1
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Koc EC, Hunter CA, Koc H. Phosphorylation of mammalian mitochondrial EF-Tu by Fyn and c-Src kinases. Cell Signal 2023; 101:110524. [PMID: 36379377 DOI: 10.1016/j.cellsig.2022.110524] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Revised: 10/31/2022] [Accepted: 11/09/2022] [Indexed: 11/14/2022]
Abstract
Src Family Kinases (SFKs) are tyrosine kinases known to regulate glucose and fatty acid metabolism as well as oxidative phosphorylation (OXPHOS) in mammalian mitochondria. We and others discovered the association of the SFK kinases Fyn and c-Src with mitochondrial translation components. This translational system is responsible for the synthesis of 13 mitochondrial (mt)-encoded subunits of the OXPHOS complexes and is, thus, essential for energy generation. Mitochondrial ribosomal proteins and various translation elongation factors including Tu (EF-Tumt) have been identified as possible Fyn and c-Src kinase targets. However, the phosphorylation of specific residues in EF-Tumt by these kinases and their roles in the regulation of protein synthesis are yet to be explored. In this study, we report the association of EF-Tumt with cSrc kinase and mapping of phosphorylated Tyr (pTyr) residues by these kinases. We determined that a specific Tyr residue in EF-Tumt at position 266 (EF-Tumt-Y266), located in a highly conserved c-Src consensus motif is one of the major phosphorylation sites. The potential role of EF-Tumt-Y266 phosphorylation in regulation of mitochondrial translation investigated by site-directed mutagenesis. Its phosphomimetic to Glu residue (EF-Tumt-E266) inhibited ternary complex (EF-Tumt•GTP•aatRNA) formation and translation in vitro. Our findings along with data mining analysis of the c-Src knock out (KO) mice proteome suggest that the SFKs have possible roles for regulation of mitochondrial protein synthesis and oxidative energy metabolism in animals.
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Affiliation(s)
- Emine C Koc
- Department of Biomedical Sciences, Joan C. Edwards School of Medicine, Marshall University, Huntington, WV 25755, United States of America.
| | - Caroline A Hunter
- Department of Biomedical Sciences, Joan C. Edwards School of Medicine, Marshall University, Huntington, WV 25755, United States of America
| | - Hasan Koc
- Department of Pharmacological Science, School of Pharmacy, Marshall University, Huntington, WV 25755, United States of America.
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2
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Structural insights of the elongation factor EF-Tu complexes in protein translation of Mycobacterium tuberculosis. Commun Biol 2022; 5:1052. [PMID: 36192483 PMCID: PMC9529903 DOI: 10.1038/s42003-022-04019-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Accepted: 09/21/2022] [Indexed: 11/09/2022] Open
Abstract
Tuberculosis (TB) caused by Mycobacterium tuberculosis (Mtb) is the second-deadliest infectious disease worldwide. Emerging evidence shows that the elongation factor EF-Tu could be an excellent target for treating Mtb infection. Here, we report the crystal structures of Mtb EF-Tu•EF-Ts and EF-Tu•GDP complexes, showing the molecular basis of EF-Tu's representative recycling and inactive forms in protein translation. Mtb EF-Tu binds with EF-Ts at a 1:1 ratio in solution and crystal packing. Mutation and SAXS analysis show that EF-Ts residues Arg13, Asn82, and His149 are indispensable for the EF-Tu/EF-Ts complex formation. The GDP binding pocket of EF-Tu dramatically changes conformations upon binding with EF-Ts, sharing a similar GDP-exchange mechanism in E. coli and T. ther. Also, the FDA-approved drug Osimertinib inhibits the growth of M. smegmatis, H37Ra, and M. bovis BCG strains by directly binding with EF-Tu. Thus, our work reveals the structural basis of Mtb EF-Tu in polypeptide synthesis and may provide a promising candidate for TB treatment.
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3
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Xu B, Liu L, Song G. Functions and Regulation of Translation Elongation Factors. Front Mol Biosci 2022; 8:816398. [PMID: 35127825 PMCID: PMC8807479 DOI: 10.3389/fmolb.2021.816398] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Accepted: 12/20/2021] [Indexed: 12/18/2022] Open
Abstract
Translation elongation is a key step of protein synthesis, during which the nascent polypeptide chain extends by one amino acid residue during one elongation cycle. More and more data revealed that the elongation is a key regulatory node for translational control in health and disease. During elongation, elongation factor Tu (EF-Tu, eEF1A in eukaryotes) is used to deliver aminoacyl-tRNA (aa-tRNA) to the A-site of the ribosome, and elongation factor G (EF-G, EF2 in eukaryotes and archaea) is used to facilitate the translocation of the tRNA2-mRNA complex on the ribosome. Other elongation factors, such as EF-Ts/eEF1B, EF-P/eIF5A, EF4, eEF3, SelB/EFsec, TetO/Tet(M), RelA and BipA, have been found to affect the overall rate of elongation. Here, we made a systematic review on the canonical and non-canonical functions and regulation of these elongation factors. In particular, we discussed the close link between translational factors and human diseases, and clarified how post-translational modifications control the activity of translational factors in tumors.
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Affiliation(s)
- Benjin Xu
- Department of Medical Laboratory Science, Fenyang College, Shanxi Medical University, Fenyang, China
- *Correspondence: Benjin Xu, ; Guangtao Song,
| | - Ling Liu
- Department of Medical Laboratory Science, Fenyang College, Shanxi Medical University, Fenyang, China
| | - Guangtao Song
- Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- *Correspondence: Benjin Xu, ; Guangtao Song,
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4
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Wang F, Zhang D, Zhang D, Li P, Gao Y. Mitochondrial Protein Translation: Emerging Roles and Clinical Significance in Disease. Front Cell Dev Biol 2021; 9:675465. [PMID: 34277617 PMCID: PMC8280776 DOI: 10.3389/fcell.2021.675465] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Accepted: 06/09/2021] [Indexed: 12/28/2022] Open
Abstract
Mitochondria are one of the most important organelles in cells. Mitochondria are semi-autonomous organelles with their own genetic system, and can independently replicate, transcribe, and translate mitochondrial DNA. Translation initiation, elongation, termination, and recycling of the ribosome are four stages in the process of mitochondrial protein translation. In this process, mitochondrial protein translation factors and translation activators, mitochondrial RNA, and other regulatory factors regulate mitochondrial protein translation. Mitochondrial protein translation abnormalities are associated with a variety of diseases, including cancer, cardiovascular diseases, and nervous system diseases. Mutation or deletion of various mitochondrial protein translation factors and translation activators leads to abnormal mitochondrial protein translation. Mitochondrial tRNAs and mitochondrial ribosomal proteins are essential players during translation and mutations in genes encoding them represent a large fraction of mitochondrial diseases. Moreover, there is crosstalk between mitochondrial protein translation and cytoplasmic translation, and the imbalance between mitochondrial protein translation and cytoplasmic translation can affect some physiological and pathological processes. This review summarizes the regulation of mitochondrial protein translation factors, mitochondrial ribosomal proteins, mitochondrial tRNAs, and mitochondrial aminoacyl-tRNA synthetases (mt-aaRSs) in the mitochondrial protein translation process and its relationship with diseases. The regulation of mitochondrial protein translation and cytoplasmic translation in multiple diseases is also summarized.
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Affiliation(s)
- Fei Wang
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao, China
| | - Deyu Zhang
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao, China
| | - Dejiu Zhang
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao, China
| | - Peifeng Li
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao, China
| | - Yanyan Gao
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao, China.,Key Laboratory of Nuclear Medicine, Ministry of Health, Jiangsu Key Laboratory of Molecular Nuclear Medicine, Jiangsu Institute of Nuclear Medicine, Wuxi, China
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5
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Mechanisms and regulation of protein synthesis in mitochondria. Nat Rev Mol Cell Biol 2021; 22:307-325. [PMID: 33594280 DOI: 10.1038/s41580-021-00332-2] [Citation(s) in RCA: 147] [Impact Index Per Article: 49.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/13/2021] [Indexed: 02/06/2023]
Abstract
Mitochondria are cellular organelles responsible for generation of chemical energy in the process called oxidative phosphorylation. They originate from a bacterial ancestor and maintain their own genome, which is expressed by designated, mitochondrial transcription and translation machineries that differ from those operating for nuclear gene expression. In particular, the mitochondrial protein synthesis machinery is structurally and functionally very different from that governing eukaryotic, cytosolic translation. Despite harbouring their own genetic information, mitochondria are far from being independent of the rest of the cell and, conversely, cellular fitness is closely linked to mitochondrial function. Mitochondria depend heavily on the import of nuclear-encoded proteins for gene expression and function, and hence engage in extensive inter-compartmental crosstalk to regulate their proteome. This connectivity allows mitochondria to adapt to changes in cellular conditions and also mediates responses to stress and mitochondrial dysfunction. With a focus on mammals and yeast, we review fundamental insights that have been made into the biogenesis, architecture and mechanisms of the mitochondrial translation apparatus in the past years owing to the emergence of numerous near-atomic structures and a considerable amount of biochemical work. Moreover, we discuss how cellular mitochondrial protein expression is regulated, including aspects of mRNA and tRNA maturation and stability, roles of auxiliary factors, such as translation regulators, that adapt mitochondrial translation rates, and the importance of inter-compartmental crosstalk with nuclear gene expression and cytosolic translation and how it enables integration of mitochondrial translation into the cellular context.
