription factor A (TFAM). Nucleic Acids Res 2021; 50:322-332. [PMID: 34928349 PMCID: PMC8754647 DOI: 10.1093/nar/gkab1230] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2021] [Revised: 11/13/2021] [Accepted: 12/10/2021] [Indexed: 11/16/2022] Open
Abstract
Mitochondrial transcription factor A (TFAM) plays a critical role in mitochondrial transcription initiation and mitochondrial DNA (mtDNA) packaging. Both functions require DNA binding, but in one case TFAM must recognize a specific promoter sequence, while packaging requires coating of mtDNA by association with non sequence-specific regions. The mechanisms by which TFAM achieves both sequence-specific and non sequence-specific recognition have not yet been determined. Existing crystal structures of TFAM bound to DNA allowed us to identify two guanine-specific interactions that are established between TFAM and the bound DNA. These interactions are observed when TFAM is bound to both specific promoter sequences and non-sequence specific DNA. These interactions are established with two guanine bases separated by 10 random nucleotides (GN10G). Our biochemical results demonstrate that the GN10G consensus is essential for transcriptional initiation and contributes to facilitating TFAM binding to DNA substrates. Furthermore, we report a crystal structure of TFAM in complex with a non sequence-specific sequence containing a GN10G consensus. The structure reveals a unique arrangement in which TFAM bridges two DNA substrates while maintaining the GN10G interactions. We propose that the GN10G consensus is key to facilitate the interaction of TFAM with DNA.
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Affiliation(s)
- Woo Suk Choi
- Department of Pharmacological Sciences, Stony Brook University, Stony Brook, NY 11794, USA
| | - Miguel Garcia-Diaz
- Department of Pharmacological Sciences, Stony Brook University, Stony Brook, NY 11794, USA
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28
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Ullah F, Rauf W, Khan K, Khan S, Bell KM, de Oliveira VC, Tariq M, Bakhshalizadeh S, Touraine P, Katsanis N, Sinclair A, He S, Tucker EJ, Baig SM, Davis EE. A recessive variant in TFAM causes mtDNA depletion associated with primary ovarian insufficiency, seizures, intellectual disability and hearing loss. Hum Genet 2021; 140:1733-1751. [PMID: 34647195 DOI: 10.1007/s00439-021-02380-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Accepted: 09/30/2021] [Indexed: 12/25/2022]
Abstract
Mitochondrial disorders are collectively common, genetically heterogeneous disorders in both pediatric and adult populations. They are caused by molecular defects in oxidative phosphorylation, failure of essential bioenergetic supply to mitochondria, and apoptosis. Here, we present three affected individuals from a consanguineous family of Pakistani origin with variable seizures and intellectual disability. Both females display primary ovarian insufficiency (POI), while the male shows abnormal sex hormone levels. We performed whole exome sequencing and identified a recessive missense variant c.694C > T, p.Arg232Cys in TFAM that segregates with disease. TFAM (mitochondrial transcription factor A) is a component of the mitochondrial replisome machinery that maintains mtDNA transcription and replication. In primary dermal fibroblasts, we show depletion of mtDNA and significantly altered mitochondrial function and morphology. Moreover, we observed reduced nucleoid numbers with significant changes in nucleoid size or shape in fibroblasts from an affected individual compared to controls. We also investigated the effect of tfam impairment in zebrafish; homozygous tfam mutants carrying an in-frame c.141_149 deletion recapitulate the mtDNA depletion and ovarian dysgenesis phenotypes observed in affected humans. Together, our genetic and functional data confirm that TFAM plays a pivotal role in gonad development and expands the repertoire of mitochondrial disease phenotypes.
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Affiliation(s)
- Farid Ullah
- National Institute for Biotechnology and Genetic Engineering (NIBGE-C), Faisalabad, Pakistan.,Pakistan Institute of Engineering and Applied Sciences (PIEAS), Islamabad, Pakistan.,Stanley Manne Children's Research Institute, Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, IL, USA
| | - Waqar Rauf
- National Institute for Biotechnology and Genetic Engineering (NIBGE-C), Faisalabad, Pakistan.,Pakistan Institute of Engineering and Applied Sciences (PIEAS), Islamabad, Pakistan
| | - Kamal Khan
- Stanley Manne Children's Research Institute, Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, IL, USA
| | - Sheraz Khan
- National Institute for Biotechnology and Genetic Engineering (NIBGE-C), Faisalabad, Pakistan.,Pakistan Institute of Engineering and Applied Sciences (PIEAS), Islamabad, Pakistan.,Stanley Manne Children's Research Institute, Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, IL, USA
| | - Katrina M Bell
- Department of Pediatrics, University of Melbourne, Melbourne, Australia.,Bioinformatics, Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne, Australia
| | - Vanessa Cristina de Oliveira
- Department of Veterinary Medicine, Faculty of Animal Science and Food Engineering, University of São Paulo, Pirassununga, São Paulo, Brazil
| | - Muhammad Tariq
- National Institute for Biotechnology and Genetic Engineering (NIBGE-C), Faisalabad, Pakistan.,Pakistan Institute of Engineering and Applied Sciences (PIEAS), Islamabad, Pakistan
| | - Shabnam Bakhshalizadeh
- Department of Pediatrics, University of Melbourne, Melbourne, Australia.,Reproductive Development, MurdochChildren's Research Institute, Royal Children's Hospital, Melbourne, Australia
| | - Philippe Touraine
- Department of Endocrinology and Reproductive Medicine, Center for Rare Endocrine and Gynecological Diseases, Sorbonne Université Pitié Salpétrière Hospital, Paris, France
| | - Nicholas Katsanis
- Stanley Manne Children's Research Institute, Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, IL, USA.,Rescindo Therapeutics, Cary, NC, USA
| | - Andrew Sinclair
- Department of Pediatrics, University of Melbourne, Melbourne, Australia.,Reproductive Development, MurdochChildren's Research Institute, Royal Children's Hospital, Melbourne, Australia
| | | | - Elena J Tucker
- Department of Pediatrics, University of Melbourne, Melbourne, Australia.,Reproductive Development, MurdochChildren's Research Institute, Royal Children's Hospital, Melbourne, Australia
| | - Shahid M Baig
- National Institute for Biotechnology and Genetic Engineering (NIBGE-C), Faisalabad, Pakistan.,Pakistan Institute of Engineering and Applied Sciences (PIEAS), Islamabad, Pakistan.,Pakistan Science Foundation, Constitution Avenue, Islamabad, Pakistan.,Department of Biological and Biomedical Sciences, Aga Khan University, Karachi, Pakistan
| | - Erica E Davis
- Stanley Manne Children's Research Institute, Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, IL, USA. .,Department of Pediatrics, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA. .,Department of Cell and Developmental Biology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA.
