1
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Platz KR, Rudisel EJ, Paluch KV, Laurin TR, Dittenhafer-Reed KE. Assessing the Role of Post-Translational Modifications of Mitochondrial RNA Polymerase. Int J Mol Sci 2023; 24:16050. [PMID: 38003238 PMCID: PMC10671485 DOI: 10.3390/ijms242216050] [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: 10/10/2023] [Revised: 11/02/2023] [Accepted: 11/02/2023] [Indexed: 11/26/2023] Open
Abstract
The mitochondrial proteome is subject to abundant post-translational modifications, including lysine acetylation and phosphorylation of serine, threonine, and tyrosine. The biological function of the majority of these protein modifications is unknown. Proteins required for the transcription and translation of mitochondrial DNA (mtDNA) are subject to modification. This suggests that reversible post-translational modifications may serve as a regulatory mechanism for mitochondrial gene transcription, akin to mechanisms controlling nuclear gene expression. We set out to determine whether acetylation or phosphorylation controls the function of mitochondrial RNA polymerase (POLRMT). Mass spectrometry was used to identify post-translational modifications on POLRMT. We analyzed three POLRMT modification sites (lysine 402, threonine 315, threonine 993) found in distinct structural regions. Amino acid point mutants that mimic the modified and unmodified forms of POLRMT were employed to measure the effect of acetylation or phosphorylation on the promoter binding ability of POLRMT in vitro. We found a slight decrease in binding affinity for the phosphomimic at threonine 315. We did not identify large changes in viability, mtDNA content, or mitochondrial transcript level upon overexpression of POLRMT modification mimics in HeLa cells. Our results suggest minimal biological impact of the POLRMT post-translational modifications studied in our system.
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2
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Potter A, Cabrera-Orefice A, Spelbrink JN. Let's make it clear: systematic exploration of mitochondrial DNA- and RNA-protein complexes by complexome profiling. Nucleic Acids Res 2023; 51:10619-10641. [PMID: 37615582 PMCID: PMC10602928 DOI: 10.1093/nar/gkad697] [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: 04/15/2023] [Revised: 07/18/2023] [Accepted: 08/11/2023] [Indexed: 08/25/2023] Open
Abstract
Complexome profiling (CP) is a powerful tool for systematic investigation of protein interactors that has been primarily applied to study the composition and dynamics of mitochondrial protein complexes. Here, we further optimized this method to extend its application to survey mitochondrial DNA- and RNA-interacting protein complexes. We established that high-resolution clear native gel electrophoresis (hrCNE) is a better alternative to preserve DNA- and RNA-protein interactions that are otherwise disrupted when samples are separated by the widely used blue native gel electrophoresis (BNE). In combination with enzymatic digestion of DNA, our CP approach improved the identification of a wide range of protein interactors of the mitochondrial gene expression system without compromising the detection of other multiprotein complexes. The utility of this approach was particularly demonstrated by analysing the complexome changes in human mitochondria with impaired gene expression after transient, chemically induced mitochondrial DNA depletion. Effects of RNase on mitochondrial protein complexes were also evaluated and discussed. Overall, our adaptations significantly improved the identification of mitochondrial DNA- and RNA-protein interactions by CP, thereby unlocking the comprehensive analysis of a near-complete mitochondrial complexome in a single experiment.
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Affiliation(s)
- Alisa Potter
- Department of Pediatrics, Amalia Children's Hospital, Radboud University Medical Center, Nijmegen, The Netherlands
- Radboud Center for Mitochondrial Medicine (RCMM), Radboud University Medical Center, Nijmegen, The Netherlands
| | - Alfredo Cabrera-Orefice
- Radboud Center for Mitochondrial Medicine (RCMM), Radboud University Medical Center, Nijmegen, The Netherlands
- Department of Medical BioSciences, Radboud University Medical Center, Nijmegen, The Netherlands
- Functional Proteomics, Institute for Cardiovascular Physiology, Goethe University, Frankfurt am Main, Germany
| | - Johannes N Spelbrink
- Department of Pediatrics, Amalia Children's Hospital, Radboud University Medical Center, Nijmegen, The Netherlands
- Radboud Center for Mitochondrial Medicine (RCMM), Radboud University Medical Center, Nijmegen, The Netherlands
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3
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Wang D, Wang W, Fang L, Qi L, Zhang Y, Liu J, Liang Y, Yang H, Wang M, Wei X, Jiang R, Liu Y, Zhou W, Fang X. Mitochondrial Protease Targeting Chimeras for Mitochondrial Matrix Protein Degradation. J Am Chem Soc 2023. [PMID: 37276358 DOI: 10.1021/jacs.3c03756] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Targeted protein degradation (TPD) is an emerging technique for protein regulation. Currently, all TPD developed in eukaryotic cells relies on either ubiquitin-proteasome or lysosomal systems, thus are powerless against target proteins in membrane organelles lacking proteasomes and lysosomes, such as mitochondria. Here, we developed a mitochondrial protease targeting chimera (MtPTAC) to address this issue. MtPTAC is a bifunctional small molecule that can bind to mitochondrial caseinolytic protease P (ClpP) at one end and target protein at the other. Mechanistically, MtPTAC activates the hydrolase activity of ClpP while simultaneously bringing target proteins into proximity with ClpP. Taking mitochondrial RNA polymerase (POLRMT) as a model protein, we have demonstrated the powerful proteolytic ability and antitumor application prospects of MtPTAC, both in vivo and in vitro. This is the first modularly designed TPD that can specifically hydrolyze target proteins inside mitochondria.
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Affiliation(s)
- Dachi Wang
- School of Chemistry and Materials, University of Science and Technology of China, Hefei, Anhui 230026, China
- Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, PR China
| | - Wenxi Wang
- Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, PR China
- School of Molecular Medicine, Hangzhou Institute for Advanced Study, UCAS, Hangzhou 310024, China
| | - Le Fang
- Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, PR China
| | - Lubin Qi
- Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, PR China
| | - Yuchao Zhang
- Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, PR China
| | - Jie Liu
- Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, PR China
| | - Yuxin Liang
- Beijing National Research Center for Molecular Sciences, Institute of Chemistry, Key Laboratory of Molecular Nanostructure and Nanotechnology, Chinese Academy of Science, Beijing 100190, China
| | - Hongwei Yang
- Beijing National Research Center for Molecular Sciences, Institute of Chemistry, Key Laboratory of Molecular Nanostructure and Nanotechnology, Chinese Academy of Science, Beijing 100190, China
| | - Mengjie Wang
- Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, PR China
| | - Xiaojian Wei
- Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, PR China
| | - Ruibin Jiang
- Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, PR China
| | - Yuan Liu
- Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, PR China
| | - Wei Zhou
- Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, PR China
| | - Xiaohong Fang
- School of Chemistry and Materials, University of Science and Technology of China, Hefei, Anhui 230026, China
- Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, PR China
- Beijing National Research Center for Molecular Sciences, Institute of Chemistry, Key Laboratory of Molecular Nanostructure and Nanotechnology, Chinese Academy of Science, Beijing 100190, China
- School of Molecular Medicine, Hangzhou Institute for Advanced Study, UCAS, Hangzhou 310024, China
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4
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Jerome MS, Nanjappa DP, Chakraborty A, Chakrabarty S. Molecular etiology of defective nuclear and mitochondrial ribosome biogenesis: Clinical phenotypes and therapy. Biochimie 2023; 207:122-136. [PMID: 36336106 DOI: 10.1016/j.biochi.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: 08/01/2022] [Revised: 10/27/2022] [Accepted: 11/01/2022] [Indexed: 11/06/2022]
Abstract
Ribosomopathies are rare congenital disorders associated with defective ribosome biogenesis due to pathogenic variations in genes that encode proteins related to ribosome function and biogenesis. Defects in ribosome biogenesis result in a nucleolar stress response involving the TP53 tumor suppressor protein and impaired protein synthesis leading to a deregulated translational output. Despite the accepted notion that ribosomes are omnipresent and essential for all cells, most ribosomopathies show tissue-specific phenotypes affecting blood cells, hair, spleen, or skin. On the other hand, defects in mitochondrial ribosome biogenesis are associated with a range of clinical manifestations affecting more than one organ. Intriguingly, the deregulated ribosomal function is also a feature in several human malignancies with a selective upregulation or downregulation of specific ribosome components. Here, we highlight the clinical conditions associated with defective ribosome biogenesis in the nucleus and mitochondria with a description of the affected genes and the implicated pathways, along with a note on the treatment strategies currently available for these disorders.
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Affiliation(s)
- Maria Sona Jerome
- Department of Cell and Molecular Biology, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, 576104, Karnataka, India
| | - Dechamma Pandyanda Nanjappa
- Division of Molecular Genetics and Cancer, Nitte University Centre for Science Education and Research (NUCSER), NITTE (Deemed to Be University), Deralakate, Mangaluru, 575018, India
| | - Anirban Chakraborty
- Division of Molecular Genetics and Cancer, Nitte University Centre for Science Education and Research (NUCSER), NITTE (Deemed to Be University), Deralakate, Mangaluru, 575018, India.
| | - Sanjiban Chakrabarty
- Department of Cell and Molecular Biology, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, 576104, Karnataka, India.
