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Baechler SA, Dalla Rosa I, Spinazzola A, Pommier Y. Beyond the unwinding: role of TOP1MT in mitochondrial translation. Cell Cycle 2019; 18:2377-2384. [PMID: 31345095 DOI: 10.1080/15384101.2019.1646563] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Mitochondria contain their own genome (mtDNA), encoding 13 proteins of the enzyme complexes of the oxidative phosphorylation. Synthesis of these 13 mitochondrial proteins requires a specific translation machinery, the mitoribosomes whose RNA components are encoded by the mtDNA, whereas more than 80 proteins are encoded by nuclear genes. It has been well established that mitochondrial topoisomerase I (TOP1MT) is important for mtDNA integrity and mitochondrial transcription as it prevents excessive mtDNA negative supercoiling and releases topological stress during mtDNA replication and transcription. We recently showed that TOP1MT also supports mitochondrial protein synthesis, and thus is critical for promoting tumor growth. Impaired mitochondrial protein synthesis leads to activation of the mitonuclear stress response through the transcription factor ATF4, and induces cytoprotective genes in order to prevent mitochondrial and cellular dysfunction. In this perspective, we highlight the novel role of TOP1MT in mitochondrial protein synthesis and as potential target for chemotherapy.
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Affiliation(s)
- Simone A Baechler
- Laboratory of Molecular Pharmacology, Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, NIH , Bethesda , MD , USA
| | - Ilaria Dalla Rosa
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology , London , UK
| | - Antonella Spinazzola
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology , London , UK
| | - Yves Pommier
- Laboratory of Molecular Pharmacology, Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, NIH , Bethesda , MD , USA
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52
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Luo Y, Su R, Wang Y, Xie W, Liu Z, Huang Y. Schizosaccharomyces pombe Mti2 and Mti3 act in conjunction during mitochondrial translation initiation. FEBS J 2019; 286:4542-4553. [PMID: 31350787 DOI: 10.1111/febs.15021] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2019] [Revised: 06/23/2019] [Accepted: 07/24/2019] [Indexed: 01/15/2023]
Abstract
Mitochondrial DNA encodes key subunits of the oxidative phosphorylation complexes essential for ATP production. Translation initiation in mitochondria requires two general factors, mtIF2 and mtIF3, whose counterparts in bacteria are essential for protein synthesis. In this study, we report the characterization of the fission yeast Schizosaccharomyces pombe mtIF2 (Mti2) and mtIF3 (Mti3). Deletion of mti2 impairs cell growth on the respiratory medium. The growth defect of the mti2 deletion mutant can be suppressed by expressing IFM1, the Saccharomyces cerevisiae homolog of Mti2, demonstrating functional conservation between the two proteins. Deletion of mti2 also impairs mitochondrial protein synthesis. Unlike mti2, deletion of mti3 does not affect cell growth on respiratory media and mitochondrial translation. However, deletion of mti3 exacerbates the growth defect of the Δmti2 mutant, suggesting that the two proteins have distinct, but partially overlapping functions during the process of mitochondrial translation initiation in S. pombe. Both Mti2 and Mti3 are associated with the small subunit of the mitochondrial ribosome (mitoribosome). Disruption of mti2, but not mti3, causes dissociation of the mitoribosome and also abolishes Mti3 binding to the small subunit of the mitoribosome. Our results suggest that Mti2 and Mti3 bind in a sequential manner to the small subunit of the mitoribosome and that Mti3 facilitates the function of Mti2 in mitochondrial translation initiation. Our findings also support the view that the importance of the mitochondrial translation initiation factors varies among the organisms.
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Affiliation(s)
- Ying Luo
- Jiangsu Key Laboratory for Microbes and Functional Genomics, School of Life Sciences, Nanjing Normal University, China
| | - Ruyue Su
- Jiangsu Key Laboratory for Microbes and Functional Genomics, School of Life Sciences, Nanjing Normal University, China
| | - Yirong Wang
- Jiangsu Key Laboratory for Microbes and Functional Genomics, School of Life Sciences, Nanjing Normal University, China
| | - Wanqiu Xie
- Jiangsu Key Laboratory for Microbes and Functional Genomics, School of Life Sciences, Nanjing Normal University, China
| | - Zecheng Liu
- Jiangsu Key Laboratory for Microbes and Functional Genomics, School of Life Sciences, Nanjing Normal University, China
| | - Ying Huang
- Jiangsu Key Laboratory for Microbes and Functional Genomics, School of Life Sciences, Nanjing Normal University, China
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53
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Maslov DA. Separating the Wheat from the Chaff: RNA Editing and Selection of Translatable mRNA in Trypanosome Mitochondria. Pathogens 2019; 8:E105. [PMID: 31323762 PMCID: PMC6789859 DOI: 10.3390/pathogens8030105] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Revised: 07/14/2019] [Accepted: 07/16/2019] [Indexed: 11/16/2022] Open
Abstract
In the mitochondria of trypanosomes and related kinetoplastid protists, most mRNAs undergo a long and sophisticated maturation pathway before they can be productively translated by mitochondrial ribosomes. Some of the aspects of this pathway (identity of the promotors, transcription initiation, and termination signals) remain obscure, and some (post-transcriptional modification by U-insertion/deletion, RNA editing, 3'-end maturation) have been illuminated by research during the last decades. The RNA editing creates an open reading frame for a productive translation, but the fully edited mRNA often represents a minor fraction in the pool of pre-edited and partially edited precursors. Therefore, it has been expected that the final stages of the mRNA processing generate molecular hallmarks, which allow for the efficient and selective recognition of translation-competent templates. The general contours and several important details of this process have become known only recently and represent the subject of this review.
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Affiliation(s)
- Dmitri A Maslov
- Department of Molecular, Cell and Systems Biology, University of California, Riverside, CA 92521, USA.
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54
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Hosseini M, Roy P, Sissler M, Zirbel CL, Westhof E, Leontis N. How to fold and protect mitochondrial ribosomal RNA with fewer guanines. Nucleic Acids Res 2019; 46:10946-10968. [PMID: 30215760 PMCID: PMC6237812 DOI: 10.1093/nar/gky762] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Accepted: 09/06/2018] [Indexed: 01/25/2023] Open
Abstract
Mammalian mitochondrial ribosomes evolved from bacterial ribosomes by reduction of ribosomal RNAs, increase of ribosomal protein content, and loss of guanine nucleotides. Guanine is the base most sensitive to oxidative damage. By systematically comparing high-quality, small ribosomal subunit RNA sequence alignments and solved 3D ribosome structures from mammalian mitochondria and bacteria, we deduce rules for folding a complex RNA with the remaining guanines shielded from solvent. Almost all conserved guanines in both bacterial and mammalian mitochondrial ribosomal RNA form guanine-specific, local or long-range, RNA–RNA or RNA–protein interactions. Many solvent-exposed guanines conserved in bacteria are replaced in mammalian mitochondria by bases less sensitive to oxidation. New guanines, conserved only in the mitochondrial alignment, are strategically positioned at solvent inaccessible sites to stabilize the ribosomal RNA structure. New mitochondrial proteins substitute for truncated RNA helices, maintain mutual spatial orientations of helices, compensate for lost RNA–RNA interactions, reduce solvent accessibility of bases, and replace guanines conserved in bacteria by forming specific amino acid–RNA interactions.
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Affiliation(s)
- Maryam Hosseini
- Department of Chemistry, Bowling Green State University, Bowling Green, OH 43403, USA
| | - Poorna Roy
- Center for RNA Biomedicine, Department of Chemistry, University of Michigan, Ann Arbor, MI 48109-1055, USA
| | - Marie Sissler
- Architecture et Réactivité de l'ARN, Université de Strasbourg, Institut de Biologie Moléculaire et Cellulaire du CNRS, Strasbourg France
| | - Craig L Zirbel
- Department of Mathematics and Statistics, Bowling Green State University, Bowling Green, OH 43403, USA
| | - Eric Westhof
- Architecture et Réactivité de l'ARN, Université de Strasbourg, Institut de Biologie Moléculaire et Cellulaire du CNRS, Strasbourg France
| | - Neocles Leontis
- Department of Chemistry, Bowling Green State University, Bowling Green, OH 43403, USA
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55
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Serfling R, Lorenz C, Etzel M, Schicht G, Böttke T, Mörl M, Coin I. Designer tRNAs for efficient incorporation of non-canonical amino acids by the pyrrolysine system in mammalian cells. Nucleic Acids Res 2019; 46:1-10. [PMID: 29177436 PMCID: PMC5758916 DOI: 10.1093/nar/gkx1156] [Citation(s) in RCA: 82] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2017] [Accepted: 11/09/2017] [Indexed: 11/12/2022] Open
Abstract
The pyrrolysyl-tRNA synthetase/tRNAPyl pair is the most versatile and widespread system for the incorporation of non-canonical amino acids (ncAAs) into proteins in mammalian cells. However, low yields of ncAA incorporation severely limit its applicability to relevant biological targets. Here, we generate two tRNAPyl variants that significantly boost the performance of the pyrrolysine system. Compared to the original tRNAPyl, the engineered tRNAs feature a canonical hinge between D- and T-loop, show higher intracellular concentrations and bear partially distinct post-transcriptional modifications. Using the new tRNAs, we demonstrate efficient ncAA incorporation into a G-protein coupled receptor (GPCR) and simultaneous ncAA incorporation at two GPCR sites. Moreover, by incorporating last-generation ncAAs for bioorthogonal chemistry, we achieve GPCR labeling with small organic fluorophores on the live cell and visualize stimulus-induced GPCR internalization. Such a robust system for incorporation of single or multiple ncAAs will facilitate the application of a wide pool of chemical tools for structural and functional studies of challenging biological targets in live mammalian cells.
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Affiliation(s)
- Robert Serfling
- Institute of Biochemistry, Faculty of Life Sciences, University of Leipzig, Brüderstraße 34, 04103 Leipzig, Germany
| | - Christian Lorenz
- Institute of Biochemistry, Faculty of Life Sciences, University of Leipzig, Brüderstraße 34, 04103 Leipzig, Germany
| | - Maja Etzel
- Institute of Biochemistry, Faculty of Life Sciences, University of Leipzig, Brüderstraße 34, 04103 Leipzig, Germany
| | - Gerda Schicht
- Institute of Biochemistry, Faculty of Life Sciences, University of Leipzig, Brüderstraße 34, 04103 Leipzig, Germany
| | - Thore Böttke
- Institute of Biochemistry, Faculty of Life Sciences, University of Leipzig, Brüderstraße 34, 04103 Leipzig, Germany
| | - Mario Mörl
- Institute of Biochemistry, Faculty of Life Sciences, University of Leipzig, Brüderstraße 34, 04103 Leipzig, Germany
| | - Irene Coin
- Institute of Biochemistry, Faculty of Life Sciences, University of Leipzig, Brüderstraße 34, 04103 Leipzig, Germany
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56
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Li G, Qin Y. Mitochondrial translation factor EF4 regulates oxidative phosphorylation complexes and the production of ROS. Free Radic Res 2019; 52:1250-1255. [PMID: 30693836 DOI: 10.1080/10715762.2018.1479063] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Mitochondrial translation system executes the biosynthesis of mitochondrial DNA encoded polypeptides that are the core subunits of oxidative phosphorylation complexes. Recently, we reported that elongation factor 4 (EF4) is a key quality control factor in bacterial and mitochondrial translation regulating tRNA translocation and modulating cellular responses via a direct cross-talk with cytoplasmic translation machinery. Here, we made a brief review on mtEF4-regulated mitochondrial translation, respiratory chain biogenesis and the production of reactive oxygen species (ROS). We will discuss the influence of mtEF4 on the electron transport chain, especially at respiratory chain complex IV, which could result in cytochrome c peroxidase formation, electron leakage from electron transport chain and ROS increase.
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Affiliation(s)
- Guichen Li
- a Key Laboratory of RNA Biology , Institute of Biophysics, Chinese Academy of Sciences , Chaoyang District , Beijing , China
| | - Yan Qin
- a Key Laboratory of RNA Biology , Institute of Biophysics, Chinese Academy of Sciences , Chaoyang District , Beijing , China.,b University of Chinese Academy of Sciences , Beijing , China
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57
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Koripella RK, Sharma MR, Risteff P, Keshavan P, Agrawal RK. Structural insights into unique features of the human mitochondrial ribosome recycling. Proc Natl Acad Sci U S A 2019; 116:8283-8288. [PMID: 30962385 PMCID: PMC6486771 DOI: 10.1073/pnas.1815675116] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Mammalian mitochondrial ribosomes (mitoribosomes) are responsible for synthesizing proteins that are essential for oxidative phosphorylation (ATP generation). Despite their common ancestry with bacteria, the composition and structure of the human mitoribosome and its translational factors are significantly different from those of their bacterial counterparts. The mammalian mitoribosome recycling factor (RRFmt) carries a mito-specific N terminus extension (NTE), which is necessary for the function of RRFmt Here we present a 3.9-Å resolution cryo-electron microscopic (cryo-EM) structure of the human 55S mitoribosome-RRFmt complex, which reveals α-helix and loop structures for the NTE that makes multiple mito-specific interactions with functionally critical regions of the mitoribosome. These include ribosomal RNA segments that constitute the peptidyl transferase center (PTC) and those that connect PTC with the GTPase-associated center and with mitoribosomal proteins L16 and L27. Our structure reveals the presence of a tRNA in the pe/E position and a rotation of the small mitoribosomal subunit on RRFmt binding. In addition, we observe an interaction between the pe/E tRNA and a mito-specific protein, mL64. These findings help understand the unique features of mitoribosome recycling.