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6
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Novel homozygous TSFM pathogenic variant associated with encephalocardiomyopathy with sensorineural hearing loss and peculiar neuroradiologic findings. Neurogenetics 2019; 20:165-172. [PMID: 31267352 DOI: 10.1007/s10048-019-00582-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2019] [Accepted: 06/09/2019] [Indexed: 10/26/2022]
Abstract
TSFM is a nuclear gene encoding the elongation factor Ts (EFTs), an essential component of mitochondrial translational machinery. Impaired mitochondrial translation is responsible for neurodegenerative disorders characterized by multiple respiratory chain complex defects, multisystemic involvement, and neuroradiological features of Leigh-like syndrome. With the use of a next-generation sequencing (NGS)-based multigene panel for mitochondrial disorders, we identified the novel TSFM homozygous variant c.547G>A (p.Gly183Ser) in a 5-year-old boy with infantile early onset encephalocardiomyopathy, sensorineural hearing loss, and peculiar partially reversible neuroimaging features. Our findings expand the phenotypic spectrum of TSFM-related encephalopathy, offering new insights into the natural history of brain involvement and suggesting that TSFM should be investigated in pediatric mitochondrial disorders with distinctive neurologic and cardiac involvement.
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7
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Hershkovitz T, Kurolap A, Gonzaga-Jauregui C, Paperna T, Mory A, Wolf SE, Overton JD, Shuldiner AR, Saada A, Mandel H, Baris Feldman H. A novel TUFM homozygous variant in a child with mitochondrial cardiomyopathy expands the phenotype of combined oxidative phosphorylation deficiency 4. J Hum Genet 2019; 64:589-595. [PMID: 30903008 DOI: 10.1038/s10038-019-0592-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2018] [Revised: 02/05/2019] [Accepted: 03/02/2019] [Indexed: 11/09/2022]
Abstract
Translation of mitochondrial-specific DNA is required for proper mitochondrial function and energy production. For this purpose, an elaborate network of dedicated molecular machinery including initiation, elongation and termination factors exists. We describe a patient with an unusual phenotype and a novel homozygous missense variant in TUFM (c.344A>C; p.His115Pro), encoding mtDNA translation elongating factor Tu (EFTu). To date, only four patients have been reported with bi-allelic mutations in TUFM, leading to combined oxidative phosphorylation deficiency 4 (COXPD4) characterized by severe early-onset lactic acidosis and progressive fatal infantile encephalopathy. The patient presented here expands the phenotypic features of TUFM-related disease, exhibiting lactic acidosis and dilated cardiomyopathy without progressive encephalopathy. This warrants the inclusion of TUFM in differential diagnosis of metabolic cardiomyopathy. Cases that further refine genotype-phenotype associations and characterize the molecular basis of mitochondrial disorders allow clinicians to predict disease prognosis, greatly impacting patient care, as well as provide families with reproductive planning options.
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Affiliation(s)
- Tova Hershkovitz
- The Genetics Institute, Rambam Health Care Campus, Haifa, Israel
| | - Alina Kurolap
- The Genetics Institute, Rambam Health Care Campus, Haifa, Israel.,The Ruth and Bruce Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, Israel
| | | | - Tamar Paperna
- The Genetics Institute, Rambam Health Care Campus, Haifa, Israel
| | - Adi Mory
- The Genetics Institute, Rambam Health Care Campus, Haifa, Israel
| | | | | | | | | | - 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
| | - Hanna Mandel
- Institute of Human Genetics and Metabolic Disorders, Western Galilee Medical Center, Naharia, Israel
| | - Hagit Baris Feldman
- The Genetics Institute, Rambam Health Care Campus, Haifa, Israel. .,The Ruth and Bruce Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, Israel.
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8
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Yang J, Hong J, Luo L, Liu K, Meng C, Ji ZL, Lin D. Biophysical characterization and ligand-binding properties of the elongation factor Tu from Mycobacterium tuberculosis. Acta Biochim Biophys Sin (Shanghai) 2019; 51:139-149. [PMID: 30615070 DOI: 10.1093/abbs/gmy164] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Revised: 11/28/2018] [Accepted: 11/30/2018] [Indexed: 02/05/2023] Open
Abstract
Mycobacterium tuberculosis (Mtb) is the key devastating bacterial pathogen responsible for tuberculosis. Increasing emergence of multi-drug-resistant, extensively drug-resistant, and rifampicin/isoniazid-resistant strains of Mtb makes the discovery of validated drug targets an urgent priority. As a vital translational component of the protein biosynthesis system, elongation factor Tu (EF-Tu) is an important molecular switch responsible for selection and binding of the cognate aminoacyl-tRNA to the acceptor site on the ribosome. In addition, EF-Tu from Mtb (MtbEF-Tu) is involved in the initial step of trans-translation which is an effective system for rescuing the stalled ribosomes from non-stop translation complexes under stress conditions. Given its crucial role in protein biosynthesis, EF-Tu is identified as an excellent molecular target for drug design. Here, we reported the recombinant expression, purification, biophysical characterization, and structural modeling of the MtbEF-Tu protein. Our results demonstrated that prokaryotic expression plasmids of pET28a-MtbEF-Tu could be expressed efficiently in Escherichia coli. We successfully purified the 6× His-tagged proteins with a yield of 16.8 mg from 1 l of Luria Bertani medium. Dynamic light scattering experiments showed that MtbEF-Tu existed in a monomeric form, and circular dichroism experiments indicated that MtbEF-Tu was well structured. Moreover, isothermal titration calorimetry experiments displayed that the purified MtbEF-Tu protein possessed intermediate binding affinities for guanosine-5'-triphosphate (GTP) and GDP. The GTP/GDP-binding sites were predicted by flexible molecular docking approach which reveals that GTP/GDP binds to MtbEF-Tu mainly through hydrogen bonds. Our work lays the essential basis for further structural and functional studies of MtbEF-Tu as well as MtbEF-Tu-related novel drug developments.
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Affiliation(s)
- Juanjuan Yang
- Institute of Pharmaceutical Biotechnology and Engineering, College of Biological Science and Biotechnology, Fuzhou University, Fuzhou, China
| | - Jing Hong
- Institute of Pharmaceutical Biotechnology and Engineering, College of Biological Science and Biotechnology, Fuzhou University, Fuzhou, China
| | - Ling Luo
- Institute of Pharmaceutical Biotechnology and Engineering, College of Biological Science and Biotechnology, Fuzhou University, Fuzhou, China
| | - Ke Liu
- State Key Laboratory of Stress Cell Biology, School of Life Sciences, Xiamen University, Xiamen, China
| | - Chun Meng
- Institute of Pharmaceutical Biotechnology and Engineering, College of Biological Science and Biotechnology, Fuzhou University, Fuzhou, China
| | - Zhi-liang Ji
- State Key Laboratory of Stress Cell Biology, School of Life Sciences, Xiamen University, Xiamen, China
| | - Donghai Lin
- High-Field NMR Center, Key Laboratory for Chemical Biology of Fujian Province, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, China
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9
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Transcriptome analysis of methicillin-resistant Staphylococcus aureus in response to stigmasterol and lupeol. J Glob Antimicrob Resist 2017; 8:48-54. [DOI: 10.1016/j.jgar.2016.10.006] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2016] [Revised: 10/09/2016] [Accepted: 10/16/2016] [Indexed: 11/22/2022] Open
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10
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Emperador S, Bayona-Bafaluy MP, Fernández-Marmiesse A, Pineda M, Felgueroso B, López-Gallardo E, Artuch R, Roca I, Ruiz-Pesini E, Couce ML, Montoya J. Molecular-genetic characterization and rescue of a TSFM mutation causing childhood-onset ataxia and nonobstructive cardiomyopathy. Eur J Hum Genet 2016; 25:153-156. [PMID: 27677415 DOI: 10.1038/ejhg.2016.124] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2016] [Revised: 08/23/2016] [Accepted: 08/24/2016] [Indexed: 01/20/2023] Open
Abstract
Oxidative phosphorylation dysfunction has been found in many different disorders. This biochemical pathway depends on mitochondrial protein synthesis. Thus, mutations in components of the mitochondrial translation system can be responsible for some of these pathologies. We identified a new homozygous missense mutation in the mitochondrial translation elongation factor Ts gene in a patient suffering from slowly progressive childhood ataxia and hypertrophic cardiomyopathy. Using cell, biochemical and molecular-genetic protocols, we confirm it as the etiologic factor of this phenotype. Moreover, as an important functional confirmation, we rescued the normal molecular phenotype by expression of the wild-type TSFM cDNA in patient's fibroblasts. Different TSFM mutations can produce the same or very different clinical phenotypes, going from abortions to moderately severe presentations. On the other hand, the same TSFM mutation can also produce same or different phenotypes within the same range of presentations, therefore suggesting the involvement of unknown factors.