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5
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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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6
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Kuthethur R, Shukla V, Mallya S, Adiga D, Kabekkodu SP, Ramachandra L, Saxena Pu P, Satyamoorthy K, Chakrabarty S. Expression analysis and function of mitochondrial genome-encoded microRNAs. J Cell Sci 2022; 135:274749. [PMID: 35297485 DOI: 10.1242/jcs.258937] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Accepted: 03/11/2022] [Indexed: 11/20/2022] Open
Abstract
MicroRNAs play a significant role in nuclear and mitochondrial anterograde and retrograde signaling. Most of the miRNAs found inside mitochondria are nuclear genome encoded, with few mitochondrial genome encoded non-coding RNAs have been reported. In this study, we have identified 13 mitochondrial genome-encoded microRNAs (mitomiRs), which were differentially expressed in breast cancer cell lines (MCF-7, MDA-MB-468, and MDA-MB-231), non-malignant breast epithelial cell line (MCF-10A), and normal and breast cancer tissue specimens. We found that mitochondrial DNA depletion and inhibition of mitochondrial transcription leads to reduced expression of mitomiRs in breast cancer cells. MitomiRs physically interact with Ago2, an RNA-induced silencing complex (RISC) protein, in the cytoplasm and inside mitochondria. MitomiRs regulate the expression of both nuclear and mitochondrial transcripts in breast cancer cells. We showed that mitomiR-5 targets PPARGC1A and regulates mtDNA copy number in breast cancer cells. MitomiRs identified in the present study may be a promising tool for expression and functional analysis in patients with a defective mitochondrial phenotype, including cancer and metabolic syndromes.
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Affiliation(s)
- Raviprasad Kuthethur
- Department of Cell and Molecular Biology, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - Vaibhav Shukla
- Department of Cell and Molecular Biology, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - Sandeep Mallya
- Department of Bioinformatics, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - Divya Adiga
- Department of Cell and Molecular Biology, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - Shama Prasada Kabekkodu
- Department of Cell and Molecular Biology, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - Lingadakai Ramachandra
- Department of Surgery, Kasturba Medical College, Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - Prakash Saxena Pu
- Department of Radiation Oncology, Kasturba Medical College, Manipal Academy of Higher Education, Mangalore, Karnataka, India
| | - Kapaettu Satyamoorthy
- Department of Cell and Molecular Biology, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - Sanjiban Chakrabarty
- Department of Cell and Molecular Biology, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, Karnataka, India
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7
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Lin KL, Chen SD, Lin KJ, Liou CW, Chuang YC, Wang PW, Chuang JH, Lin TK. Quality Matters? The Involvement of Mitochondrial Quality Control in Cardiovascular Disease. Front Cell Dev Biol 2021; 9:636295. [PMID: 33829016 PMCID: PMC8019794 DOI: 10.3389/fcell.2021.636295] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Accepted: 03/02/2021] [Indexed: 12/12/2022] Open
Abstract
Cardiovascular diseases are one of the leading causes of death and global health problems worldwide. Multiple factors are known to affect the cardiovascular system from lifestyles, genes, underlying comorbidities, and age. Requiring high workload, metabolism of the heart is largely dependent on continuous power supply via mitochondria through effective oxidative respiration. Mitochondria not only serve as cellular power plants, but are also involved in many critical cellular processes, including the generation of intracellular reactive oxygen species (ROS) and regulating cellular survival. To cope with environmental stress, mitochondrial function has been suggested to be essential during bioenergetics adaptation resulting in cardiac pathological remodeling. Thus, mitochondrial dysfunction has been advocated in various aspects of cardiovascular pathology including the response to ischemia/reperfusion (I/R) injury, hypertension (HTN), and cardiovascular complications related to type 2 diabetes mellitus (DM). Therefore, mitochondrial homeostasis through mitochondrial dynamics and quality control is pivotal in the maintenance of cardiac health. Impairment of the segregation of damaged components and degradation of unhealthy mitochondria through autophagic mechanisms may play a crucial role in the pathogenesis of various cardiac disorders. This article provides in-depth understanding of the current literature regarding mitochondrial remodeling and dynamics in cardiovascular diseases.
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Affiliation(s)
- Kai-Lieh Lin
- Center for Mitochondrial Research and Medicine, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung, Taiwan.,Department of Anesthesiology, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung, Taiwan
| | - Shang-Der Chen
- Center for Mitochondrial Research and Medicine, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung, Taiwan.,Department of Neurology, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung, Taiwan.,Center of Parkinson's Disease, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung, Taiwan
| | - Kai-Jung Lin
- Center for Mitochondrial Research and Medicine, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung, Taiwan
| | - Chia-Wei Liou
- Center for Mitochondrial Research and Medicine, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung, Taiwan.,Department of Neurology, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung, Taiwan.,Center of Parkinson's Disease, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung, Taiwan
| | - Yao-Chung Chuang
- Center for Mitochondrial Research and Medicine, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung, Taiwan.,Department of Neurology, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung, Taiwan.,Center of Parkinson's Disease, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung, Taiwan
| | - Pei-Wen Wang
- Center for Mitochondrial Research and Medicine, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung, Taiwan.,Department of Metabolism, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung, Taiwan
| | - Jiin-Haur Chuang
- Center for Mitochondrial Research and Medicine, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung, Taiwan.,Department of Pediatric Surgery, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung, Taiwan
| | - Tsu-Kung Lin
- Center for Mitochondrial Research and Medicine, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung, Taiwan.,Department of Neurology, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung, Taiwan.,Center of Parkinson's Disease, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung, Taiwan
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8
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Gonçalves AM, Pereira-Santos AR, Esteves AR, Cardoso SM, Empadinhas N. The Mitochondrial Ribosome: A World of Opportunities for Mitochondrial Dysfunction Toward Parkinson's Disease. Antioxid Redox Signal 2021; 34:694-711. [PMID: 32098485 DOI: 10.1089/ars.2019.7997] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Significance: Mitochondrial ribosomes (mitoribosomes) are organelles that translate mitochondrial messenger RNA in the matrix and, in mammals, have evolved to translate 13 polypeptides of the pathway that performs oxidative phosphorylation (OXPHOS). Although a number of devastating diseases result from defects in this mitochondrial translation apparatus, most are associated with genetic mutations and little is known about allelopathic defects caused by antibiotics, toxins, or nonproteinogenic amino acids. Recent Advances: The levels of mitochondrial ribosomal subunits 12S and 16S ribosomal RNA (rRNA) in cells/tissues from patients carrying mutations in these genes have been associated with alterations in mitochondrial translation efficiency and with impaired OXPHOS activities, as well as with the severity of clinical phenotypes. In recent decades, important studies revealed a prominent role of mitochondrial dysfunction in Parkinson's disease (PD); however, the involvement of mitoribosomes remains largely unknown. Critical Issues: Considering that mitoribosomal structure and function can determine the efficiency of OXPHOS and that an impaired mitochondrial respiratory chain is a common finding in PD, we argue that the mitoribosome may be key to disease onset and progression. With this review, we comprehensively integrate the available knowledge on the composition, assembly, and role of the mitoribosome in mitochondrial efficiency, reflecting on its possible involvement in the etiopathogenesis of this epidemic disease as an appealing research avenue. Future Directions: If a direct correlation between mitoribosome failure and PD pathology is demonstrated, these mitochondrial organelles will provide valuable early clinical markers and potentially attractive targets for the development of innovative PD-directed therapeutic agents.
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Affiliation(s)
- Ana Mafalda Gonçalves
- CNC-Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal.,CIBB-Centre for Innovative Biomedicine and Biotechnology, University of Coimbra, Coimbra, Portugal.,Faculty of Medicine, University of Coimbra, Coimbra, Portugal
| | - Ana Raquel Pereira-Santos
- CNC-Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal.,CIBB-Centre for Innovative Biomedicine and Biotechnology, University of Coimbra, Coimbra, Portugal
| | - Ana Raquel Esteves
- CNC-Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal.,CIBB-Centre for Innovative Biomedicine and Biotechnology, University of Coimbra, Coimbra, Portugal
| | - Sandra M Cardoso
- CNC-Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal.,CIBB-Centre for Innovative Biomedicine and Biotechnology, University of Coimbra, Coimbra, Portugal.,Faculty of Medicine, University of Coimbra, Coimbra, Portugal
| | - Nuno Empadinhas
- CNC-Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal.,CIBB-Centre for Innovative Biomedicine and Biotechnology, University of Coimbra, Coimbra, Portugal.,IIIUC-Institute for Interdisciplinary Research, University of Coimbra, Coimbra, Portugal
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9
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Laptev I, Dontsova O, Sergiev P. Epitranscriptomics of Mammalian Mitochondrial Ribosomal RNA. Cells 2020; 9:E2181. [PMID: 32992603 PMCID: PMC7600485 DOI: 10.3390/cells9102181] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 09/20/2020] [Accepted: 09/23/2020] [Indexed: 12/16/2022] Open
Abstract
Modified nucleotides are present in all ribosomal RNA molecules. Mitochondrial ribosomes are unique to have a set of methylated residues that includes universally conserved ones, those that could be found either in bacterial or in archaeal/eukaryotic cytosolic ribosomes and those that are present exclusively in mitochondria. A single pseudouridine within the mt-rRNA is located in the peptidyltransferase center at a position similar to that in bacteria. After recent completion of the list of enzymes responsible for the modification of mammalian mitochondrial rRNA it became possible to summarize an evolutionary history, functional role of mt-rRNA modification enzymes and an interplay of the mt-rRNA modification and mitoribosome assembly process, which is a goal of this review.