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Affiliation(s)
- Ravi K Koripella
- Division of Translational Medicine, Wadsworth Center, New York State Department of Health, Albany, NY 12201-0509
| | - Manjuli R Sharma
- Division of Translational Medicine, Wadsworth Center, New York State Department of Health, Albany, NY 12201-0509
| | - Paul Risteff
- Division of Translational Medicine, Wadsworth Center, New York State Department of Health, Albany, NY 12201-0509
| | - Pooja Keshavan
- Division of Translational Medicine, Wadsworth Center, New York State Department of Health, Albany, NY 12201-0509
| | - Rajendra K Agrawal
- Division of Translational Medicine, Wadsworth Center, New York State Department of Health, Albany, NY 12201-0509;
- Department of Biomedical Sciences, School of Public Health, State University of New York at Albany, Albany, NY
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58
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González-Serrano LE, Chihade JW, Sissler M. When a common biological role does not imply common disease outcomes: Disparate pathology linked to human mitochondrial aminoacyl-tRNA synthetases. J Biol Chem 2019; 294:5309-5320. [PMID: 30647134 PMCID: PMC6462531 DOI: 10.1074/jbc.rev118.002953] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Mitochondrial aminoacyl-tRNA synthetases (mt-aaRSs) are essential components of the mitochondrial translation machinery. The correlation of mitochondrial disorders with mutations in these enzymes has raised the interest of the scientific community over the past several years. Most surprising has been the wide-ranging presentation of clinical manifestations in patients with mt-aaRS mutations, despite the enzymes' common biochemical role. Even among cases where a common physiological system is affected, phenotypes, severity, and age of onset varies depending on which mt-aaRS is mutated. Here, we review work done thus far and propose a categorization of diseases based on tissue specificity that highlights emerging patterns. We further discuss multiple in vitro and in cellulo efforts to characterize the behavior of WT and mutant mt-aaRSs that have shaped hypotheses about the molecular causes of these pathologies. Much remains to do in order to complete our understanding of these proteins. We expect that futher work is likely to result in the discovery of new roles for the mt-aaRSs in addition to their fundamental function in mitochondrial translation, informing the development of treatment strategies and diagnoses.
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Affiliation(s)
- Ligia Elena González-Serrano
- From the Université de Strasbourg, CNRS, Architecture et Réactivité de l'ARN, UPR9002, F-67000 Strasbourg, France and
| | - Joseph W Chihade
- the Department of Chemistry, Carleton College, Northfield, Minnesota 55057
| | - Marie Sissler
- From the Université de Strasbourg, CNRS, Architecture et Réactivité de l'ARN, UPR9002, F-67000 Strasbourg, France and
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59
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Borna NN, Kishita Y, Kohda M, Lim SC, Shimura M, Wu Y, Mogushi K, Yatsuka Y, Harashima H, Hisatomi Y, Fushimi T, Ichimoto K, Murayama K, Ohtake A, Okazaki Y. Mitochondrial ribosomal protein PTCD3 mutations cause oxidative phosphorylation defects with Leigh syndrome. Neurogenetics 2019; 20:9-25. [PMID: 30607703 DOI: 10.1007/s10048-018-0561-9] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2018] [Accepted: 12/06/2018] [Indexed: 02/06/2023]
Abstract
Pentatricopeptide repeat domain proteins are a large family of RNA-binding proteins involved in mitochondrial RNA editing, stability, and translation. Mitochondrial translation machinery defects are an expanding group of genetic diseases in humans. We describe a patient who presented with low birth weight, mental retardation, and optic atrophy. Brain MRI showed abnormal bilateral signals at the basal ganglia and brainstem, and the patient was diagnosed as Leigh syndrome. Exome sequencing revealed two potentially loss-of-function variants [c.415-2A>G, and c.1747_1748insCT (p.Phe583Serfs*3)] in PTCD3 (also known as MRPS39). PTCD3, a member of the pentatricopeptide repeat domain protein family, is a component of the small mitoribosomal subunit. The patient had marked decreases in mitochondrial complex I and IV levels and activities, oxygen consumption and ATP biosynthesis, and generalized mitochondrial translation defects in fibroblasts. Quantitative proteomic analysis revealed decreased levels of the small mitoribosomal subunits. Complementation experiments rescued oxidative phosphorylation complex I and IV levels and activities, ATP biosynthesis, and MT-RNR1 rRNA transcript level, providing functional validation of the pathogenicity of identified variants. This is the first report of an association of PTCD3 mutations with Leigh syndrome along with combined oxidative phosphorylation deficiencies caused by defects in the mitochondrial translation machinery.
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Affiliation(s)
- Nurun Nahar Borna
- Diagnostics and Therapeutics of Intractable Diseases, Intractable Disease Research Center, Graduate School of Medicine, Juntendo University, Hongo 2-1-1, Bunkyo-ku, Tokyo, 113-8421, Japan
| | - Yoshihito Kishita
- Diagnostics and Therapeutics of Intractable Diseases, Intractable Disease Research Center, Graduate School of Medicine, Juntendo University, Hongo 2-1-1, Bunkyo-ku, Tokyo, 113-8421, Japan
| | - Masakazu Kohda
- Diagnostics and Therapeutics of Intractable Diseases, Intractable Disease Research Center, Graduate School of Medicine, Juntendo University, Hongo 2-1-1, Bunkyo-ku, Tokyo, 113-8421, Japan
| | - Sze Chern Lim
- Diagnostics and Therapeutics of Intractable Diseases, Intractable Disease Research Center, Graduate School of Medicine, Juntendo University, Hongo 2-1-1, Bunkyo-ku, Tokyo, 113-8421, Japan
| | - Masaru Shimura
- Department of Metabolism, Chiba Children's Hospital, Midori, Chiba, 266-0007, Japan
| | - Yibo Wu
- Laboratory for Comprehensive Genomic Analysis, RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, 230-0045, Japan
| | - Kaoru Mogushi
- Diagnostics and Therapeutics of Intractable Diseases, Intractable Disease Research Center, Graduate School of Medicine, Juntendo University, Hongo 2-1-1, Bunkyo-ku, Tokyo, 113-8421, Japan
| | - Yukiko Yatsuka
- Diagnostics and Therapeutics of Intractable Diseases, Intractable Disease Research Center, Graduate School of Medicine, Juntendo University, Hongo 2-1-1, Bunkyo-ku, Tokyo, 113-8421, Japan
| | - Hiroko Harashima
- Department of Pediatrics, Saitama Medical University, Moroyama, Saitama, 350-0495, Japan
| | - Yuichiro Hisatomi
- Department of Pediatrics, Kumamoto City Hospital, Higashi-ku, Kumamoto, 862-8505, Japan
| | - Takuya Fushimi
- Department of Metabolism, Chiba Children's Hospital, Midori, Chiba, 266-0007, Japan
| | - Keiko Ichimoto
- Department of Metabolism, Chiba Children's Hospital, Midori, Chiba, 266-0007, Japan
| | - Kei Murayama
- Department of Metabolism, Chiba Children's Hospital, Midori, Chiba, 266-0007, Japan
| | - Akira Ohtake
- Department of Pediatrics, Saitama Medical University, Moroyama, Saitama, 350-0495, Japan
| | - Yasushi Okazaki
- Diagnostics and Therapeutics of Intractable Diseases, Intractable Disease Research Center, Graduate School of Medicine, Juntendo University, Hongo 2-1-1, Bunkyo-ku, Tokyo, 113-8421, Japan. .,Laboratory for Comprehensive Genomic Analysis, RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, 230-0045, Japan.
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60
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Koripella RK, Sharma MR, Haque ME, Risteff P, Spremulli LL, Agrawal RK. Structure of Human Mitochondrial Translation Initiation Factor 3 Bound to the Small Ribosomal Subunit. iScience 2019; 12:76-86. [PMID: 30677741 PMCID: PMC6352543 DOI: 10.1016/j.isci.2018.12.030] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Revised: 12/11/2018] [Accepted: 12/27/2018] [Indexed: 11/20/2022] Open
Abstract
The human mitochondrial translational initiation factor 3 (IF3mt) carries mitochondrial-specific amino acid extensions at both its N and C termini (N- and C-terminal extensions [NTE and CTE, respectively]), when compared with its eubacterial counterpart. Here we present 3.3- to 3.5-Å-resolution cryoelectron microscopic structures of the mammalian 28S mitoribosomal subunit in complex with human IF3mt. Unique contacts observed between the 28S subunit and N-terminal domain of IF3mt explain its unusually high affinity for the 28S subunit, whereas the position of the mito-specific NTE suggests NTE's role in binding of initiator tRNA to the 28S subunit. The location of the C-terminal domain (CTD) clarifies its anti-association activity, whereas the orientation of the mito-specific CTE provides a mechanistic explanation for its role in destabilizing initiator tRNA in the absence of mRNA. Furthermore, our structure hints at a possible role of the CTD in recruiting leaderless mRNAs for translation initiation. Our findings highlight unique features of IF3mt in mitochondrial translation initiation. High-resolution cryo-EM study of the mammalian 28S mitoribosome-IF3mt complex Interaction between the 28S and IF3mt's NTD explains NTD's unusual high affinity Provides insights into role of IF3mt's N-terminal extension in initiator tRNA binding Provides insights into roles of IF3mt's CTD and C-terminal extension in mRNA sensing
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Affiliation(s)
- Ravi K Koripella
- Division of Translational Medicine, Wadsworth Center, New York State Department of Health, Albany, NY 12201-0509, USA
| | - Manjuli R Sharma
- Division of Translational Medicine, Wadsworth Center, New York State Department of Health, Albany, NY 12201-0509, USA
| | - Md Emdadul Haque
- Department of Chemistry, Campus Box 3290, University of North Carolina, Chapel Hill, NC, USA
| | - Paul Risteff
- Division of Translational Medicine, Wadsworth Center, New York State Department of Health, Albany, NY 12201-0509, USA
| | - Linda L Spremulli
- Department of Chemistry, Campus Box 3290, University of North Carolina, Chapel Hill, NC, USA
| | - Rajendra K Agrawal
- Division of Translational Medicine, Wadsworth Center, New York State Department of Health, Albany, NY 12201-0509, USA; Department of Biomedical Sciences, School of Public Health, University at Albany, SUNY, Albany, NY, USA.
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61
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Yehudai D, Liyanage SU, Hurren R, Rizoska B, Albertella M, Gronda M, Jeyaraju DV, Wang X, Barghout SH, MacLean N, Siriwardena TP, Jitkova Y, Targett-Adams P, Schimmer AD. The thymidine dideoxynucleoside analog, alovudine, inhibits the mitochondrial DNA polymerase γ, impairs oxidative phosphorylation and promotes monocytic differentiation in acute myeloid leukemia. Haematologica 2018; 104:963-972. [PMID: 30573504 PMCID: PMC6518883 DOI: 10.3324/haematol.2018.195172] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2018] [Accepted: 12/17/2018] [Indexed: 12/23/2022] Open
Abstract
Mitochondrial DNA encodes 13 proteins that comprise components of the respiratory chain that maintain oxidative phosphorylation. The replication of mitochondrial DNA is performed by the sole mitochondrial DNA polymerase γ. As acute myeloid leukemia (AML) cells and stem cells have an increased reliance on oxidative phosphorylation, we sought to evaluate polymerase γ inhibitors in AML. The thymidine dideoxynucleoside analog, alovudine, is an inhibitor of polymerase γ. In AML cells, alovudine depleted mitochondrial DNA, reduced mitochondrial encoded proteins, decreased basal oxygen consumption, and decreased cell proliferation and viability. To evaluate the effects of polymerase γ inhibition with alovudine in vivo, mice were xenografted with OCI-AML2 cells and then treated with alovudine. Systemic administration of alovudine reduced leukemic growth without evidence of toxicity and decreased levels of mitochondrial DNA in the leukemic cells. We also showed that alovudine increased the monocytic differentiation of AML cells. Genetic knockdown and other chemical inhibitors of polymerase γ also promoted AML differentiation, but the effects on AML differentiation were independent of reductions in oxidative phosphorylation or respiratory chain proteins. Thus, we have identified a novel mechanism by which mitochondria regulate AML fate and differentiation independent of oxidative phosphorylation. Moreover, we highlight polymerase γ inhibitors, such as alovudine, as novel therapeutic agents for AML.
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Affiliation(s)
- Dana Yehudai
- Princess Margaret Cancer Centre, University Health Network, ON, Canada.,Medivir AB, Huddinge, Sweden
| | | | - Rose Hurren
- Princess Margaret Cancer Centre, University Health Network, ON, Canada
| | | | - Mark Albertella
- Princess Margaret Cancer Centre, University Health Network, ON, Canada
| | - Marcela Gronda
- Princess Margaret Cancer Centre, University Health Network, ON, Canada
| | - Danny V Jeyaraju
- Princess Margaret Cancer Centre, University Health Network, ON, Canada
| | - Xiaoming Wang
- Princess Margaret Cancer Centre, University Health Network, ON, Canada
| | - Samir H Barghout
- Princess Margaret Cancer Centre, University Health Network, ON, Canada
| | - Neil MacLean
- Princess Margaret Cancer Centre, University Health Network, ON, Canada
| | | | - Yulia Jitkova
- Princess Margaret Cancer Centre, University Health Network, ON, Canada
| | | | - Aaron D Schimmer
- Princess Margaret Cancer Centre, University Health Network, ON, Canada
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62
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Derbikova K, Kuzmenko A, Levitskii S, Klimontova M, Chicherin I, Baleva MV, Krasheninnikov IA, Kamenski P. Biological and Evolutionary Significance of Terminal Extensions of Mitochondrial Translation Initiation Factor 3. Int J Mol Sci 2018; 19:ijms19123861. [PMID: 30518034 PMCID: PMC6321546 DOI: 10.3390/ijms19123861] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Revised: 11/27/2018] [Accepted: 11/30/2018] [Indexed: 01/14/2023] Open
Abstract
Protein biosynthesis in mitochondria is organized in a bacterial manner. However, during evolution, mitochondrial translation mechanisms underwent many organelle-specific changes. In particular, almost all mitochondrial translation factors, being orthologous to bacterial proteins, are characterized by some unique elements of primary or secondary structure. In the case of the organellar initiation factor 3 (IF3), these elements are several dozen amino acids long N- and C-terminal extensions. This study focused on the terminal extensions of baker's yeast mitochondrial IF3, Aim23p. By in vivo deletion and complementation analysis, we show that at least one extension is necessary for Aim23p function. At the same time, human mitochondrial IF3 is fully functional in yeast mitochondria even without both terminal extensions. While Escherichia coli IF3 itself is poorly active in yeast mitochondria, adding Aim23p terminal extensions makes the resulting chimeric protein as functional as the cognate factor. Our results show that the terminal extensions of IF3 have evolved as the "adaptors" that accommodate the translation factor of bacterial origin to the evolutionary changed protein biosynthesis system in mitochondria.