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Affiliation(s)
- Sonia Emperador
- Departamento de Bioquímica, Biología Molecular y Celular, Universidad de Zaragoza, Zaragoza, Spain.,Centro de Investigaciones Biomédicas en Red de Enfermedades Raras (CIBERER), Madrid, Spain.,Instituto de Investigación Sanitaria de Aragón (IIS Aragón), Universidad de Zaragoza, Zaragoza, Spain
| | - M Pilar Bayona-Bafaluy
- Departamento de Bioquímica, Biología Molecular y Celular, Universidad de Zaragoza, Zaragoza, Spain.,Instituto de Investigación Sanitaria de Aragón (IIS Aragón), Universidad de Zaragoza, Zaragoza, Spain
| | - Ana Fernández-Marmiesse
- Centro de Investigaciones Biomédicas en Red de Enfermedades Raras (CIBERER), Madrid, Spain.,Departamento de Pediatría, Hospital Clínico Universitario de Santiago de Compostela, Instituto de Investigación Sanitaria de Santiago de Compostela (IDIS), Santiago de Compostela, Spain
| | - Mercedes Pineda
- Centro de Investigaciones Biomédicas en Red de Enfermedades Raras (CIBERER), Madrid, Spain.,Departamento de Neuropediatría, Hospital San Joan de Deu, Institut de Recerca Pediàtrica (IRP-HSJD), Barcelona, Spain
| | - Blanca Felgueroso
- Departamento de Neurología Pediátrica, Hospital Materno Infantil Teresa Herrera, A Coruña, Spain
| | - Ester López-Gallardo
- Departamento de Bioquímica, Biología Molecular y Celular, Universidad de Zaragoza, Zaragoza, Spain.,Centro de Investigaciones Biomédicas en Red de Enfermedades Raras (CIBERER), Madrid, Spain.,Instituto de Investigación Sanitaria de Aragón (IIS Aragón), Universidad de Zaragoza, Zaragoza, Spain
| | - Rafael Artuch
- Centro de Investigaciones Biomédicas en Red de Enfermedades Raras (CIBERER), Madrid, Spain.,Departamento de Neuropediatría, Hospital San Joan de Deu, Institut de Recerca Pediàtrica (IRP-HSJD), Barcelona, Spain
| | - Iria Roca
- Departamento de Pediatría, Hospital Clínico Universitario de Santiago de Compostela, Instituto de Investigación Sanitaria de Santiago de Compostela (IDIS), Santiago de Compostela, Spain
| | - Eduardo Ruiz-Pesini
- Departamento de Bioquímica, Biología Molecular y Celular, Universidad de Zaragoza, Zaragoza, Spain.,Centro de Investigaciones Biomédicas en Red de Enfermedades Raras (CIBERER), Madrid, Spain.,Instituto de Investigación Sanitaria de Aragón (IIS Aragón), Universidad de Zaragoza, Zaragoza, Spain.,Fundación ARAID, Universidad de Zaragoza, Zaragoza, Spain
| | - María Luz Couce
- Centro de Investigaciones Biomédicas en Red de Enfermedades Raras (CIBERER), Madrid, Spain.,Departamento de Pediatría, Hospital Clínico Universitario de Santiago de Compostela, Instituto de Investigación Sanitaria de Santiago de Compostela (IDIS), Santiago de Compostela, Spain
| | - Julio Montoya
- Departamento de Bioquímica, Biología Molecular y Celular, Universidad de Zaragoza, Zaragoza, Spain. .,Centro de Investigaciones Biomédicas en Red de Enfermedades Raras (CIBERER), Madrid, Spain. .,Instituto de Investigación Sanitaria de Aragón (IIS Aragón), Universidad de Zaragoza, Zaragoza, Spain.
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11
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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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12
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Thirup SS, Van LB, Nielsen TK, Knudsen CR. Structural outline of the detailed mechanism for elongation factor Ts-mediated guanine nucleotide exchange on elongation factor Tu. J Struct Biol 2015; 191:10-21. [PMID: 26073967 DOI: 10.1016/j.jsb.2015.06.011] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2015] [Revised: 06/05/2015] [Accepted: 06/11/2015] [Indexed: 11/26/2022]
Abstract
Translation elongation factor EF-Tu belongs to the superfamily of guanine-nucleotide binding proteins, which play key cellular roles as regulatory switches. All G-proteins require activation via exchange of GDP for GTP to carry out their respective tasks. Often, guanine-nucleotide exchange factors are essential to this process. During translation, EF-Tu:GTP transports aminoacylated tRNA to the ribosome. GTP is hydrolyzed during this process, and subsequent reactivation of EF-Tu is catalyzed by EF-Ts. The reaction path of guanine-nucleotide exchange is structurally poorly defined for EF-Tu and EF-Ts. We have determined the crystal structures of the following reaction intermediates: two structures of EF-Tu:GDP:EF-Ts (2.2 and 1.8Å resolution), EF-Tu:PO4:EF-Ts (1.9Å resolution), EF-Tu:GDPNP:EF-Ts (2.2Å resolution) and EF-Tu:GDPNP:pulvomycin:Mg(2+):EF-Ts (3.5Å resolution). These structures provide snapshots throughout the entire exchange reaction and suggest a mechanism for the release of EF-Tu in its GTP conformation. An inferred sequence of events during the exchange reaction is presented.
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Affiliation(s)
- Søren S Thirup
- Aarhus University, Department of Molecular Biology and Genetics, Center for Structural Biology, DK-8000 Aarhus C, Denmark.
| | - Lan Bich Van
- Aarhus University, Department of Molecular Biology and Genetics, Center for Structural Biology, DK-8000 Aarhus C, Denmark
| | - Tine K Nielsen
- Aarhus University, Department of Molecular Biology and Genetics, Center for Structural Biology, DK-8000 Aarhus C, Denmark
| | - Charlotte R Knudsen
- Aarhus University, Department of Molecular Biology and Genetics, Center for Structural Biology, DK-8000 Aarhus C, Denmark
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13
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Parihar P, Solanki I, Mansuri ML, Parihar MS. Mitochondrial sirtuins: emerging roles in metabolic regulations, energy homeostasis and diseases. Exp Gerontol 2014; 61:130-41. [PMID: 25482473 DOI: 10.1016/j.exger.2014.12.004] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2014] [Revised: 11/19/2014] [Accepted: 12/03/2014] [Indexed: 12/18/2022]
Abstract
The energy production and metabolic homeostasis are well-orchestrated networks of carbohydrate, lipid and protein metabolism. These metabolic pathways are integrated by a key cytoplasmic organelle, the mitochondria, leading to production of many metabolic intermediates and harvest cellular energy in the form of ATP. Sirtuins are a highly conserved family of proteins that mediate cellular physiology and energy demands in response to metabolic inputs. Mitochondria inhabit three main types of sirtuins classified as Sirt3, Sirt4 and Sirt5. These sirtuins regulate mitochondrial metabolic functions mainly through controlling post-translational modifications of mitochondrial protein. However, the biological mechanism involved in controlling mitochondrial metabolic functions is not well understood at this stage. In this review the current knowledge on how mitochondrial sirtuins govern mitochondrial functions including energy production, metabolism, biogenesis and their involvement in different metabolic pathways are discussed. The identifications of potential pharmacological targets of sirtuins in the mitochondria and the bioactive compounds that target mitochondrial sirtuins will increase our understanding on regulation of mitochondrial metabolism in normal and disease state.
