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Ma J, Sun L, Gao W, Li Y, Dong D. RNA binding protein: coordinated expression between the nuclear and mitochondrial genomes in tumors. J Transl Med 2023; 21:512. [PMID: 37507746 PMCID: PMC10386658 DOI: 10.1186/s12967-023-04373-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Accepted: 07/18/2023] [Indexed: 07/30/2023] Open
Abstract
Mitochondria are the only organelles regulated by two genomes. The coordinated translation of nuclear DNA (nDNA) and mitochondrial DNA (mtDNA), which together co-encode the subunits of the oxidative phosphorylation (OXPHOS) complex, is critical for determining the metabolic plasticity of tumor cells. RNA-binding protein (RBP) is a post-transcriptional regulatory factor that plays a pivotal role in determining the fate of mRNA. RBP rapidly and effectively reshapes the mitochondrial proteome in response to intracellular and extracellular stressors, mediating the cytoplasmic and mitochondrial translation balance to adjust mitochondrial respiratory capacity and provide energy for tumor cells to adapt to different environmental pressures and growth needs. This review highlights the ability of RBPs to use liquid-liquid phase separation (LLPS) as a platform for translation regulation, integrating nuclear-mitochondrial positive and retrograde signals to coordinate cross-department translation, reshape mitochondrial energy metabolism, and promote the development and survival of tumor cells.
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Affiliation(s)
- Jiaoyan Ma
- Department of Pathophysiology, College of Basic Medical Sciences, Jilin University, Changchun, 130021, China
| | - Liankun Sun
- Department of Pathophysiology, College of Basic Medical Sciences, Jilin University, Changchun, 130021, China
| | - Weinan Gao
- Department of Pathophysiology, College of Basic Medical Sciences, Jilin University, Changchun, 130021, China
| | - Yang Li
- Department of Physiology, College of Basic Medical Sciences, Jilin University, Changchun, 130021, China
| | - Delu Dong
- Department of Pathophysiology, College of Basic Medical Sciences, Jilin University, Changchun, 130021, China.
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2
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Kumar R, Harilal S, Thomas Parambi DG, Kanthlal S, Rahman MA, Alexiou A, Batiha GES, Mathew B. The Role of Mitochondrial Genes in Neurodegenerative Disorders. Curr Neuropharmacol 2022; 20:824-835. [PMID: 34503413 PMCID: PMC9881096 DOI: 10.2174/1570159x19666210908163839] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2021] [Revised: 07/09/2021] [Accepted: 09/07/2021] [Indexed: 11/22/2022] Open
Abstract
Mitochondrial disorders are clinically heterogeneous, resulting from nuclear gene and mitochondrial mutations that disturb the mitochondrial functions and dynamics. There is a lack of evidence linking mtDNA mutations to neurodegenerative disorders, mainly due to the absence of noticeable neuropathological lesions in postmortem samples. This review describes various gene mutations in Alzheimer's disease, Parkinson's disease, amyotrophic lateral sclerosis, multiple sclerosis, and stroke. These abnormalities, including PINK1, Parkin, and SOD1 mutations, seem to reveal mitochondrial dysfunctions due to either mtDNA mutation or deletion, the mechanism of which remains unclear in depth.
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Affiliation(s)
- Rajesh Kumar
- Department of Pharmacy, Kerala University of Health Sciences, Thrissur, Kerala, India
| | - Seetha Harilal
- Department of Pharmacy, Kerala University of Health Sciences, Thrissur, Kerala, India
| | - Della Grace Thomas Parambi
- Department of Pharmaceutical Chemistry, College of Pharmacy, Jouf University, Sakaka, Al Jouf-2014, Saudi Arabia
| | - S.K. Kanthlal
- Department of Pharmacology, Amrita School of Pharmacy, Amrita Vishwa Vidyapeetham, AIMS Health Sciences Campus, Kochi-682 041, India
| | - Md Atiar Rahman
- Department of Biochemistry and Molecular Biology, University of Chittagong, Chittagong, Bangladesh
| | - Athanasios Alexiou
- Novel Global Community Educational Foundation, Hebersham, Australia;,AFNP Med Austria, Wien, Austria
| | - Gaber El-Saber Batiha
- Department of Pharmacology and Therapeutics, Faculty of Veterinary Medicine, Damanhour University, Damanhour 22511, AlBeheira, Egypt
| | - Bijo Mathew
- Department of Pharmaceutical Chemistry, Amrita School of Pharmacy, Amrita Vishwa Vidyapeetham, AIMS Health Sciences Campus, Kochi-682 041, India,Address correspondence to this author at the Department of Pharmaceutical Chemistry, Amrita School of Pharmacy, Amrita Vishwa Vidyapeetham, AIMS Health Sciences Campus, Kochi-682 041, India; E-mails: ;
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3
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Bioenergetic roles of mitochondrial fusion. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2016; 1857:1277-1283. [DOI: 10.1016/j.bbabio.2016.04.002] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2016] [Revised: 03/18/2016] [Accepted: 04/05/2016] [Indexed: 11/17/2022]
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4
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Woellhaf MW, Hansen KG, Garth C, Herrmann JM. Import of ribosomal proteins into yeast mitochondria. Biochem Cell Biol 2014; 92:489-98. [PMID: 24943357 DOI: 10.1139/bcb-2014-0029] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Mitochondrial ribosomes of baker's yeast contain at least 78 protein subunits. All but one of these proteins are nuclear-encoded, synthesized on cytosolic ribosomes, and imported into the matrix for biogenesis. The import of matrix proteins typically relies on N-terminal mitochondrial targeting sequences that form positively charged amphipathic helices. Interestingly, the N-terminal regions of many ribosomal proteins do not closely match the characteristics of matrix targeting sequences, suggesting that the import processes of these proteins might deviate to some extent from the general import route. So far, the biogenesis of only two ribosomal proteins, Mrpl32 and Mrp10, was studied experimentally and indeed showed surprising differences to the import of other preproteins. In this review article we summarize the current knowledge on the transport of proteins into the mitochondrial matrix, and thereby specifically focus on proteins of the mitochondrial ribosome.