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Affiliation(s)
- Ksenia Derbikova
- Faculty of Biology, M.V. Lomonosov Moscow State University, 119991 Moskva, Russia.
| | - Anton Kuzmenko
- Faculty of Biology, M.V. Lomonosov Moscow State University, 119991 Moskva, Russia.
- Institute of Molecular Genetics, Russian Academy of Science, 119991 Moskva, Russia.
| | - Sergey Levitskii
- Faculty of Biology, M.V. Lomonosov Moscow State University, 119991 Moskva, Russia.
| | - Maria Klimontova
- Faculty of Biology, M.V. Lomonosov Moscow State University, 119991 Moskva, Russia.
- Faculty of Biosciences, Heidelberg University, 69117 Heidelberg, Germany.
| | - Ivan Chicherin
- Faculty of Biology, M.V. Lomonosov Moscow State University, 119991 Moskva, Russia.
| | - Maria V Baleva
- Faculty of Biology, M.V. Lomonosov Moscow State University, 119991 Moskva, Russia.
| | | | - Piotr Kamenski
- Faculty of Biology, M.V. Lomonosov Moscow State University, 119991 Moskva, Russia.
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63
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Janvier S, De Spiegeleer B, Vanhee C, Deconinck E. Falsification of biotechnology drugs: current dangers and/or future disasters? J Pharm Biomed Anal 2018; 161:175-191. [DOI: 10.1016/j.jpba.2018.08.037] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Revised: 08/01/2018] [Accepted: 08/16/2018] [Indexed: 02/06/2023]
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64
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Yokokawa T, Kido K, Suga T, Isaka T, Hayashi T, Fujita S. Exercise-induced mitochondrial biogenesis coincides with the expression of mitochondrial translation factors in murine skeletal muscle. Physiol Rep 2018; 6:e13893. [PMID: 30369085 PMCID: PMC6204255 DOI: 10.14814/phy2.13893] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Accepted: 09/24/2018] [Indexed: 01/01/2023] Open
Abstract
The process of mitochondrial translation, in which mitochondrial (mt)DNA-encoded genes are translated into proteins, is crucial for mitochondrial function and biogenesis. In each phase, a series of mitochondrial translation factors is required for the synthesis of mtDNA-encoded mitochondrial proteins. Two mitochondrial initiation factors (mtIF2 and mtIF3), three mitochondrial elongation factors (mtEFTu, mtEFTs, and mtEFG1), one mitochondrial release factor (mtRF1L), and two mitochondrial recycling factors (mtRRF1 and mtRRF2) are mitochondrial translation factors that coordinate each translational phase. Exercise increases both nuclear DNA- and mtDNA-encoded mitochondrial proteins, resulting in mitochondrial biogenesis in skeletal muscles. Therefore, mitochondrial translation factors are likely regulated by exercise; however, it is unclear whether exercise affects mitochondrial translation factors in the skeletal muscles. We investigated whether exercise training comprehensively increases this series of mitochondrial translation factors, as well as mtDNA-encoded proteins, in the skeletal muscle. Mice were randomly assigned to either the sedentary or exercise group and housed in standard cages with or without a running wheel for 1 and 8 weeks. The expression levels of mitochondrial translation factors in the plantaris and soleus muscles were then measured. Exercise training concomitantly upregulated mitochondrial translation factors and mitochondrial proteins in the plantaris muscle. However, in the soleus muscle, these comprehensive upregulations were not detected. These results indicate that exercise-induced mitochondrial biogenesis coincides with the upregulation of mitochondrial translation factors.
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Affiliation(s)
- Takumi Yokokawa
- Laboratory of Sports and Exercise MedicineGraduate School of Human and Environmental StudiesKyoto UniversityKyotoJapan
| | - Kohei Kido
- Faculty of Sport and Health ScienceRitsumeikan UniversityKusatsuShigaJapan
| | - Tadashi Suga
- Faculty of Sport and Health ScienceRitsumeikan UniversityKusatsuShigaJapan
| | - Tadao Isaka
- Faculty of Sport and Health ScienceRitsumeikan UniversityKusatsuShigaJapan
| | - Tatsuya Hayashi
- Laboratory of Sports and Exercise MedicineGraduate School of Human and Environmental StudiesKyoto UniversityKyotoJapan
| | - Satoshi Fujita
- Faculty of Sport and Health ScienceRitsumeikan UniversityKusatsuShigaJapan
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65
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Akbergenov R, Duscha S, Fritz AK, Juskeviciene R, Oishi N, Schmitt K, Shcherbakov D, Teo Y, Boukari H, Freihofer P, Isnard-Petit P, Oettinghaus B, Frank S, Thiam K, Rehrauer H, Westhof E, Schacht J, Eckert A, Wolfer D, Böttger EC. Mutant MRPS5 affects mitoribosomal accuracy and confers stress-related behavioral alterations. EMBO Rep 2018; 19:embr.201846193. [PMID: 30237157 PMCID: PMC6216279 DOI: 10.15252/embr.201846193] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Revised: 08/21/2018] [Accepted: 08/24/2018] [Indexed: 12/30/2022] Open
Abstract
The 1555 A to G substitution in mitochondrial 12S A‐site rRNA is associated with maternally transmitted deafness of variable penetrance in the absence of otherwise overt disease. Here, we recapitulate the suggested A1555G‐mediated pathomechanism in an experimental model of mitoribosomal mistranslation by directed mutagenesis of mitoribosomal protein MRPS5. We first establish that the ratio of cysteine/methionine incorporation and read‐through of mtDNA‐encoded MT‐CO1 protein constitute reliable measures of mitoribosomal misreading. Next, we demonstrate that human HEK293 cells expressing mutant V336Y MRPS5 show increased mitoribosomal mistranslation. As for immortalized lymphocytes of individuals with the pathogenic A1555G mutation, we find little changes in the transcriptome of mutant V336Y MRPS5 HEK cells, except for a coordinated upregulation of transcripts for cytoplasmic ribosomal proteins. Homozygous knock‐in mutant Mrps5 V338Y mice show impaired mitochondrial function and a phenotype composed of enhanced susceptibility to noise‐induced hearing damage and anxiety‐related behavioral alterations. The experimental data in V338Y mutant mice point to a key role of mitochondrial translation and function in stress‐related behavioral and physiological adaptations.
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Affiliation(s)
- Rashid Akbergenov
- Institut für Medizinische Mikrobiologie, Universität Zürich, Zürich, Switzerland
| | - Stefan Duscha
- Institut für Medizinische Mikrobiologie, Universität Zürich, Zürich, Switzerland
| | - Ann-Kristina Fritz
- Anatomisches Institut, Universität Zürich, Zürich, Switzerland.,Institut für Bewegungswissenschaften und Sport, ETH Zürich, Zürich, Switzerland
| | - Reda Juskeviciene
- Institut für Medizinische Mikrobiologie, Universität Zürich, Zürich, Switzerland
| | - Naoki Oishi
- Department of Otolaryngology, Kresge Hearing Research Institute, University of Michigan, Ann Arbor, MI, USA
| | - Karen Schmitt
- Transfaculty Research Platform Molecular and Cognitive Neurosciences, Universitäre Psychiatrische Kliniken Basel, Basel, Switzerland
| | - Dimitri Shcherbakov
- Institut für Medizinische Mikrobiologie, Universität Zürich, Zürich, Switzerland
| | - Youjin Teo
- Institut für Medizinische Mikrobiologie, Universität Zürich, Zürich, Switzerland
| | - Heithem Boukari
- Institut für Medizinische Mikrobiologie, Universität Zürich, Zürich, Switzerland
| | - Pietro Freihofer
- Institut für Medizinische Mikrobiologie, Universität Zürich, Zürich, Switzerland
| | | | - Björn Oettinghaus
- Neuro- und Ophthalmopathologie, Universitätsspital Basel, Basel, Switzerland
| | - Stephan Frank
- Neuro- und Ophthalmopathologie, Universitätsspital Basel, Basel, Switzerland
| | | | - Hubert Rehrauer
- Functional Genomics Center Zurich, ETH Zürich und Universität Zürich, Zürich, Switzerland
| | - Eric Westhof
- Institut de biologie moléculaire et cellulaire du CNRS, Université de Strasbourg, Strasbourg, France
| | - Jochen Schacht
- Department of Otolaryngology, Kresge Hearing Research Institute, University of Michigan, Ann Arbor, MI, USA
| | - Anne Eckert
- Transfaculty Research Platform Molecular and Cognitive Neurosciences, Universitäre Psychiatrische Kliniken Basel, Basel, Switzerland
| | - David Wolfer
- Anatomisches Institut, Universität Zürich, Zürich, Switzerland.,Institut für Bewegungswissenschaften und Sport, ETH Zürich, Zürich, Switzerland
| | - Erik C Böttger
- Institut für Medizinische Mikrobiologie, Universität Zürich, Zürich, Switzerland
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66
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Unique features of mammalian mitochondrial translation initiation revealed by cryo-EM. Nature 2018; 560:263-267. [PMID: 30089917 DOI: 10.1038/s41586-018-0373-y] [Citation(s) in RCA: 79] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Accepted: 05/17/2018] [Indexed: 11/09/2022]
Abstract
Mitochondria maintain their own specialized protein synthesis machinery, which in mammals is used exclusively for the synthesis of the membrane proteins responsible for oxidative phosphorylation1,2. The initiation of protein synthesis in mitochondria differs substantially from bacterial or cytosolic translation systems. Mitochondrial translation initiation lacks initiation factor 1, which is essential in all other translation systems from bacteria to mammals3,4. Furthermore, only one type of methionyl transfer RNA (tRNAMet) is used for both initiation and elongation4,5, necessitating that the initiation factor specifically recognizes the formylated version of tRNAMet (fMet-tRNAMet). Lastly, most mitochondrial mRNAs do not possess 5' leader sequences to promote mRNA binding to the ribosome2. There is currently little mechanistic insight into mammalian mitochondrial translation initiation, and it is not clear how mRNA engagement, initiator-tRNA recruitment and start-codon selection occur. Here we determine the cryo-EM structure of the complete translation initiation complex from mammalian mitochondria at 3.2 Å. We describe the function of an additional domain insertion that is present in the mammalian mitochondrial initiation factor 2 (mtIF2). By closing the decoding centre, this insertion stabilizes the binding of leaderless mRNAs and induces conformational changes in the rRNA nucleotides involved in decoding. We identify unique features of mtIF2 that are required for specific recognition of fMet-tRNAMet and regulation of its GTPase activity. Finally, we observe that the ribosomal tunnel in the initiating ribosome is blocked by insertion of the N-terminal portion of mitochondrial protein mL45, which becomes exposed as the ribosome switches to elongation mode and may have an additional role in targeting of mitochondrial ribosomes to the protein-conducting pore in the inner mitochondrial membrane.
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67
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Arguello T, Köhrer C, RajBhandary UL, Moraes CT. Mitochondrial methionyl N-formylation affects steady-state levels of oxidative phosphorylation complexes and their organization into supercomplexes. J Biol Chem 2018; 293:15021-15032. [PMID: 30087118 DOI: 10.1074/jbc.ra118.003838] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2018] [Revised: 08/02/2018] [Indexed: 12/20/2022] Open
Abstract
N-Formylation of the Met-tRNAMet by the nuclearly encoded mitochondrial methionyl-tRNA formyltransferase (MTFMT) has been found to be a key determinant of protein synthesis initiation in mitochondria. In humans, mutations in the MTFMT gene result in Leigh syndrome, a progressive and severe neurometabolic disorder. However, the absolute requirement of formylation of Met-tRNAMet for protein synthesis in mammalian mitochondria is still debated. Here, we generated a Mtfmt-KO mouse fibroblast cell line and demonstrated that N-formylation of the first methionine via fMet-tRNAMet by MTFMT is not an absolute requirement for initiation of protein synthesis. However, it differentially affected the efficiency of synthesis of mtDNA-coded polypeptides. Lack of methionine N-formylation did not compromise the stability of these individual subunits but had a marked effect on the assembly and stability of the OXPHOS complexes I and IV and on their supercomplexes. In summary, N-formylation is not essential for mitochondrial protein synthesis but is critical for efficient synthesis of several mitochondrially encoded peptides and for OXPHOS complex stability and assembly into supercomplexes.
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Affiliation(s)
- Tania Arguello
- From the Department of Neurology, University of Miami School of Medicine, Miami, Florida 33136 and
| | - Caroline Köhrer
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139
| | - Uttam L RajBhandary
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139
| | - Carlos T Moraes
- From the Department of Neurology, University of Miami School of Medicine, Miami, Florida 33136 and
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68
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Zhu P, Liu Y, Zhang F, Bai X, Chen Z, Shangguan F, Zhang B, Zhang L, Chen Q, Xie D, Lan L, Xue X, Liang XJ, Lu B, Wei T, Qin Y. Human Elongation Factor 4 Regulates Cancer Bioenergetics by Acting as a Mitochondrial Translation Switch. Cancer Res 2018; 78:2813-2824. [PMID: 29572227 DOI: 10.1158/0008-5472.can-17-2059] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Revised: 01/01/2018] [Accepted: 03/20/2018] [Indexed: 11/16/2022]
Abstract
Mitochondria regulate cellular bioenergetics and redox states and influence multiple signaling pathways required for tumorigenesis. In this study, we determined that the mitochondrial translation elongation factor 4 (EF4) is a critical component of tumor progression. EF4 was ubiquitous in human tissues with localization to the mitochondria (mtEF4) and performed quality control on respiratory chain biogenesis. Knockout of mtEF4 induced respiratory chain complex defects and apoptosis, while its overexpression stimulated cancer development. In multiple cancers, expression of mtEF4 was increased in patient tumor tissues. These findings reveal that mtEF4 expression may promote tumorigenesis via an imbalance in the regulation of mitochondrial activities and subsequent variation of cellular redox. Thus, dysregulated mitochondrial translation may play a vital role in the etiology and development of diverse human cancers.Significance: Dysregulated mitochondrial translation drives tumor development and progression. Cancer Res; 78(11); 2813-24. ©2018 AACR.