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Affiliation(s)
- Priyanka Parihar
- School of Studies in Zoology & Biotechnology, Vikram University, Ujjain, MP, India
| | - Isha Solanki
- School of Studies in Zoology & Biotechnology, Vikram University, Ujjain, MP, India
| | | | - Mordhwaj S Parihar
- School of Studies in Zoology & Biotechnology, Vikram University, Ujjain, MP, India.
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14
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Ahola S, Isohanni P, Euro L, Brilhante V, Palotie A, Pihko H, Lönnqvist T, Lehtonen T, Laine J, Tyynismaa H, Suomalainen A. Mitochondrial EFTs defects in juvenile-onset Leigh disease, ataxia, neuropathy, and optic atrophy. Neurology 2014; 83:743-51. [PMID: 25037205 DOI: 10.1212/wnl.0000000000000716] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
OBJECTIVE We report novel defects of mitochondrial translation elongation factor Ts (EFTs), with high carrier frequency in Finland and expand the manifestations of this disease group from infantile cardiomyopathy to juvenile neuropathy/encephalopathy disorders. METHODS DNA analysis, whole-exome analysis, protein biochemistry, and protein modeling. RESULTS We used whole-exome sequencing to find the genetic cause of infantile-onset mitochondrial cardiomyopathy, progressing to juvenile-onset Leigh syndrome, neuropathy, and optic atrophy in 2 siblings. We found novel compound heterozygous mutations, c.944G>A [p.C315Y] and c.856C>T [p.Q286X], in the TSFM gene encoding mitochondrial EFTs. The same p.Q286X variant was found as compound heterozygous with a splice site change in a patient from a second family, with juvenile-onset optic atrophy, peripheral neuropathy, and ataxia. Our molecular modeling predicted the coding-region mutations to cause protein instability, which was experimentally confirmed in cultured patient cells, with mitochondrial translation defect and lacking EFTs. Only a single TSFM mutation has been previously described in different populations, leading to an infantile fatal multisystem disorder with cardiomyopathy. Sequence data from 35,000 Finnish population controls indicated that the heterozygous carrier frequency of p.Q286X change was exceptionally high in Finland, 1:80, but no homozygotes were found in the population, in our mitochondrial disease patient collection, or in an intrauterine fetal death material, suggesting early developmental lethality of the homozygotes. CONCLUSIONS We show that in addition to early-onset cardiomyopathy, TSFM mutations should be considered in childhood and juvenile encephalopathies with optic and/or peripheral neuropathy, ataxia, or Leigh disease.
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Affiliation(s)
- Sofia Ahola
- From the Research Programs Unit, Molecular Neurology, Biomedicum Helsinki (S.A., P.I., L.E., V.B., H.T., A.S.), Institute for Molecular Medicine Finland (A.P.), Department of Medical Genetics, Haartman Institute (H.T.), and Neuroscience Center (A.S.), University of Helsinki; Department of Child Neurology, Children's Hospital (P.I., H.P., T. Lönnqvist), and Department of Neurology (A.S.), Helsinki University Central Hospital, Finland; Analytic and Translational Genetics Unit, Department of Medicine (A.P.), and Psychiatric & Neurodevelopmental Genetics Unit, Department of Psychiatry (A.P.), Massachusetts General Hospital, Boston; Program in Medical and Population Genetics (A.P.), Broad Institute of MIT and Harvard, Cambridge, MA; and Department of Pathology (T. Lehtonen, J.L.), University of Turku, Finland
| | - Pirjo Isohanni
- From the Research Programs Unit, Molecular Neurology, Biomedicum Helsinki (S.A., P.I., L.E., V.B., H.T., A.S.), Institute for Molecular Medicine Finland (A.P.), Department of Medical Genetics, Haartman Institute (H.T.), and Neuroscience Center (A.S.), University of Helsinki; Department of Child Neurology, Children's Hospital (P.I., H.P., T. Lönnqvist), and Department of Neurology (A.S.), Helsinki University Central Hospital, Finland; Analytic and Translational Genetics Unit, Department of Medicine (A.P.), and Psychiatric & Neurodevelopmental Genetics Unit, Department of Psychiatry (A.P.), Massachusetts General Hospital, Boston; Program in Medical and Population Genetics (A.P.), Broad Institute of MIT and Harvard, Cambridge, MA; and Department of Pathology (T. Lehtonen, J.L.), University of Turku, Finland
| | - Liliya Euro
- From the Research Programs Unit, Molecular Neurology, Biomedicum Helsinki (S.A., P.I., L.E., V.B., H.T., A.S.), Institute for Molecular Medicine Finland (A.P.), Department of Medical Genetics, Haartman Institute (H.T.), and Neuroscience Center (A.S.), University of Helsinki; Department of Child Neurology, Children's Hospital (P.I., H.P., T. Lönnqvist), and Department of Neurology (A.S.), Helsinki University Central Hospital, Finland; Analytic and Translational Genetics Unit, Department of Medicine (A.P.), and Psychiatric & Neurodevelopmental Genetics Unit, Department of Psychiatry (A.P.), Massachusetts General Hospital, Boston; Program in Medical and Population Genetics (A.P.), Broad Institute of MIT and Harvard, Cambridge, MA; and Department of Pathology (T. Lehtonen, J.L.), University of Turku, Finland
| | - Virginia Brilhante
- From the Research Programs Unit, Molecular Neurology, Biomedicum Helsinki (S.A., P.I., L.E., V.B., H.T., A.S.), Institute for Molecular Medicine Finland (A.P.), Department of Medical Genetics, Haartman Institute (H.T.), and Neuroscience Center (A.S.), University of Helsinki; Department of Child Neurology, Children's Hospital (P.I., H.P., T. Lönnqvist), and Department of Neurology (A.S.), Helsinki University Central Hospital, Finland; Analytic and Translational Genetics Unit, Department of Medicine (A.P.), and Psychiatric & Neurodevelopmental Genetics Unit, Department of Psychiatry (A.P.), Massachusetts General Hospital, Boston; Program in Medical and Population Genetics (A.P.), Broad Institute of MIT and Harvard, Cambridge, MA; and Department of Pathology (T. Lehtonen, J.L.), University of Turku, Finland
| | - Aarno Palotie
- From the Research Programs Unit, Molecular Neurology, Biomedicum Helsinki (S.A., P.I., L.E., V.B., H.T., A.S.), Institute for Molecular Medicine Finland (A.P.), Department of Medical Genetics, Haartman Institute (H.T.), and Neuroscience Center (A.S.), University of Helsinki; Department of Child Neurology, Children's Hospital (P.I., H.P., T. Lönnqvist), and Department of Neurology (A.S.), Helsinki University Central Hospital, Finland; Analytic and Translational Genetics Unit, Department of Medicine (A.P.), and Psychiatric & Neurodevelopmental Genetics Unit, Department of Psychiatry (A.P.), Massachusetts General Hospital, Boston; Program in Medical and Population Genetics (A.P.), Broad Institute of MIT and Harvard, Cambridge, MA; and Department of Pathology (T. Lehtonen, J.L.), University of Turku, Finland
| | - Helena Pihko
- From the Research Programs Unit, Molecular Neurology, Biomedicum Helsinki (S.A., P.I., L.E., V.B., H.T., A.S.), Institute for Molecular Medicine Finland (A.P.), Department of Medical Genetics, Haartman Institute (H.T.), and Neuroscience Center (A.S.), University of Helsinki; Department of Child Neurology, Children's Hospital (P.I., H.P., T. Lönnqvist), and Department of Neurology (A.S.), Helsinki University Central Hospital, Finland; Analytic and Translational Genetics Unit, Department of Medicine (A.P.), and Psychiatric & Neurodevelopmental Genetics Unit, Department of Psychiatry (A.P.), Massachusetts General Hospital, Boston; Program in Medical and Population Genetics (A.P.), Broad Institute of MIT and Harvard, Cambridge, MA; and Department of Pathology (T. Lehtonen, J.L.), University of Turku, Finland
| | - Tuula Lönnqvist
- From the Research Programs Unit, Molecular Neurology, Biomedicum Helsinki (S.A., P.I., L.E., V.B., H.T., A.S.), Institute for Molecular Medicine Finland (A.P.), Department of Medical Genetics, Haartman Institute (H.T.), and Neuroscience Center (A.S.), University of Helsinki; Department of Child Neurology, Children's Hospital (P.I., H.P., T. Lönnqvist), and Department of Neurology (A.S.), Helsinki University Central Hospital, Finland; Analytic and Translational Genetics Unit, Department of Medicine (A.P.), and Psychiatric & Neurodevelopmental Genetics Unit, Department of Psychiatry (A.P.), Massachusetts General Hospital, Boston; Program in Medical and Population Genetics (A.P.), Broad Institute of MIT and Harvard, Cambridge, MA; and Department of Pathology (T. Lehtonen, J.L.), University of Turku, Finland