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Affiliation(s)
- Michael W Woellhaf
- a Cell Biology, University of Kaiserslautern, Erwin-Schrödinger-Strasse 13, 67663 Kaiserslautern, Germany
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5
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Weckbecker D, Herrmann JM. Methods to study the biogenesis of membrane proteins in yeast mitochondria. Methods Mol Biol 2014; 1033:307-22. [PMID: 23996186 DOI: 10.1007/978-1-62703-487-6_20] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
Abstract
The biogenesis of mitochondrial membrane proteins is an intricate process that relies on the import and submitochondrial sorting of nuclear-encoded preproteins and on the synthesis of mitochondrial translation products in the matrix. Subsequently, these polypeptides need to be inserted into the outer and the inner membranes of the organelle where many of them assemble into multisubunit complexes. In this chapter we provide established protocols to study these different processes experimentally using mitochondria of budding yeast. In particular, methods are described in detail to purify mitochondria, to study mitochondrial protein synthesis, to follow the import of radiolabeled preproteins into isolated mitochondria, and to assess membrane association and the aggregation of mitochondrial proteins by fractionation. These protocols and a list of dos and don'ts shall enable beginners and experienced scientists to address the targeting and assembly of mitochondrial membrane proteins.
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6
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Cristodero M, Mani J, Oeljeklaus S, Aeberhard L, Hashimi H, Ramrath DJF, Lukeš J, Warscheid B, Schneider A. Mitochondrial translation factors of Trypanosoma brucei: elongation factor-Tu has a unique subdomain that is essential for its function. Mol Microbiol 2013; 90:744-55. [PMID: 24033548 DOI: 10.1111/mmi.12397] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/07/2013] [Indexed: 11/28/2022]
Abstract
Mitochondrial translation in the parasitic protozoan Trypanosoma brucei relies on imported eukaryotic-type tRNAs as well as on bacterial-type ribosomes that have the shortest known rRNAs. Here we have identified the mitochondrial translation elongation factors EF-Tu, EF-Ts, EF-G1 and release factor RF1 of trypanosomatids and show that their ablation impairs growth and oxidative phosphorylation. In vivo labelling experiments and a SILAC-based analysis of the global proteomic changes induced by EF-Tu RNAi directly link EF-Tu to mitochondrial translation. Moreover, EF-Tu RNAi reveals downregulation of many nuclear encoded subunits of cytochrome oxidase as well as of components of the bc1-complex, whereas most cytosolic ribosomal proteins were upregulated. Interestingly, T. brucei EF-Tu has a 30-amino-acid-long, highly charged subdomain, which is unique to trypanosomatids. A combination of RNAi and complementation experiments shows that this subdomain is essential for EF-Tu function, but that it can be replaced by a similar sequence found in eukaryotic EF-1a, the cytosolic counterpart of EF-Tu. A recent cryo-electron microscopy study revealed that trypanosomatid mitochondrial ribosomes have a unique intersubunit space that likely harbours the EF-Tu binding site. These findings suggest that the trypanosomatid-specific EF-Tu subdomain serves as an adaption for binding to these unusual mitochondrial ribosomes.
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Affiliation(s)
- Marina Cristodero
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, CH-3012, Bern, Switzerland
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Dhillon VS, Fenech M. Mutations that affect mitochondrial functions and their association with neurodegenerative diseases. MUTATION RESEARCH-REVIEWS IN MUTATION RESEARCH 2013; 759:1-13. [PMID: 24055911 DOI: 10.1016/j.mrrev.2013.09.001] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2013] [Revised: 09/05/2013] [Accepted: 09/08/2013] [Indexed: 12/20/2022]
Abstract
Mitochondria are essential for mammalian and human cell function as they generate ATP via aerobic respiration. The proteins required in the electron transport chain are mainly encoded by the circular mitochondrial genome but other essential mitochondrial proteins such as DNA repair genes, are coded in the nuclear genome and require transport into the mitochondria. In this review we summarize current knowledge on the association of point mutations and deletions in the mitochondrial genome that are detrimental to mitochondrial function and are associated with accelerated ageing and neurological disorders including Alzheimer's, Parkinson's, Huntington's and Amyotrophic lateral sclerosis (ALS). Mutations in the nuclear encoded genes that disrupt mitochondrial functions are also discussed. It is evident that a greater understanding of the causes of mutations that adversely affect mitochondrial metabolism is required to develop preventive measures against accelerated ageing and neurological disorders caused by mitochondrial dysfunction.