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29
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Tang J, Zhao W, Hendricks NG, Zhao L. High-Resolution Mapping of Amino Acid Residues in DNA-Protein Cross-Links Enabled by Ribonucleotide-Containing DNA. Anal Chem 2021; 93:13398-13406. [PMID: 34559515 DOI: 10.1021/acs.analchem.1c03481] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
DNA-protein cross-links have broad applications in mapping DNA-protein interactions and provide structural insights into macromolecular structures. However, high-resolution mapping of DNA-interacting amino acid residues with tandem mass spectrometry remains challenging due to difficulties in sample preparation and data analysis. Herein, we developed a method for identifying cross-linking amino residues in DNA-protein cross-links at single amino acid resolution. We leveraged the alkaline lability of ribonucleotides and designed ribonucleotide-containing DNA to produce structurally defined nucleic acid-peptide cross-links under our optimized ribonucleotide cleavage conditions. The structurally defined oligonucleotide-peptide heteroconjugates improved ionization, reduced the database search space, and facilitated the identification of cross-linking residues in peptides. We applied the workflow to identifying abasic (AP) site-interacting residues in human mitochondrial transcription factor A (TFAM)-DNA cross-links. With sub-nmol sample input, we obtained high-quality fragmentation spectra for nucleic acid-peptide cross-links and identified 14 cross-linked lysine residues with the home-built AP_CrosslinkFinder program. Semi-quantification based on integrated peak areas revealed that K186 of TFAM is the major cross-linking residue, consistent with K186 being the closest (to the AP modification) lysine residue in solved TFAM:DNA crystal structures. Additional cross-linking lysine residues (K69, K76, K136, K154) support the dynamic characteristics of TFAM:DNA complexes. Overall, our combined workflow using ribonucleotide as a chemically cleavable DNA modification together with optimized sample preparation and data analysis offers a simple yet powerful approach for mapping cross-linking sites in DNA-protein cross-links. The method is amendable to other chemical or photo-cross-linking systems and can be extended to complex biological samples.
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Affiliation(s)
- Jin Tang
- Department of Chemistry, University of California, Riverside, Riverside, California 92521, United States
| | - Wenxin Zhao
- Department of Chemistry, University of California, Riverside, Riverside, California 92521, United States
| | - Nathan G Hendricks
- Proteomics Core, Institute for Integrative Genome Biology, University of California, Riverside, Riverside, California 92521, United States
| | - Linlin Zhao
- Department of Chemistry, University of California, Riverside, Riverside, California 92521, United States.,Environmental Toxicology Graduate Program, University of California, Riverside, Riverside, California 92521, United States
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30
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Bonekamp NA, Jiang M, Motori E, Garcia Villegas R, Koolmeister C, Atanassov I, Mesaros A, Park CB, Larsson NG. High levels of TFAM repress mammalian mitochondrial DNA transcription in vivo. Life Sci Alliance 2021; 4:4/11/e202101034. [PMID: 34462320 PMCID: PMC8408345 DOI: 10.26508/lsa.202101034] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Revised: 08/10/2021] [Accepted: 08/20/2021] [Indexed: 01/04/2023] Open
Abstract
Mitochondrial transcription factor A (TFAM) is compacting mitochondrial DNA (dmtDNA) into nucleoids and directly controls mtDNA copy number. Here, we show that the TFAM-to-mtDNA ratio is critical for maintaining normal mtDNA expression in different mouse tissues. Moderately increased TFAM protein levels increase mtDNA copy number but a normal TFAM-to-mtDNA ratio is maintained resulting in unaltered mtDNA expression and normal whole animal metabolism. Mice ubiquitously expressing very high TFAM levels develop pathology leading to deficient oxidative phosphorylation (OXPHOS) and early postnatal lethality. The TFAM-to-mtDNA ratio varies widely between tissues in these mice and is very high in skeletal muscle leading to strong repression of mtDNA expression and OXPHOS deficiency. In the heart, increased mtDNA copy number results in a near normal TFAM-to-mtDNA ratio and maintained OXPHOS capacity. In liver, induction of LONP1 protease and mitochondrial RNA polymerase expression counteracts the silencing effect of high TFAM levels. TFAM thus acts as a general repressor of mtDNA expression and this effect can be counterbalanced by tissue-specific expression of regulatory factors.
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Affiliation(s)
- Nina A Bonekamp
- Department of Mitochondrial Biology, Max Planck Institute for Biology of Ageing, Cologne, Germany
| | - Min Jiang
- Department of Mitochondrial Biology, Max Planck Institute for Biology of Ageing, Cologne, Germany.,Zhejiang Provincial Laboratory of Life Sciences and Biomedicine, Key Laboratory of Growth Regulation and Transformation Research of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, China
| | - Elisa Motori
- Department of Mitochondrial Biology, Max Planck Institute for Biology of Ageing, Cologne, Germany.,Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), Cologne, Germany
| | | | - Camilla Koolmeister
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Ilian Atanassov
- Proteomics Core Facility, Max Planck Institute for Biology of Ageing, Cologne, Germany
| | - Andrea Mesaros
- Phenotyping Core Facility, Max Planck Institute for Biology of Ageing, Cologne, Germany
| | | | - Nils-Göran Larsson
- Department of Mitochondrial Biology, Max Planck Institute for Biology of Ageing, Cologne, Germany .,Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
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31
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Menger KE, Rodríguez-Luis A, Chapman J, Nicholls TJ. Controlling the topology of mammalian mitochondrial DNA. Open Biol 2021; 11:210168. [PMID: 34547213 PMCID: PMC8455175 DOI: 10.1098/rsob.210168] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The genome of mitochondria, called mtDNA, is a small circular DNA molecule present at thousands of copies per human cell. MtDNA is packaged into nucleoprotein complexes called nucleoids, and the density of mtDNA packaging affects mitochondrial gene expression. Genetic processes such as transcription, DNA replication and DNA packaging alter DNA topology, and these topological problems are solved by a family of enzymes called topoisomerases. Within mitochondria, topoisomerases are involved firstly in the regulation of mtDNA supercoiling and secondly in disentangling interlinked mtDNA molecules following mtDNA replication. The loss of mitochondrial topoisomerase activity leads to defects in mitochondrial function, and variants in the dual-localized type IA topoisomerase TOP3A have also been reported to cause human mitochondrial disease. We review the current knowledge on processes that alter mtDNA topology, how mtDNA topology is modulated by the action of topoisomerases, and the consequences of altered mtDNA topology for mitochondrial function and human health.
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Affiliation(s)
- Katja E. Menger
- Wellcome Centre for Mitochondrial Research, Biosciences Institute, Newcastle University, Framlington Place, Newcastle upon Tyne NE2 4HH, UK
| | - Alejandro Rodríguez-Luis
- Wellcome Centre for Mitochondrial Research, Biosciences Institute, Newcastle University, Framlington Place, Newcastle upon Tyne NE2 4HH, UK
| | - James Chapman
- Wellcome Centre for Mitochondrial Research, Biosciences Institute, Newcastle University, Framlington Place, Newcastle upon Tyne NE2 4HH, UK
| | - Thomas J. Nicholls
- Wellcome Centre for Mitochondrial Research, Biosciences Institute, Newcastle University, Framlington Place, Newcastle upon Tyne NE2 4HH, UK
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32
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Chew K, Zhao L. Interactions of Mitochondrial Transcription Factor A with DNA Damage: Mechanistic Insights and Functional Implications. Genes (Basel) 2021; 12:genes12081246. [PMID: 34440420 PMCID: PMC8393399 DOI: 10.3390/genes12081246] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Revised: 08/11/2021] [Accepted: 08/13/2021] [Indexed: 12/17/2022] Open
Abstract
Mitochondria have a plethora of functions in eukaryotic cells, including cell signaling, programmed cell death, protein cofactor synthesis, and various aspects of metabolism. The organelles carry their own genomic DNA, which encodes transfer and ribosomal RNAs and crucial protein subunits in the oxidative phosphorylation system. Mitochondria are vital for cellular and organismal functions, and alterations of mitochondrial DNA (mtDNA) have been linked to mitochondrial disorders and common human diseases. As such, how the cell maintains the integrity of the mitochondrial genome is an important area of study. Interactions of mitochondrial proteins with mtDNA damage are critically important for repairing, regulating, and signaling mtDNA damage. Mitochondrial transcription factor A (TFAM) is a key player in mtDNA transcription, packaging, and maintenance. Due to the extensive contact of TFAM with mtDNA, it is likely to encounter many types of mtDNA damage and secondary structures. This review summarizes recent research on the interaction of human TFAM with different forms of non-canonical DNA structures and discusses the implications on mtDNA repair and packaging.