| | - Tanita Lehtonen
- From the Research Programs Unit, Molecular Neurology, Biomedicum Helsinki (S.A., P.I., L.E., V.B., H.T., A.S.), Institute for Molecular Medicine Finland (A.P.), Department of Medical Genetics, Haartman Institute (H.T.), and Neuroscience Center (A.S.), University of Helsinki; Department of Child Neurology, Children's Hospital (P.I., H.P., T. Lönnqvist), and Department of Neurology (A.S.), Helsinki University Central Hospital, Finland; Analytic and Translational Genetics Unit, Department of Medicine (A.P.), and Psychiatric & Neurodevelopmental Genetics Unit, Department of Psychiatry (A.P.), Massachusetts General Hospital, Boston; Program in Medical and Population Genetics (A.P.), Broad Institute of MIT and Harvard, Cambridge, MA; and Department of Pathology (T. Lehtonen, J.L.), University of Turku, Finland
| | - Jukka Laine
- From the Research Programs Unit, Molecular Neurology, Biomedicum Helsinki (S.A., P.I., L.E., V.B., H.T., A.S.), Institute for Molecular Medicine Finland (A.P.), Department of Medical Genetics, Haartman Institute (H.T.), and Neuroscience Center (A.S.), University of Helsinki; Department of Child Neurology, Children's Hospital (P.I., H.P., T. Lönnqvist), and Department of Neurology (A.S.), Helsinki University Central Hospital, Finland; Analytic and Translational Genetics Unit, Department of Medicine (A.P.), and Psychiatric & Neurodevelopmental Genetics Unit, Department of Psychiatry (A.P.), Massachusetts General Hospital, Boston; Program in Medical and Population Genetics (A.P.), Broad Institute of MIT and Harvard, Cambridge, MA; and Department of Pathology (T. Lehtonen, J.L.), University of Turku, Finland
| | - Henna Tyynismaa
- From the Research Programs Unit, Molecular Neurology, Biomedicum Helsinki (S.A., P.I., L.E., V.B., H.T., A.S.), Institute for Molecular Medicine Finland (A.P.), Department of Medical Genetics, Haartman Institute (H.T.), and Neuroscience Center (A.S.), University of Helsinki; Department of Child Neurology, Children's Hospital (P.I., H.P., T. Lönnqvist), and Department of Neurology (A.S.), Helsinki University Central Hospital, Finland; Analytic and Translational Genetics Unit, Department of Medicine (A.P.), and Psychiatric & Neurodevelopmental Genetics Unit, Department of Psychiatry (A.P.), Massachusetts General Hospital, Boston; Program in Medical and Population Genetics (A.P.), Broad Institute of MIT and Harvard, Cambridge, MA; and Department of Pathology (T. Lehtonen, J.L.), University of Turku, Finland
| | - Anu Suomalainen
- From the Research Programs Unit, Molecular Neurology, Biomedicum Helsinki (S.A., P.I., L.E., V.B., H.T., A.S.), Institute for Molecular Medicine Finland (A.P.), Department of Medical Genetics, Haartman Institute (H.T.), and Neuroscience Center (A.S.), University of Helsinki; Department of Child Neurology, Children's Hospital (P.I., H.P., T. Lönnqvist), and Department of Neurology (A.S.), Helsinki University Central Hospital, Finland; Analytic and Translational Genetics Unit, Department of Medicine (A.P.), and Psychiatric & Neurodevelopmental Genetics Unit, Department of Psychiatry (A.P.), Massachusetts General Hospital, Boston; Program in Medical and Population Genetics (A.P.), Broad Institute of MIT and Harvard, Cambridge, MA; and Department of Pathology (T. Lehtonen, J.L.), University of Turku, Finland.
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15
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Kuzmenko AV, Levitskii SA, Vinogradova EN, Atkinson GC, Hauryliuk V, Zenkin N, Kamenski PA. Protein biosynthesis in mitochondria. BIOCHEMISTRY (MOSCOW) 2014; 78:855-66. [PMID: 24228873 DOI: 10.1134/s0006297913080014] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Translation, that is biosynthesis of polypeptides in accordance with information encoded in the genome, is one of the most important processes in the living cell, and it has been in the spotlight of international research for many years. The mechanisms of protein biosynthesis in bacteria and in the eukaryotic cytoplasm are now understood in great detail. However, significantly less is known about translation in eukaryotic mitochondria, which is characterized by a number of unusual features. In this review, we summarize current knowledge about mitochondrial translation in different organisms while paying special attention to the aspects of this process that differ from cytoplasmic protein biosynthesis.
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Affiliation(s)
- A V Kuzmenko
- Department of Molecular Biology, Faculty of Biology, Lomonosov Moscow State University, Moscow, 119991, Russia.
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16
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Cloning and characterization of EF-Tu and EF-Ts from Pseudomonas aeruginosa. BIOMED RESEARCH INTERNATIONAL 2013; 2013:585748. [PMID: 23984384 PMCID: PMC3747624 DOI: 10.1155/2013/585748] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/01/2013] [Accepted: 07/12/2013] [Indexed: 11/17/2022]
Abstract
We have cloned genes encoding elongation factors EF-Tu and EF-Ts from Pseudomonas aeruginosa and expressed and purified the proteins to greater than 95% homogeneity. Sequence analysis indicated that P. aeruginosa EF-Tu and EF-Ts are 84% and 55% identical to E. coli counterparts, respectively. P. aeruginosa EF-Tu was active when assayed in GDP exchange assays. Kinetic parameters for the interaction of EF-Tu with GDP in the absence of EF-Ts were observed to be K M = 33 μM, k cat (obs) = 0.003 s(-1), and the specificity constant k cat (obs)/K M was 0.1 × 10(-3) s(-1) μM(-1). In the presence of EF-Ts, these values were shifted to K M = 2 μM, k cat (obs) = 0.005 s(-1), and the specificity constant k(cat)(obs)/K M was 2.5 × 10(-3) s(-1) μM(-1). The equilibrium dissociation constants governing the binding of EF-Tu to GDP (K GDP) were 30-75 nM and to GTP (K GTP) were 125-200 nM. EF-Ts stimulated the exchange of GDP by EF-Tu 10-fold. P. aeruginosa EF-Tu was active in forming a ternary complex with GTP and aminoacylated tRNA and was functional in poly(U)-dependent binding of Phe-tRNA(Phe) at the A-site of P. aeruginosa ribosomes. P. aeruginosa EF-Tu was active in poly(U)-programmed polyphenylalanine protein synthesis system composed of all P. aeruginosa components.
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17
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Hebert AS, Dittenhafer-Reed KE, Yu W, Bailey DJ, Selen ES, Boersma MD, Carson JJ, Tonelli M, Balloon A, Higbee AJ, Westphall MS, Pagliarini DJ, Prolla TA, Assadi-Porter F, Roy S, Denu JM, Coon JJ. Calorie restriction and SIRT3 trigger global reprogramming of the mitochondrial protein acetylome. Mol Cell 2013; 49:186-99. [PMID: 23201123 PMCID: PMC3704155 DOI: 10.1016/j.molcel.2012.10.024] [Citation(s) in RCA: 500] [Impact Index Per Article: 45.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2012] [Revised: 09/11/2012] [Accepted: 10/23/2012] [Indexed: 12/18/2022]
Abstract
Calorie restriction (CR) extends life span in diverse species. Mitochondria play a key role in CR adaptation; however, the molecular details remain elusive. We developed and applied a quantitative mass spectrometry method to probe the liver mitochondrial acetyl-proteome during CR versus control diet in mice that were wild-type or lacked the protein deacetylase SIRT3. Quantification of 3,285 acetylation sites-2,193 from mitochondrial proteins-rendered a comprehensive atlas of the acetyl-proteome and enabled global site-specific, relative acetyl occupancy measurements between all four experimental conditions. Bioinformatic and biochemical analyses provided additional support for the effects of specific acetylation on mitochondrial protein function. Our results (1) reveal widespread reprogramming of mitochondrial protein acetylation in response to CR and SIRT3, (2) identify three biochemically distinct classes of acetylation sites, and (3) provide evidence that SIRT3 is a prominent regulator in CR adaptation by coordinately deacetylating proteins involved in diverse pathways of metabolism and mitochondrial maintenance.