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Affiliation(s)
- Ping Zhu
- Key Laboratory of RNA Biology, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Chaoyang District, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Yongzhang Liu
- Attardi Institute of Mitochondrial Biomedicine, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
| | - Fenglin Zhang
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Chaoyang District, Beijing, China
| | - Xiufeng Bai
- Key Laboratory of RNA Biology, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Chaoyang District, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Zilei Chen
- Key Laboratory of RNA Biology, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Chaoyang District, Beijing, China.,Attardi Institute of Mitochondrial Biomedicine, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
| | - Fugen Shangguan
- Key Laboratory of RNA Biology, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Chaoyang District, Beijing, China.,Attardi Institute of Mitochondrial Biomedicine, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
| | - Bo Zhang
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Chaoyang District, Beijing, China
| | - Lingyun Zhang
- Key Laboratory of RNA Biology, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Chaoyang District, Beijing, China
| | - Qianqian Chen
- University of Chinese Academy of Sciences, Beijing, China.,National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Chaoyang District, Beijing, China
| | - Deyao Xie
- Departments of Cardiothoracic Surgery, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Linhua Lan
- Attardi Institute of Mitochondrial Biomedicine, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
| | - Xiangdong Xue
- Laboratory of Controllable Nanopharmaceuticals, CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, National Center for Nanoscience and Technology of China, Zhongguancun, Beijing, China
| | - Xing-Jie Liang
- Laboratory of Controllable Nanopharmaceuticals, CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, National Center for Nanoscience and Technology of China, Zhongguancun, Beijing, China
| | - Bin Lu
- Attardi Institute of Mitochondrial Biomedicine, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China.
| | - Taotao Wei
- University of Chinese Academy of Sciences, Beijing, China. .,National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Chaoyang District, Beijing, China
| | - Yan Qin
- Key Laboratory of RNA Biology, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Chaoyang District, Beijing, China. .,University of Chinese Academy of Sciences, Beijing, China
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69
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Sissler M, González-Serrano LE, Westhof E. Recent Advances in Mitochondrial Aminoacyl-tRNA Synthetases and Disease. Trends Mol Med 2017; 23:693-708. [DOI: 10.1016/j.molmed.2017.06.002] [Citation(s) in RCA: 95] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2017] [Revised: 06/08/2017] [Accepted: 06/14/2017] [Indexed: 01/02/2023]
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70
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Gao Y, Li F, Zhou H, Yang Y, Wu R, Chen Y, Li W, Li Y, Xu X, Ke C, Pei Z. Down-regulation of MRPS23 inhibits rat breast cancer proliferation and metastasis. Oncotarget 2017; 8:71772-71781. [PMID: 29069745 PMCID: PMC5641088 DOI: 10.18632/oncotarget.17888] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2016] [Accepted: 04/28/2017] [Indexed: 11/25/2022] Open
Abstract
Mitochondrial ribosomal protein S23 (MRPS23) has been shown to be involved in breast cancer cell proliferation and metastatic phenotypes of cervical cancer. Here we investigated its biological features in breast cancer for the first time. It demonstrated that knockdown of MRPS23 reduced breast cancer cell proliferation and induced apoptosis in vitro. Besides, shRNA targeting MRPS23 (shMRPS23) inhibited tumour proliferation and metastasis by blocking tumor angiogenesis in breast cancer xenograft rat model. Small animal positron emission tomography/computed tomography (PET/CT) with 2′-deoxy-2′-[18F] fluoro-D-glucose (FDG) was performed at four weeks after tumour cell injection. We found that FDG maximum standardized uptake value (SUVmax) significantly decreased by 31 ± 3% in the shMRPS23-treated group. But this change was not independent of metabolic tumour size. In addition, we also found that shMRPS23 could significantly suppress breast cancer metastasis through inhibiting epithelial mesenchymal transition (EMT) phenotype. The epithelial marker E-cadherin was increased, whereas the metastasis associated gene vimentin was decreased. Mechanistically, shMRPS23-treated tumours failed to progress through p53 and p21WAF1/CIP1 activation, but not cytochrome c-mediated pathway. These findings suggest that MRPS23 is a potential therapeutic target for interference of breast cancer proliferation, angiogenesis and metastasis.
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Affiliation(s)
- Yan Gao
- Department of PET Center and Institute of Anesthesiology and Pain, Taihe Hospital, Hubei University of medicine, Hubei, China
| | - Fuyan Li
- Department of PET Center and Institute of Anesthesiology and Pain, Taihe Hospital, Hubei University of medicine, Hubei, China
| | - Hong Zhou
- Department of PET Center and Institute of Anesthesiology and Pain, Taihe Hospital, Hubei University of medicine, Hubei, China
| | - Yi Yang
- Department of PET Center and Institute of Anesthesiology and Pain, Taihe Hospital, Hubei University of medicine, Hubei, China
| | - Ruimin Wu
- Department of PET Center and Institute of Anesthesiology and Pain, Taihe Hospital, Hubei University of medicine, Hubei, China
| | - Yijia Chen
- Department of PET Center and Institute of Anesthesiology and Pain, Taihe Hospital, Hubei University of medicine, Hubei, China
| | - Wei Li
- Department of PET Center and Institute of Anesthesiology and Pain, Taihe Hospital, Hubei University of medicine, Hubei, China
| | - Yang Li
- Department of PET Center and Institute of Anesthesiology and Pain, Taihe Hospital, Hubei University of medicine, Hubei, China
| | - Xueqin Xu
- Department of PET Center and Institute of Anesthesiology and Pain, Taihe Hospital, Hubei University of medicine, Hubei, China
| | - Changbin Ke
- Department of PET Center and Institute of Anesthesiology and Pain, Taihe Hospital, Hubei University of medicine, Hubei, China
| | - Zhijun Pei
- Department of PET Center and Institute of Anesthesiology and Pain, Taihe Hospital, Hubei University of medicine, Hubei, China
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71
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Huttanus HM, Feng X. Compartmentalized metabolic engineering for biochemical and biofuel production. Biotechnol J 2017; 12. [DOI: 10.1002/biot.201700052] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Revised: 03/07/2017] [Accepted: 03/20/2017] [Indexed: 11/09/2022]
Affiliation(s)
- Herbert M. Huttanus
- Biological Systems Engineering; Virginia Polytechnic Institute and State University; Blacksburg VA USA
| | - Xueyang Feng
- Biological Systems Engineering; Virginia Polytechnic Institute and State University; Blacksburg VA USA
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72
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Abstract
Mitochondria play fundamental roles in the regulation of life and death of eukaryotic cells. They mediate aerobic energy conversion through the oxidative phosphorylation (OXPHOS) system, and harbor and control the intrinsic pathway of apoptosis. As a descendant of a bacterial endosymbiont, mitochondria retain a vestige of their original genome (mtDNA), and its corresponding full gene expression machinery. Proteins encoded in the mtDNA, all components of the multimeric OXPHOS enzymes, are synthesized in specialized mitochondrial ribosomes (mitoribosomes). Mitoribosomes are therefore essential in the regulation of cellular respiration. Additionally, an increasing body of literature has been reporting an alternative role for several mitochondrial ribosomal proteins as apoptosis-inducing factors. No surprisingly, the expression of genes encoding for mitoribosomal proteins, mitoribosome assembly factors and mitochondrial translation factors is modified in numerous cancers, a trait that has been linked to tumorigenesis and metastasis. In this article, we will review the current knowledge regarding the dual function of mitoribosome components in protein synthesis and apoptosis and their association with cancer susceptibility and development. We will also highlight recent developments in targeting mitochondrial ribosomes for the treatment of cancer.
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73
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Simon MT, Ng BG, Friederich MW, Wang RY, Boyer M, Kircher M, Collard R, Buckingham KJ, Chang R, Shendure J, Nickerson DA, Bamshad MJ, Van Hove JLK, Freeze HH, Abdenur JE. Activation of a cryptic splice site in the mitochondrial elongation factor GFM1 causes combined OXPHOS deficiency. Mitochondrion 2017; 34:84-90. [PMID: 28216230 DOI: 10.1016/j.mito.2017.02.004] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2016] [Revised: 01/11/2017] [Accepted: 02/10/2017] [Indexed: 11/17/2022]
Abstract
We report the clinical, biochemical, and molecular findings in two brothers with encephalopathy and multi-systemic disease. Abnormal transferrin glycoforms were suggestive of a type I congenital disorder of glycosylation (CDG). While exome sequencing was negative for CDG related candidate genes, the testing revealed compound heterozygous mutations in the mitochondrial elongation factor G gene (GFM1). One of the mutations had been reported previously while the second, novel variant was found deep in intron 6, activating a cryptic splice site. Functional studies demonstrated decreased GFM1 protein levels, suggested disrupted assembly of mitochondrial complexes III and V and decreased activities of mitochondrial complexes I and IV, all indicating combined OXPHOS deficiency.
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Affiliation(s)
- Mariella T Simon
- Division of Metabolic Disorders, CHOC Children's, Orange, CA, USA; Department of Developmental and Cell Biology, University of California Irvine, Irvine, CA, USA
| | - Bobby G Ng
- Human Genetics Program, Sanford Children's Health Research Center, Sanford-Burnham-Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - Marisa W Friederich
- Department of Pediatrics, Section of Clinical Genetics and Metabolism, University of Colorado, Aurora, CO, USA
| | - Raymond Y Wang
- Division of Metabolic Disorders, CHOC Children's, Orange, CA, USA; Department of Pediatrics, University of California Irvine, Irvine, CA, USA
| | - Monica Boyer
- Division of Metabolic Disorders, CHOC Children's, Orange, CA, USA
| | - Martin Kircher
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Renata Collard
- Department of Pediatrics, Section of Clinical Genetics and Metabolism, University of Colorado, Aurora, CO, USA
| | - Kati J Buckingham
- Department of Pediatrics, University of Washington, Seattle, WA, USA
| | - Richard Chang
- Division of Metabolic Disorders, CHOC Children's, Orange, CA, USA; Department of Pediatrics, University of California Irvine, Irvine, CA, USA
| | - Jay Shendure
- Department of Genome Sciences, University of Washington, Seattle, WA, USA; Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA
| | | | - Michael J Bamshad
- Department of Genome Sciences, University of Washington, Seattle, WA, USA; Department of Pediatrics, University of Washington, Seattle, WA, USA
| | - Johan L K Van Hove
- Department of Pediatrics, Section of Clinical Genetics and Metabolism, University of Colorado, Aurora, CO, USA
| | - Hudson H Freeze
- Human Genetics Program, Sanford Children's Health Research Center, Sanford-Burnham-Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - Jose E Abdenur
- Division of Metabolic Disorders, CHOC Children's, Orange, CA, USA; Department of Pediatrics, University of California Irvine, Irvine, CA, USA.
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74
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Di Nottia M, Montanari A, Verrigni D, Oliva R, Torraco A, Fernandez-Vizarra E, Diodato D, Rizza T, Bianchi M, Catteruccia M, Zeviani M, Dionisi-Vici C, Francisci S, Bertini E, Carrozzo R. Novel mutation in mitochondrial Elongation Factor EF-Tu associated to dysplastic leukoencephalopathy and defective mitochondrial DNA translation. Biochim Biophys Acta Mol Basis Dis 2017; 1863:961-967. [PMID: 28132884 PMCID: PMC5335904 DOI: 10.1016/j.bbadis.2017.01.022] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2016] [Revised: 12/20/2016] [Accepted: 01/25/2017] [Indexed: 12/27/2022]
Abstract
The mitochondrial Elongation Factor Tu (EF-Tu), encoded by the TUFM gene, is a highly conserved GTPase, which is part of the mitochondrial protein translation machinery. In its activated form it delivers the aminoacyl-tRNAs to the A site of the mitochondrial ribosome. We report here on a baby girl with severe infantile macrocystic leukodystrophy with micropolygyria and a combined defect of complexes I and IV in muscle biopsy, caused by a novel mutation identified in TUFM. Using human mutant cells and the yeast model, we demonstrate the pathological role of the novel variant. Moreover, results of a molecular modeling study suggest that the mutant is inactive in mitochondrial polypeptide chain elongation, probably as a consequence of its reduced ability to bind mitochondrial aa-tRNAs. Four patients have so far been described with mutations in TUFM, and, following the first description of the disease in a single patient, we describe similar clinical and neuroradiological features in an additional patient.
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Affiliation(s)
- Michela Di Nottia
- Unit of Muscular and Neurodegenerative Disorders, Laboratory of Molecular Medicine, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Arianna Montanari
- Pasteur Institute Italy - Cenci Bolognetti Foundation, Italy; Department of Biology and Biotechnologies "Charles Darwin", Sapienza University of Rome, Rome, Italy
| | - Daniela Verrigni
- Unit of Muscular and Neurodegenerative Disorders, Laboratory of Molecular Medicine, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Romina Oliva
- Department of Sciences and Technologies, University Parthenope of Naples, Centro Direzionale Isola C4, I-80143 Naples, Italy
| | - Alessandra Torraco
- Unit of Muscular and Neurodegenerative Disorders, Laboratory of Molecular Medicine, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | | | - Daria Diodato
- Unit of Muscular and Neurodegenerative Disorders, Laboratory of Molecular Medicine, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Teresa Rizza
- Unit of Muscular and Neurodegenerative Disorders, Laboratory of Molecular Medicine, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Marzia Bianchi
- Unit of Muscular and Neurodegenerative Disorders, Laboratory of Molecular Medicine, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Michela Catteruccia
- Unit of Muscular and Neurodegenerative Disorders, Laboratory of Molecular Medicine, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Massimo Zeviani
- Mitochondrial Biology Unit, Medical Research Council, Cambridge, UK
| | - Carlo Dionisi-Vici
- Division of Metabolism, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Silvia Francisci
- Department of Biology and Biotechnologies "Charles Darwin", Sapienza University of Rome, Rome, Italy
| | - Enrico Bertini
- Unit of Muscular and Neurodegenerative Disorders, Laboratory of Molecular Medicine, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Rosalba Carrozzo
- Unit of Muscular and Neurodegenerative Disorders, Laboratory of Molecular Medicine, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy.