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33
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Mitochondrial DNA in innate immune responses against infectious diseases. Biochem Soc Trans 2021; 48:2823-2838. [PMID: 33155647 DOI: 10.1042/bst20200687] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Revised: 09/18/2020] [Accepted: 10/12/2020] [Indexed: 12/30/2022]
Abstract
Mitochondrial DNA (mtDNA) can initiate an innate immune response when mislocalized in a compartment other than the mitochondrial matrix. mtDNA plays significant roles in regulating mitochondrial dynamics as well as mitochondrial unfolded protein response (UPR). The mislocalized extra-mtDNA can elicit innate immune response via cGAS-STING (cyclic GMP-AMP synthase-stimulator of interferon genes) pathway, inducing the expression of the interferon-stimulated genes (ISGs). Also, cytosolic damaged mtDNA is cleared up by various pathways which are responsible for participating in the activation of inflammatory responses. Four pathways of extra-mitochondrial mtDNA clearance are highlighted in this review - the inflammasome activation mechanism, neutrophil extracellular traps formation, recognition by Toll-like receptor 9 and transfer of mtDNA between cells packaged into extracellular vesicles. Anomalies in these pathways are associated with various diseases. We posit our review in the present pandemic situation and discuss how mtDNA elicits innate immune responses against different viruses and bacteria. This review gives a comprehensive picture of the role of extra-mitochondrial mtDNA in infectious diseases and speculates that research towards its understanding would help establish its therapeutic potential.
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34
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Feric M, Misteli T. Phase separation in genome organization across evolution. Trends Cell Biol 2021; 31:671-685. [PMID: 33771451 PMCID: PMC8286288 DOI: 10.1016/j.tcb.2021.03.001] [Citation(s) in RCA: 54] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Revised: 02/17/2021] [Accepted: 03/01/2021] [Indexed: 02/06/2023]
Abstract
Phase separation is emerging as a paradigm to explain the self-assembly and organization of membraneless bodies in the cell. Recent advances show that this principle also extends to nucleoprotein complexes, including DNA-based structures. We discuss here recent observations on the role of phase separation in genome organization across the evolutionary spectrum from bacteria to mammals. These findings suggest that molecular interactions amongst DNA-binding proteins evolved to form a variety of biomolecular condensates with distinct material properties that affect genome organization and function. We suggest that phase separation contributes to genome organization across evolution and that the resulting phase behavior of genomes may underlie regulatory mechanisms and disease.
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Affiliation(s)
- Marina Feric
- National Cancer Institute, National Institutes of Health (NIH), Bethesda, MD, USA; National Institute of General Medical Sciences, NIH, Bethesda, MD, USA.
| | - Tom Misteli
- National Cancer Institute, National Institutes of Health (NIH), Bethesda, MD, USA.
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35
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YAF2-Mediated YY1-Sirtuin6 Interactions Responsible for Mitochondrial Downregulation in Aging Tunicates. Mol Cell Biol 2021; 41:e0004721. [PMID: 33875574 DOI: 10.1128/mcb.00047-21] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
In budding tunicates, aging accompanies a decrease in the gene expression of mitochondrial transcription factor A (Tfam), and the in vivo transfection of Tfam mRNA stimulates the mitochondrial respiratory activity of aged animals. The gene expression of both the transcriptional repressor Yin-Yang-1 (YY1) and corepressor Sirtuin6 (Sirt6) increased during aging, and the cotransfection of synthetic mRNA of YY1 and Sirt6 synergistically downregulated Tfam gene expression. Pulldown assays of proteins indicated that YY1-associated factor 2 (YAF2) was associated with both YY1 and SIRT6. Protein cross-linking confirmed that YAF2 bound YY1 and SIRT6 with a molar ratio of 1:1. YY1 was bound to CCAT- or ACAT-containing oligonucleotides in the 5' flanking region of the Tfam gene. Chromatin immunoprecipitation-quantitative PCR (ChIP-qPCR) showed that SIRT6 specifically induced the histone H3 lysine 9 (H3K9) deacetylation of the Tfam upstream region. YY1 and YAF2 accelerated SIRT6-induced H3K9 deacetylation. YY1 and Sirt6 mRNA transfection attenuated mitochondrial respiratory gene expression and blocked MitoTracker fluorescence. In contrast, the SIRT6 inhibitor and Tfam mRNA antagonized the inhibitory effects of YY1 and Sirt6, indicating that Tfam acts on mitochondria downstream of YY1 and Sirt6. We concluded that in the budding tunicate Polyandrocarpa misakiensis, YY1 recruits SIRT6 via YAF2 to the TFAM gene, resulting in aging-related mitochondrial downregulation.
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36
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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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37
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Feric M, Demarest TG, Tian J, Croteau DL, Bohr VA, Misteli T. Self-assembly of multi-component mitochondrial nucleoids via phase separation. EMBO J 2021; 40:e107165. [PMID: 33619770 DOI: 10.15252/embj.2020107165] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 01/08/2021] [Accepted: 01/19/2021] [Indexed: 11/09/2022] Open
Abstract
Mitochondria contain an autonomous and spatially segregated genome. The organizational unit of their genome is the nucleoid, which consists of mitochondrial DNA (mtDNA) and associated architectural proteins. Here, we show that phase separation is the primary physical mechanism for assembly and size control of the mitochondrial nucleoid (mt-nucleoid). The major mtDNA-binding protein TFAM spontaneously phase separates in vitro via weak, multivalent interactions into droplets with slow internal dynamics. TFAM and mtDNA form heterogenous, viscoelastic structures in vitro, which recapitulate the dynamics and behavior of mt-nucleoids in vivo. Mt-nucleoids coalesce into larger droplets in response to various forms of cellular stress, as evidenced by the enlarged and transcriptionally active nucleoids in mitochondria from patients with the premature aging disorder Hutchinson-Gilford Progeria Syndrome (HGPS). Our results point to phase separation as an evolutionarily conserved mechanism of genome organization.