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Affiliation(s)
- Alexander S. Hebert
- Department of Biomolecular Chemistry, University of Wisconsin, Madison, Wisconsin, United States
| | | | - Wei Yu
- Department of Biomolecular Chemistry, University of Wisconsin, Madison, Wisconsin, United States
| | - Derek J. Bailey
- Department of Chemistry, University of Wisconsin, Madison, Wisconsin, United States
| | - Ebru Selin Selen
- Department of Biochemistry, University of Wisconsin, Madison, Wisconsin, United States
| | - Melissa D. Boersma
- Department of Biomolecular Chemistry, University of Wisconsin, Madison, Wisconsin, United States
| | - Joshua J. Carson
- Department of Biochemistry, University of Wisconsin, Madison, Wisconsin, United States
| | - Marco Tonelli
- National Magnetic Resonance Facility at Madison, University of Wisconsin, Madison, Wisconsin, United States
| | - Allison Balloon
- Department of Chemistry, University of Wisconsin, Madison, Wisconsin, United States
| | - Alan J. Higbee
- Genome Center of Wisconsin, University of Wisconsin, Madison, Wisconsin, United States
| | - Michael S. Westphall
- Genome Center of Wisconsin, University of Wisconsin, Madison, Wisconsin, United States
| | - David J. Pagliarini
- Department of Biochemistry, University of Wisconsin, Madison, Wisconsin, United States
| | - Tomas A. Prolla
- Genetics and Medical Genetics, University of Wisconsin, Madison, Wisconsin, United States
| | - Fariba Assadi-Porter
- Department of Biochemistry, University of Wisconsin, Madison, Wisconsin, United States
- National Magnetic Resonance Facility at Madison, University of Wisconsin, Madison, Wisconsin, United States
| | - Sushmita Roy
- Department of Biostatistics and Medical Informatics, University of Wisconsin, Madison, Wisconsin, United States
| | - John M. Denu
- Department of Biomolecular Chemistry, University of Wisconsin, Madison, Wisconsin, United States
| | - Joshua J. Coon
- Department of Biomolecular Chemistry, University of Wisconsin, Madison, Wisconsin, United States
- Department of Chemistry, University of Wisconsin, Madison, Wisconsin, United States
- Genome Center of Wisconsin, University of Wisconsin, Madison, Wisconsin, United States
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18
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Newman MA, Sundelin T, Nielsen JT, Erbs G. MAMP (microbe-associated molecular pattern) triggered immunity in plants. FRONTIERS IN PLANT SCIENCE 2013; 4:139. [PMID: 23720666 PMCID: PMC3655273 DOI: 10.3389/fpls.2013.00139] [Citation(s) in RCA: 262] [Impact Index Per Article: 23.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2013] [Accepted: 04/23/2013] [Indexed: 05/18/2023]
Abstract
Plants are sessile organisms that are under constant attack from microbes. They rely on both preformed defenses, and their innate immune system to ward of the microbial pathogens. Preformed defences include for example the cell wall and cuticle, which act as physical barriers to microbial colonization. The plant immune system is composed of surveillance systems that perceive several general microbe elicitors, which allow plants to switch from growth and development into a defense mode, rejecting most potentially harmful microbes. The elicitors are essential structures for pathogen survival and are conserved among pathogens. The conserved microbe-specific molecules, referred to as microbe- or pathogen-associated molecular patterns (MAMPs or PAMPs), are recognized by the plant innate immune systems pattern recognition receptors (PRRs). General elicitors like flagellin (Flg), elongation factor Tu (EF-Tu), peptidoglycan (PGN), lipopolysaccharides (LPS), Ax21 (Activator of XA21-mediated immunity in rice), fungal chitin, and β-glucans from oomycetes are recognized by plant surface localized PRRs. Several of the MAMPs and their corresponding PRRs have, in recent years, been identified. This review focuses on the current knowledge regarding important MAMPs from bacteria, fungi, and oomycetes, their structure, the plant PRRs that recognizes them, and how they induce MAMP-triggered immunity (MTI) in plants.
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Affiliation(s)
- Mari-Anne Newman
- *Correspondence: Mari-Anne Newman, Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg C, Denmark. e-mail:
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19
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Rackham O, Mercer TR, Filipovska A. The human mitochondrial transcriptome and the RNA-binding proteins that regulate its expression. WILEY INTERDISCIPLINARY REVIEWS-RNA 2012; 3:675-95. [DOI: 10.1002/wrna.1128] [Citation(s) in RCA: 81] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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20
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Christian BE, Spremulli LL. Mechanism of protein biosynthesis in mammalian mitochondria. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2011; 1819:1035-54. [PMID: 22172991 DOI: 10.1016/j.bbagrm.2011.11.009] [Citation(s) in RCA: 135] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2011] [Revised: 11/03/2011] [Accepted: 11/08/2011] [Indexed: 01/25/2023]
Abstract
Protein synthesis in mammalian mitochondria produces 13 proteins that are essential subunits of the oxidative phosphorylation complexes. This review provides a detailed outline of each phase of mitochondrial translation including initiation, elongation, termination, and ribosome recycling. The roles of essential proteins involved in each phase are described. All of the products of mitochondrial protein synthesis in mammals are inserted into the inner membrane. Several proteins that may help bind ribosomes to the membrane during translation are described, although much remains to be learned about this process. Mutations in mitochondrial or nuclear genes encoding components of the translation system often lead to severe deficiencies in oxidative phosphorylation, and a summary of these mutations is provided. This article is part of a Special Issue entitled: Mitochondrial Gene Expression.
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Affiliation(s)
- Brooke E Christian
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
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Wieden HJ, Mercier E, Gray J, Steed B, Yawney D. A combined molecular dynamics and rapid kinetics approach to identify conserved three-dimensional communication networks in elongation factor Tu. Biophys J 2011; 99:3735-43. [PMID: 21112298 DOI: 10.1016/j.bpj.2010.10.013] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2010] [Revised: 09/30/2010] [Accepted: 10/04/2010] [Indexed: 10/18/2022] Open
Abstract
Elongation factor (EF) Tu delivers aminoacyl-tRNAs to the actively translating bacterial ribosome in a GTP-hydrolysis-dependent process. Rapid recycling of EF-Tu, catalyzed by EF-Ts, is required for efficient protein synthesis in vivo. Here we report a combined theoretical and experimental approach aimed at identifying three-dimensional communication networks in EF-Tu. As an example, we focus on the mechanistic role of second-shell residue Asp(109). We constructed full-length structural models of EF-Tu from Escherichia coli in the GDP-/GTP-bound state and performed several 10-ns-long molecular-dynamics simulations. During these simulations, the side chain of Asp(109) formed a previously undetected transient hydrogen bond to His(22), an invariant residue in the phosphate-binding loop (P-loop). To experimentally validate our molecular-dynamics results and further analyze the role of this hydrogen bond, we determined all rate constants for the multistep reaction between EF-Tu (wild-type and two mutants), EF-Ts, GDP, and GTP using the stopped-flow technique. This mutational analysis revealed that the side chain of Asp(109) is important for acceleration of GDP, but not for GTP dissociation by EF-Ts. The possibility that the Asp(109) side chain has a role in transition-state stabilization and coupling of P-loop movements with rearrangements at the base side of the nucleotide is discussed.
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Affiliation(s)
- Hans-Joachim Wieden
- Department of Chemistry and Biochemistry, University of Lethbridge, Lethbridge, Canada.