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75
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The Assembly Pathway of Mitochondrial Respiratory Chain Complex I. Cell Metab 2017; 25:128-139. [PMID: 27720676 DOI: 10.1016/j.cmet.2016.09.002] [Citation(s) in RCA: 281] [Impact Index Per Article: 40.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/25/2016] [Revised: 07/21/2016] [Accepted: 09/10/2016] [Indexed: 11/20/2022]
Abstract
Mitochondrial complex I is the largest integral membrane enzyme of the respiratory chain and consists of 44 different subunits encoded in the mitochondrial and nuclear genome. Its biosynthesis is a highly complicated and multifaceted process involving at least 14 additional assembly factors. How these subunits assemble into a functional complex I and where the assembly factors come into play is largely unknown. Here, we applied a dynamic complexome profiling approach to elucidate the assembly of human mitochondrial complex I and its further incorporation into respiratory chain supercomplexes. We delineate the stepwise incorporation of all but one subunit into a series of distinct assembly intermediates and their association with known and putative assembly factors, which had not been implicated in this process before. The resulting detailed and comprehensive model of complex I assembly is fully consistent with recent structural data and the remarkable modular architecture of this multiprotein complex.
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76
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Lee DE, Brown JL, Rosa ME, Brown LA, Perry RA, Washington TA, Greene N. Translational machinery of mitochondrial mRNA is promoted by physical activity in Western diet-induced obese mice. Acta Physiol (Oxf) 2016; 218:167-177. [PMID: 27061106 DOI: 10.1111/apha.12687] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2015] [Revised: 04/06/2016] [Accepted: 04/07/2016] [Indexed: 12/23/2022]
Abstract
AIM Mitochondria-encoded proteins are necessary for oxidative phosphorylation; however, no report has examined how physical activity (PA) and obesity affect mitochondrial mRNA translation machinery. Our purpose was to determine whether Western diet (WD)-induced obesity and voluntary wheel running (VWR) impact mitochondrial mRNA translation machinery and whether expression of this machinery is dictated by oxidative phenotype. METHODS Obesity was induced with 8-wk WD feeding, and in the final 4 wks, half of mice were allowed VWR. Mitochondrial mRNA translation machinery including initiation factors (mtIF2/3), elongation factor Tu (TUFM) and translational activator (TACO1), and mitochondria-encoded proteins (CytB and ND4) was assessed by immunoblotting. The relation of mitochondrial mRNA translation to muscle oxidative phenotype was assessed using PGC-1α transgenic overexpression (MCK-PGC-1α vs. wild-type mice) and comparing across muscle groups in wild-type mice. RESULTS mtIF3 and TACO1 proteins were ~45% greater in VWR than sedentary (SED), and TACO1 and mtIF2 proteins were ~60% and 125% greater in WD than normal chow (NC). TUFM protein was ~50% lower in WD-SED than NC-SED, but ~50% greater in WD-VWR compared to NC-SED. CytB and ND4 were ~40% greater in VWR and ND4 was twofold greater with WD. TUFM, TACO1, ND4 and CytB were greater in MCK-PGC-1α compared to wild-type, and mtIF2/3 contents were not different. In oxidative muscle (soleus), mitochondrial translation machinery was elevated compared to mixed (gastrocnemius) or glycolytic (extensor digitorum longus) muscles. CONCLUSION These data suggest a novel mechanism promoting mitochondrial function by translation of mitochondrial protein following PA. This may act to promote muscle health by PA in obesity.
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Affiliation(s)
- D. E. Lee
- Integrative Muscle Metabolism Laboratory; Human Performance Laboratory; Department of Health, Human Performance and Recreation; University of Arkansas; Fayetteville AR USA
| | - J. L. Brown
- Integrative Muscle Metabolism Laboratory; Human Performance Laboratory; Department of Health, Human Performance and Recreation; University of Arkansas; Fayetteville AR USA
| | - M. E. Rosa
- Integrative Muscle Metabolism Laboratory; Human Performance Laboratory; Department of Health, Human Performance and Recreation; University of Arkansas; Fayetteville AR USA
| | - L. A. Brown
- Exercise Muscle Biology Laboratory; Human Performance Laboratory; Department of Health; Human Performance and Recreation; University of Arkansas; Fayetteville AR USA
| | - R. A. Perry
- Exercise Muscle Biology Laboratory; Human Performance Laboratory; Department of Health; Human Performance and Recreation; University of Arkansas; Fayetteville AR USA
| | - T. A. Washington
- Exercise Muscle Biology Laboratory; Human Performance Laboratory; Department of Health; Human Performance and Recreation; University of Arkansas; Fayetteville AR USA
| | - N. P. Greene
- Integrative Muscle Metabolism Laboratory; Human Performance Laboratory; Department of Health, Human Performance and Recreation; University of Arkansas; Fayetteville AR USA
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77
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Cao X, Qin Y. Mitochondrial translation factors reflect coordination between organelles and cytoplasmic translation via mTOR signaling: Implication in disease. Free Radic Biol Med 2016; 100:231-237. [PMID: 27101739 DOI: 10.1016/j.freeradbiomed.2016.04.010] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/18/2016] [Revised: 04/11/2016] [Accepted: 04/13/2016] [Indexed: 12/24/2022]
Abstract
Mitochondria are semi-autonomous organelle possessing their own translation machinery to biosynthesize mitochondrial DNA (mtDNA)-encoded polypeptides, which are the core subunits of oxidative phosphorylation (OXPHOS) complexes. Mitochondrial translation elongation factor 4 (mtEF4) is a key quality control factor in mitochondrial translation (mt-translation) that regulates mitochondrial tRNA translocation and modulates cellular responses by influencing cytoplasmic translation (ct-translation). In addition to mtEF4, mt-translational activators, mitochondrial microRNAs (mitomiRs), and MITRAC have been reported recently as crucial mt-translation regulators. Here, we focus on the novel ways how these factors regulate mt-translation, discuss the main cellular response of mammalian target of rapamycin (mTOR) signalling upon mt-translation defects, and summarize the related human diseases.
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Affiliation(s)
- Xintao Cao
- Key Laboratory of RNA Biology, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Chaoyang District, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yan Qin
- Key Laboratory of RNA Biology, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Chaoyang District, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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Abstract
Synthesis of polypeptides from mRNA (translation) is a fundamental cellular process that is coordinated and catalyzed by a set of canonical ‘translation factors’. Surprisingly, the translation factors of Drosophila melanogaster have not yet been systematically identified, leading to inconsistencies in their nomenclature and shortcomings in functional (Gene Ontology, GO) annotations. Here, we describe the complete set of translation factors in D. melanogaster, applying nomenclature already in widespread use in other species, and revising their functional annotation. The collection comprises 43 initiation factors, 12 elongation factors, 3 release factors and 6 recycling factors, totaling 64 of which 55 are cytoplasmic and 9 are mitochondrial. We also provide an overview of notable findings and particular insights derived from Drosophila about these factors. This catalog, together with the incorporation of the improved nomenclature and GO annotation into FlyBase, will greatly facilitate access to information about the functional roles of these important proteins.
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Affiliation(s)
- Steven J Marygold
- a FlyBase, Department of Physiology , Development and Neuroscience, University of Cambridge , Cambridge , UK
| | - Helen Attrill
- a FlyBase, Department of Physiology , Development and Neuroscience, University of Cambridge , Cambridge , UK
| | - Paul Lasko
- b Department of Biology , McGill University , Bellini Life Sciences Complex, Montreal, Quebec , Canada
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79
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Duechler M, Leszczyńska G, Sochacka E, Nawrot B. Nucleoside modifications in the regulation of gene expression: focus on tRNA. Cell Mol Life Sci 2016; 73:3075-95. [PMID: 27094388 PMCID: PMC4951516 DOI: 10.1007/s00018-016-2217-y] [Citation(s) in RCA: 89] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2015] [Revised: 03/25/2016] [Accepted: 04/04/2016] [Indexed: 01/10/2023]
Abstract
Both, DNA and RNA nucleoside modifications contribute to the complex multi-level regulation of gene expression. Modified bases in tRNAs modulate protein translation rates in a highly dynamic manner. Synonymous codons, which differ by the third nucleoside in the triplet but code for the same amino acid, may be utilized at different rates according to codon-anticodon affinity. Nucleoside modifications in the tRNA anticodon loop can favor the interaction with selected codons by stabilizing specific base pairs. Similarly, weakening of base pairing can discriminate against binding to near-cognate codons. mRNAs enriched in favored codons are translated in higher rates constituting a fine-tuning mechanism for protein synthesis. This so-called codon bias establishes a basic protein level, but sometimes it is necessary to further adjust the production rate of a particular protein to actual requirements, brought by, e.g., stages in circadian rhythms, cell cycle progression or exposure to stress. Such an adjustment is realized by the dynamic change of tRNA modifications resulting in the preferential translation of mRNAs coding for example for stress proteins to facilitate cell survival. Furthermore, tRNAs contribute in an entirely different way to another, less specific stress response consisting in modification-dependent tRNA cleavage that contributes to the general down-regulation of protein synthesis. In this review, we summarize control functions of nucleoside modifications in gene regulation with a focus on recent findings on protein synthesis control by tRNA base modifications.
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Affiliation(s)
- Markus Duechler
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112, 90-363, Lodz, Poland.
| | - Grażyna Leszczyńska
- Institute of Organic Chemistry, Lodz University of Technology, Zeromskiego 116, 90-924, Lodz, Poland
| | - Elzbieta Sochacka
- Institute of Organic Chemistry, Lodz University of Technology, Zeromskiego 116, 90-924, Lodz, Poland
| | - Barbara Nawrot
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112, 90-363, Lodz, Poland
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80
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Abstract
Oxidative phosphorylation (OXPHOS) is the mechanism whereby ATP, the major energy source for the cell, is produced by harnessing cellular respiration in the mitochondrion. This is facilitated by five multi-subunit complexes housed within the inner mitochondrial membrane. These complexes, with the exception of complex II, are of a dual genetic origin, requiring expression from nuclear and mitochondrial genes. Mitochondrially encoded mRNA is translated on the mitochondrial ribosome (mitoribosome) and the recent release of the near atomic resolution structure of the mammalian mitoribosome has highlighted its peculiar features. However, whereas some aspects of mitochondrial translation are understood, much is to be learnt about the presentation of mitochondrial mRNA to the mitoribosome, the biogenesis of the machinery, the exact role of the membrane, the constitution of the translocon/insertion machinery and the regulation of translation in the mitochondrion. This review addresses our current knowledge of mammalian mitochondrial gene expression, highlights key questions and indicates how defects in this process can result in profound mitochondrial disease.
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81
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Affiliation(s)
- Martin Ott
- Department of Biochemistry and Biophysics, Stockholm University, SE-106 91 Stockholm, Sweden;
| | - Alexey Amunts
- Department of Biochemistry and Biophysics, Stockholm University, SE-106 91 Stockholm, Sweden;
- Science for Life Laboratory, Stockholm University, SE-171 21 Solna, Sweden;
| | - Alan Brown
- Laboratory of Molecular Biology, Medical Research Council, Cambridge CB2 0QH, United Kingdom;
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82
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Ostojić J, Panozzo C, Bourand-Plantefol A, Herbert CJ, Dujardin G, Bonnefoy N. Ribosome recycling defects modify the balance between the synthesis and assembly of specific subunits of the oxidative phosphorylation complexes in yeast mitochondria. Nucleic Acids Res 2016; 44:5785-97. [PMID: 27257059 PMCID: PMC4937339 DOI: 10.1093/nar/gkw490] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2016] [Accepted: 05/20/2016] [Indexed: 01/07/2023] Open
Abstract
Mitochondria have their own translation machinery that produces key subunits of the OXPHOS complexes. This machinery relies on the coordinated action of nuclear-encoded factors of bacterial origin that are well conserved between humans and yeast. In humans, mutations in these factors can cause diseases; in yeast, mutations abolishing mitochondrial translation destabilize the mitochondrial DNA. We show that when the mitochondrial genome contains no introns, the loss of the yeast factors Mif3 and Rrf1 involved in ribosome recycling neither blocks translation nor destabilizes mitochondrial DNA. Rather, the absence of these factors increases the synthesis of the mitochondrially-encoded subunits Cox1, Cytb and Atp9, while strongly impairing the assembly of OXPHOS complexes IV and V. We further show that in the absence of Rrf1, the COX1 specific translation activator Mss51 accumulates in low molecular weight forms, thought to be the source of the translationally-active form, explaining the increased synthesis of Cox1. We propose that Rrf1 takes part in the coordination between translation and OXPHOS assembly in yeast mitochondria. These interactions between general and specific translation factors might reveal an evolutionary adaptation of the bacterial translation machinery to the set of integral membrane proteins that are translated within mitochondria.
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Affiliation(s)
- Jelena Ostojić
- Institute of Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, UEVE, 91198, Gif-sur-Yvette cedex, France
| | - Cristina Panozzo
- Institute of Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, UEVE, 91198, Gif-sur-Yvette cedex, France
| | - Alexa Bourand-Plantefol
- Institute of Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, UEVE, 91198, Gif-sur-Yvette cedex, France
| | - Christopher J Herbert
- Institute of Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, UEVE, 91198, Gif-sur-Yvette cedex, France
| | - Geneviève Dujardin
- Institute of Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, UEVE, 91198, Gif-sur-Yvette cedex, France
| | - Nathalie Bonnefoy
- Institute of Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, UEVE, 91198, Gif-sur-Yvette cedex, France
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83
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He K, Guo X, Liu Y, Li J, Hu Y, Wang D, Song J. TUFM downregulation induces epithelial-mesenchymal transition and invasion in lung cancer cells via a mechanism involving AMPK-GSK3β signaling. Cell Mol Life Sci 2016; 73:2105-21. [PMID: 26781467 PMCID: PMC11108297 DOI: 10.1007/s00018-015-2122-9] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2015] [Revised: 11/25/2015] [Accepted: 12/15/2015] [Indexed: 12/30/2022]
Abstract
Mitochondrial dysfunction and epithelial-to-mesenchymal transition (EMT) play important roles in cancer development and metastasis. However, very little is known about the connection between mitochondrial dysfunction and EMT. Tu translation elongation factor, mitochondrial (TUFM), a key factor in the translational expression of mitochondrial DNA, plays an important role in the control of mitochondrial function. Here, we show that TUFM is downregulated in human cancer tissues. TUFM expression level was positively correlated with that of E-cadherin and decreased significantly during the progression of human lung cancer. TUFM knockdown induced EMT, reduced mitochondrial respiratory chain activity, and increased glycolytic function and the production of reactive oxygen species (ROS). Mechanistically, TUFM knockdown activated AMPK and phosphorylated GSK3β and increased the nuclear accumulation of β-catenin, leading to the induction of EMT and increased migration and metastasis of A549 lung cancer cells. Although TUFM knockdown also induced EMT of MCF7 breast cancer cells, the underlying mechanism appeared somewhat different from that in lung cancer cells. Our work identifies TUFM as a novel regulator of EMT and suggests a molecular link between mitochondrial dysfunction and EMT induction.