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Affiliation(s)
- Marina Feric
- National Cancer Institute, NIH, Bethesda, MD, USA.,National Institute of General Medical Sciences, NIH, Bethesda, MD, USA
| | | | - Jane Tian
- National Institute on Aging, NIH, Baltimore, MD, USA
| | | | | | - Tom Misteli
- National Cancer Institute, NIH, Bethesda, MD, USA
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38
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Kotrasová V, Keresztesová B, Ondrovičová G, Bauer JA, Havalová H, Pevala V, Kutejová E, Kunová N. Mitochondrial Kinases and the Role of Mitochondrial Protein Phosphorylation in Health and Disease. Life (Basel) 2021; 11:life11020082. [PMID: 33498615 PMCID: PMC7912454 DOI: 10.3390/life11020082] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Revised: 01/19/2021] [Accepted: 01/20/2021] [Indexed: 02/07/2023] Open
Abstract
The major role of mitochondria is to provide cells with energy, but no less important are their roles in responding to various stress factors and the metabolic changes and pathological processes that might occur inside and outside the cells. The post-translational modification of proteins is a fast and efficient way for cells to adapt to ever changing conditions. Phosphorylation is a post-translational modification that signals these changes and propagates these signals throughout the whole cell, but it also changes the structure, function and interaction of individual proteins. In this review, we summarize the influence of kinases, the proteins responsible for phosphorylation, on mitochondrial biogenesis under various cellular conditions. We focus on their role in keeping mitochondria fully functional in healthy cells and also on the changes in mitochondrial structure and function that occur in pathological processes arising from the phosphorylation of mitochondrial proteins.
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Affiliation(s)
- Veronika Kotrasová
- Institute of Molecular Biology, Slovak Academy of Sciences, Dúbravská Cesta 21, 845 51 Bratislava, Slovakia; (V.K.); (B.K.); (G.O.); (J.A.B.); (H.H.); (V.P.)
| | - Barbora Keresztesová
- Institute of Molecular Biology, Slovak Academy of Sciences, Dúbravská Cesta 21, 845 51 Bratislava, Slovakia; (V.K.); (B.K.); (G.O.); (J.A.B.); (H.H.); (V.P.)
- First Faculty of Medicine, Institute of Biology and Medical Genetics, Charles University, 128 00 Prague, Czech Republic
| | - Gabriela Ondrovičová
- Institute of Molecular Biology, Slovak Academy of Sciences, Dúbravská Cesta 21, 845 51 Bratislava, Slovakia; (V.K.); (B.K.); (G.O.); (J.A.B.); (H.H.); (V.P.)
| | - Jacob A. Bauer
- Institute of Molecular Biology, Slovak Academy of Sciences, Dúbravská Cesta 21, 845 51 Bratislava, Slovakia; (V.K.); (B.K.); (G.O.); (J.A.B.); (H.H.); (V.P.)
| | - Henrieta Havalová
- Institute of Molecular Biology, Slovak Academy of Sciences, Dúbravská Cesta 21, 845 51 Bratislava, Slovakia; (V.K.); (B.K.); (G.O.); (J.A.B.); (H.H.); (V.P.)
| | - Vladimír Pevala
- Institute of Molecular Biology, Slovak Academy of Sciences, Dúbravská Cesta 21, 845 51 Bratislava, Slovakia; (V.K.); (B.K.); (G.O.); (J.A.B.); (H.H.); (V.P.)
| | - Eva Kutejová
- Institute of Molecular Biology, Slovak Academy of Sciences, Dúbravská Cesta 21, 845 51 Bratislava, Slovakia; (V.K.); (B.K.); (G.O.); (J.A.B.); (H.H.); (V.P.)
- Correspondence: (E.K.); (N.K.)
| | - Nina Kunová
- Institute of Molecular Biology, Slovak Academy of Sciences, Dúbravská Cesta 21, 845 51 Bratislava, Slovakia; (V.K.); (B.K.); (G.O.); (J.A.B.); (H.H.); (V.P.)
- First Faculty of Medicine, Institute of Biology and Medical Genetics, Charles University, 128 00 Prague, Czech Republic
- Correspondence: (E.K.); (N.K.)
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He X, Wang P, Wang Y. Mitochondrial Transcription Factor A Binds to and Promotes Mutagenic Transcriptional Bypass of O4-Alkylthymidine Lesions. Anal Chem 2021; 93:1161-1169. [PMID: 33290046 PMCID: PMC7904241 DOI: 10.1021/acs.analchem.0c04224] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
O2- and O4-alkylated thymidine lesions are known to be poorly repaired and persist in mammalian tissues. To understand how mammalian cells sense the presence and regulate the repair of these lesions, we employed a quantitative proteomic method to discover regioisomeric O2- and O4-n-butylthymidine (O2- and O4-nBudT)-binding proteins. We were able to identify 21 and 74 candidate DNA damage recognition proteins for O2-nBudT- and O4-nBudT-bearing DNA probes, respectively. Among these proteins, DDB1 and DDB2 selectively bind to O2-nBudT-containing DNA, whereas three high-mobility group (HMG) proteins (i.e., HMGB1, HMGB2, and mitochondrial transcription factor A (TFAM)) exhibit preferential binding to O4-nBudT-bearing DNA. We further demonstrated that TFAM binds directly and selectively with O4-alkyldT-harboring DNA, and the binding capacity depends mainly on the HMG box-A domain of TFAM. We also found that TFAM promotes transcriptional mutagenesis of O4-nBudT and O4-pyridyloxobutylthymidine, which is a DNA adduct induced by tobacco-specific N-nitrosamines, in vitro and in human cells. Together, we explored, for the first time, the interaction proteomes of O-alkyldT lesions, and our study expanded the functions of TFAM by revealing its capability in the recognition of O4-alkyldT-bearing DNA and uncovering its modulation of transcriptional mutagenesis of these lesions in human cells.
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Affiliation(s)
- Xiaomei He
- Department of Chemistry, University of California, Riverside, California 92521-0403, United States
| | - Pengcheng Wang
- Department of Chemistry, University of California, Riverside, California 92521-0403, United States
| | - Yinsheng Wang
- Department of Chemistry, University of California, Riverside, California 92521-0403, United States
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40
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Basu U, Bostwick AM, Das K, Dittenhafer-Reed KE, Patel SS. Structure, mechanism, and regulation of mitochondrial DNA transcription initiation. J Biol Chem 2020; 295:18406-18425. [PMID: 33127643 PMCID: PMC7939475 DOI: 10.1074/jbc.rev120.011202] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2020] [Revised: 10/29/2020] [Indexed: 12/14/2022] Open
Abstract
Mitochondria are specialized compartments that produce requisite ATP to fuel cellular functions and serve as centers of metabolite processing, cellular signaling, and apoptosis. To accomplish these roles, mitochondria rely on the genetic information in their small genome (mitochondrial DNA) and the nucleus. A growing appreciation for mitochondria's role in a myriad of human diseases, including inherited genetic disorders, degenerative diseases, inflammation, and cancer, has fueled the study of biochemical mechanisms that control mitochondrial function. The mitochondrial transcriptional machinery is different from nuclear machinery. The in vitro re-constituted transcriptional complexes of Saccharomyces cerevisiae (yeast) and humans, aided with high-resolution structures and biochemical characterizations, have provided a deeper understanding of the mechanism and regulation of mitochondrial DNA transcription. In this review, we will discuss recent advances in the structure and mechanism of mitochondrial transcription initiation. We will follow up with recent discoveries and formative findings regarding the regulatory events that control mitochondrial DNA transcription, focusing on those involved in cross-talk between the mitochondria and nucleus.