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Affiliation(s)
- Ivan Laptev
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119992 Moscow, Russia; (I.L.); (O.D.)
| | - Olga Dontsova
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119992 Moscow, Russia; (I.L.); (O.D.)
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Skolkovo, 143028 Moscow Region, Russia
- Department of Chemistry, Lomonosov Moscow State University, 119992 Moscow, Russia
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, 117997 Moscow, Russia
| | - Petr Sergiev
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119992 Moscow, Russia; (I.L.); (O.D.)
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Skolkovo, 143028 Moscow Region, Russia
- Department of Chemistry, Lomonosov Moscow State University, 119992 Moscow, Russia
- Institute of Functional Genomics, Lomonosov Moscow State University, 119992 Moscow, Russia
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10
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Gupta A, Shrivastava D, Shakya AK, Gupta K, Pratap JV, Habib S. PfKsgA1 functions as a transcription initiation factor and interacts with the N-terminal region of the mitochondrial RNA polymerase of Plasmodium falciparum. Int J Parasitol 2020; 51:23-37. [PMID: 32896572 DOI: 10.1016/j.ijpara.2020.07.010] [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: 05/05/2020] [Revised: 07/13/2020] [Accepted: 07/16/2020] [Indexed: 10/23/2022]
Abstract
The small mitochondrial genome (mtDNA) of the malaria parasite is known to transcribe its genes polycistonically, although promoter element(s) have not yet been identified. An unusually large Plasmodium falciparum candidate mitochondrial phage-like RNA polymerase (PfmtRNAP) with an extended N-terminal region is encoded by the parasite nuclear genome. Using specific antibodies against the enzyme, we established that PfmtRNAP was targeted exclusively to the mitochondrion and interacted with mtDNA. Phylogenetic analysis showed that it is part of a separate apicomplexan clade. A search for PfmtRNAP-associated transcription initiation factors using sequence homology and in silico protein-protein interaction network analysis identified PfKsgA1. PfKsgA1 is a dual cytosol- and mitochondrion-targeted protein that functions as a small subunit rRNA dimethyltransferase in ribosome biogenesis. Chromatin immunoprecipitation showed that PfKsgA1 interacts with mtDNA, and in vivo crosslinking and pull-down experiments confirmed PfmtRNAP-PfKsgA1 interaction. The ability of PfKsgA1 to serve as a transcription initiation factor was demonstrated by complementation of yeast mitochondrial transcription factor Mtf1 function in Rpo41-driven in vitro transcription. Pull-down experiments using PfKsgA1 and PfmtRNAP domains indicated that the N-terminal region of PfmtRNAP interacts primarily with the PfKsgA1 C-terminal domain with some contacts being made with the linker and N-terminal domain of PfKsgA1. In the absence of full-length recombinant PfmtRNAP, solution structures of yeast mitochondrial RNA polymerase Rpo41 complexes with Mtf1 or PfKsgA1 were determined by small-angle X-ray scattering. Protein interaction interfaces thus identified matched with those reported earlier for Rpo41-Mtf1 interaction and overlaid with the PfmtRNAP-interfacing region identified experimentally for PfKsgA1. Our results indicate that in addition to a role in mitochondrial ribosome biogenesis, PfKsgA1 has an independent function as a transcription initiation factor for PfmtRNAP.
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Affiliation(s)
- Ankit Gupta
- Division of Molecular and Structural Biology, CSIR-Central Drug Research Institute, Lucknow 226031, India
| | - Deepti Shrivastava
- Division of Molecular and Structural Biology, CSIR-Central Drug Research Institute, Lucknow 226031, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Anil Kumar Shakya
- Division of Molecular and Structural Biology, CSIR-Central Drug Research Institute, Lucknow 226031, India
| | - Kirti Gupta
- Division of Molecular and Structural Biology, CSIR-Central Drug Research Institute, Lucknow 226031, India
| | - J V Pratap
- Division of Molecular and Structural Biology, CSIR-Central Drug Research Institute, Lucknow 226031, India
| | - Saman Habib
- Division of Molecular and Structural Biology, CSIR-Central Drug Research Institute, Lucknow 226031, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India.
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11
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Gupta K, Gupta A, Habib S. Characterization of a Plasmodium falciparum rRNA methyltransferase. Mol Biochem Parasitol 2018; 223:13-18. [DOI: 10.1016/j.molbiopara.2018.06.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Revised: 06/12/2018] [Accepted: 06/12/2018] [Indexed: 12/29/2022]
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12
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Ferreira N, Rackham O, Filipovska A. Regulation of a minimal transcriptome by repeat domain proteins. Semin Cell Dev Biol 2018; 76:132-141. [DOI: 10.1016/j.semcdb.2017.08.037] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2017] [Revised: 08/15/2017] [Accepted: 08/18/2017] [Indexed: 01/19/2023]
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13
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Oran AR, Adams CM, Zhang XY, Gennaro VJ, Pfeiffer HK, Mellert HS, Seidel HE, Mascioli K, Kaplan J, Gaballa MR, Shen C, Rigoutsos I, King MP, Cotney JL, Arnold JJ, Sharma SD, Martinez-Outschoorn UE, Vakoc CR, Chodosh LA, Thompson JE, Bradner JE, Cameron CE, Shadel GS, Eischen CM, McMahon SB. Multi-focal control of mitochondrial gene expression by oncogenic MYC provides potential therapeutic targets in cancer. Oncotarget 2018; 7:72395-72414. [PMID: 27590350 PMCID: PMC5340124 DOI: 10.18632/oncotarget.11718] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2016] [Accepted: 08/25/2016] [Indexed: 12/14/2022] Open
Abstract
Despite ubiquitous activation in human cancer, essential downstream effector pathways of the MYC transcription factor have been difficult to define and target. Using a structure/function-based approach, we identified the mitochondrial RNA polymerase (POLRMT) locus as a critical downstream target of MYC. The multifunctional POLRMT enzyme controls mitochondrial gene expression, a process required both for mitochondrial function and mitochondrial biogenesis. We further demonstrate that inhibition of this newly defined MYC effector pathway causes robust and selective tumor cell apoptosis, via an acute, checkpoint-like mechanism linked to aberrant electron transport chain complex assembly and mitochondrial reactive oxygen species (ROS) production. Fortuitously, MYC-dependent tumor cell death can be induced by inhibiting the mitochondrial gene expression pathway using a variety of strategies, including treatment with FDA-approved antibiotics. In vivo studies using a mouse model of Burkitt's Lymphoma provide pre-clinical evidence that these antibiotics can successfully block progression of MYC-dependent tumors.