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Affiliation(s)
- Kai He
- State Key Laboratory of Cell Biology, Innovation Center for Cell Signalling Network, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 320 Yue-Yang Road, Shanghai, 200031, China
| | - Xiaojie Guo
- State Key Laboratory of Cell Biology, Innovation Center for Cell Signalling Network, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 320 Yue-Yang Road, Shanghai, 200031, China
| | - Yi Liu
- State Key Laboratory of Cell Biology, Innovation Center for Cell Signalling Network, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 320 Yue-Yang Road, Shanghai, 200031, China
| | - Jingsong Li
- State Key Laboratory of Cell Biology, Innovation Center for Cell Signalling Network, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 320 Yue-Yang Road, Shanghai, 200031, China
| | - Ying Hu
- State Key Laboratory of Cell Biology, Innovation Center for Cell Signalling Network, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 320 Yue-Yang Road, Shanghai, 200031, China
| | - Dongmei Wang
- State Key Laboratory of Cell Biology, Innovation Center for Cell Signalling Network, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 320 Yue-Yang Road, Shanghai, 200031, China
| | - Jianguo Song
- State Key Laboratory of Cell Biology, Innovation Center for Cell Signalling Network, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 320 Yue-Yang Road, Shanghai, 200031, China.
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84
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Potluri P, Procaccio V, Scheffler IE, Wallace DC. High throughput gene complementation screening permits identification of a mammalian mitochondrial protein synthesis (ρ(-)) mutant. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2016; 1857:1336-1343. [PMID: 26946086 DOI: 10.1016/j.bbabio.2016.02.021] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2016] [Revised: 02/24/2016] [Accepted: 02/25/2016] [Indexed: 12/26/2022]
Abstract
To identify nuclear DNA (nDNA) oxidative phosphorylation (OXPHOS) gene mutations using cultured cells, we have developed a complementation system based on retroviral transduction with a full length cDNA expression library and selection for OXHOS function by growth in galactose. We have used this system to transduce the Chinese hamster V79-G7 OXPHOS mutant cell line with a defect in mitochondrial protein synthesis. The complemented cells were found to have acquired the cDNA for the bS6m polypeptide of the small subunit of the mitochondrial ribosome. bS6m is a 14 kDa polypeptide located on the outside of the mitochondrial 28S ribosomal subunit and interacts with the rRNA. The V79-G7 mutant protein was found to harbor a methionine to threonine missense mutation at codon 13. The hamster bS6m null mutant could also be complemented by its orthologs from either mouse or human. bS6m protein tagged at its C-terminus by HA, His or GFP localized to the mitochondrion and was fully functional. Through site-directed mutagenesis we identified the probable RNA interacting residues of the bS6m peptide and tested the functional significance of mammalian specific C-terminal region. The N-terminus of the bS6m polypeptide functionally corresponds to that of the prokaryotic small ribosomal subunit, but deletion of C-terminal residues along with the zinc ion coordinating cysteine had no functional effect. Since mitochondrial diseases can result from hundreds to thousands of different nDNA gene mutations, this one step viral complementation cloning may facilitate the molecular diagnosis of a range of nDNA mitochondrial disease mutations. This article is part of a Special Issue entitled 'EBEC 2016: 19th European Bioenergetics Conference, Riva del Garda, Italy, July 2-6, 2016', edited by Prof. Paolo Bernardi.
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Affiliation(s)
- Prasanth Potluri
- Center for Mitochondrial and Epigenomic Medicine, The Children's Hospital of Philadelphia, Department of Pathology and Laboratory of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Vincent Procaccio
- Dépt. de Biochimie et Génétique, Centre Hospitalier Universitaire d'Angers, Angers, France
| | - Immo E Scheffler
- Division of Biological Sciences, University of California - San Diego, La Jolla, CA, United States
| | - Douglas C Wallace
- Center for Mitochondrial and Epigenomic Medicine, The Children's Hospital of Philadelphia, Department of Pathology and Laboratory of Medicine, University of Pennsylvania, Philadelphia, PA, United States.
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85
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Lasserre JP, Dautant A, Aiyar RS, Kucharczyk R, Glatigny A, Tribouillard-Tanvier D, Rytka J, Blondel M, Skoczen N, Reynier P, Pitayu L, Rötig A, Delahodde A, Steinmetz LM, Dujardin G, Procaccio V, di Rago JP. Yeast as a system for modeling mitochondrial disease mechanisms and discovering therapies. Dis Model Mech 2016; 8:509-26. [PMID: 26035862 PMCID: PMC4457039 DOI: 10.1242/dmm.020438] [Citation(s) in RCA: 101] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Mitochondrial diseases are severe and largely untreatable. Owing to the many essential processes carried out by mitochondria and the complex cellular systems that support these processes, these diseases are diverse, pleiotropic, and challenging to study. Much of our current understanding of mitochondrial function and dysfunction comes from studies in the baker's yeast Saccharomyces cerevisiae. Because of its good fermenting capacity, S. cerevisiae can survive mutations that inactivate oxidative phosphorylation, has the ability to tolerate the complete loss of mitochondrial DNA (a property referred to as ‘petite-positivity’), and is amenable to mitochondrial and nuclear genome manipulation. These attributes make it an excellent model system for studying and resolving the molecular basis of numerous mitochondrial diseases. Here, we review the invaluable insights this model organism has yielded about diseases caused by mitochondrial dysfunction, which ranges from primary defects in oxidative phosphorylation to metabolic disorders, as well as dysfunctions in maintaining the genome or in the dynamics of mitochondria. Owing to the high level of functional conservation between yeast and human mitochondrial genes, several yeast species have been instrumental in revealing the molecular mechanisms of pathogenic human mitochondrial gene mutations. Importantly, such insights have pointed to potential therapeutic targets, as have genetic and chemical screens using yeast. Summary: In this Review, we discuss the use of budding yeast to understand mitochondrial diseases and help in the search for their treatments.
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Affiliation(s)
- Jean-Paul Lasserre
- University Bordeaux-CNRS, IBGC, UMR 5095, 1 rue Camille Saint-Saëns, Bordeaux F-33000, France
| | - Alain Dautant
- University Bordeaux-CNRS, IBGC, UMR 5095, 1 rue Camille Saint-Saëns, Bordeaux F-33000, France
| | - Raeka S Aiyar
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Meyerhofstrasse 1, Heidelberg 69117, Germany
| | - Roza Kucharczyk
- Department of Genetics, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw 02-106, Poland
| | - Annie Glatigny
- Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CEA, CNRS, Université Paris-Sud, 1 avenue de la terrasse, Gif-sur-Yvette 91198, France
| | - Déborah Tribouillard-Tanvier
- Institut National de la Santé et de la Recherche Médicale UMR1078, Université de Bretagne Occidentale, Faculté de Médecine et des Sciences de la Santé, Etablissement Français du Sang (EFS) Bretagne, CHRU Brest, Hôpital Morvan, Laboratoire de Génétique Moléculaire, Brest F-29200, France
| | - Joanna Rytka
- Department of Genetics, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw 02-106, Poland
| | - Marc Blondel
- Institut National de la Santé et de la Recherche Médicale UMR1078, Université de Bretagne Occidentale, Faculté de Médecine et des Sciences de la Santé, Etablissement Français du Sang (EFS) Bretagne, CHRU Brest, Hôpital Morvan, Laboratoire de Génétique Moléculaire, Brest F-29200, France
| | - Natalia Skoczen
- University Bordeaux-CNRS, IBGC, UMR 5095, 1 rue Camille Saint-Saëns, Bordeaux F-33000, France Department of Genetics, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw 02-106, Poland
| | - Pascal Reynier
- UMR CNRS 6214-INSERM U1083, Angers 49933, Cedex 9, France Département de Biochimie et Génétique, Centre Hospitalier Universitaire d'Angers, Angers 49933, Cedex 9, France
| | - Laras Pitayu
- Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CEA, CNRS, Université Paris-Sud, rue Gregor Mendel, Orsay 91405, France
| | - Agnès Rötig
- Inserm U1163, Hôpital Necker-Enfants-Malades, Institut Imagine, Université Paris Descartes-Sorbonne Paris Cité, 149 rue de Sèvres, Paris 75015, France
| | - Agnès Delahodde
- Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CEA, CNRS, Université Paris-Sud, rue Gregor Mendel, Orsay 91405, France
| | - Lars M Steinmetz
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Meyerhofstrasse 1, Heidelberg 69117, Germany Stanford Genome Technology Center, Department of Biochemistry, Stanford University, Palo Alto, CA 94304, USA Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305-5301, USA
| | - Geneviève Dujardin
- Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CEA, CNRS, Université Paris-Sud, 1 avenue de la terrasse, Gif-sur-Yvette 91198, France
| | - Vincent Procaccio
- UMR CNRS 6214-INSERM U1083, Angers 49933, Cedex 9, France Département de Biochimie et Génétique, Centre Hospitalier Universitaire d'Angers, Angers 49933, Cedex 9, France
| | - Jean-Paul di Rago
- University Bordeaux-CNRS, IBGC, UMR 5095, 1 rue Camille Saint-Saëns, Bordeaux F-33000, France
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86
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Richter U, Lahtinen T, Marttinen P, Suomi F, Battersby BJ. Quality control of mitochondrial protein synthesis is required for membrane integrity and cell fitness. J Cell Biol 2016; 211:373-89. [PMID: 26504172 PMCID: PMC4621829 DOI: 10.1083/jcb.201504062] [Citation(s) in RCA: 84] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Impaired turnover of newly synthesized mitochondrial proteins of the oxidative phosphorylation complexes leads to protein over-accumulation in the inner mitochondrial membrane, thereby generating a stress that dissipates the mitochondrial membrane potential and therefore compromises organelle and cellular fitness. Mitochondrial ribosomes synthesize a subset of hydrophobic proteins required for assembly of the oxidative phosphorylation complexes. This process requires temporal and spatial coordination and regulation, so quality control of mitochondrial protein synthesis is paramount to maintain proteostasis. We show how impaired turnover of de novo mitochondrial proteins leads to aberrant protein accumulation in the mitochondrial inner membrane. This creates a stress in the inner membrane that progressively dissipates the mitochondrial membrane potential, which in turn stalls mitochondrial protein synthesis and fragments the mitochondrial network. The mitochondrial m-AAA protease subunit AFG3L2 is critical to this surveillance mechanism that we propose acts as a sensor to couple the synthesis of mitochondrial proteins with organelle fitness, thus ensuring coordinated assembly of the oxidative phosphorylation complexes from two sets of ribosomes.
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Affiliation(s)
- Uwe Richter
- Research Programs for Molecular Neurology, Biomedicum Helsinki, University of Helsinki, 00290 Helsinki, Finland
| | - Taina Lahtinen
- Research Programs for Molecular Neurology, Biomedicum Helsinki, University of Helsinki, 00290 Helsinki, Finland
| | - Paula Marttinen
- Research Programs for Molecular Neurology, Biomedicum Helsinki, University of Helsinki, 00290 Helsinki, Finland
| | - Fumi Suomi
- Research Programs for Molecular Neurology, Biomedicum Helsinki, University of Helsinki, 00290 Helsinki, Finland
| | - Brendan J Battersby
- Research Programs for Molecular Neurology, Biomedicum Helsinki, University of Helsinki, 00290 Helsinki, Finland
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Imagawa E, Fattal-Valevski A, Eyal O, Miyatake S, Saada A, Nakashima M, Tsurusaki Y, Saitsu H, Miyake N, Matsumoto N. Homozygous p.V116* mutation in C12orf65 results in Leigh syndrome. J Neurol Neurosurg Psychiatry 2016; 87:212-6. [PMID: 25995486 DOI: 10.1136/jnnp-2014-310084] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/19/2014] [Accepted: 05/05/2015] [Indexed: 11/03/2022]
Abstract
BACKGROUND Leigh syndrome (LS) is an early-onset progressive neurodegenerative disorder associated with mitochondrial dysfunction. LS is characterised by elevated lactate and pyruvate and bilateral symmetric hyperintense lesions in the basal ganglia, thalamus, brainstem, cerebral white matter or spinal cord on T2-weighted MRI. LS is a genetically heterogeneous disease, and to date mutations in approximately 40 genes related to mitochondrial function have been linked to the disorder. METHODS We investigated a pair of female monozygotic twins diagnosed with LS from consanguineous healthy parents of Indian origin. Their common clinical features included optic atrophy, ophthalmoplegia, spastic paraparesis and mild intellectual disability. High-blood lactate and high-intensity signal in the brainstem on T2-weighted MRI were consistent with a clinical diagnosis of LS. To identify the genetic cause of their condition, we performed whole exome sequencing. RESULTS We identified a homozygous nonsense mutation in C12orf65 (NM_001143905; c.346delG, p.V116*) in the affected twins. Interestingly, the identical mutation was previously reported in an Indian family with Charcot-Marie Tooth disease type 6, which displayed some overlapping clinical features with the twins. CONCLUSIONS We demonstrate that the identical nonsense mutation in C12orf65 can result in different clinical features, suggesting the involvement of unknown modifiers.
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Affiliation(s)
- Eri Imagawa
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Aviva Fattal-Valevski
- Paediatric Neurology Unit, Tel Aviv Sourasky Medical Centre, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Ori Eyal
- Paediatric Endocrinology Unit, Tel Aviv Sourasky Medical Centre, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Satoko Miyatake
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Ann Saada
- Monique and Jacques Roboh Department of Genetic Research and the Department of Genetic and Metabolic Diseases, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | - Mitsuko Nakashima
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Yoshinori Tsurusaki
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Hirotomo Saitsu
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Noriko Miyake
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Naomichi Matsumoto
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
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88
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Grzybkowska A, Jędrzejczyk D, Rostkowski M, Chworos A, Dybala-Defratyka A. RNA model evaluation based on MD simulation of four tRNA analogs. RSC Adv 2016. [DOI: 10.1039/c6ra14933b] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
Characteristic of 3D structures of tRNA analogs generated from primary sequence, subjected to all-atom MD simulation and assessed using selected RNA model evaluation methods.