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Affiliation(s)
- Urmimala Basu
- Department of Biochemistry and Molecular Biology, Rutgers Robert Wood Johnson Medical School, Piscataway, New Jersey, USA; Graduate School of Biomedical Sciences, Rutgers Robert Wood Johnson Medical School, Piscataway, New Jersey, USA
| | | | - Kalyan Das
- Department of Microbiology, Immunology, and Transplantation, Rega Institute for Medical Research, KU Leuven, Leuven, Belgium
| | | | - Smita S Patel
- Department of Biochemistry and Molecular Biology, Rutgers Robert Wood Johnson Medical School, Piscataway, New Jersey, USA.
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41
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Filograna R, Mennuni M, Alsina D, Larsson NG. Mitochondrial DNA copy number in human disease: the more the better? FEBS Lett 2020; 595:976-1002. [PMID: 33314045 PMCID: PMC8247411 DOI: 10.1002/1873-3468.14021] [Citation(s) in RCA: 209] [Impact Index Per Article: 52.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Revised: 11/02/2020] [Accepted: 11/26/2020] [Indexed: 12/19/2022]
Abstract
Most of the genetic information has been lost or transferred to the nucleus during the evolution of mitochondria. Nevertheless, mitochondria have retained their own genome that is essential for oxidative phosphorylation (OXPHOS). In mammals, a gene‐dense circular mitochondrial DNA (mtDNA) of about 16.5 kb encodes 13 proteins, which constitute only 1% of the mitochondrial proteome. Mammalian mtDNA is present in thousands of copies per cell and mutations often affect only a fraction of them. Most pathogenic human mtDNA mutations are recessive and only cause OXPHOS defects if present above a certain critical threshold. However, emerging evidence strongly suggests that the proportion of mutated mtDNA copies is not the only determinant of disease but that also the absolute copy number matters. In this review, we critically discuss current knowledge of the role of mtDNA copy number regulation in various types of human diseases, including mitochondrial disorders, neurodegenerative disorders and cancer, and during ageing. We also provide an overview of new exciting therapeutic strategies to directly manipulate mtDNA to restore OXPHOS in mitochondrial diseases.
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Affiliation(s)
- Roberta Filograna
- Division of Molecular Metabolism, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden.,Max Planck Institute for Biology of Ageing - Karolinska Institutet Laboratory, Karolinska Institutet, Stockholm, Sweden
| | - Mara Mennuni
- Division of Molecular Metabolism, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden.,Max Planck Institute for Biology of Ageing - Karolinska Institutet Laboratory, Karolinska Institutet, Stockholm, Sweden
| | - David Alsina
- Division of Molecular Metabolism, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden.,Max Planck Institute for Biology of Ageing - Karolinska Institutet Laboratory, Karolinska Institutet, Stockholm, Sweden
| | - Nils-Göran Larsson
- Division of Molecular Metabolism, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden.,Max Planck Institute for Biology of Ageing - Karolinska Institutet Laboratory, Karolinska Institutet, Stockholm, Sweden
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Vozáriková V, Kunová N, Bauer JA, Frankovský J, Kotrasová V, Procházková K, Džugasová V, Kutejová E, Pevala V, Nosek J, Tomáška Ľ. Mitochondrial HMG-Box Containing Proteins: From Biochemical Properties to the Roles in Human Diseases. Biomolecules 2020; 10:biom10081193. [PMID: 32824374 PMCID: PMC7463775 DOI: 10.3390/biom10081193] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2020] [Revised: 08/11/2020] [Accepted: 08/13/2020] [Indexed: 12/14/2022] Open
Abstract
Mitochondrial DNA (mtDNA) molecules are packaged into compact nucleo-protein structures called mitochondrial nucleoids (mt-nucleoids). Their compaction is mediated in part by high-mobility group (HMG)-box containing proteins (mtHMG proteins), whose additional roles include the protection of mtDNA against damage, the regulation of gene expression and the segregation of mtDNA into daughter organelles. The molecular mechanisms underlying these functions have been identified through extensive biochemical, genetic, and structural studies, particularly on yeast (Abf2) and mammalian mitochondrial transcription factor A (TFAM) mtHMG proteins. The aim of this paper is to provide a comprehensive overview of the biochemical properties of mtHMG proteins, the structural basis of their interaction with DNA, their roles in various mtDNA transactions, and the evolutionary trajectories leading to their rapid diversification. We also describe how defects in the maintenance of mtDNA in cells with dysfunctional mtHMG proteins lead to different pathologies at the cellular and organismal level.
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Affiliation(s)
- Veronika Vozáriková
- Department of Genetics, Faculty of Natural Sciences, Comenius University in Bratislava, Ilkovičova 6, Mlynská dolina B-1, 842 15 Bratislava, Slovakia; (V.V.); (J.F.); (K.P.); (V.D.)
| | - Nina Kunová
- Institute of Molecular Biology, Slovak Academy of Sciences, Dúbravská cesta 21, 845 51 Bratislava, Slovakia; (N.K.); (J.A.B.); (V.K.); (E.K.); (V.P.)
| | - Jacob A. Bauer
- Institute of Molecular Biology, Slovak Academy of Sciences, Dúbravská cesta 21, 845 51 Bratislava, Slovakia; (N.K.); (J.A.B.); (V.K.); (E.K.); (V.P.)
| | - Ján Frankovský
- Department of Genetics, Faculty of Natural Sciences, Comenius University in Bratislava, Ilkovičova 6, Mlynská dolina B-1, 842 15 Bratislava, Slovakia; (V.V.); (J.F.); (K.P.); (V.D.)
| | - Veronika Kotrasová
- Institute of Molecular Biology, Slovak Academy of Sciences, Dúbravská cesta 21, 845 51 Bratislava, Slovakia; (N.K.); (J.A.B.); (V.K.); (E.K.); (V.P.)
| | - Katarína Procházková
- Department of Genetics, Faculty of Natural Sciences, Comenius University in Bratislava, Ilkovičova 6, Mlynská dolina B-1, 842 15 Bratislava, Slovakia; (V.V.); (J.F.); (K.P.); (V.D.)
| | - Vladimíra Džugasová
- Department of Genetics, Faculty of Natural Sciences, Comenius University in Bratislava, Ilkovičova 6, Mlynská dolina B-1, 842 15 Bratislava, Slovakia; (V.V.); (J.F.); (K.P.); (V.D.)
| | - Eva Kutejová
- Institute of Molecular Biology, Slovak Academy of Sciences, Dúbravská cesta 21, 845 51 Bratislava, Slovakia; (N.K.); (J.A.B.); (V.K.); (E.K.); (V.P.)
| | - Vladimír Pevala
- Institute of Molecular Biology, Slovak Academy of Sciences, Dúbravská cesta 21, 845 51 Bratislava, Slovakia; (N.K.); (J.A.B.); (V.K.); (E.K.); (V.P.)
| | - Jozef Nosek
- Department of Biochemistry, Faculty of Natural Sciences, Comenius University in Bratislava, Ilkovičova 6, Mlynská dolina CH-1, 842 15 Bratislava, Slovakia;
| | - Ľubomír Tomáška
- Department of Genetics, Faculty of Natural Sciences, Comenius University in Bratislava, Ilkovičova 6, Mlynská dolina B-1, 842 15 Bratislava, Slovakia; (V.V.); (J.F.); (K.P.); (V.D.)