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Affiliation(s)
- Amanda R Oran
- Department of Cancer Biology, Thomas Jefferson University, Philadelphia, PA, USA
| | - Clare M Adams
- Department of Cancer Biology, Thomas Jefferson University, Philadelphia, PA, USA
| | - Xiao-Yong Zhang
- Department of Cancer Biology, Thomas Jefferson University, Philadelphia, PA, USA
| | - Victoria J Gennaro
- Department of Cancer Biology, Thomas Jefferson University, Philadelphia, PA, USA
| | - Harla K Pfeiffer
- Department of Cancer Biology, Thomas Jefferson University, Philadelphia, PA, USA
| | - Hestia S Mellert
- Biomedical Graduate Studies, University of Pennsylvania, Philadelphia, PA, USA
| | - Hans E Seidel
- Department of Cancer Biology and Abramson Family Cancer Research Institute, University of Pennsylvania School of Medicine, Philadelphia, PA, USA
| | - Kirsten Mascioli
- Department of Cancer Biology, Thomas Jefferson University, Philadelphia, PA, USA
| | - Jordan Kaplan
- Department of Cancer Biology, Thomas Jefferson University, Philadelphia, PA, USA
| | - Mahmoud R Gaballa
- Department of Cancer Biology, Thomas Jefferson University, Philadelphia, PA, USA
| | - Chen Shen
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA.,Molecular and Cellular Biology Program, Stony Brook University, Stony Brook, NY, USA
| | - Isidore Rigoutsos
- Department of Cancer Biology, Thomas Jefferson University, Philadelphia, PA, USA
| | - Michael P King
- Department of Biochemistry, Thomas Jefferson University, Philadelphia, PA, USA
| | - Justin L Cotney
- Genetics and Genome Sciences, University of Connecticut Health, Farmington, CT, USA
| | - Jamie J Arnold
- Department of Biochemistry & Molecular Biology, The Pennsylvania State University, University Park, PA, USA
| | - Suresh D Sharma
- Department of Biochemistry & Molecular Biology, The Pennsylvania State University, University Park, PA, USA
| | | | | | - Lewis A Chodosh
- Department of Cancer Biology and Abramson Family Cancer Research Institute, University of Pennsylvania School of Medicine, Philadelphia, PA, USA
| | - James E Thompson
- Leukemia Service, Department of Medicine, Roswell Park Cancer Institute, Buffalo, NY, USA
| | - James E Bradner
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA,USA
| | - Craig E Cameron
- Department of Biochemistry & Molecular Biology, The Pennsylvania State University, University Park, PA, USA
| | - Gerald S Shadel
- Department of Pathology, Yale School of Medicine, New Haven, CT, USA.,Department of Genetics, Yale School of Medicine, New Haven, CT, USA
| | - Christine M Eischen
- Department of Cancer Biology, Thomas Jefferson University, Philadelphia, PA, USA
| | - Steven B McMahon
- Department of Cancer Biology, Thomas Jefferson University, Philadelphia, PA, USA
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14
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Abstract
Mitochondrial dysfunction underlines a multitude of pathologies; however, studies are scarce that rescue the mitochondria for cellular resuscitation. Exploration into the protective role of mitochondrial transcription factor A (TFAM) and its mitochondrial functions respective to cardiomyocyte death are in need of further investigation. TFAM is a gene regulator that acts to mitigate calcium mishandling and ROS production by wrapping around mitochondrial DNA (mtDNA) complexes. TFAM's regulatory functions over serca2a, NFAT, and Lon protease contribute to cardiomyocyte stability. Calcium- and ROS-dependent proteases, calpains, and matrix metalloproteinases (MMPs) are abundantly found upregulated in the failing heart. TFAM's regulatory role over ROS production and calcium mishandling leads to further investigation into the cardioprotective role of exogenous TFAM. In an effort to restabilize physiological and contractile activity of cardiomyocytes in HF models, we propose that TFAM-packed exosomes (TFAM-PE) will act therapeutically by mitigating mitochondrial dysfunction. Notably, this is the first mention of exosomal delivery of transcription factors in the literature. Here we elucidate the role of TFAM in mitochondrial rescue and focus on its therapeutic potential.
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Affiliation(s)
- George H Kunkel
- Department of Physiology and Biophysics, Health Sciences Centre, 1216, School of Medicine, University of Louisville, 500, South Preston Street, Louisville, KY, 40202, USA
| | - Pankaj Chaturvedi
- Department of Physiology and Biophysics, Health Sciences Centre, 1216, School of Medicine, University of Louisville, 500, South Preston Street, Louisville, KY, 40202, USA.
| | - Suresh C Tyagi
- Department of Physiology and Biophysics, Health Sciences Centre, 1216, School of Medicine, University of Louisville, 500, South Preston Street, Louisville, KY, 40202, USA
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15
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Boot A, Oosting J, van Eendenburg JDH, Kuppen PJK, Morreau H, van Wezel T. Methylation associated transcriptional repression of ELOVL5 in novel colorectal cancer cell lines. PLoS One 2017; 12:e0184900. [PMID: 28931069 PMCID: PMC5607170 DOI: 10.1371/journal.pone.0184900] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2017] [Accepted: 09/03/2017] [Indexed: 01/16/2023] Open
Abstract
Genetic and epigenetic alterations mark colorectal cancer (CRC). Global hypomethylation is observed in nearly all CRC, but a distinct subset of CRC show the CpG Island Methylator Phenotype (CIMP). These tumors show DNA hypermethylation of a specific subset of CpG islands, resulting in transcriptional downregulation of nearby genes. Recently we reported the establishment of novel CRC cell lines derived from primary and metastatic CRC tissues. In this study we describe the DNA methylation profiling of these low passage CRC cell lines. We generated global DNA methylation profiles with Infinium HumanMethylation450 BeadChips and analysed them in conjunction with matching gene expression profiles. Multidimensional scaling of the DNA methylation and gene expression datasets showed that BRAF mutated cell lines form a distinct group. In this group we investigated the 706 loci which we have previously identified to be hypermethylated in BRAF mutant CRC. We validated the significant findings in the The Cancer Genome Atlas colon adenocarcinoma dataset. Our analysis identified ELOVL5, FAM127B, MTERF1, ZNF606 to be subject to transcriptional downregulation through DNA hypermethylation in CRC. We further investigated ELOVL5 with qPCR and immunohistochemical staining, validating our results, but did not find a clear relation between ELOVL5 expression and tumor stage or relapse free survival. ELOVL5, FAM127B, MTERF1, ZNF606 are involved in important cellular processes such as apoptosis, lipogenesis and the downstream transcriptional effect of the MAPK-pathway. We have identified a DNA methylation profile regulating key cellular processes in CRC, resulting in a growth advantage to the tumor cells.
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Affiliation(s)
- Arnoud Boot
- Department of Pathology, Leiden University Medical Center, Leiden, The Netherlands
| | - Jan Oosting
- Department of Pathology, Leiden University Medical Center, Leiden, The Netherlands
| | | | - Peter J. K. Kuppen
- Department of Surgery, Leiden University Medical Center, Leiden, The Netherlands
| | - Hans Morreau
- Department of Pathology, Leiden University Medical Center, Leiden, The Netherlands
| | - Tom van Wezel
- Department of Pathology, Leiden University Medical Center, Leiden, The Netherlands
- * E-mail:
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16
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De Silva D, Poliquin S, Zeng R, Zamudio-Ochoa A, Marrero N, Perez-Martinez X, Fontanesi F, Barrientos A. The DEAD-box helicase Mss116 plays distinct roles in mitochondrial ribogenesis and mRNA-specific translation. Nucleic Acids Res 2017; 45:6628-6643. [PMID: 28520979 PMCID: PMC5499750 DOI: 10.1093/nar/gkx426] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2017] [Revised: 04/27/2017] [Accepted: 05/03/2017] [Indexed: 11/21/2022] Open
Abstract
Members of the DEAD-box family are often multifunctional proteins involved in several RNA transactions. Among them, yeast Saccharomyces cerevisiae Mss116 participates in mitochondrial intron splicing and, under cold stress, also in mitochondrial transcription elongation. Here, we show that Mss116 interacts with the mitoribosome assembly factor Mrh4, is required for efficient mitoribosome biogenesis, and consequently, maintenance of the overall mitochondrial protein synthesis rate. Additionally, Mss116 is required for efficient COX1 mRNA translation initiation and elongation. Mss116 interacts with a COX1 mRNA-specific translational activator, the pentatricopeptide repeat protein Pet309. In the absence of Mss116, Pet309 is virtually absent, and although mitoribosome loading onto COX1 mRNA can occur, activation of COX1 mRNA translation is impaired. Mutations abolishing the helicase activity of Mss116 do not prevent the interaction of Mss116 with Pet309 but also do not allow COX1 mRNA translation. We propose that Pet309 acts as an adaptor protein for Mss116 action on the COX1 mRNA 5΄-UTR to promote efficient Cox1 synthesis. Overall, we conclude that the different functions of Mss116 in the biogenesis and functioning of the mitochondrial translation machinery depend on Mss116 interplay with its protein cofactors.
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Affiliation(s)
- Dasmanthie De Silva
- Department of Biochemistry and Molecular Biology, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Sarah Poliquin
- Department of Biochemistry and Molecular Biology, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Rui Zeng
- Department of Biochemistry and Molecular Biology, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Angelica Zamudio-Ochoa
- Departamento de Genetica Molecular, Instituto de Fisiología Celular, Universidad Nacional Autonoma de Mexico, Mexico City 04510, Mexico
| | - Natalie Marrero
- Department of Neurology, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Xochitl Perez-Martinez
- Departamento de Genetica Molecular, Instituto de Fisiología Celular, Universidad Nacional Autonoma de Mexico, Mexico City 04510, Mexico
| | - Flavia Fontanesi
- Department of Biochemistry and Molecular Biology, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Antoni Barrientos
- Department of Biochemistry and Molecular Biology, University of Miami Miller School of Medicine, Miami, FL 33136, USA
- Department of Neurology, University of Miami Miller School of Medicine, Miami, FL 33136, USA
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17
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Mitochondrial protein interactome elucidated by chemical cross-linking mass spectrometry. Proc Natl Acad Sci U S A 2017; 114:1732-1737. [PMID: 28130547 PMCID: PMC5321032 DOI: 10.1073/pnas.1617220114] [Citation(s) in RCA: 133] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Mitochondrial protein interactions and complexes facilitate mitochondrial function. These complexes range from simple dimers to the respirasome supercomplex consisting of oxidative phosphorylation complexes I, III, and IV. To improve understanding of mitochondrial function, we used chemical cross-linking mass spectrometry to identify 2,427 cross-linked peptide pairs from 327 mitochondrial proteins in whole, respiring murine mitochondria. In situ interactions were observed in proteins throughout the electron transport chain membrane complexes, ATP synthase, and the mitochondrial contact site and cristae organizing system (MICOS) complex. Cross-linked sites showed excellent agreement with empirical protein structures and delivered complementary constraints for in silico protein docking. These data established direct physical evidence of the assembly of the complex I-III respirasome and enabled prediction of in situ interfacial regions of the complexes. Finally, we established a database and tools to harness the cross-linked interactions we observed as molecular probes, allowing quantification of conformation-dependent protein interfaces and dynamic protein complex assembly.