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Affiliation(s)
- Anna Grzybkowska
- Institute of Applied Radiation Chemistry
- Faculty of Chemistry
- Lodz University of Technology
- Lodz
- Poland
| | - Dominika Jędrzejczyk
- Center of Molecular and Macromolecular Studies
- Polish Academy of Sciences
- 90-363 Lodz
- Poland
| | - Michał Rostkowski
- Institute of Applied Radiation Chemistry
- Faculty of Chemistry
- Lodz University of Technology
- Lodz
- Poland
| | - Arkadiusz Chworos
- Center of Molecular and Macromolecular Studies
- Polish Academy of Sciences
- 90-363 Lodz
- Poland
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89
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Kartvelishvili E, Peretz M, Tworowski D, Moor N, Safro M. Chimeric human mitochondrial PheRS exhibits editing activity to discriminate nonprotein amino acids. Protein Sci 2015; 25:618-26. [PMID: 26645192 DOI: 10.1002/pro.2855] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2015] [Accepted: 11/10/2015] [Indexed: 11/11/2022]
Abstract
Mitochondria are considered as the primary source of reactive oxygen species (ROS) in nearly all eukaryotic cells during respiration. The harmful effects of these compounds range from direct neurotoxicity to incorporation into proteins producing aberrant molecules with multiple physiological problems. Phenylalanine exposure to ROS produces multiple oxidized isomers: tyrosine, Levodopa, ortho-Tyr, meta-Tyr (m-Tyr), and so on. Cytosolic phenylalanyl-tRNA synthetase (PheRS) exerts control over the translation accuracy, hydrolyzing misacylated products, while monomeric mitochondrial PheRS lacks the editing activity. Recently we showed that "teamwork" of cytosolic and mitochondrial PheRSs cannot prevent incorporation of m-Tyr and l-Dopa into proteins. Here, we present human mitochondrial chimeric PheRS with implanted editing module taken from EcPheRS. The monomeric mitochondrial chimera possesses editing activity, while in bacterial and cytosolic PheRSs this type of activity was detected for the (αβ)2 architecture only. The fusion protein catalyzes aminoacylation of tRNA(Phe) with cognate phenylalanine and effectively hydrolyzes the noncognate aminoacyl-tRNAs: Tyr-tRNA(Phe) and m-Tyr-tRNA(Phe) .
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Affiliation(s)
| | - Moshe Peretz
- Department of Structural Biology, Weizmann Institute of Science, Rehovot, 76100, Israel
| | - Dmitry Tworowski
- Department of Structural Biology, Weizmann Institute of Science, Rehovot, 76100, Israel
| | - Nina Moor
- Institute of Chemical Biology and Fundamental Medicine, Novosibirsk, 630090, Russia
| | - Mark Safro
- Department of Structural Biology, Weizmann Institute of Science, Rehovot, 76100, Israel
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90
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Demarquoy J, Le Borgne F. Crosstalk between mitochondria and peroxisomes. World J Biol Chem 2015; 6:301-9. [PMID: 26629313 PMCID: PMC4657118 DOI: 10.4331/wjbc.v6.i4.301] [Citation(s) in RCA: 78] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/21/2015] [Revised: 06/30/2015] [Accepted: 08/10/2015] [Indexed: 02/05/2023] Open
Abstract
Mitochondria and peroxisomes are small ubiquitous organelles. They both play major roles in cell metabolism, especially in terms of fatty acid metabolism, reactive oxygen species (ROS) production, and ROS scavenging, and it is now clear that they metabolically interact with each other. These two organelles share some properties, such as great plasticity and high potency to adapt their form and number according to cell requirements. Their functions are connected, and any alteration in the function of mitochondria may induce changes in peroxisomal physiology. The objective of this paper was to highlight the interconnection and the crosstalk existing between mitochondria and peroxisomes. Special emphasis was placed on the best known connections between these organelles: origin, structure, and metabolic interconnections.
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91
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D'Aquila P, Giordano M, Montesanto A, De Rango F, Passarino G, Bellizzi D. Age-and gender-related pattern of methylation in the MT-RNR1 gene. Epigenomics 2015; 7:707-16. [PMID: 26343273 DOI: 10.2217/epi.15.30] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
AIM We evaluated the methylation of two CpG sites located within human mitochondrial 12S and 16S ribosomal RNA (MT-RNR1 and MT-RNR2) genes. MATERIALS & METHODS Methylation was measured through bisulfite sequencing and qPCR assays on DNA samples collected from 381 differently aged human subjects. RESULTS Analyses revealed the methylation of the site in the MT-RNR1 gene and the co-presence of both unmethylated and methylated cytosines in most samples. High methylation levels (>10%) were more frequent in old women with respect to younger controls. A 9-year-long follow-up survey showed that subjects with high methylation levels exhibit a mortality risk significantly higher than subjects with low levels. CONCLUSION Our data further support the presence of methylation within human mitochondrial DNA and suggest that high levels of methylation of the MT-RNR1 site may reflect a condition of the cell or of the organism unfavorable to survival.
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Affiliation(s)
- Patrizia D'Aquila
- Department of Biology, Ecology & Earth Science (DIBEST), University of Calabria, 87036 Rende, Italy
| | - Marco Giordano
- Department of Biology, Ecology & Earth Science (DIBEST), University of Calabria, 87036 Rende, Italy
| | - Alberto Montesanto
- Department of Biology, Ecology & Earth Science (DIBEST), University of Calabria, 87036 Rende, Italy
| | - Francesco De Rango
- Department of Biology, Ecology & Earth Science (DIBEST), University of Calabria, 87036 Rende, Italy
| | - Giuseppe Passarino
- Department of Biology, Ecology & Earth Science (DIBEST), University of Calabria, 87036 Rende, Italy
| | - Dina Bellizzi
- Department of Biology, Ecology & Earth Science (DIBEST), University of Calabria, 87036 Rende, Italy
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92
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Impaired mitochondrial protein synthesis in head and neck squamous cell carcinoma. Mitochondrion 2015; 24:113-21. [DOI: 10.1016/j.mito.2015.07.123] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2015] [Revised: 07/24/2015] [Accepted: 07/29/2015] [Indexed: 01/31/2023]
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93
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Lagouge M, Mourier A, Lee HJ, Spåhr H, Wai T, Kukat C, Silva Ramos E, Motori E, Busch JD, Siira S, Kremmer E, Filipovska A, Larsson NG. SLIRP Regulates the Rate of Mitochondrial Protein Synthesis and Protects LRPPRC from Degradation. PLoS Genet 2015; 11:e1005423. [PMID: 26247782 PMCID: PMC4527767 DOI: 10.1371/journal.pgen.1005423] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2015] [Accepted: 07/04/2015] [Indexed: 12/17/2022] Open
Abstract
We have studied the in vivo role of SLIRP in regulation of mitochondrial DNA (mtDNA) gene expression and show here that it stabilizes its interacting partner protein LRPPRC by protecting it from degradation. Although SLIRP is completely dependent on LRPPRC for its stability, reduced levels of LRPPRC persist in the absence of SLIRP in vivo. Surprisingly, Slirp knockout mice are apparently healthy and only display a minor weight loss, despite a 50-70% reduction in the steady-state levels of mtDNA-encoded mRNAs. In contrast to LRPPRC, SLIRP is dispensable for polyadenylation of mtDNA-encoded mRNAs. Instead, deep RNA sequencing (RNAseq) of mitochondrial ribosomal fractions and additional molecular analyses show that SLIRP is required for proper association of mRNAs to the mitochondrial ribosome and efficient translation. Our findings thus establish distinct functions for SLIRP and LRPPRC within the LRPPRC-SLIRP complex, with a novel role for SLIRP in mitochondrial translation. Very surprisingly, our results also demonstrate that mammalian mitochondria have a great excess of transcripts under basal physiological conditions in vivo.
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Affiliation(s)
- Marie Lagouge
- Department of Mitochondrial Biology, Max Planck Institute for Biology of Ageing, Cologne, Germany
| | - Arnaud Mourier
- Department of Mitochondrial Biology, Max Planck Institute for Biology of Ageing, Cologne, Germany
| | - Hyun Ju Lee
- Department of Mitochondrial Biology, Max Planck Institute for Biology of Ageing, Cologne, Germany
| | - Henrik Spåhr
- Department of Mitochondrial Biology, Max Planck Institute for Biology of Ageing, Cologne, Germany
| | - Timothy Wai
- CECAD Research Center, University of Cologne, Cologne, Germany
| | - Christian Kukat
- FACS and Imaging facility, Max Planck Institute for Biology of Ageing, Cologne, Germany
| | - Eduardo Silva Ramos
- Department of Mitochondrial Biology, Max Planck Institute for Biology of Ageing, Cologne, Germany
| | - Elisa Motori
- Department of Mitochondrial Biology, Max Planck Institute for Biology of Ageing, Cologne, Germany
| | - Jakob D. Busch
- Department of Mitochondrial Biology, Max Planck Institute for Biology of Ageing, Cologne, Germany
| | - Stefan Siira
- Harry Perkins Institute of Medical Research, Centre for Medical Research and School of Chemistry and Biochemistry, The University of Western Australia, Perth, Australia
| | - German Mouse Clinic Consortium
- German Mouse Clinic, Helmholtz Zentrum München, German Research Center for Environmental Health GmbH, Neuherberg, Germany
| | - Elisabeth Kremmer
- Helmholtz Zentrum München, Institute of Molecular Immunology, Munich, Germany
| | - Aleksandra Filipovska
- Harry Perkins Institute of Medical Research, Centre for Medical Research and School of Chemistry and Biochemistry, The University of Western Australia, Perth, Australia
- * E-mail: (AF); (NGL)
| | - Nils-Göran Larsson
- Department of Mitochondrial Biology, Max Planck Institute for Biology of Ageing, Cologne, Germany
- Department of Laboratory Medicine, Karolinska Institute, Stockholm, Sweden
- * E-mail: (AF); (NGL)
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94
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Tigano M, Ruotolo R, Dallabona C, Fontanesi F, Barrientos A, Donnini C, Ottonello S. Elongator-dependent modification of cytoplasmic tRNALysUUU is required for mitochondrial function under stress conditions. Nucleic Acids Res 2015; 43:8368-80. [PMID: 26240381 PMCID: PMC4787798 DOI: 10.1093/nar/gkv765] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2014] [Accepted: 07/15/2015] [Indexed: 11/12/2022] Open
Abstract
To gain a wider view of the pathways that regulate mitochondrial function, we combined the effect of heat stress on respiratory capacity with the discovery potential of a genome-wide screen in Saccharomyces cerevisiae. We identified 105 new genes whose deletion impairs respiratory growth at 37°C by interfering with processes such as transcriptional regulation, ubiquitination and cytosolic tRNA wobble uridine modification via 5-methoxycarbonylmethyl-2-thiouridine formation. The latter process, specifically required for efficient decoding of AA-ending codons under stress conditions, was covered by multiple genes belonging to the Elongator (e.g. ELP3) and urmylation (e.g., NCS6) pathways. ELP3 or NCS6 deletants had impaired mitochondrial protein synthesis. Their respiratory deficiency was selectively rescued by overexpression of tRNA(Lys) UUU as well by overexpression of genes (BCK1 and HFM1) with a strong bias for the AAA codon read by this tRNA. These data extend the mitochondrial regulome, demonstrate that heat stress can impair respiration by disturbing cytoplasmic translation of proteins critically involved in mitochondrial function and document, for the first time, the involvement in such process of the Elongator and urmylation pathways. Given the conservation of these pathways, the present findings may pave the way to a better understanding of the human mitochondrial regulome in health and disease.
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Affiliation(s)
- Marco Tigano
- Department of Life Sciences, University of Parma, 43124 Parma, Italy
| | - Roberta Ruotolo
- Department of Life Sciences, University of Parma, 43124 Parma, Italy
| | | | - 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
| | - Claudia Donnini
- Department of Life Sciences, University of Parma, 43124 Parma, Italy
| | - Simone Ottonello
- Department of Life Sciences, University of Parma, 43124 Parma, Italy
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95
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De Silva D, Tu YT, Amunts A, Fontanesi F, Barrientos A. Mitochondrial ribosome assembly in health and disease. Cell Cycle 2015; 14:2226-50. [PMID: 26030272 DOI: 10.1080/15384101.2015.1053672] [Citation(s) in RCA: 130] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
The ribosome is a structurally and functionally conserved macromolecular machine universally responsible for catalyzing protein synthesis. Within eukaryotic cells, mitochondria contain their own ribosomes (mitoribosomes), which synthesize a handful of proteins, all essential for the biogenesis of the oxidative phosphorylation system. High-resolution cryo-EM structures of the yeast, porcine and human mitoribosomal subunits and of the entire human mitoribosome have uncovered a wealth of new information to illustrate their evolutionary divergence from their bacterial ancestors and their adaptation to synthesis of highly hydrophobic membrane proteins. With such structural data becoming available, one of the most important remaining questions is that of the mitoribosome assembly pathway and factors involved. The regulation of mitoribosome biogenesis is paramount to mitochondrial respiration, and thus to cell viability, growth and differentiation. Moreover, mutations affecting the rRNA and protein components produce severe human mitochondrial disorders. Despite its biological and biomedical significance, knowledge on mitoribosome biogenesis and its deviations from the much-studied bacterial ribosome assembly processes is scarce, especially the order of rRNA processing and assembly events and the regulatory factors required to achieve fully functional particles. This article focuses on summarizing the current available information on mitoribosome assembly pathway, factors that form the mitoribosome assembly machinery, and the effect of defective mitoribosome assembly on human health.