- Correspondence: ; Tel.: +421-2-90149-433
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Rajakumara E, Satish M, Abhishek S. In vitro studies on non-canonical DNA binding specificities of KAP6 and HMO1 and mechanistic insights into DNA bound and unbinding dynamics of KAP6. Int J Biol Macromol 2020; 160:925-933. [PMID: 32497665 DOI: 10.1016/j.ijbiomac.2020.05.228] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Revised: 05/25/2020] [Accepted: 05/26/2020] [Indexed: 12/26/2022]
Abstract
High mobility group box (HMGB) members are DNA binding proteins with varied functions present across kingdoms. The mechanism by which HMGBs with varying number of HMG boxes are able to carry out similar functions, are poorly understood. Moreover, how non-canonical DNAs are recognized by HMGB proteins is not clear. To address these, we carried out detailed biochemical and computational studies to characterize two HMGB members- Kinetoplast associated protein (KAP6) of Trypanosoma and High mobility group protein 1 (HMO1) from yeast. Here, we report that KAP6 binds non-canonical DNAs tighter than B-form DNA. Among non-canonical DNAs, KAP6 has the highest affinity for splayed and flap structures, but least for Holliday Junction (HJ). In contrast, HMO1 binds tighter to HJ. Computational analysis show that the secondary structural elements involved in DNA interaction are conserved in HMGB members KAP6 and mitochondrial transcription factor A. Simulation analyses revealed that the ~90° bend in DNA induced by KAP6 HMG box is a result of two ~45° bends, by Helix 1 and Helix 2 of the protein. Our data also suggests that the orthologs of HMO1 and KAP6 are oligomers in solution, which could be necessary for their functioning such as DNA bending and looping.
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Affiliation(s)
- Eerappa Rajakumara
- Macromolecular Structural Biology Lab, Department of Biotechnology, Indian Institute of Technology Hyderabad, Kandi, Sangareddy, Telangana 502285, India.
| | - Mutyala Satish
- Macromolecular Structural Biology Lab, Department of Biotechnology, Indian Institute of Technology Hyderabad, Kandi, Sangareddy, Telangana 502285, India
| | - Suman Abhishek
- Macromolecular Structural Biology Lab, Department of Biotechnology, Indian Institute of Technology Hyderabad, Kandi, Sangareddy, Telangana 502285, India
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Fang Y, Akimoto M, Mayanagi K, Hatano A, Matsumoto M, Matsuda S, Yasukawa T, Kang D. Chemical acetylation of mitochondrial transcription factor A occurs on specific lysine residues and affects its ability to change global DNA topology. Mitochondrion 2020; 53:99-108. [PMID: 32439622 DOI: 10.1016/j.mito.2020.05.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Revised: 05/08/2020] [Accepted: 05/14/2020] [Indexed: 12/20/2022]
Abstract
Chemical acetylation is postulated to occur in mitochondria. Mitochondrial transcription factor A (TFAM or mtTFA), a mitochondrial transcription initiation factor as well as the major mitochondrial nucleoid protein coating the entire mitochondrial genome, is proposed to be acetylated in animals and cultured cells. This study investigated the properties of human TFAM, in conjunction with the mechanism and effects of TFAM acetylation in vitro. Using highly purified recombinant human TFAM and 3 kb circular DNA as a downsized mtDNA model, we studied how the global TFAM-DNA interaction is affected/regulated by the quantitative TFAM-DNA relationship and TFAM acetylation. Results showed that the TFAM-DNA ratio strictly affects the TFAM property to unwind circular DNA in the presence of topoisomerase I. Mass spectrometry analysis showed that in vitro chemical acetylation of TFAM with acetyl-coenzyme A occurs preferentially on specific lysine residues, including those reported to be acetylated in exogenously expressed TFAM in cultured human cells, indicating that chemical acetylation plays a crucial role in TFAM acetylation in mitochondria. Intriguingly, the modification significantly decreased TFAM's DNA-unwinding ability, while its DNA-binding ability was largely unaffected. Altogether, we propose TFAM is chemically acetylated in vivo, which could change mitochondrial DNA topology, leading to copy number and gene expression modulation.
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Affiliation(s)
- Yuan Fang
- Department of Clinical Chemistry and Laboratory Medicine, Graduate School of Medical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka-shi, Fukuoka 812-8582, Japan
| | - Masaru Akimoto
- Department of Clinical Chemistry and Laboratory Medicine, Graduate School of Medical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka-shi, Fukuoka 812-8582, Japan; Department of Clinical Chemistry and Laboratory Medicine, Kyushu University Hospital, 3-1-1 Maidashi, Higashi-ku, Fukuoka-shi, Fukuoka 812-8582, Japan
| | - Kouta Mayanagi
- Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka-shi, Fukuoka 812-8582, Japan
| | - Atsushi Hatano
- Department of Omics and Systems Biology, Graduate School of Medical and Dental Sciences, Niigata University, 757 Ichibancho, Asahimachi-dori, Chuo-ku, Niigata-shi, Niigata 951-8510, Japan
| | - Masaki Matsumoto
- Department of Omics and Systems Biology, Graduate School of Medical and Dental Sciences, Niigata University, 757 Ichibancho, Asahimachi-dori, Chuo-ku, Niigata-shi, Niigata 951-8510, Japan
| | - Shigeru Matsuda
- Department of Clinical Chemistry and Laboratory Medicine, Graduate School of Medical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka-shi, Fukuoka 812-8582, Japan
| | - Takehiro Yasukawa
- Department of Clinical Chemistry and Laboratory Medicine, Graduate School of Medical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka-shi, Fukuoka 812-8582, Japan.
| | - Dongchon Kang
- Department of Clinical Chemistry and Laboratory Medicine, Graduate School of Medical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka-shi, Fukuoka 812-8582, Japan
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Cuppari A, Fernández-Millán P, Battistini F, Tarrés-Solé A, Lyonnais S, Iruela G, Ruiz-López E, Enciso Y, Rubio-Cosials A, Prohens R, Pons M, Alfonso C, Tóth K, Rivas G, Orozco M, Solà M. DNA specificities modulate the binding of human transcription factor A to mitochondrial DNA control region. Nucleic Acids Res 2020; 47:6519-6537. [PMID: 31114891 PMCID: PMC6614842 DOI: 10.1093/nar/gkz406] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Revised: 04/30/2019] [Accepted: 05/15/2019] [Indexed: 12/18/2022] Open
Abstract
Human mitochondrial DNA (h-mtDNA) codes for 13 subunits of the oxidative phosphorylation pathway, the essential route that produces ATP. H-mtDNA transcription and replication depends on the transcription factor TFAM, which also maintains and compacts this genome. It is well-established that TFAM activates the mtDNA promoters LSP and HSP1 at the mtDNA control region where DNA regulatory elements cluster. Previous studies identified still uncharacterized, additional binding sites at the control region downstream from and slightly similar to LSP, namely sequences X and Y (Site-X and Site-Y) (Fisher et al., Cell 50, pp 247-258, 1987). Here, we explore TFAM binding at these two sites and compare them to LSP by multiple experimental and in silico methods. Our results show that TFAM binding is strongly modulated by the sequence-dependent properties of Site-X, Site-Y and LSP. The high binding versatility of Site-Y or the considerable stiffness of Site-X tune TFAM interactions. In addition, we show that increase in TFAM/DNA complex concentration induces multimerization, which at a very high concentration triggers disruption of preformed complexes. Therefore, our results suggest that mtDNA sequences induce non-uniform TFAM binding and, consequently, direct an uneven distribution of TFAM aggregation sites during the essential process of mtDNA compaction.