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Affiliation(s)
- Varinderpal S Dhillon
- Preventative-Health Flagship, Gate 13, Kintore Avenue, Adelaide, SA 5000, Australia; CSIRO Animal, Food and Health Sciences, Gate 13, Kintore Avenue, Adelaide, SA 5000, Australia.
| | - Michael Fenech
- Preventative-Health Flagship, Gate 13, Kintore Avenue, Adelaide, SA 5000, Australia; CSIRO Animal, Food and Health Sciences, Gate 13, Kintore Avenue, Adelaide, SA 5000, Australia
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8
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Jhas B, Sriskanthadevan S, Skrtic M, Sukhai MA, Voisin V, Jitkova Y, Gronda M, Hurren R, Laister RC, Bader GD, Minden MD, Schimmer AD. Metabolic adaptation to chronic inhibition of mitochondrial protein synthesis in acute myeloid leukemia cells. PLoS One 2013; 8:e58367. [PMID: 23520503 PMCID: PMC3592803 DOI: 10.1371/journal.pone.0058367] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2012] [Accepted: 02/04/2013] [Indexed: 12/19/2022] Open
Abstract
Recently, we demonstrated that the anti-bacterial agent tigecycline preferentially induces death in leukemia cells through the inhibition of mitochondrial protein synthesis. Here, we sought to understand mechanisms of resistance to tigecycline by establishing a leukemia cell line resistant to the drug. TEX leukemia cells were treated with increasing concentrations of tigecycline over 4 months and a population of cells resistant to tigecycline (RTEX+TIG) was selected. Compared to wild type cells, RTEX+TIG cells had undetectable levels of mitochondrially translated proteins Cox-1 and Cox-2, reduced oxygen consumption and increased rates of glycolysis. Moreover, RTEX+TIG cells were more sensitive to inhibitors of glycolysis and more resistant to hypoxia. By electron microscopy, RTEX+TIG cells had abnormally swollen mitochondria with irregular cristae structures. RNA sequencing demonstrated a significant over-representation of genes with binding sites for the HIF1α:HIF1β transcription factor complex in their promoters. Upregulation of HIF1α mRNA and protein in RTEX+TIG cells was confirmed by Q-RTPCR and immunoblotting. Strikingly, upon removal of tigecycline from RTEX+TIG cells, the cells re-established aerobic metabolism. Levels of Cox-1 and Cox-2, oxygen consumption, glycolysis, mitochondrial mass and mitochondrial membrane potential returned to wild type levels, but HIF1α remained elevated. However, upon re-treatment with tigecycline for 72 hours, the glycolytic phenotype was re-established. Thus, we have generated cells with a reversible metabolic phenotype by chronic treatment with an inhibitor of mitochondrial protein synthesis. These cells will provide insight into cellular adaptations used to cope with metabolic stress.
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MESH Headings
- Anti-Bacterial Agents/pharmacology
- Cell Line, Tumor
- Drug Resistance, Neoplasm
- Electron Transport Complex IV/biosynthesis
- Electron Transport Complex IV/genetics
- Gene Expression Regulation, Leukemic/drug effects
- Gene Expression Regulation, Leukemic/genetics
- Glycolysis/drug effects
- Glycolysis/genetics
- Humans
- Hypoxia-Inducible Factor 1, alpha Subunit/biosynthesis
- Hypoxia-Inducible Factor 1, alpha Subunit/genetics
- Leukemia, Myeloid, Acute/drug therapy
- Leukemia, Myeloid, Acute/genetics
- Leukemia, Myeloid, Acute/metabolism
- Leukemia, Myeloid, Acute/pathology
- Minocycline/analogs & derivatives
- Minocycline/pharmacology
- Mitochondrial Proteins/biosynthesis
- Mitochondrial Proteins/genetics
- Neoplasm Proteins/biosynthesis
- Neoplasm Proteins/genetics
- Oxygen Consumption/drug effects
- Oxygen Consumption/genetics
- Protein Biosynthesis
- Tigecycline
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Affiliation(s)
- Bozhena Jhas
- The Princess Margaret Hospital and The Ontario Cancer Institute, University Health Network, Toronto, Canada
| | - Shrivani Sriskanthadevan
- The Princess Margaret Hospital and The Ontario Cancer Institute, University Health Network, Toronto, Canada
| | - Marko Skrtic
- The Princess Margaret Hospital and The Ontario Cancer Institute, University Health Network, Toronto, Canada
| | - Mahadeo A. Sukhai
- The Princess Margaret Hospital and The Ontario Cancer Institute, University Health Network, Toronto, Canada
| | | | - Yulia Jitkova
- The Princess Margaret Hospital and The Ontario Cancer Institute, University Health Network, Toronto, Canada
| | - Marcela Gronda
- The Princess Margaret Hospital and The Ontario Cancer Institute, University Health Network, Toronto, Canada
| | - Rose Hurren
- The Princess Margaret Hospital and The Ontario Cancer Institute, University Health Network, Toronto, Canada
| | - Rob C. Laister
- The Princess Margaret Hospital and The Ontario Cancer Institute, University Health Network, Toronto, Canada
| | - Gary D. Bader
- The Donnelly Centre, University of Toronto, Toronto, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Canada
| | - Mark D. Minden