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18
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Shokolenko IN, Alexeyev MF. Mitochondrial transcription in mammalian cells. Front Biosci (Landmark Ed) 2017; 22:835-853. [PMID: 27814650 DOI: 10.2741/4520] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
As a consequence of recent discoveries of intimate involvement of mitochondria with key cellular processes, there has been a resurgence of interest in all aspects of mitochondrial biology, including the intricate mechanisms of mitochondrial DNA maintenance and expression. Despite four decades of research, there remains a lot to be learned about the processes that enable transcription of genetic information from mitochondrial DNA to RNA, as well as their regulation. These processes are vitally important, as evidenced by the lethality of inactivating the central components of mitochondrial transcription machinery. Here, we review the current understanding of mitochondrial transcription and its regulation in mammalian cells. We also discuss key theories in the field and highlight controversial subjects and future directions as we see them.
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Affiliation(s)
- Inna N Shokolenko
- University of South Alabama, Patt Capps Covey College of Allied Health Professions, Biomedical Sciences Department, 5721 USA Drive N, HAHN 4021, Mobile, AL 36688-0002, USA
| | - Mikhail F Alexeyev
- Department of Physiology and Cell Biology, University of South Alabama, 5851 USA Dr. North, MSB3074, Mobile, AL 36688, USA,
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19
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Banerjee Mustafi S, Aznar N, Dwivedi SKD, Chakraborty PK, Basak R, Mukherjee P, Ghosh P, Bhattacharya R. Mitochondrial BMI1 maintains bioenergetic homeostasis in cells. FASEB J 2016; 30:4042-4055. [PMID: 27613804 PMCID: PMC5102112 DOI: 10.1096/fj.201600321r] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2016] [Accepted: 08/15/2016] [Indexed: 12/14/2022]
Abstract
The polycomb complex proto-oncogene BMI1 [B lymphoma Mo-MLV insertion region 1 homolog (mouse)] is essential for self-renewal of normal and cancer stem cells. BMI1-null mice show severe defects in growth, development, and survival. Although BMI1 is known to exert its effect in the nucleus via repression of 2 potent cell-cycle regulators that are encoded by the Ink4a/Arf locus, deletion of this locus only partially rescues BMI1-null phenotypes, which is indicative of alternate mechanisms of action of BMI1. Here, we show that an extranuclear pool of BMI1 localizes to inner mitochondrial membrane and directly regulates mitochondrial RNA (mtRNA) homeostasis and bioenergetics. These mitochondrial functions of BMI1 are independent of its previously described nuclear functions because a nuclear localization-defective mutant BMI1 rescued several bioenergetic defects that we observed in BMI1-depleted cells, for example, mitochondrial respiration, cytochrome c oxidase activity, and ATP production. Mechanistically, BMI1 coprecipitated with polynucleotide phosphorylase, a ribonuclease that is responsible for decay of mtRNA transcripts. Loss of BMI1 enhanced ribonuclease activity of polynucleotide phosphorylase and reduced mtRNA stability. These findings not only establish a novel extranuclear role of BMI1 in the regulation of mitochondrial bioenergetics, but also provide new mechanistic insights into the role of this proto-oncogene in stem cell differentiation, neuronal aging, and cancer.-Banerjee Mustafi, S., Aznar, N., Dwivedi, S. K. D., Chakraborty, P. K., Basak, R., Mukherjee, P., Ghosh, P., Bhattacharya, R. Mitochondrial BMI1 maintains bioenergetic homeostasis in cells.
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Affiliation(s)
- Soumyajit Banerjee Mustafi
- Department of Obstetrics and Gynecology, Stephenson Cancer Center, University of Oklahoma Health Science Center, Oklahoma City, Oklahoma, USA
| | - Nicolas Aznar
- Department of Medicine, University of California, San Diego, La Jolla, California, USA
| | - Shailendra Kumar Dhar Dwivedi
- Department of Obstetrics and Gynecology, Stephenson Cancer Center, University of Oklahoma Health Science Center, Oklahoma City, Oklahoma, USA
| | - Prabir Kumar Chakraborty
- Department of Pathology, Stephenson Cancer Center, University of Oklahoma Health Science Center, Oklahoma City, Oklahoma, USA; and
| | - Rumki Basak
- Department of Obstetrics and Gynecology, Stephenson Cancer Center, University of Oklahoma Health Science Center, Oklahoma City, Oklahoma, USA
| | - Priyabrata Mukherjee
- Department of Pathology, Stephenson Cancer Center, University of Oklahoma Health Science Center, Oklahoma City, Oklahoma, USA; and
| | - Pradipta Ghosh
- Department of Medicine, University of California, San Diego, La Jolla, California, USA
| | - Resham Bhattacharya
- Department of Obstetrics and Gynecology, Stephenson Cancer Center, University of Oklahoma Health Science Center, Oklahoma City, Oklahoma, USA;
- Department of Cell Biology, University of Oklahoma College of Medicine, Oklahoma City, Oklahoma, USA
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20
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Bralha FN, Liyanage SU, Hurren R, Wang X, Son MH, Fung TA, Chingcuanco FB, Tung AYW, Andreazza AC, Psarianos P, Schimmer AD, Salmena L, Laposa RR. Targeting mitochondrial RNA polymerase in acute myeloid leukemia. Oncotarget 2016; 6:37216-28. [PMID: 26484416 PMCID: PMC4741925 DOI: 10.18632/oncotarget.6129] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2015] [Accepted: 09/25/2015] [Indexed: 01/29/2023] Open
Abstract
Acute myeloid leukemia (AML) cells have high oxidative phosphorylation and mitochondrial mass and low respiratory chain spare reserve capacity. We reasoned that targeting the mitochondrial RNA polymerase (POLRMT), which indirectly controls oxidative phosphorylation, represents a therapeutic strategy for AML. POLRMT-knockdown OCI-AML2 cells exhibited decreased mitochondrial gene expression, decreased levels of assembled complex I, decreased levels of mitochondrially-encoded Cox-II and decreased oxidative phosphorylation. POLRMT-knockdown cells exhibited an increase in complex II of the electron transport chain, a complex comprised entirely of subunits encoded by nuclear genes, and POLRMT-knockdown cells were resistant to a complex II inhibitor theonyltrifluoroacetone. POLRMT-knockdown cells showed a prominent increase in cell death. Treatment of OCI-AML2 cells with 10-50 µM 2-C-methyladenosine (2-CM), a chain terminator of mitochondrial transcription, reduced mitochondrial gene expression and oxidative phosphorylation, and increased cell death in a concentration-dependent manner. Treatment of normal human hematopoietic cells with 2-CM at concentrations of up to 100 µMdid not alter clonogenic growth, suggesting a therapeutic window. In an OCI-AML2 xenograft model, treatment with 2-CM (70 mg/kg, i.p., daily) decreased the volume and mass of tumours to half that of vehicle controls. 2-CM did not cause toxicity to major organs. Overall, our results in a preclinical model contribute to the functional validation of the utility of targeting the mitochondrial RNA polymerase as a therapeutic strategy for AML.