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Affiliation(s)
- Anna Cuppari
- Structural MitoLab, Structural Biology Department, Maria de Maeztu Unit of Excellence, Molecular Biology Institute Barcelona (IBMB-CSIC), 08028 Barcelona, Spain
| | - Pablo Fernández-Millán
- Structural MitoLab, Structural Biology Department, Maria de Maeztu Unit of Excellence, Molecular Biology Institute Barcelona (IBMB-CSIC), 08028 Barcelona, Spain
| | - Federica Battistini
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, 08028 Barcelona, Spain
| | - Aleix Tarrés-Solé
- Structural MitoLab, Structural Biology Department, Maria de Maeztu Unit of Excellence, Molecular Biology Institute Barcelona (IBMB-CSIC), 08028 Barcelona, Spain
| | - Sébastien Lyonnais
- Structural MitoLab, Structural Biology Department, Maria de Maeztu Unit of Excellence, Molecular Biology Institute Barcelona (IBMB-CSIC), 08028 Barcelona, Spain
| | - Guillermo Iruela
- BioNMR Laboratory, Inorganic and Organic Chemistry Department, Universitat de Barcelona, 08028 Barcelona, Spain
| | - Elena Ruiz-López
- Structural MitoLab, Structural Biology Department, Maria de Maeztu Unit of Excellence, Molecular Biology Institute Barcelona (IBMB-CSIC), 08028 Barcelona, Spain
| | - Yuliana Enciso
- Structural MitoLab, Structural Biology Department, Maria de Maeztu Unit of Excellence, Molecular Biology Institute Barcelona (IBMB-CSIC), 08028 Barcelona, Spain
| | - Anna Rubio-Cosials
- Structural MitoLab, Structural Biology Department, Maria de Maeztu Unit of Excellence, Molecular Biology Institute Barcelona (IBMB-CSIC), 08028 Barcelona, Spain
| | - Rafel Prohens
- Unitat de Polimorfisme i Calorimetria, Centres Científics i Tecnològics, University of Barcelona, 08028 Barcelona, Spain
| | - Miquel Pons
- BioNMR Laboratory, Inorganic and Organic Chemistry Department, Universitat de Barcelona, 08028 Barcelona, Spain
| | - Carlos Alfonso
- Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas (CSIC), 28040 Madrid, Spain
| | - Katalin Tóth
- Deutsches Krebsforschungszentrum, Division Biophysics of Macromolecules, Heidelberg, Germany
| | - Germán Rivas
- Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas (CSIC), 28040 Madrid, Spain
| | - Modesto Orozco
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, 08028 Barcelona, Spain.,Department of Biochemistry and Biomedicine, University of Barcelona, Barcelona 08028, Spain
| | - Maria Solà
- Structural MitoLab, Structural Biology Department, Maria de Maeztu Unit of Excellence, Molecular Biology Institute Barcelona (IBMB-CSIC), 08028 Barcelona, Spain
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Flood BA, Higgs EF, Li S, Luke JJ, Gajewski TF. STING pathway agonism as a cancer therapeutic. Immunol Rev 2020; 290:24-38. [PMID: 31355488 DOI: 10.1111/imr.12765] [Citation(s) in RCA: 210] [Impact Index Per Article: 52.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2019] [Accepted: 04/04/2019] [Indexed: 12/13/2022]
Abstract
The fact that a subset of human cancers showed evidence for a spontaneous adaptive immune response as reflected by the T cell-inflamed tumor microenvironment phenotype led to the search for candidate innate immune pathways that might be driving such endogenous responses. Preclinical studies indicated a major role for the host STING pathway, a cytosolic DNA sensing pathway, as a proximal event required for optimal type I interferon production, dendritic cell activation, and priming of CD8+ T cells against tumor-associated antigens. STING agonists are therefore being developed as a novel cancer therapeutic, and a greater understanding of STING pathway regulation is leading to a broadened list of candidate immune regulatory targets. Early phase clinical trials of intratumoral STING agonists are already showing promise, alone and in combination with checkpoint blockade. Further advancement will derive from a deeper understanding of STING pathway biology as well as mechanisms of response vs resistance in individual cancer patients.
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Affiliation(s)
- Blake A Flood
- Department of Pathology, The University of Chicago, Chicago, Illinois
| | - Emily F Higgs
- Department of Pathology, The University of Chicago, Chicago, Illinois
| | - Shuyin Li
- Department of Pathology, The University of Chicago, Chicago, Illinois
| | - Jason J Luke
- Department of Medicine, Section of Hematology/Oncology, The University of Chicago, Chicago, Illinois
| | - Thomas F Gajewski
- Department of Pathology, The University of Chicago, Chicago, Illinois.,Department of Medicine, Section of Hematology/Oncology, The University of Chicago, Chicago, Illinois
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47
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Mishmar D, Levin R, Naeem MM, Sondheimer N. Higher Order Organization of the mtDNA: Beyond Mitochondrial Transcription Factor A. Front Genet 2019; 10:1285. [PMID: 31998357 PMCID: PMC6961661 DOI: 10.3389/fgene.2019.01285] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Accepted: 11/21/2019] [Indexed: 01/09/2023] Open
Abstract
The higher order organization of eukaryotic and prokaryotic genomes is pivotal in the regulation of gene expression. Specifically, chromatin accessibility in eukaryotes and nucleoid accessibility in bacteria are regulated by a cohort of proteins to alter gene expression in response to diverse physiological conditions. By contrast, prior studies have suggested that the mitochondrial genome (mtDNA) is coated solely by mitochondrial transcription factor A (TFAM), whose increased cellular concentration was proposed to be the major determinant of mtDNA packaging in the mitochondrial nucleoid. Nevertheless, recent analysis of DNase-seq and ATAC-seq experiments from multiple human and mouse samples suggest gradual increase in mtDNA occupancy during the course of embryonic development to generate a conserved footprinting pattern which correlate with sites that have low TFAM occupancy in vivo (ChIP-seq) and tend to adopt G-quadruplex structures. These findings, along with recent identification of mtDNA binding by known modulators of chromatin accessibility such as MOF, suggest that mtDNA higher order organization is generated by cross talk with the nuclear regulatory system, may have a role in mtDNA regulation, and is more complex than once thought.