- The Princess Margaret Hospital and The Ontario Cancer Institute, University Health Network, Toronto, Canada
| | - Aaron D. Schimmer
- The Princess Margaret Hospital and The Ontario Cancer Institute, University Health Network, Toronto, Canada
- * E-mail:
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9
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Wredenberg A, Lagouge M, Bratic A, Metodiev MD, Spåhr H, Mourier A, Freyer C, Ruzzenente B, Tain L, Grönke S, Baggio F, Kukat C, Kremmer E, Wibom R, Polosa PL, Habermann B, Partridge L, Park CB, Larsson NG. MTERF3 regulates mitochondrial ribosome biogenesis in invertebrates and mammals. PLoS Genet 2013; 9:e1003178. [PMID: 23300484 PMCID: PMC3536695 DOI: 10.1371/journal.pgen.1003178] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2012] [Accepted: 10/31/2012] [Indexed: 11/18/2022] Open
Abstract
Regulation of mitochondrial DNA (mtDNA) expression is critical for the control of oxidative phosphorylation in response to physiological demand, and this regulation is often impaired in disease and aging. We have previously shown that mitochondrial transcription termination factor 3 (MTERF3) is a key regulator that represses mtDNA transcription in the mouse, but its molecular mode of action has remained elusive. Based on the hypothesis that key regulatory mechanisms for mtDNA expression are conserved in metazoans, we analyzed Mterf3 knockout and knockdown flies. We demonstrate here that decreased expression of MTERF3 not only leads to activation of mtDNA transcription, but also impairs assembly of the large mitochondrial ribosomal subunit. This novel function of MTERF3 in mitochondrial ribosomal biogenesis is conserved in the mouse, thus we identify a novel and unexpected role for MTERF3 in coordinating the crosstalk between transcription and translation for the regulation of mammalian mtDNA gene expression.
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Affiliation(s)
- Anna Wredenberg
- Max-Planck Institute for Biology of Ageing, Köln, Germany
- Department Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Marie Lagouge
- Max-Planck Institute for Biology of Ageing, Köln, Germany
| | - Ana Bratic
- Max-Planck Institute for Biology of Ageing, Köln, Germany
- Department Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden
| | | | - Henrik Spåhr
- Max-Planck Institute for Biology of Ageing, Köln, Germany
| | - Arnaud Mourier
- Max-Planck Institute for Biology of Ageing, Köln, Germany
| | - Christoph Freyer
- Max-Planck Institute for Biology of Ageing, Köln, Germany
- Department Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden
| | | | - Luke Tain
- Max-Planck Institute for Biology of Ageing, Köln, Germany
| | | | | | | | - Elisabeth Kremmer
- Helmholtz Center, Institute for Molecular Immunology, Munich, Germany
| | - Rolf Wibom
- Department Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Paola Loguercio Polosa
- Department of Biosciences, Biotechnologies, and Pharmacological Sciences, University of Bari Aldo Moro, Bari, Italy
| | | | | | - Chan Bae Park
- Institute for Medical Sciences, Ajou University School of Medicine, Suwon, Korea
- Mitochondria Hub Regulation Center, Dong-A University College of Medicine, Busan, Republic of Korea
- * E-mail: (CBP); (N-GL)
| | - Nils-Göran Larsson
- Max-Planck Institute for Biology of Ageing, Köln, Germany
- Department Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden
- * E-mail: (CBP); (N-GL)
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Yagi M, Uchiumi T, Takazaki S, Okuno B, Nomura M, Yoshida SI, Kanki T, Kang D. p32/gC1qR is indispensable for fetal development and mitochondrial translation: importance of its RNA-binding ability. Nucleic Acids Res 2012; 40:9717-37. [PMID: 22904065 PMCID: PMC3479211 DOI: 10.1093/nar/gks774] [Citation(s) in RCA: 113] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
p32 is an evolutionarily conserved and ubiquitously expressed multifunctional protein. Although p32 exists at diverse intra and extracellular sites, it is predominantly localized to the mitochondrial matrix near the nucleoid associated with mitochondrial transcription factor A. Nonetheless, its function in the matrix is poorly understood. Here, we determined p32 function via generation of p32-knockout mice. p32-deficient mice exhibited mid-gestation lethality associated with a severe developmental defect of the embryo. Primary embryonic fibroblasts isolated from p32-knockout embryos showed severe dysfunction of the mitochondrial respiratory chain, because of severely impaired mitochondrial protein synthesis. Recombinant p32 binds RNA, not DNA, and endogenous p32 interacts with all mitochondrial messenger RNA species in vivo. The RNA-binding ability of p32 is well correlated with the mitochondrial translation. Co-immunoprecipitation revealed the close association of p32 with the mitoribosome. We propose that p32 is required for functional mitoribosome formation to synthesize proteins within mitochondria.
