1
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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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2
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Liu K, Li W, Xiao Y, Lei M, Zhang M, Min J. Molecular mechanism of specific DNA sequence recognition by NRF1. Nucleic Acids Res 2024; 52:953-966. [PMID: 38055835 PMCID: PMC10810270 DOI: 10.1093/nar/gkad1162] [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: 08/08/2023] [Revised: 11/09/2023] [Accepted: 11/17/2023] [Indexed: 12/08/2023] Open
Abstract
Nuclear respiratory factor 1 (NRF1) regulates the expression of genes that are vital for mitochondrial biogenesis, respiration, and various other cellular processes. While NRF1 has been reported to bind specifically to GC-rich promoters as a homodimer, the precise molecular mechanism governing its recognition of target gene promoters has remained elusive. To unravel the recognition mechanism, we have determined the crystal structure of the NRF1 homodimer bound to an ATGCGCATGCGCAT dsDNA. In this complex, NRF1 utilizes a flexible linker to connect its dimerization domain (DD) and DNA binding domain (DBD). This configuration allows one NRF1 monomer to adopt a U-turn conformation, facilitating the homodimer to specifically bind to the two TGCGC motifs in the GCGCATGCGC consensus sequence from opposite directions. Strikingly, while the NRF1 DBD alone could also bind to the half-site (TGCGC) DNA of the consensus sequence, the cooperativity between DD and DBD is essential for the binding of the intact GCGCATGCGC sequence and the transcriptional activity of NRF1. Taken together, our results elucidate the molecular mechanism by which NRF1 recognizes specific DNA sequences in the promoters to regulate gene expression.
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Affiliation(s)
- Ke Liu
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan 430079, PR China
| | - Weifang Li
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan 430079, PR China
| | - Yuqing Xiao
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan 430079, PR China
| | - Ming Lei
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan 430079, PR China
| | - Ming Zhang
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan 430079, PR China
| | - Jinrong Min
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan 430079, PR China
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3
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Heo J, Park YJ, Kim Y, Lee HS, Kim J, Kwon SH, Kang MG, Rhee HW, Sun W, Lee JH, Cho H. Mitochondrial E3 ligase MARCH5 is a safeguard against DNA-PKcs-mediated immune signaling in mitochondria-damaged cells. Cell Death Dis 2023; 14:788. [PMID: 38040710 PMCID: PMC10692114 DOI: 10.1038/s41419-023-06315-9] [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: 04/04/2023] [Revised: 11/10/2023] [Accepted: 11/15/2023] [Indexed: 12/03/2023]
Abstract
Mitochondrial dysfunction is important in various chronic degenerative disorders, and aberrant immune responses elicited by cytoplasmic mitochondrial DNA (mtDNA) may be related. Here, we developed mtDNA-targeted MTERF1-FokI and TFAM-FokI endonuclease systems to induce mitochondrial DNA double-strand breaks (mtDSBs). In these cells, the mtDNA copy number was significantly reduced upon mtDSB induction. Interestingly, in cGAS knockout cells, synthesis of interferon β1 and interferon-stimulated gene was increased upon mtDSB induction. We found that mtDSBs activated DNA-PKcs and HSPA8 in a VDAC1-dependent manner. Importantly, the mitochondrial E3 ligase MARCH5 bound active DNA-PKcs in cells with mtDSBs and reduced the type І interferon response through the degradation of DNA-PKcs. Likewise, mitochondrial damage caused by LPS treatment in RAW264.7 macrophage cells increased phospho-HSPA8 levels and the synthesis of mIFNB1 mRNA in a DNA-PKcs-dependent manner. Accordingly, in March5 knockout macrophages, phospho-HSPA8 levels and the synthesis of mIFNB1 mRNA were prolonged after LPS stimulation. Together, cytoplasmic mtDNA elicits a cellular immune response through DNA-PKcs, and mitochondrial MARCH5 may be a safeguard to prevent persistent inflammatory reactions.
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Affiliation(s)
- June Heo
- Department of Biochemistry and Molecular Biology, Ajou University School of Medicine, Suwon, South Korea
- Department of Biomedical Sciences, Graduate School of Ajou University, Suwon, South Korea
| | - Yeon-Ji Park
- Department of Biochemistry and Molecular Biology, Ajou University School of Medicine, Suwon, South Korea
| | - Yonghyeon Kim
- Department of Biochemistry and Molecular Biology, Ajou University School of Medicine, Suwon, South Korea
- Department of Biomedical Sciences, Graduate School of Ajou University, Suwon, South Korea
| | - Ho-Soo Lee
- Department of Biochemistry and Molecular Biology, Ajou University School of Medicine, Suwon, South Korea
| | - Jeongah Kim
- Department of Anatomy, College of medicine, Korea University, Seoul, South Korea
| | - Soon-Hwan Kwon
- Department of Infectious Diseases, Research Center of Infectious and Environmental Diseases, Armed Forces Medical Research Institute, Daejeon, South Korea
| | - Myeong-Gyun Kang
- Department of Chemistry, Seoul National University, Seoul, South Korea
| | - Hyun-Woo Rhee
- Department of Chemistry, Seoul National University, Seoul, South Korea
| | - Woong Sun
- Department of Anatomy, College of medicine, Korea University, Seoul, South Korea
| | - Jae-Ho Lee
- Department of Biochemistry and Molecular Biology, Ajou University School of Medicine, Suwon, South Korea.