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Affiliation(s)
- Dan Mishmar
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Rotem Levin
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Mansur M Naeem
- Institute of Medical Sciences and the Department of Paediatrics, The University of Toronto, Toronto, ON, Canada
| | - Neal Sondheimer
- Institute of Medical Sciences and the Department of Paediatrics, The University of Toronto, Toronto, ON, Canada
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Loth K, Largillière J, Coste F, Culard F, Landon C, Castaing B, Delmas AF, Paquet F. New protein-DNA complexes in archaea: a small monomeric protein induces a sharp V-turn DNA structure. Sci Rep 2019; 9:14253. [PMID: 31582767 PMCID: PMC6776556 DOI: 10.1038/s41598-019-50211-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Accepted: 09/05/2019] [Indexed: 01/02/2023] Open
Abstract
MC1, a monomeric nucleoid-associated protein (NAP), is structurally unrelated to other DNA-binding proteins. The protein participates in the genome organization of several Euryarchaea species through an atypical compaction mechanism. It is also involved in DNA transcription and cellular division through unknown mechanisms. We determined the 3D solution structure of a new DNA-protein complex formed by MC1 and a strongly distorted 15 base pairs DNA. While the protein just needs to adapt its conformation slightly, the DNA undergoes a dramatic curvature (the first two bend angles of 55° and 70°, respectively) and an impressive torsional stress (dihedral angle of 106°) due to several kinks upon binding of MC1 to its concave side. Thus, it adopts a V-turn structure. For longer DNAs, MC1 stabilizes multiple V-turn conformations in a flexible and dynamic manner. The existence of such V-turn conformations of the MC1-DNA complexes leads us to propose two binding modes of the protein, as a bender (primary binding mode) and as a wrapper (secondary binding mode). Moreover, it opens up new opportunities for studying and understanding the repair, replication and transcription molecular machineries of Archaea.
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Affiliation(s)
- Karine Loth
- Centre de Biophysique Moléculaire, Centre National de la Recherche Scientifique UPR 4301, rue Charles Sadron, F-45071, Orléans, Cedex 2, France. .,UFR Collegium Sciences et Techniques, Université d'Orléans, rue de Chartres, 45100, Orléans, France.
| | - Justine Largillière
- Centre de Biophysique Moléculaire, Centre National de la Recherche Scientifique UPR 4301, rue Charles Sadron, F-45071, Orléans, Cedex 2, France
| | - Franck Coste
- Centre de Biophysique Moléculaire, Centre National de la Recherche Scientifique UPR 4301, rue Charles Sadron, F-45071, Orléans, Cedex 2, France
| | - Françoise Culard
- Centre de Biophysique Moléculaire, Centre National de la Recherche Scientifique UPR 4301, rue Charles Sadron, F-45071, Orléans, Cedex 2, France
| | - Céline Landon
- Centre de Biophysique Moléculaire, Centre National de la Recherche Scientifique UPR 4301, rue Charles Sadron, F-45071, Orléans, Cedex 2, France
| | - Bertrand Castaing
- Centre de Biophysique Moléculaire, Centre National de la Recherche Scientifique UPR 4301, rue Charles Sadron, F-45071, Orléans, Cedex 2, France
| | - Agnès F Delmas
- Centre de Biophysique Moléculaire, Centre National de la Recherche Scientifique UPR 4301, rue Charles Sadron, F-45071, Orléans, Cedex 2, France
| | - Françoise Paquet
- Centre de Biophysique Moléculaire, Centre National de la Recherche Scientifique UPR 4301, rue Charles Sadron, F-45071, Orléans, Cedex 2, France.
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Sharma N, Pasala MS, Prakash A. Mitochondrial DNA: Epigenetics and environment. ENVIRONMENTAL AND MOLECULAR MUTAGENESIS 2019; 60:668-682. [PMID: 31335990 PMCID: PMC6941438 DOI: 10.1002/em.22319] [Citation(s) in RCA: 98] [Impact Index Per Article: 19.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2019] [Revised: 07/08/2019] [Accepted: 07/11/2019] [Indexed: 05/22/2023]
Abstract
Maintenance of the mitochondrial genome is essential for proper cellular function. For this purpose, mitochondrial DNA (mtDNA) needs to be faithfully replicated, transcribed, translated, and repaired in the face of constant onslaught from endogenous and environmental agents. Although only 13 polypeptides are encoded within mtDNA, the mitochondrial proteome comprises over 1500 proteins that are encoded by nuclear genes and translocated to the mitochondria for the purpose of maintaining mitochondrial function. Regulation of mtDNA and mitochondrial proteins by epigenetic changes and post-translational modifications facilitate crosstalk between the nucleus and the mitochondria and ultimately lead to the maintenance of cellular health and homeostasis. DNA methyl transferases have been identified in the mitochondria implicating that methylation occurs within this organelle; however, the extent to which mtDNA is methylated has been debated for many years. Mechanisms of demethylation within this organelle have also been postulated, but the exact mechanisms and their outcomes is still an active area of research. Mitochondrial dysfunction in the form of altered gene expression and ATP production, resulting from epigenetic changes, can lead to various conditions including aging-related neurodegenerative disorders, altered metabolism, changes in circadian rhythm, and cancer. Here, we provide an overview of the epigenetic regulation of mtDNA via methylation, long and short noncoding RNAs, and post-translational modifications of nucleoid proteins (as mitochondria lack histones). We also highlight the influence of xenobiotics such as airborne environmental pollutants, contamination from heavy metals, and therapeutic drugs on mtDNA methylation. Environ. Mol. Mutagen., 60:668-682, 2019. © 2019 Wiley Periodicals, Inc.
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Mitochondrial transcription factor A promotes DNA strand cleavage at abasic sites. Proc Natl Acad Sci U S A 2019; 116:17792-17799. [PMID: 31413200 DOI: 10.1073/pnas.1911252116] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
In higher eukaryotic cells, mitochondria are essential subcellular organelles for energy production, cell signaling, and the biosynthesis of biomolecules. The mitochondrial DNA (mtDNA) genome is indispensable for mitochondrial function because it encodes protein subunits of the electron transport chain and a full set of transfer and ribosomal RNAs. MtDNA degradation has emerged as an essential quality control measure to maintain mtDNA and to cope with mtDNA damage resulting from endogenous and environmental factors. Among all types of DNA damage known, abasic (AP) sites, sourced from base excision repair and spontaneous base loss, are the most abundant endogenous DNA lesions in cells. In mitochondria, AP sites trigger rapid DNA loss; however, the mechanism and molecular factors involved in the process remain elusive. Herein, we demonstrate that the stability of AP sites is reduced dramatically upon binding to a major mtDNA packaging protein, mitochondrial transcription factor A (TFAM). The half-life of AP lesions within TFAM-DNA complexes is 2 to 3 orders of magnitude shorter than that in free DNA, depending on their position. The TFAM-catalyzed AP-DNA destabilization occurs with nonspecific DNA or mitochondrial light-strand promoter sequence, yielding DNA single-strand breaks and DNA-TFAM cross-links. TFAM-DNA cross-link intermediates prior to the strand scission were also observed upon treating AP-DNA with mitochondrial extracts of human cells. In situ trapping of the reaction intermediates (DNA-TFAM cross-links) revealed that the reaction proceeds via Schiff base chemistry facilitated by lysine residues. Collectively, our data suggest a novel role of TFAM in facilitating the turnover of abasic DNA.
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