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Affiliation(s)
- Mikako Yagi
- Department of Clinical Chemistry and Laboratory Medicine, Graduate School of Medical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
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11
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Rackham O, Mercer TR, Filipovska A. The human mitochondrial transcriptome and the RNA-binding proteins that regulate its expression. WILEY INTERDISCIPLINARY REVIEWS-RNA 2012; 3:675-95. [DOI: 10.1002/wrna.1128] [Citation(s) in RCA: 81] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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12
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The role of TFAM-associated proteins in mitochondrial RNA metabolism. Biochim Biophys Acta Gen Subj 2011; 1820:565-70. [PMID: 21920408 DOI: 10.1016/j.bbagen.2011.08.014] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2011] [Revised: 08/18/2011] [Accepted: 08/25/2011] [Indexed: 11/22/2022]
Abstract
BACKGROUND Mammalian mitochondrial DNA (mtDNA) takes on a higher structure called the nucleoid or mitochromosome, which corresponds to that of nuclear DNA. Mitochondrial transcription factor A (TFAM), which was cloned as a transcription factor for mitochondrial DNA, is critical for forming this higher structure and for maintenance of mtDNA. SCOPE OF REVIEW To investigate the functional aspects of the nucleoid, we have identified many RNA-binding proteins to be candidate TFAM interactors, including ERAL1 and p32. MAJOR CONCLUSIONS In this review, we would like to describe that ERAL1 binds to the mitochondrial rRNA component of the ribosomal small subunit and is an important constituent of this subunit. p32, which is involved in mitochondrial translation, may be a novel marker of clinical progression in prostate cancer. Here we describe these proteins, all of which are involved in translation within the mitochondrial matrix. GENERAL SIGNIFICANCE This review highlights the results from the mitochondrial nucleoid research in organic biochemistry. This article is part of a Special Issue entitled Biochemistry of Mitochondria.
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Rorbach J, Nicholls TJJ, Minczuk M. PDE12 removes mitochondrial RNA poly(A) tails and controls translation in human mitochondria. Nucleic Acids Res 2011; 39:7750-63. [PMID: 21666256 PMCID: PMC3177208 DOI: 10.1093/nar/gkr470] [Citation(s) in RCA: 84] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
Polyadenylation of mRNA in human mitochondria is crucial for gene expression and perturbation of poly(A) tail length has been linked to a human neurodegenerative disease. Here we show that 2′-phosphodiesterase (2′-PDE), (hereafter PDE12), is a mitochondrial protein that specifically removes poly(A) extensions from mitochondrial mRNAs both in vitro and in mitochondria of cultured cells. In eukaryotes, poly(A) tails generally stabilize mature mRNAs, whereas in bacteria they increase mRNA turnover. In human mitochondria, the effects of increased PDE12 expression were transcript dependent. An excess of PDE12 led to an increase in the level of three mt-mRNAs (ND1, ND2 and CytB) and two (CO1 and CO2) were less abundant than in mitochondria of control cells and there was no appreciable effect on the steady-state level of the remainder of the mitochondrial transcripts. The alterations in poly(A) tail length accompanying elevated PDE12 expression were associated with severe inhibition of mitochondrial protein synthesis, and consequently respiratory incompetence. Therefore, we propose that mRNA poly(A) tails are important in regulating protein synthesis in human mitochondria, as it is the case for nuclear-encoded eukaryotic mRNA.
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Affiliation(s)
- Joanna Rorbach
- MRC Mitochondrial Biology Unit, Wellcome Trust/MRC Building, Cambridge CB2 0XY, UK
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14
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Gubina NE, Merekina OS, Ushakova TE. Mitochondrial DNA transcription in mouse liver, skeletal muscle, and brain following lethal x-ray irradiation. BIOCHEMISTRY (MOSCOW) 2010; 75:777-83. [PMID: 20636270 DOI: 10.1134/s0006297910060131] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Using quantitative real-time PCR, the levels of mitochondrial DNA transcripts in murine tissues (skeletal muscle, liver, and brain) were determined at different time points (1, 5, and 24 h) following X-ray irradiation at the dose of 10 Gy. One hour after irradiation the levels of mitochondrial transcripts ND2, ND4, CYTB, and ATP6 dramatically decreased by 85-95% and remained at the same minimum level for 24 h in all analyzed tissues. This decrease was not associated with depletion of mtDNA as a matrix for transcription, since mtDNA copy number increased after irradiation in all tissues. The decrease in mitochondrial transcription in liver, brain, and skeletal muscle did not generally result from the damage of cell transcription apparatus, because the transcription level of nuclear housekeeping gene BETA-ACTIN remained virtually unchanged after irradiation. The mitochondrial gene transcription decreased after irradiation in the same manner as that of the nuclear gene TFB2M encoding mitochondrial transcription factor, whose regulatory role under normal conditions is well understood.