- Department of Biomedical Sciences, Graduate School of Ajou University, Suwon, South Korea.
| | - Hyeseong Cho
- Department of Biochemistry and Molecular Biology, Ajou University School of Medicine, Suwon, South Korea.
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4
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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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5
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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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6
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Oliveira VCD, Roballo KCS, Mariano Junior CG, Ambrósio CE. Gene Editing Technologies Targeting TFAM and Its Relation to Mitochondrial Diseases. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2023; 1429:173-189. [PMID: 37486522 DOI: 10.1007/978-3-031-33325-5_10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/25/2023]
Abstract
Mitochondria are organelles present in the cytoplasm of eukaryotic cells; they play a key role in adenosine triphosphate (ATP) synthesis and oxidative phosphorylation. Mitochondria have their own DNA, mitochondrial DNA (mtDNA), keeping the function of the mitochondria. Mitochondrial transcription factor A (TFAM) is a member of the HMGB subfamily that binds to mtDNA promoters is and considered essential in mtDNA replication and transcription. More recently, TFAM has been shown to play a central role in the maintenance and regulation of mitochondrial copy number, inflammatory response, expression regulation, and mitochondrial genome activity. Gene editing tools such as the CRISPR-Cas 9 technique, TALENs, and other gene editing tools have been used to investigate the role of TFAM in mitochondrial mechanics and biogenesis as well as its correlation to mitochondrial disorders. Thus this chapter brings a summary of mitochondria function, dysfunction, the importance of TFAM in the maintenance of mitochondria, and state of the art of gene editing tools involving TFAM and mtDNA.
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Affiliation(s)
- Vanessa Cristina de Oliveira
- Department of Veterinary Medicine, Faculty of Animal Science and Food Engineering, University of São Paulo, Pirassununga, SP, Brazil.
| | - Kelly Cristine Santos Roballo
- Biomedical Affairs and Research, Edward Via College of Osteopathic Medicine, Blacksburg, VA, USA
- Department of Biomedical Sciences and Pathobiology, Virginia Maryland College of Veterinary Medicine, Virginia Tech, Blacksburg, VA, USA
| | - Clesio Gomes Mariano Junior
- Department of Veterinary Medicine, Faculty of Animal Science and Food Engineering, University of São Paulo, Pirassununga, SP, Brazil
| | - Carlos Eduardo Ambrósio
- Department of Veterinary Medicine, Faculty of Animal Science and Food Engineering, University of São Paulo, Pirassununga, SP, Brazil
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7
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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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8
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Tan BG, Mutti CD, Shi Y, Xie X, Zhu X, Silva-Pinheiro P, Menger KE, Díaz-Maldonado H, Wei W, Nicholls TJ, Chinnery PF, Minczuk M, Falkenberg M, Gustafsson CM. The human mitochondrial genome contains a second light strand promoter. Mol Cell 2022; 82:3646-3660.e9. [PMID: 36044900 DOI: 10.1016/j.molcel.2022.08.011] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Revised: 07/21/2022] [Accepted: 08/07/2022] [Indexed: 11/30/2022]
Abstract
The human mitochondrial genome must be replicated and expressed in a timely manner to maintain energy metabolism and supply cells with adequate levels of adenosine triphosphate. Central to this process is the idea that replication primers and gene products both arise via transcription from a single light strand promoter (LSP) such that primer formation can influence gene expression, with no consensus as to how this is regulated. Here, we report the discovery of a second light strand promoter (LSP2) in humans, with features characteristic of a bona fide mitochondrial promoter. We propose that the position of LSP2 on the mitochondrial genome allows replication and gene expression to be orchestrated from two distinct sites, which expands our long-held understanding of mitochondrial gene expression in humans.
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Affiliation(s)
- Benedict G Tan
- Department of Medical Biochemistry and Cell Biology, University of Gothenburg, Gothenburg 405 30, Sweden
| | - Christian D Mutti
- Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Cambridge CB2 0XY, UK
| | - Yonghong Shi
- Department of Medical Biochemistry and Cell Biology, University of Gothenburg, Gothenburg 405 30, Sweden
| | - Xie Xie
- Department of Medical Biochemistry and Cell Biology, University of Gothenburg, Gothenburg 405 30, Sweden
| | - Xuefeng Zhu
- Department of Medical Biochemistry and Cell Biology, University of Gothenburg, Gothenburg 405 30, Sweden
| | - Pedro Silva-Pinheiro
- Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Cambridge CB2 0XY, UK
| | - Katja E Menger
- Wellcome Centre for Mitochondrial Research, Biosciences Institute, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Héctor Díaz-Maldonado
- Department of Medical Biochemistry and Cell Biology, University of Gothenburg, Gothenburg 405 30, Sweden
| | - Wei Wei
- Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Cambridge CB2 0XY, UK; Department of Clinical Neurosciences, School of Clinical Medicine, University of Cambridge, Cambridge, UK
| | - Thomas J Nicholls
- Wellcome Centre for Mitochondrial Research, Biosciences Institute, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Patrick F Chinnery
- Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Cambridge CB2 0XY, UK; Department of Clinical Neurosciences, School of Clinical Medicine, University of Cambridge, Cambridge, UK
| | - Michal Minczuk
- Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Cambridge CB2 0XY, UK.
| | - Maria Falkenberg
- Department of Medical Biochemistry and Cell Biology, University of Gothenburg, Gothenburg 405 30, Sweden.
| | - Claes M Gustafsson
- Department of Medical Biochemistry and Cell Biology, University of Gothenburg, Gothenburg 405 30, Sweden.
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9
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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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