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Affiliation(s)
- Fernando N Bralha
- Department of Pharmacology and Toxicology, Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Sanduni U Liyanage
- Princess Margaret Cancer Centre, University Health Network, Toronto, Canada
| | - Rose Hurren
- Princess Margaret Cancer Centre, University Health Network, Toronto, Canada
| | - Xiaoming Wang
- Princess Margaret Cancer Centre, University Health Network, Toronto, Canada
| | - Meong Hi Son
- Department of Pharmacology and Toxicology, Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada.,Princess Margaret Cancer Centre, University Health Network, Toronto, Canada
| | - Thomas A Fung
- Department of Pharmacology and Toxicology, Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Francine B Chingcuanco
- Department of Pharmacology and Toxicology, Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Aveline Y W Tung
- Department of Pharmacology and Toxicology, Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Ana C Andreazza
- Department of Pharmacology and Toxicology, Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada.,Department of Psychiatry, Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada.,Centre for Addiction and Mental Health, Toronto, Ontario, Canada
| | - Pamela Psarianos
- Department of Pharmacology and Toxicology, Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Aaron D Schimmer
- Princess Margaret Cancer Centre, University Health Network, Toronto, Canada
| | - Leonardo Salmena
- Department of Pharmacology and Toxicology, Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada.,Princess Margaret Cancer Centre, University Health Network, Toronto, Canada
| | - Rebecca R Laposa
- Department of Pharmacology and Toxicology, Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
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21
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Nouws J, Goswami AV, Bestwick M, McCann BJ, Surovtseva YV, Shadel GS. Mitochondrial Ribosomal Protein L12 Is Required for POLRMT Stability and Exists as Two Forms Generated by Alternative Proteolysis during Import. J Biol Chem 2015; 291:989-97. [PMID: 26586915 DOI: 10.1074/jbc.m115.689299] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2015] [Indexed: 01/21/2023] Open
Abstract
To translate the 13 mtDNA-encoded mRNAs involved in oxidative phosphorylation (OXPHOS), mammalian mitochondria contain a dedicated set of ribosomes comprising rRNAs encoded by the mitochondrial genome and mitochondrial ribosomal proteins (MRPs) that are encoded by nuclear genes and imported into the matrix. In addition to their role in the ribosome, several MRPs have auxiliary functions or have been implicated in other cellular processes like cell cycle regulation and apoptosis. For example, we have shown that human MRPL12 binds and activates mitochondrial RNA polymerase (POLRMT), and hence has distinct functions in the ribosome and mtDNA transcription. Here we provide concrete evidence that there are two mature forms of mammalian MRPL12 that are generated by a two-step cleavage during import, involving efficient cleavage by mitochondrial processing protease and a second inefficient or regulated cleavage by mitochondrial intermediate protease. We also show that knock-down of MRPL12 by RNAi results in instability of POLRMT, but not other primary mitochondrial transcription components, and a corresponding decrease in mitochondrial transcription rates. Knock-down of MRPL10, the binding partner of MRPL12 in the ribosome, results in selective degradation of the mature long form of MRPL12, but has no effect on POLRMT. We propose that the two forms of MRPL12 are involved in homeostatic regulation of mitochondrial transcription and ribosome biogenesis that likely contribute to cell cycle, growth regulation, and longevity pathways to which MRPL12 has been linked.
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Affiliation(s)
| | | | - Megan Bestwick
- From the Departments of Pathology and the Department of Chemistry, Linfield College, McMinnville, Oregon 97128, and
| | - Beverly Jo McCann
- From the Departments of Pathology and the Department of Biology, Technische Universität Darmstadt, 64287 Darmstadt, Germany
| | | | - Gerald S Shadel
- From the Departments of Pathology and Genetics, Yale School of Medicine, New Haven, Connecticut 06520-8023,
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22
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McKay SE, Yan W, Nouws J, Thormann MJ, Raimundo N, Khan A, Santos-Sacchi J, Song L, Shadel GS. Auditory Pathology in a Transgenic mtTFB1 Mouse Model of Mitochondrial Deafness. THE AMERICAN JOURNAL OF PATHOLOGY 2015; 185:3132-40. [PMID: 26552864 DOI: 10.1016/j.ajpath.2015.08.014] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2014] [Revised: 07/31/2015] [Accepted: 08/14/2015] [Indexed: 12/13/2022]
Abstract
The A1555G mutation in the 12S rRNA gene of human mitochondrial DNA causes maternally inherited, nonsyndromic deafness, an extreme case of tissue-specific mitochondrial pathology. A transgenic mouse strain that robustly overexpresses the mitochondrial 12S ribosomal RNA methyltransferase TFB1M (Tg-mtTFB1 mice) exhibits progressive hearing loss that we proposed models aspects of A1555G-related pathology in humans. Although our previous studies of Tg-mtTFB1 mice implicated apoptosis in the spiral ganglion and stria vascularis because of mitochondrial reactive oxygen species-mediated activation of AMP kinase (AMPK) and the nuclear transcription factor E2F1, detailed auditory pathology was not delineated. Herein, we show that Tg-mtTFB1 mice have reduced endocochlear potential, indicative of significant stria vascularis dysfunction, but without obvious signs of strial atrophy. We also observed decreased auditory brainstem response peak 1 amplitude and prolonged wave I latency, consistent with apoptosis of spiral ganglion neurons. Although no major loss of hair cells was observed, there was a mild impairment of voltage-dependent electromotility of outer hair cells. On the basis of these results, we propose that these events conspire to produce the progressive hearing loss phenotype in Tg-mtTFB1 mice. Finally, genetically reducing AMPK α1 rescues hearing loss in Tg-mtTFB1 mice, confirming that aberrant up-regulation of AMPK signaling promotes the observed auditory pathology. The relevance of these findings to human A1555G patients and the potential therapeutic value of reducing AMPK activity are discussed.
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Affiliation(s)
- Sharen E McKay
- Department of Pathology, Yale School of Medicine, New Haven, Connecticut; Department of Psychology, University of Bridgeport, Bridgeport, Connecticut
| | - Wayne Yan
- Department of Surgery, Yale School of Medicine, New Haven, Connecticut
| | - Jessica Nouws
- Department of Pathology, Yale School of Medicine, New Haven, Connecticut
| | | | - Nuno Raimundo
- Institute of Cell Biology, University Medical Center Göettingen, Göttingen, Germany
| | - Abdul Khan
- Department of Pathology, Yale School of Medicine, New Haven, Connecticut
| | - Joseph Santos-Sacchi
- Department of Surgery, Yale School of Medicine, New Haven, Connecticut; Department of Cellular and Molecular Physiology, Yale School of Medicine, New Haven, Connecticut; Department of Neurobiology, Yale School of Medicine, New Haven, Connecticut.
| | - Lei Song
- Department of Surgery, Yale School of Medicine, New Haven, Connecticut.
| | - Gerald S Shadel
- Department of Pathology, Yale School of Medicine, New Haven, Connecticut; Department of Genetics, Yale School of Medicine, New Haven, Connecticut.
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23
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Brown TA, Tkachuk AN, Clayton DA. Mitochondrial Transcription Factor A (TFAM) Binds to RNA Containing 4-Way Junctions and Mitochondrial tRNA. PLoS One 2015; 10:e0142436. [PMID: 26545237 PMCID: PMC4636309 DOI: 10.1371/journal.pone.0142436] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2015] [Accepted: 10/21/2015] [Indexed: 11/26/2022] Open
Abstract
Mitochondrial DNA (mtDNA) is maintained within nucleoprotein complexes known as nucleoids. These structures are highly condensed by the DNA packaging protein, mitochondrial Transcription Factor A (TFAM). Nucleoids also include RNA, RNA:DNA hybrids, and are associated with proteins involved with RNA processing and mitochondrial ribosome biogenesis. Here we characterize the ability of TFAM to bind various RNA containing substrates in order to determine their role in TFAM distribution and function within the nucleoid. We find that TFAM binds to RNA-containing 4-way junctions but does not bind appreciably to RNA hairpins, internal loops, or linear RNA:DNA hybrids. Therefore the RNA within nucleoids largely excludes TFAM, and its distribution is not grossly altered with removal of RNA. Within the cell, TFAM binds to mitochondrial tRNAs, consistent with our RNA 4-way junction data. Kinetic binding assays and RNase-insensitive TFAM distribution indicate that DNA remains the preferred substrate within the nucleoid. However, TFAM binds to tRNA with nanomolar affinity and these complexes are not rare. TFAM-immunoprecipitated tRNAs have processed ends, suggesting that binding is not specific to RNA precursors. The amount of each immunoprecipitated tRNA is not well correlated with tRNA celluar abundance, indicating unequal TFAM binding preferences. TFAM-mt-tRNA interaction suggests potentially new functions for this protein.