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Affiliation(s)
- N E Gubina
- Institute of Theoretical and Experimental Biophysics, Russian Academy of Sciences, Pushchino, Moscow Region, Russia.
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15
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Mazunin IO, Volodko NV, Starikovskaya EB, Sukernik RI. Mitochondrial genome and human mitochondrial diseases. Mol Biol 2010. [DOI: 10.1134/s0026893310050018] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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16
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Abstract
From their very beginning to the present day, mitochondria have evolved to become a crucial organelle within the cell. The mitochondrial genome encodes only 37 genes, but its compact structure and minimal redundancy results in mutations on the mitochondrial genome being an important cause of genetic disease. In the present chapter we describe the up-to-date knowledge about mitochondrial DNA structure and function, and describe some of the consequences of defective function including disease and aging.
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17
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Young DJ, Edgar CD, Murphy J, Fredebohm J, Poole ES, Tate WP. Bioinformatic, structural, and functional analyses support release factor-like MTRF1 as a protein able to decode nonstandard stop codons beginning with adenine in vertebrate mitochondria. RNA (NEW YORK, N.Y.) 2010; 16:1146-55. [PMID: 20421313 PMCID: PMC2874167 DOI: 10.1261/rna.1970310] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Vertebrate mitochondria use stop codons UAA and UAG decoded by the release factor (RF) MTRF1L and two reassigned arginine codons, AGA and AGG. A second highly conserved RF-like factor, MTRF1, which evolved from a gene duplication of an ancestral mitochondrial RF1 and not a RF2, is a good candidate for recognizing the nonstandard codons. MTRF1 differs from other RFs by having insertions in the two external loops important for stop codon recognition (tip of helix alpha5 and recognition loop) and by having key substitutions that are involved in stop codon interactions in eubacterial RF/ribosome structures. These changes may allow recognition of the larger purine base in the first position of AGA/G and, uniquely for RFs, only of G at position 2. In contrast, residues that support A and G recognition in the third position in RF1 are conserved as would be required for recognition of AGA and AGG. Since an assay with vertebrate mitochondrial ribosomes has not been established, we modified Escherichia coli RF1 at the helix alpha5 and recognition loop regions to mimic MTRF1. There was loss of peptidyl-tRNA hydrolysis activity with standard stop codons beginning with U (e.g., UAG), but a gain of activity with codons beginning with A (AAG in particular). A lower level of activity with AGA could be enhanced by solvent modification. These observations imply that MTRF1 has the characteristics to recognize A as the first base of a stop codon as would be required to decode the nonstandard codons AGA and AGG.
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Affiliation(s)
- David J Young
- Department of Biochemistry, University of Otago, Dunedin 9054, New Zealand
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Uchiumi T, Ohgaki K, Yagi M, Aoki Y, Sakai A, Matsumoto S, Kang D. ERAL1 is associated with mitochondrial ribosome and elimination of ERAL1 leads to mitochondrial dysfunction and growth retardation. Nucleic Acids Res 2010; 38:5554-68. [PMID: 20430825 PMCID: PMC2938226 DOI: 10.1093/nar/gkq305] [Citation(s) in RCA: 83] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
ERAL1, a homologue of Era protein in Escherichia coli, is a member of conserved GTP-binding proteins with RNA-binding activity. Depletion of prokaryotic Era inhibits cell division without affecting chromosome segregation. Previously, we isolated ERAL1 protein as one of proteins which were associated with mitochondrial transcription factor A by using immunoprecipitation. In this study, we analysed the localization and function of ERAL1 in mammalian cells. ERAL1 was localized in mitochondrial matrix and associated with mitoribosomal proteins including the 12S rRNA. siRNA knockdown of ERAL1 decreased mitochondrial translation, caused redistribution of ribosomal small subunits and reduced 12S rRNA. The knockdown of ERAL1 in human HeLa cells elevated mitochondrial superoxide production and slightly decreased mitochondrial membrane potential. The knockdown inhibited the growth of HeLa cells with an accumulation of apoptotic cells. These results suggest that ERAL1 is localized in a small subunit of the mitochondrial ribosome, plays an important role in the small ribosomal constitution, and is also involved in cell viability.
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Affiliation(s)
- Takeshi Uchiumi
- Department of Clinical Chemistry and Laboratory Medicine, Kyushu University Graduate School of Medical Sciences, 3-1-1, Maidashi, Higashi-ku, Fukuoka 812-8582, Japan.
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19
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Abstract
Mitochondrial dysfunction is heavily implicated in the multifactorial aging process. Aging humans have increased levels of somatic mtDNA mutations that tend to undergo clonal expansion to cause mosaic respiratory chain deficiency in various tissues, such as heart, brain, skeletal muscle, and gut. Genetic mouse models have shown that somatic mtDNA mutations and cell type-specific respiratory chain dysfunction can cause a variety of phenotypes associated with aging and age-related disease. There is thus strong observational and experimental evidence to implicate somatic mtDNA mutations and mosaic respiratory chain dysfunction in the mammalian aging process. The hypothesis that somatic mtDNA mutations are generated by oxidative damage has not been conclusively proven. Emerging data instead suggest that the inherent error rate of mitochondrial DNA (mtDNA) polymerase gamma (Pol gamma) may be responsible for the majority of somatic mtDNA mutations. The roles for mtDNA damage and replication errors in aging need to be further experimentally addressed.