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Affiliation(s)
- Dasmanthie De Silva
- a Department of Biochemistry and Molecular Biology ; University of Miami Miller School of Medicine ; Miami , FL USA
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96
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Zhang X, Gao X, Coots RA, Conn CS, Liu B, Qian SB. Translational control of the cytosolic stress response by mitochondrial ribosomal protein L18. Nat Struct Mol Biol 2015; 22:404-10. [PMID: 25866880 PMCID: PMC4424103 DOI: 10.1038/nsmb.3010] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2014] [Accepted: 03/13/2015] [Indexed: 12/27/2022]
Abstract
In response to stress, cells attenuate global protein synthesis but permit efficient translation of mRNAs encoding heat-shock proteins (HSPs). Although decades have passed since the first description of the heat-shock response, how cells achieve translational control of HSP synthesis remains enigmatic. Here we report an unexpected role for mitochondrial ribosomal protein L18 (MRPL18) in the mammalian cytosolic stress response. MRPL18 bears a downstream CUG start codon and generates a cytosolic isoform in a stress-dependent manner. Cytosolic MRPL18 incorporates into the 80S ribosome and facilitates ribosome engagement on mRNAs selected for translation during stress. MRPL18 knockdown has minimal effects on mitochondrial function but substantially dampens cytosolic HSP expression at the level of translation. Our results uncover a hitherto-uncharacterized stress-adaptation mechanism in mammalian cells, which involves formation of a 'hybrid' ribosome responsible for translational regulation during the cytosolic stress response.
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Affiliation(s)
- Xingqian Zhang
- Division of Nutritional Sciences, Cornell University, Ithaca, New York, USA
| | - Xiangwei Gao
- Division of Nutritional Sciences, Cornell University, Ithaca, New York, USA
| | - Ryan Alex Coots
- 1] Division of Nutritional Sciences, Cornell University, Ithaca, New York, USA. [2] Graduate Field of Nutritional Sciences, Cornell University, Ithaca, New York, USA
| | - Crystal S Conn
- Graduate Field of Genetics, Genomics and Development, Cornell University, Ithaca, New York, USA
| | - Botao Liu
- Graduate Field of Genetics, Genomics and Development, Cornell University, Ithaca, New York, USA
| | - Shu-Bing Qian
- 1] Division of Nutritional Sciences, Cornell University, Ithaca, New York, USA. [2] Graduate Field of Nutritional Sciences, Cornell University, Ithaca, New York, USA. [3] Graduate Field of Genetics, Genomics and Development, Cornell University, Ithaca, New York, USA
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97
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Kaushal PS, Sharma MR, Agrawal RK. The 55S mammalian mitochondrial ribosome and its tRNA-exit region. Biochimie 2015; 114:119-26. [PMID: 25797916 DOI: 10.1016/j.biochi.2015.03.013] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2014] [Accepted: 03/12/2015] [Indexed: 11/25/2022]
Abstract
Mitochondria carry their own genetic material and gene-expression machinery, including ribosomes, which are responsible for synthesizing polypeptides that form essential components of the complexes involved in oxidative phosphorylation (or ATP generation) for the eukaryotic cell. Mitochondrial ribosomes (mitoribosomes) are quite divergent from cytoplasmic ribosomes in both composition and structure even as their main functional cores, such as the mRNA decoding and peptidyl transferase sites, are highly conserved. Remarkable progress has been made recently towards understanding the structure of mitoribosomes, by obtaining high-resolution cryo-electron microscopic (cryo-EM) maps. These studies confirm previous structural findings that had revealed that a significant reduction in size of ribosomal RNAs has caused topological changes in some of the functionally relevant regions, including the transfer RNA (tRNA)-binding sites and the nascent polypeptide-exit tunnel, within the structure of the mammalian mitoribosome. In addition, these studies provide unprecedented detailed views of the molecular architecture of those regions. In this review, we summarize the current state of knowledge of the structure of the mammalian mitoribosome and describe the molecular environment of its tRNA-exit region.
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Affiliation(s)
- Prem S Kaushal
- Division of Translational Medicine, Wadsworth Center, New York State Department of Health, Albany, NY 12201-0509, USA
| | - Manjuli R Sharma
- Division of Translational Medicine, Wadsworth Center, New York State Department of Health, Albany, NY 12201-0509, USA
| | - Rajendra K Agrawal
- Division of Translational Medicine, Wadsworth Center, New York State Department of Health, Albany, NY 12201-0509, USA; Department of Biomedical Sciences, School of Public Health, State University of New York at Albany, Albany, NY, USA.
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98
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Abstract
Metabolic and mitochondrial myopathies encompass a heterogeneous group of disorders that result in impaired energy production in skeletal muscle. Symptoms of premature muscle fatigue, sometimes leading to myalgia, rhabdomyolysis, and myoglobinuria, typically occur with exercise that would normally depend on the defective metabolic pathway. But in another group of these disorders, the dominant muscle symptom is weakness. This article reviews the clinical features, diagnosis, and management of these diseases with emphasis on the recent literature.
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Affiliation(s)
- Lydia J Sharp
- Department of Neurology and Neurotherapeutics, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390, USA; Neuromuscular Center, Institute for Exercise and Environmental Medicine, Texas Health Presbyterian Hospital, 7232 Greenville Avenue, Dallas, TX 75231, USA
| | - Ronald G Haller
- Department of Neurology and Neurotherapeutics, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390, USA; Neuromuscular Center, Institute for Exercise and Environmental Medicine, Texas Health Presbyterian Hospital, 7232 Greenville Avenue, Dallas, TX 75231, USA; North Texas VA Medical Center, 4500 South Lancaster Road, Dallas, TX 75216, USA.
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99
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Audano M, Ferrari A, Fiorino E, Kuenzl M, Caruso D, Mitro N, Crestani M, De Fabiani E. Energizing Genetics and Epi-genetics: Role in the Regulation of Mitochondrial Function. Curr Genomics 2015; 15:436-56. [PMID: 25646072 PMCID: PMC4311388 DOI: 10.2174/138920291506150106151119] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2014] [Revised: 11/11/2014] [Accepted: 11/18/2014] [Indexed: 12/15/2022] Open
Abstract
Energy metabolism and mitochondrial function hold a core position in cellular homeostasis. Oxidative metabolism is regulated at multiple levels, ranging from gene transcription to allosteric modulation. To accomplish the fine tuning of these multiple regulatory circuits, the nuclear and mitochondrial compartments are tightly and reciprocally controlled. The fact that nuclear encoded factors, PPARγ coactivator 1α and mitochondrial transcription factor A, play pivotal roles in the regulation of oxidative metabolism and mitochondrial biogenesis is paradigmatic of this crosstalk. Here we provide an updated survey of the genetic and epigenetic mechanisms involved in the control of energy metabolism and mitochondrial function. Chromatin dynamics highly depends on post-translational modifications occurring at specific amino acids in histone proteins and other factors associated to nuclear DNA. In addition to the well characterized enzymes responsible for histone methylation/demethylation and acetylation/deacetylation, other factors have gone on the "metabolic stage". This is the case of the new class of α-ketoglutarate-regulated demethylases (Jumonji C domain containing demethylases) and of the NAD+-dependent deacetylases, also known as sirtuins. Moreover, unexpected features of the machineries involved in mitochondrial DNA (mtDNA) replication and transcription, mitochondrial RNA processing and maturation have recently emerged. Mutations or defects of any component of these machineries profoundly affect mitochondrial activity and oxidative metabolism. Finally, recent evidences support the importance of mtDNA packaging in replication and transcription. These observations, along with the discovery that non-classical CpG islands present in mtDNA undergo methylation, indicate that epigenetics also plays a role in the regulation of the mitochondrial genome function.
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Affiliation(s)
- Matteo Audano
- Dipartimento di Scienze Farmacologiche e Biomolecolari, Università degli Studi di Milano, Italy
| | - Alessandra Ferrari
- Dipartimento di Scienze Farmacologiche e Biomolecolari, Università degli Studi di Milano, Italy
| | - Erika Fiorino
- Dipartimento di Scienze Farmacologiche e Biomolecolari, Università degli Studi di Milano, Italy
| | - Martin Kuenzl
- Dipartimento di Scienze Farmacologiche e Biomolecolari, Università degli Studi di Milano, Italy
| | - Donatella Caruso
- Dipartimento di Scienze Farmacologiche e Biomolecolari, Università degli Studi di Milano, Italy
| | - Nico Mitro
- Dipartimento di Scienze Farmacologiche e Biomolecolari, Università degli Studi di Milano, Italy
| | - Maurizio Crestani
- Dipartimento di Scienze Farmacologiche e Biomolecolari, Università degli Studi di Milano, Italy
| | - Emma De Fabiani
- Dipartimento di Scienze Farmacologiche e Biomolecolari, Università degli Studi di Milano, Italy
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100
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Weiss SL, Cvijanovich NZ, Allen GL, Thomas NJ, Freishtat RJ, Anas N, Meyer K, Checchia PA, Shanley TP, Bigham MT, Fitzgerald J, Banschbach S, Beckman E, Howard K, Frank E, Harmon K, Wong HR. Differential expression of the nuclear-encoded mitochondrial transcriptome in pediatric septic shock. CRITICAL CARE : THE OFFICIAL JOURNAL OF THE CRITICAL CARE FORUM 2014; 18:623. [PMID: 25410281 PMCID: PMC4247726 DOI: 10.1186/s13054-014-0623-9] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/07/2014] [Accepted: 10/28/2014] [Indexed: 01/09/2023]
Abstract
Introduction Increasing evidence supports a role for mitochondrial dysfunction in organ injury and immune dysregulation in sepsis. Although differential expression of mitochondrial genes in blood cells has been reported for several diseases in which bioenergetic failure is a postulated mechanism, there are no data about the blood cell mitochondrial transcriptome in pediatric sepsis. Methods We conducted a focused analysis using a multicenter genome-wide expression database of 180 children ≤10 years of age with septic shock and 53 healthy controls. Using total RNA isolated from whole blood within 24 hours of PICU admission for septic shock, we evaluated 296 nuclear-encoded mitochondrial genes using a false discovery rate of 1%. A series of bioinformatic approaches were applied to compare differentially expressed genes across previously validated gene expression-based subclasses (groups A, B, and C) of pediatric septic shock. Results In total, 118 genes were differentially regulated in subjects with septic shock compared to healthy controls, including 48 genes that were upregulated and 70 that were downregulated. The top scoring canonical pathway was oxidative phosphorylation, with general downregulation of the 51 genes corresponding to the electron transport system (ETS). The top two gene networks were composed primarily of mitochondrial ribosomal proteins highly connected to ETS complex I, and genes encoding for ETS complexes I, II, and IV that were highly connected to the peroxisome proliferator activated receptor (PPAR) family. There were 162 mitochondrial genes differentially regulated between groups A, B, and C. Group A, which had the highest maximum number of organ failures and mortality, exhibited a greater downregulation of mitochondrial genes compared to groups B and C. Conclusions Based on a focused analysis of a pediatric septic shock transcriptomic database, nuclear-encoded mitochondrial genes were differentially regulated early in pediatric septic shock compared to healthy controls, as well as across genotypic and phenotypic distinct pediatric septic shock subclasses. The nuclear genome may be an important mechanism contributing to alterations in mitochondrial bioenergetic function and outcomes in pediatric sepsis. Electronic supplementary material The online version of this article (doi:10.1186/s13054-014-0623-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Scott L Weiss
- Division of Critical Care Medicine, Department of Anesthesia and Critical Care, The Children's Hospital of Philadelphia, University of Pennsylvania Perelman School of Medicine, 3620 Hamilton Walk, Philadelphia, PA, 19104, USA. .,Center for Resuscitation Science, University of Pennsylvania Perelman School of Medicine, 3620 Hamilton Walk, Philadelphia, PA, 19104, USA.
| | - Natalie Z Cvijanovich
- UCSF Benioff Children's Hospital Oakland, 1411 East 31st Street, Oakland, CA, 94602, USA.
| | - Geoffrey L Allen
- Children's Mercy Hospital, 2401 Gillham Road, Kansas City, MO, 64108, USA.
| | - Neal J Thomas
- Penn State Children's Hospital, 500 University Drive, Hershey, PA, 17033, USA.
| | - Robert J Freishtat
- Children's National Medical Center, 111 Michigan Avenue NW, Washington, DC, 20010, USA.
| | - Nick Anas
- Children's Hospital of Orange County, 1201 W La Veta Avenue, Orange, CA, 92868, USA.
| | - Keith Meyer
- Miami Children's Hospital, 3100 SW 62nd Avenue, Miami, FL, 33155, USA.
| | - Paul A Checchia
- Texas Children's Hospital, 6621 Fannin Street, Houston, TX, 77030, USA.
| | - Thomas P Shanley
- CS Mott Children's Hospital at the University of Michigan, 1540 E Hospital Drive, Ann Arbor, MI, 48109, USA.
| | - Michael T Bigham
- Akron Children's Hospital, 1 Perkins Square, Akron, OH, 44302, USA.
| | - Julie Fitzgerald
- Division of Critical Care Medicine, Department of Anesthesia and Critical Care, The Children's Hospital of Philadelphia, University of Pennsylvania Perelman School of Medicine, 3620 Hamilton Walk, Philadelphia, PA, 19104, USA.
| | - Sharon Banschbach
- Division of Critical Care Medicine, Cincinnati Children's Hospital Medical Center and Cincinnati Children's Research Foundation, 3333 Burnet Avenue, MLC 2005, Cincinnati, OH, 45229, USA.
| | - Eileen Beckman
- Division of Critical Care Medicine, Cincinnati Children's Hospital Medical Center and Cincinnati Children's Research Foundation, 3333 Burnet Avenue, MLC 2005, Cincinnati, OH, 45229, USA.
| | - Kelli Howard
- Division of Critical Care Medicine, Cincinnati Children's Hospital Medical Center and Cincinnati Children's Research Foundation, 3333 Burnet Avenue, MLC 2005, Cincinnati, OH, 45229, USA.
| | - Erin Frank
- Division of Critical Care Medicine, Cincinnati Children's Hospital Medical Center and Cincinnati Children's Research Foundation, 3333 Burnet Avenue, MLC 2005, Cincinnati, OH, 45229, USA.
| | - Kelli Harmon
- Division of Critical Care Medicine, Cincinnati Children's Hospital Medical Center and Cincinnati Children's Research Foundation, 3333 Burnet Avenue, MLC 2005, Cincinnati, OH, 45229, USA.
| | - Hector R Wong
- Division of Critical Care Medicine, Cincinnati Children's Hospital Medical Center and Cincinnati Children's Research Foundation, 3333 Burnet Avenue, MLC 2005, Cincinnati, OH, 45229, USA. .,Department of Pediatrics, University of Cincinnati College of Medicine, 3230 Eden Avenue, Cincinnati, OH, 45267, USA.
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