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Affiliation(s)
- Timothy A. Brown
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia, United States of America
- * E-mail:
| | - Ariana N. Tkachuk
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia, United States of America
| | - David A. Clayton
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia, United States of America
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24
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van der Lee R, Szklarczyk R, Smeitink J, Smeets HJM, Huynen MA, Vogel R. Transcriptome analysis of complex I-deficient patients reveals distinct expression programs for subunits and assembly factors of the oxidative phosphorylation system. BMC Genomics 2015; 16:691. [PMID: 26369791 PMCID: PMC4570683 DOI: 10.1186/s12864-015-1883-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2015] [Accepted: 08/27/2015] [Indexed: 12/17/2022] Open
Abstract
Background Transcriptional control of mitochondrial metabolism is essential for cellular function. A better understanding of this process will aid the elucidation of mitochondrial disorders, in particular of the many genetically unsolved cases of oxidative phosphorylation (OXPHOS) deficiency. Yet, to date only few studies have investigated nuclear gene regulation in the context of OXPHOS deficiency. In this study we performed RNA sequencing of two control and two complex I-deficient patient cell lines cultured in the presence of compounds that perturb mitochondrial metabolism: chloramphenicol, AICAR, or resveratrol. We combined this with a comprehensive analysis of mitochondrial and nuclear gene expression patterns, co-expression calculations and transcription factor binding sites. Results Our analyses show that subsets of mitochondrial OXPHOS genes respond opposingly to chloramphenicol and AICAR, whereas the response of nuclear OXPHOS genes is less consistent between cell lines and treatments. Across all samples nuclear OXPHOS genes have a significantly higher co-expression with each other than with other genes, including those encoding mitochondrial proteins. We found no evidence for complex-specific mRNA expression regulation: subunits of different OXPHOS complexes are similarly (co-)expressed and regulated by a common set of transcription factors. However, we did observe significant differences between the expression of nuclear genes for OXPHOS subunits versus assembly factors, suggesting divergent transcription programs. Furthermore, complex I co-expression calculations identified 684 genes with a likely role in OXPHOS biogenesis and function. Analysis of evolutionarily conserved transcription factor binding sites in the promoters of these genes revealed almost all known OXPHOS regulators (including GABP, NRF1/2, SP1, YY1, E-box factors) and a set of novel candidates (ELK1, KLF7, SP4, EHF, ZNF143, and TEL2). Conclusions OXPHOS genes share an expression program distinct from other genes encoding mitochondrial proteins, indicative of targeted nuclear regulation of a mitochondrial sub-process. Within the subset of OXPHOS genes we established a difference in expression between mitochondrial and nuclear genes, and between nuclear genes encoding subunits and assembly factors. Most transcription regulators of genes that co-express with complex I are well-established factors for OXPHOS biogenesis. For the remaining six factors we here suggest for the first time a link with transcription regulation in OXPHOS deficiency. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1883-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Robin van der Lee
- Centre for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, Radboud university medical center, PO BOX 9101, 6500 HB, Nijmegen, The Netherlands.
| | - Radek Szklarczyk
- Centre for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, Radboud university medical center, PO BOX 9101, 6500 HB, Nijmegen, The Netherlands. .,Department of Clinical Genetics, Unit Clinical Genomics, Maastricht University Medical Centre, 6200 MD, Maastricht, The Netherlands.
| | - Jan Smeitink
- Nijmegen Center for Mitochondrial Disorders, Department of Pediatrics, Radboud Institute for Molecular Life Sciences, Radboud university medical center, PO BOX 9101, 6500 HB, Nijmegen, The Netherlands.
| | - Hubert J M Smeets
- Unit Clinical Genomics, Department of Genetics and Cell Biology, School for Growth and Development and for Cardiovascular Research, Maastricht University Medical Centre, Maastricht, The Netherlands.
| | - Martijn A Huynen
- Centre for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, Radboud university medical center, PO BOX 9101, 6500 HB, Nijmegen, The Netherlands.
| | - Rutger Vogel
- Nijmegen Center for Mitochondrial Disorders, Department of Pediatrics, Radboud Institute for Molecular Life Sciences, Radboud university medical center, PO BOX 9101, 6500 HB, Nijmegen, The Netherlands.
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25
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Moustafa IM, Uchida A, Wang Y, Yennawar N, Cameron CE. Structural models of mammalian mitochondrial transcription factor B2. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2015; 1849:987-1002. [PMID: 26066983 DOI: 10.1016/j.bbagrm.2015.05.010] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2015] [Revised: 05/22/2015] [Accepted: 05/25/2015] [Indexed: 11/26/2022]
Abstract
Mammalian mitochondrial DNA (mtDNA) encodes 13 core proteins of oxidative phosphorylation, 12S and 16S ribosomal RNAs, and 22 transfer RNAs. Mutations and deletions of mtDNA and/or nuclear genes encoding mitochondrial proteins have been implicated in a wide range of diseases. Thus, cell survival and health of the organism require some steady-state level of the mitochondrial genome and its expression. In mammalian systems, the mitochondrial transcription factor B2 (mtTFB2 or TFB2M) is indispensable for transcription initiation. TFB2M along with two other proteins, mitochondrial RNA polymerase (mtRNAP or POLRMT) and mitochondrial transcription factor A (mtTFA or TFAM), are key components of the core mitochondrial transcription apparatus. Structural information for POLRMT and TFAM from humans is available; however, there is no available structure for TFB2M. In the present study, three-dimensional structure of TFB2M from humans was modeled using a combination of homology modeling and small-angle X-ray scattering (SAXS). The TFB2M structural model adds substantively to our understanding of TFB2M function. An explanation for the low or absent RNA methyltransferase activity is provided. A putative nucleic acid-binding site is revealed. The amino and carboxy termini, while likely lacking defined secondary structure, appear to adopt compact, globular conformations, thus "capping" the ends of the protein. Finally, sites of interaction of TFB2M with other factors, protein and/or nucleic acid, are suggested by the identification of species-specific clusters on the surface of the protein.
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Affiliation(s)
- Ibrahim M Moustafa
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA.
| | - Akira Uchida
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA
| | - Yao Wang
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA
| | - Neela Yennawar
- Huck Institutes of Life Sciences, Pennsylvania State University, University Park, PA 16802, USA
| | - Craig E Cameron
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA.
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26
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Lightowlers RN, Rozanska A, Chrzanowska-Lightowlers ZM. Mitochondrial protein synthesis: figuring the fundamentals, complexities and complications, of mammalian mitochondrial translation. FEBS Lett 2014; 588:2496-503. [PMID: 24911204 PMCID: PMC4099522 DOI: 10.1016/j.febslet.2014.05.054] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2014] [Revised: 05/28/2014] [Accepted: 05/29/2014] [Indexed: 12/28/2022]
Abstract
Mitochondrial protein synthesis is essential for all mammals, being responsible for providing key components of the oxidative phosphorylation complexes. Although only thirteen different polypeptides are made, the molecular details of this deceptively simple process remain incomplete. Central to this process is a non-canonical ribosome, the mitoribosome, which has evolved to address its unique mandate. In this review, we integrate the current understanding of the molecular aspects of mitochondrial translation with recent advances in structural biology. We identify numerous key questions that we will need to answer if we are to increase our knowledge of the molecular mechanisms underlying mitochondrial protein synthesis.
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Affiliation(s)
- Robert N Lightowlers
- The Wellcome Trust Centre for Mitochondrial Research, Institute for Cell and Molecular Biosciences, Newcastle University, The Medical School, Framlington Place, Newcastle upon Tyne NE2 4HH, UK.
| | - Agata Rozanska
- The Wellcome Trust Centre for Mitochondrial Research, Institute for Cell and Molecular Biosciences, Newcastle University, The Medical School, Framlington Place, Newcastle upon Tyne NE2 4HH, UK
| | - Zofia M Chrzanowska-Lightowlers
- The Wellcome Trust Centre for Mitochondrial Research, Institute of Neuroscience, Newcastle University, The Medical School, Framlington Place, Newcastle upon Tyne NE2 4HH, UK.
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27
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Kuzmenko AV, Levitskii SA, Vinogradova EN, Atkinson GC, Hauryliuk V, Zenkin N, Kamenski PA. Protein biosynthesis in mitochondria. BIOCHEMISTRY (MOSCOW) 2014; 78:855-66. [PMID: 24228873 DOI: 10.1134/s0006297913080014] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Translation, that is biosynthesis of polypeptides in accordance with information encoded in the genome, is one of the most important processes in the living cell, and it has been in the spotlight of international research for many years. The mechanisms of protein biosynthesis in bacteria and in the eukaryotic cytoplasm are now understood in great detail. However, significantly less is known about translation in eukaryotic mitochondria, which is characterized by a number of unusual features. In this review, we summarize current knowledge about mitochondrial translation in different organisms while paying special attention to the aspects of this process that differ from cytoplasmic protein biosynthesis.
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Affiliation(s)
- A V Kuzmenko
- Department of Molecular Biology, Faculty of Biology, Lomonosov Moscow State University, Moscow, 119991, Russia.
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28
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De Silva D, Fontanesi F, Barrientos A. The DEAD box protein Mrh4 functions in the assembly of the mitochondrial large ribosomal subunit. Cell Metab 2013; 18:712-25. [PMID: 24206665 PMCID: PMC3857544 DOI: 10.1016/j.cmet.2013.10.007] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/20/2013] [Revised: 09/04/2013] [Accepted: 10/08/2013] [Indexed: 12/24/2022]
Abstract
Proteins in a cell are universally synthesized by ribosomes. Mitochondria contain their own ribosomes, which specialize in the synthesis of a handful of proteins required for oxidative phosphorylation. The pathway of mitoribosomal biogenesis and factors involved are poorly characterized. An example is the DEAD box proteins, widely known to participate in the biogenesis of bacterial and cytoplasmic eukaryotic ribosomes as either RNA helicases or RNA chaperones, whose mitochondrial counterparts remain completely unknown. Here, we have identified the Saccharomyces cerevisiae mitochondrial DEAD box protein Mrh4 as essential for large mitoribosome subunit biogenesis. Mrh4 interacts with the 21S rRNA, mitoribosome subassemblies, and fully assembled mitoribosomes. In the absence of Mrh4, the 21S rRNA is matured and forms part of a large on-pathway assembly intermediate missing proteins Mrpl16 and Mrpl39. We conclude that Mrh4 plays an essential role during the late stages of mitoribosome assembly by promoting remodeling of the 21S rRNA-protein interactions.