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Turnbull HE, Lax NZ, Diodato D, Ansorge O, Turnbull DM. The mitochondrial brain: From mitochondrial genome to neurodegeneration. BIOCHIMICA ET BIOPHYSICA ACTA 2010; 1802:111-21. [PMID: 19647794 PMCID: PMC2795853 DOI: 10.1016/j.bbadis.2009.07.010] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/15/2009] [Revised: 07/21/2009] [Accepted: 07/23/2009] [Indexed: 11/26/2022]
Abstract
Mitochondrial DNA mutations are an important cause of neurological disease. The clinical presentation is very varied in terms of age of onset and different neurological signs and symptoms. The clinical course varies considerably but in many patients there is a progressive decline, and in some evidence of marked neurodegeneration. Our understanding of the mechanisms involved is limited due in part to limited availability of animal models of disease. However, studies on human post-mortem brains, combined with clinical and radiological studies, are giving important insights into specific neuronal involvement.
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Affiliation(s)
- Helen E Turnbull
- Mitochondrial Research Group, Institute for Ageing and Health, Newcastle University, NE24HH, UK.
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21
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Valente L, Shigi N, Suzuki T, Zeviani M. The R336Q mutation in human mitochondrial EFTu prevents the formation of an active mt-EFTu.GTP.aa-tRNA ternary complex. Biochim Biophys Acta Mol Basis Dis 2009; 1792:791-5. [PMID: 19524667 DOI: 10.1016/j.bbadis.2009.06.002] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2009] [Revised: 05/06/2009] [Accepted: 06/08/2009] [Indexed: 11/18/2022]
Abstract
The mitochondrial translational machinery allows the genes encoded by mitochondrial DNA (mtDNA) to be translated in situ. Mitochondrial translation requires a number of nucleus-encoded protein factors, some of which have been found to carry mutations in patients affected by mitochondrial encephalomyopathies. We have previously described the first, and so far only, mutation in the mitochondrial elongation factor Tu, mt-EFTu, in a baby girl with polycystic encephalopathy, micropolygyria, and leukodystrophic changes. Despite that the mutant mt-EFTu was present in normal amount in the patient's tissues, mitochondrial translation was severely reduced, determining multiple defects in the amount and activity of mtDNA-dependent respiratory chain complexes. By an in-vitro reconstructed translational system, we here provide evidence that the mutant mt-EFTu variant fails to bind to aminoacylated mitochondrial tRNAs, thus explaining the observed impairment of mitochondrial translation. This is the first analysis on the molecular mechanism of a mtDNA translation defect due to a nuclear gene mutation.
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Affiliation(s)
- Lucia Valente
- Unit of Molecular Neurogenetics, IRCCS Foundation, Neurological Institute C. Besta, 20126 Milano, Italy
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22
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Jiang YJ, Sun Q, Fang XS, Wang X. Comparative mitochondrial proteomic analysis of Rji cells exposed to adriamycin. Mol Med 2009; 15:173-82. [PMID: 19209238 DOI: 10.2119/molmed.2008.00129] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2009] [Accepted: 02/04/2009] [Indexed: 02/01/2023] Open
Abstract
The antitumor mechanisms of adriamycin (ADR) have been thought to contribute to induction of apoptosis and inefficiency of DNA repair, processes that are to a large extent mediated by mitochondria. This study aimed to investigate characteristics of ADR, including its antineoplastic activity, drug resistance, and unexpected toxicity in non-Hodgkin lymphoma (NHL) Raji cells at the mitochondrial proteomic level. The alterations of the mitochondrial proteome of Raji cells treated with ADR were analyzed by two-dimensional differential in-gel electrophoresis (2D-DIGE) coupled with linear ion trap quadrupole-electrospray ionization tandem mass spectrometry (LTQ-ESI-MS/MS).The altered patterns of three identified proteins were validated by Western blot and analyzed by pathway studio software. The results showed that 34 proteins were downregulated and 3 proteins upregulated in the study group compared with the control group. The differentially expressed proteins distributed their functions in reduction-oxidation reactions, DNA repair, cell cycle regulation, transporters and channels, and oxidative phosphorylation. Furthermore, heat shock protein 70 (HSP70), ATP-binding cassette transporter isoform B6 (ABCB6), and prohibitin (PHB) identified in this study may be closely related to chemoresistance and could serve as potential chemotherapeutic targets for NHL. Collectively, these results suggest that specific mitochondrial proteins are uniquely susceptible to alterations in abundance following exposure to ADR and carry implications for the investigation of therapeutic and prognostic markers. Further studies focusing on these identified proteins will be used to predict treatment response and reverse apoptosis resistance,and to explore drug-combination strategies associated with ADR for NHL therapy.