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22
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Biswas S, Lim EE, Gupta A, Saqib U, Mir SS, Siddiqi MI, Ralph SA, Habib S. Interaction of apicoplast-encoded elongation factor (EF) EF-Tu with nuclear-encoded EF-Ts mediates translation in the Plasmodium falciparum plastid. Int J Parasitol 2011; 41:417-27. [DOI: 10.1016/j.ijpara.2010.11.003] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2010] [Revised: 11/08/2010] [Accepted: 11/08/2010] [Indexed: 11/16/2022]
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23
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Kulczycka K, Długosz M, Trylska J. Molecular dynamics of ribosomal elongation factors G and Tu. EUROPEAN BIOPHYSICS JOURNAL : EBJ 2011; 40:289-303. [PMID: 21152913 PMCID: PMC3045518 DOI: 10.1007/s00249-010-0647-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/27/2010] [Revised: 11/09/2010] [Accepted: 11/16/2010] [Indexed: 11/04/2022]
Abstract
Translation on the ribosome is controlled by external factors. During polypeptide lengthening, elongation factors EF-Tu and EF-G consecutively interact with the bacterial ribosome. EF-Tu binds and delivers an aminoacyl-tRNA to the ribosomal A site and EF-G helps translocate the tRNAs between their binding sites after the peptide bond is formed. These processes occur at the expense of GTP. EF-Tu:tRNA and EF-G are of similar shape, share a common binding site, and undergo large conformational changes on interaction with the ribosome. To characterize the internal motion of these two elongation factors, we used 25 ns long all-atom molecular dynamics simulations. We observed enhanced mobility of EF-G domains III, IV, and V and of tRNA in the EF-Tu:tRNA complex. EF-Tu:GDP complex acquired a configuration different from that found in the crystal structure of EF-Tu with a GTP analogue, showing conformational changes in the switch I and II regions. The calculated electrostatic properties of elongation factors showed no global similarity even though matching electrostatic surface patches were found around the domain I that contacts the ribosome, and in the GDP/GTP binding region.
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Affiliation(s)
- Katarzyna Kulczycka
- Interdisciplinary Centre for Mathematical and Computational Modelling, University of Warsaw, Pawinskiego 5A, 02-106 Warsaw, Poland
- College of Inter-Faculty Individual Studies in Mathematics and Natural Science, University of Warsaw, Zwirki i Wigury 93, 02-089 Warsaw, Poland
| | - Maciej Długosz
- Interdisciplinary Centre for Mathematical and Computational Modelling, University of Warsaw, Pawinskiego 5A, 02-106 Warsaw, Poland
| | - Joanna Trylska
- Interdisciplinary Centre for Mathematical and Computational Modelling, University of Warsaw, Pawinskiego 5A, 02-106 Warsaw, Poland
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24
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Berger CN, Brown DJ, Shaw RK, Minuzzi F, Feys B, Frankel G. Salmonella enterica strains belonging to O serogroup 1,3,19 induce chlorosis and wilting of Arabidopsis thaliana leaves. Environ Microbiol 2011; 13:1299-308. [DOI: 10.1111/j.1462-2920.2011.02429.x] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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25
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Berisio R, Ruggiero A, Vitagliano L. Elongation Factors EFIA and EF-Tu: Their Role in Translation and Beyond. Isr J Chem 2010. [DOI: 10.1002/ijch.201000005] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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26
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Akama K, Christian BE, Jones CN, Ueda T, Takeuchi N, Spremulli LL. Analysis of the functional consequences of lethal mutations in mitochondrial translational elongation factors. Biochim Biophys Acta Mol Basis Dis 2010; 1802:692-8. [PMID: 20435138 DOI: 10.1016/j.bbadis.2010.04.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2010] [Revised: 04/14/2010] [Accepted: 04/16/2010] [Indexed: 11/29/2022]
Abstract
Mammalian mitochondria synthesize a set of thirteen proteins that are essential for energy generation via oxidative phosphorylation. The genes for all of the factors required for synthesis of the mitochondrially encoded proteins are located in the nuclear genome. A number of disease-causing mutations have been identified in these genes. In this manuscript, we have elucidated the mechanisms of translational failure for two disease states characterized by lethal mutations in mitochondrial elongation factor Ts (EF-Ts(mt)) and elongation factor Tu (EF-Tu(mt)). EF-Tu(mt) delivers the aminoacyl-tRNA (aa-tRNA) to the ribosome during the elongation phase of protein synthesis. EF-Ts(mt) regenerates EF-Tu(mt):GTP from EF-Tu(mt):GDP. A mutation of EF-Ts(mt) (R325W) leads to a two-fold reduction in its ability to stimulate the activity of EF-Tu(mt) in poly(U)-directed polypeptide chain elongation. This loss of activity is caused by a significant reduction in the ability of EF-Ts(mt) R325W to bind EF-Tu(mt), leading to a defect in nucleotide exchange. A mutation of Arg336 to Gln in EF-Tu(mt) causes infantile encephalopathy caused by defects in mitochondrial translation. EF-Tu(mt) R336Q is as active as the wild-type protein in polymerization using Escherichia coli 70S ribosomes and E. coli [(14)C]Phe-tRNA but is inactive in polymerization with mitochondrial [(14)C]Phe-tRNA and mitochondrial 55S ribosomes. The R336Q mutation causes a two-fold decrease in ternary complex formation with E. coli aa-tRNA but completely inactivates EF-Tu(mt) for binding to mitochondrial aa-tRNA. Clearly the R336Q mutation in EF-Tu(mt) has a far more drastic effect on its interaction with mitochondrial aa-tRNAs than bacterial aa-tRNAs.
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Affiliation(s)
- Kenta Akama
- Department of Medical Genome Sciences, Graduate school of Frontier Sciences, University of Tokyo, Bunkyo, Tokyo113-8656, Japan
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27
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Valente L, Shigi N, Suzuki T, Zeviani M. The R336Q mutation in human mitochondrial EFTu prevents the formation of an active mt-EFTu.GTP.aa-tRNA ternary complex. Biochim Biophys Acta Mol Basis Dis 2009; 1792:791-5. [PMID: 19524667 DOI: 10.1016/j.bbadis.2009.06.002] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2009] [Revised: 05/06/2009] [Accepted: 06/08/2009] [Indexed: 11/18/2022]
Abstract
The mitochondrial translational machinery allows the genes encoded by mitochondrial DNA (mtDNA) to be translated in situ. Mitochondrial translation requires a number of nucleus-encoded protein factors, some of which have been found to carry mutations in patients affected by mitochondrial encephalomyopathies. We have previously described the first, and so far only, mutation in the mitochondrial elongation factor Tu, mt-EFTu, in a baby girl with polycystic encephalopathy, micropolygyria, and leukodystrophic changes. Despite that the mutant mt-EFTu was present in normal amount in the patient's tissues, mitochondrial translation was severely reduced, determining multiple defects in the amount and activity of mtDNA-dependent respiratory chain complexes. By an in-vitro reconstructed translational system, we here provide evidence that the mutant mt-EFTu variant fails to bind to aminoacylated mitochondrial tRNAs, thus explaining the observed impairment of mitochondrial translation. This is the first analysis on the molecular mechanism of a mtDNA translation defect due to a nuclear gene mutation.
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Affiliation(s)
- Lucia Valente
- Unit of Molecular Neurogenetics, IRCCS Foundation, Neurological Institute C. Besta, 20126 Milano, Italy
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Lu Y, Jiao R, Chen X, Zhong J, Ji J, Shen P. Methylene blue-mediated photodynamic therapy induces mitochondria-dependent apoptosis in HeLa cell. J Cell Biochem 2009; 105:1451-60. [PMID: 18980251 DOI: 10.1002/jcb.21965] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Methylene blue (MB), a widely studied reagent, is investigated in this work for its usage in photodynamic therapy (PDT). PDT has been proved to be highly effective in the treatment of different types of cancers. Previous studies showed MB has both high affinity for mitochondria and high photodynamic efficiency. To elucidate the effects of MB in PDT, we analyzed PDT-induced apoptosis in HeLa cells by introducing different doses of MB into the culture media. Our data showed that MB-mediated PDT triggered intense apoptotic cell death through a series of steps, beginning with photochemical generation of reactive oxygen species. The release of cytochrome c and activation of caspase-3 indicated that MB-PDT-mediated apoptosis in HeLa cells was executed by the mitochondria-dependent apoptotic pathway. Importantly, proteomic studies confirmed that expression levels of several mitochondrial proteins were altered in MB-PDT-induced apoptosis, including TRAP1, mitochondrial elongation factor Tu and peroxiredoxin 3 isoform b. Western blot data showed that phosphorylation of ERK1/2 and PKA were reduced in MB-PDT treated cells, indicating several signal molecules participating in this apoptotic cascade. Moreover, MB-PDT induced an increase in the strength of interaction between Bcl-xL and dephosphorylated Bad. This led to loss of the pro-survival function of Bcl-xL and resulted in mitochondria-mediated apoptosis. This study provides solid evidence of a strong induction by MB-PDT of a mitochondria-dependent apoptosis cascade in HeLa cells.