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Affiliation(s)
- Dasmanthie De Silva
- Department of Biochemistry and Molecular Biology, University of Miami Miller School of Medicine, Miami, FL-33136 (USA)
| | - Flavia Fontanesi
- Department of Biochemistry and Molecular Biology, University of Miami Miller School of Medicine, Miami, FL-33136 (USA)
| | - Antoni Barrientos
- Department of Biochemistry and Molecular Biology, University of Miami Miller School of Medicine, Miami, FL-33136 (USA)
- Department of Neurology University of Miami Miller School of Medicine, Miami, FL-33136 (USA)
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29
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Lee KW, Okot-Kotber C, LaComb JF, Bogenhagen DF. Mitochondrial ribosomal RNA (rRNA) methyltransferase family members are positioned to modify nascent rRNA in foci near the mitochondrial DNA nucleoid. J Biol Chem 2013; 288:31386-99. [PMID: 24036117 DOI: 10.1074/jbc.m113.515692] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
We have identified RNMTL1, MRM1, and MRM2 (FtsJ2) as members of the RNA methyltransferase family that may be responsible for the three known 2'-O-ribose modifications of the 16 S rRNA core of the large mitochondrial ribosome subunit. These proteins are confined to foci located in the vicinity of mtDNA nucleoids. They show distinct patterns of association with mtDNA nucleoids and/or mitochondrial ribosomes in cell fractionation studies. We focused on the role of the least studied protein in this set, RNMTL1, to show that this protein interacts with the large ribosomal subunit as well as with a series of non-ribosomal proteins that may be involved in coupling of the rate of rRNA transcription and ribosome assembly in mitochondria. siRNA-directed silencing of RNMTL1 resulted in a significant inhibition of translation on mitochondrial ribosomes. Our results are consistent with a role for RNMTL1 in methylation of G(1370) of human 16 S rRNA.
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Affiliation(s)
- Ken-Wing Lee
- From the Department of Pharmacological Sciences, Stony Brook University, Stony Brook, New York 11794-8651
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30
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Manna S, Le P, Barth C. A unique mitochondrial transcription factor B protein in Dictyostelium discoideum. PLoS One 2013; 8:e70614. [PMID: 23923009 PMCID: PMC3724811 DOI: 10.1371/journal.pone.0070614] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2013] [Accepted: 06/20/2013] [Indexed: 11/19/2022] Open
Abstract
Unlike their bacteriophage homologs, mitochondrial RNA polymerases require the assistance of transcription factors in order to transcribe mitochondrial DNA efficiently. The transcription factor A family has been shown to be important for transcription of the human mitochondrial DNA, with some of its regulatory activity located in its extended C-terminal tail. The mitochondrial transcription factor B family often has functions not only in transcription, but also in mitochondrial rRNA modification, a hallmark of its α-proteobacterial origin. We have identified and characterised a mitochondrial transcription factor B homolog in the soil dwelling cellular slime mould Dictyostelium discoideum, an organism widely established as a model for studying eukaryotic cell biology. Using in bacterio functional assays, we demonstrate that the mitochondrial transcription factor B homolog not only functions as a mitochondrial transcription factor, but that it also has a role in rRNA methylation. Additionally, we show that the transcriptional activation properties of the D. discoideum protein are located in its extended C-terminal tail, a feature not seen before in the mitochondrial transcription factor B family, but reminiscent of the human mitochondrial transcription factor A. This report contributes to our current understanding of the complexities of mitochondrial transcription, and its evolution in eukaryotes.
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Affiliation(s)
- Sam Manna
- Department of Microbiology, La Trobe University, Melbourne, Victoria, Australia
| | - Phuong Le
- Tokyo Metropolitan University, Department of Biological Science, Tokyo, Japan
| | - Christian Barth
- Department of Microbiology, La Trobe University, Melbourne, Victoria, Australia
- * E-mail:
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31
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Guja KE, Venkataraman K, Yakubovskaya E, Shi H, Mejia E, Hambardjieva E, Karzai AW, Garcia-Diaz M. Structural basis for S-adenosylmethionine binding and methyltransferase activity by mitochondrial transcription factor B1. Nucleic Acids Res 2013; 41:7947-59. [PMID: 23804760 PMCID: PMC3763538 DOI: 10.1093/nar/gkt547] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Eukaryotic transcription factor B (TFB) proteins are homologous to KsgA/Dim1 ribosomal RNA (rRNA) methyltransferases. The mammalian TFB1, mitochondrial (TFB1M) factor is an essential protein necessary for mitochondrial gene expression. TFB1M mediates an rRNA modification in the small ribosomal subunit and thus plays a role analogous to KsgA/Dim1 proteins. This modification has been linked to mitochondrial dysfunctions leading to maternally inherited deafness, aminoglycoside sensitivity and diabetes. Here, we present the first structural characterization of the mammalian TFB1 factor. We have solved two X-ray crystallographic structures of TFB1M with (2.1 Å) and without (2.0 Å) its cofactor S-adenosyl-L-methionine. These structures reveal that TFB1M shares a conserved methyltransferase core with other KsgA/Dim1 methyltransferases and shed light on the structural basis of S-adenosyl-L-methionine binding and methyltransferase activity. Together with mutagenesis studies, these data suggest a model for substrate binding and provide insight into the mechanism of methyl transfer, clarifying the role of this factor in an essential process for mitochondrial function.
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Affiliation(s)
- Kip E Guja
- Department of Pharmacological Sciences, Stony Brook University, Stony Brook, NY 11794, USA, Medical Scientist Training Program, Stony Brook University Medical Center, Stony Brook, NY 11794, USA and Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY 11794, USA
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32
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Bestwick ML, Shadel GS. Accessorizing the human mitochondrial transcription machinery. Trends Biochem Sci 2013; 38:283-91. [PMID: 23632312 PMCID: PMC3698603 DOI: 10.1016/j.tibs.2013.03.006] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2013] [Revised: 03/18/2013] [Accepted: 03/26/2013] [Indexed: 12/29/2022]
Abstract
The human genome comprises large chromosomes in the nucleus and mitochondrial DNA (mtDNA) housed in the dynamic mitochondrial network. Human cells contain up to thousands of copies of the double-stranded, circular mtDNA molecule that encodes essential subunits of the oxidative phosphorylation complexes and the rRNAs and tRNAs needed to translate these in the organelle matrix. Transcription of human mtDNA is directed by a single-subunit RNA polymerase, POLRMT, which requires two primary transcription factors, TFB2M (transcription factor B2, mitochondrial) and TFAM (transcription factor A, mitochondrial), to achieve basal regulation of the system. Here, we review recent advances in understanding the structure and function of the primary human transcription machinery and the other factors that facilitate steps in transcription beyond initiation and provide more intricate control over the system.
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Affiliation(s)
- Megan L. Bestwick
- Department of Pathology, Yale University School of Medicine, New Haven, CT 06520
| | - Gerald S. Shadel
- Department of Pathology, Yale University School of Medicine, New Haven, CT 06520
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06520
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33
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Lightowlers RN, Chrzanowska-Lightowlers ZMA. Human pentatricopeptide proteins: only a few and what do they do? RNA Biol 2013; 10:1433-8. [PMID: 23635806 PMCID: PMC3858426 DOI: 10.4161/rna.24770] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
Pentatricopeptide repeat (PPR) proteins constitute a large family of RNA-binding proteins that contain a canonical 35 residue repeat motif. Originally identified in Arabidopsis thaliana, family members are found in protists, fungi, and metazoan but are by far most abundant in plant organelles. Seven examples have been identified in human mitochondria and roles have been tentatively ascribed to each. In this review, we briefly outline each of these PPR proteins and discuss the role each is believed to play in facilitating mitochondrial gene expression.
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Affiliation(s)
- Robert N Lightowlers
- The Wellcome Trust Centre for Mitochondrial Research; Institute for Cell and Molecular Biosciences; Newcastle University; The Medical School; Framlington Place; Newcastle upon Tyne, UK
| | - Zofia M A Chrzanowska-Lightowlers
- The Wellcome Trust Centre for Mitochondrial Research; Institute for Ageing and Health; Newcastle University; The Medical School; Framlington Place; Newcastle upon Tyne, UK
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