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Affiliation(s)
- Yu-Jie Jiang
- Department of Hematology, Provincial Hospital affiliated to Shandong University, Jinan, China
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23
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Torraco A, Diaz F, Vempati UD, Moraes CT. Mouse models of oxidative phosphorylation defects: powerful tools to study the pathobiology of mitochondrial diseases. BIOCHIMICA ET BIOPHYSICA ACTA 2009; 1793:171-80. [PMID: 18601959 PMCID: PMC2652735 DOI: 10.1016/j.bbamcr.2008.06.003] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2008] [Revised: 05/28/2008] [Accepted: 06/04/2008] [Indexed: 01/14/2023]
Abstract
Defects in the oxidative phosphorylation system (OXPHOS) are responsible for a group of extremely heterogeneous and pleiotropic pathologies commonly known as mitochondrial diseases. Although many mutations have been found to be responsible for OXPHOS defects, their pathogenetic mechanisms are still poorly understood. An important contribution to investigate the in vivo function of several mitochondrial proteins and their role in mitochondrial dysfunction, has been provided by mouse models. Thanks to their genetic and physiologic similarity to humans, mouse models represent a powerful tool to investigate the impact of pathological mutations on metabolic pathways. In this review we discuss the main mouse models of mitochondrial disease developed, focusing on the ones that directly affect the OXPHOS system.
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Affiliation(s)
- Alessandra Torraco
- Department of Neurology, University of Miami Miller School of Medicine, 1095 NW 14th Terrace, Miami, FL 33136, USA
| | - Francisca Diaz
- Department of Neurology, University of Miami Miller School of Medicine, 1095 NW 14th Terrace, Miami, FL 33136, USA
| | - Uma D. Vempati
- Department of Neurology, University of Miami Miller School of Medicine, 1095 NW 14th Terrace, Miami, FL 33136, USA
| | - Carlos T. Moraes
- Department of Neurology, University of Miami Miller School of Medicine, 1095 NW 14th Terrace, Miami, FL 33136, USA
- Department of Cell Biology and Anatomy, University of Miami Miller School of Medicine, 1095 NW 14th Terrace, Miami, FL 33136, USA
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Khrapko K, Vijg J. Mitochondrial DNA mutations and aging: devils in the details? Trends Genet 2008; 25:91-8. [PMID: 19110336 DOI: 10.1016/j.tig.2008.11.007] [Citation(s) in RCA: 85] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2008] [Revised: 11/14/2008] [Accepted: 11/24/2008] [Indexed: 01/07/2023]
Abstract
Although several lines of evidence support a role for accumulating somatic mitochondrial DNA (mtDNA) mutations in the etiology of aging, it remains unclear if they are a major cause of age-related deterioration and death. Mouse models that harbor elevated mtDNA mutation frequencies age prematurely; these findings were thought to provide conclusive evidence for a causal role of such mutations in aging. Yet, the presence of several conflicting reports has sparked controversy in the field and this is further aggravated by discrepancies in the estimates of mtDNA mutant fractions, which disagree by orders of magnitude. Here, we briefly review the evidence and some of the unresolved questions surrounding a causative role for accumulating mtDNA mutations in aging.
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Affiliation(s)
- Konstantin Khrapko
- Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, MA 02115, USA.
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Mammalian mitochondria have the innate ability to import tRNAs by a mechanism distinct from protein import. Proc Natl Acad Sci U S A 2008; 105:9186-91. [PMID: 18587046 DOI: 10.1073/pnas.0804283105] [Citation(s) in RCA: 107] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Mitochondrial genomes generally encode a minimal set of tRNAs necessary for protein synthesis. However, a number of eukaryotes import tRNAs from the cytoplasm into their mitochondria. For instance, Saccharomyces cerevisiae imports cytoplasmic tRNA(Gln) into the mitochondrion without any added protein factors. Here, we examine the existence of a similar active tRNA import system in mammalian mitochondria. We have used subcellular RNA fractions from rat liver and human cells to perform RT-PCR with oligonucleotide primers specific for nucleus-encoded tRNA(CUG)(Gln) and tRNA(UUG)(Gln) species, and we show that these tRNAs are present in rat and human mitochondria in vivo. Import of in vitro transcribed tRNAs, but not of heterologous RNAs, into isolated mitochondria also demonstrates that this process is tRNA-specific and does not require the addition of cytosolic factors. Although this in vitro system requires ATP, it is resistant to inhibitors of the mitochondrial electrochemical gradient, a key component of protein import. tRNA(Gln) import into mammalian mitochondria proceeds by a mechanism distinct from protein import. We also show that both tRNA(Gln) species and a bacterial pre-tRNA(Asp) can be imported in vitro into mitochondria isolated from myoclonic epilepsy with ragged-red fiber cells if provided with sufficient ATP (2 mM). This work suggests that tRNA import is more widespread than previously thought and may be a universal trait of mitochondria. Mutations in mitochondrial tRNA genes have been associated with human disease; the tRNA import system described here could possibly be exploited for the manipulation of defective mitochondria.
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