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Affiliation(s)
- Yan Lu
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210093, China
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Pittman YR, Kandl K, Lewis M, Valente L, Kinzy TG. Coordination of eukaryotic translation elongation factor 1A (eEF1A) function in actin organization and translation elongation by the guanine nucleotide exchange factor eEF1Balpha. J Biol Chem 2008; 284:4739-47. [PMID: 19095653 DOI: 10.1074/jbc.m807945200] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Eukaryotic translation elongation factor 1A (eEF1A) both shuttles aminoacyl-tRNA (aa-tRNA) to the ribosome and binds and bundles actin. A single domain of eEF1A is proposed to bind actin, aa-tRNA and the guanine nucleotide exchange factor eEF1Balpha. We show that eEF1Balpha has the ability to disrupt eEF1A-induced actin organization. Mutational analysis of eEF1Balpha F163, which binds in this domain, demonstrates effects on growth, eEF1A binding, nucleotide exchange activity, and cell morphology. These phenotypes can be partially restored by an intragenic W130A mutation. Furthermore, the combination of F163A with the lethal K205A mutation restores viability by drastically reducing eEF1Balpha affinity for eEF1A. This also results in a consistent increase in actin bundling and partially corrected morphology. The consequences of the overlapping functions in this eEF1A domain and its unique differences from the bacterial homologs provide a novel function for eEF1Balpha to balance the dual roles in actin bundling and protein synthesis.
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Affiliation(s)
- Yvette R Pittman
- Department of Molecular Genetics, Microbiology, and Immunology, University of Medicine and Dentistry of New Jersey Robert Wood Johnson Medical School, Piscataway, New Jersey 08854, USA
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Abstract
This theoretical work covers structural and biochemical aspects of nucleotide binding and GDP/GTP exchange of GTP hydrolases belonging to the family of small GTPases. Current models of GDP/GTP exchange regulation are often based on two specific assumptions. The first is that the conformation of a GTPase is switched by the exchange of the bound nucleotide from GDP to GTP or vice versa. The second is that GDP/GTP exchange is regulated by a guanine nucleotide exchange factor, which stabilizes a GTPase conformation with low nucleotide affinity. Since, however, recent biochemical and structural data seem to contradict this view, we present a generalized scheme for GTPase action. This novel ansatz accounts for those important cases when conformational switching in addition to guanine nucleotide exchange requires the presence of cofactors, and gives a more nuanced picture of how the nucleotide exchange is regulated. The scheme is also used to discuss some problems of interpretation that may arise when guanine nucleotide exchange mechanisms are inferred from experiments with analogs of GTP, like GDPNP, GDPCP, and GDP gamma S.
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Schümmer T, Gromadski KB, Rodnina MV. Mechanism of EF-Ts-catalyzed guanine nucleotide exchange in EF-Tu: contribution of interactions mediated by helix B of EF-Tu. Biochemistry 2007; 46:4977-84. [PMID: 17397188 DOI: 10.1021/bi602486c] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Elongation factor Tu (EF-Tu) belongs to the family of GTP-binding proteins and requires elongation factor Ts (EF-Ts) for nucleotide exchange. Crystal structures suggested that one of the salient features in the EF-Tu x EF-Ts complex is a conformation change in the switch II region of EF-Tu that is initiated by intrusion of Phe81 of EF-Ts between His84 and His118 of EF-Tu and may result in a destabilization of Mg2+ coordination and guanine nucleotide release. In the present paper, the contribution of His84 to nucleotide release was studied by pre-steady-state kinetic analysis of nucleotide exchange in mutant EF-Tu in which His84 was replaced by Ala. Both intrinsic and EF-Ts-catalyzed nucleotide release was affected by the mutation, resulting in a 10-fold faster spontaneous GDP release and a 4-fold faster EF-Ts-catalyzed release of GTP and GDP. Removal of Mg2+ from the EF-Tu x EF-Ts complex increased the rate constant of GDP release 2-fold, suggesting a small contribution to nucleotide exchange. Together with published data on the effects of mutations interfering with other putative interactions between EF-Tu and EF-Ts, the results suggest that each of the contacts in the EF-Tu x EF-Ts complex alone contributes moderately to nucleotide destabilization, but together they act synergistically to bring about the overall 60,000-fold acceleration of nucleotide exchange in EF-Tu by EF-Ts.
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Affiliation(s)
- Tobias Schümmer
- Institute of Physical Biochemistry, University of Witten/Herdecke, D-58448 Witten, Germany
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Valente L, Tiranti V, Marsano RM, Malfatti E, Fernandez-Vizarra E, Donnini C, Mereghetti P, De Gioia L, Burlina A, Castellan C, Comi GP, Savasta S, Ferrero I, Zeviani M. Infantile encephalopathy and defective mitochondrial DNA translation in patients with mutations of mitochondrial elongation factors EFG1 and EFTu. Am J Hum Genet 2007; 80:44-58. [PMID: 17160893 PMCID: PMC1785320 DOI: 10.1086/510559] [Citation(s) in RCA: 155] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2006] [Accepted: 10/25/2006] [Indexed: 11/03/2022] Open
Abstract
Mitochondrial protein translation is a complex process performed within mitochondria by an apparatus composed of mitochondrial DNA (mtDNA)-encoded RNAs and nuclear DNA-encoded proteins. Although the latter by far outnumber the former, the vast majority of mitochondrial translation defects in humans have been associated with mutations in RNA-encoding mtDNA genes, whereas mutations in protein-encoding nuclear genes have been identified in a handful of cases. Genetic investigation involving patients with defective mitochondrial translation led us to the discovery of novel mutations in the mitochondrial elongation factor G1 (EFG1) in one affected baby and, for the first time, in the mitochondrial elongation factor Tu (EFTu) in another one. Both patients were affected by severe lactic acidosis and rapidly progressive, fatal encephalopathy. The EFG1-mutant patient had early-onset Leigh syndrome, whereas the EFTu-mutant patient had severe infantile macrocystic leukodystrophy with micropolygyria. Structural modeling enabled us to make predictions about the effects of the mutations at the molecular level. Yeast and mammalian cell systems proved the pathogenic role of the mutant alleles by functional complementation in vivo. Nuclear-gene abnormalities causing mitochondrial translation defects represent a new, potentially broad field of mitochondrial medicine. Investigation of these defects is important to expand the molecular characterization of mitochondrial disorders and also may contribute to the elucidation of the complex control mechanisms, which regulate this fundamental pathway of mtDNA homeostasis.
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Affiliation(s)
- Lucia Valente
- Pierfranco and Luisa Mariani Center for Research on Children's Mitochondrial Disorders, Division of Molecular Neurogenetics, National Neurological Institute "Carlo Besta," Milano, Italy
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Smeitink JAM, Elpeleg O, Antonicka H, Diepstra H, Saada A, Smits P, Sasarman F, Vriend G, Jacob-Hirsch J, Shaag A, Rechavi G, Welling B, Horst J, Rodenburg RJ, van den Heuvel B, Shoubridge EA. Distinct clinical phenotypes associated with a mutation in the mitochondrial translation elongation factor EFTs. Am J Hum Genet 2006; 79:869-77. [PMID: 17033963 PMCID: PMC1698578 DOI: 10.1086/508434] [Citation(s) in RCA: 134] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2006] [Accepted: 08/14/2006] [Indexed: 01/06/2023] Open
Abstract
The 13 polypeptides encoded in mitochondrial DNA (mtDNA) are synthesized in the mitochondrial matrix on a dedicated protein-translation apparatus that resembles that found in prokaryotes. Here, we have investigated the genetic basis for a mitochondrial protein-synthesis defect associated with a combined oxidative phosphorylation enzyme deficiency in two patients, one of whom presented with encephalomyopathy and the other with hypertrophic cardiomyopathy. Sequencing of candidate genes revealed the same homozygous mutation (C997T) in both patients in TSFM, a gene coding for the mitochondrial translation elongation factor EFTs. EFTs functions as a guanine nucleotide exchange factor for EFTu, another translation elongation factor that brings aminoacylated transfer RNAs to the ribosomal A site as a ternary complex with guanosine triphosphate. The mutation predicts an Arg333Trp substitution at an evolutionarily conserved site in a subdomain of EFTs that interacts with EFTu. Molecular modeling showed that the substitution disrupts local subdomain structure and the dimerization interface. The steady-state levels of EFTs and EFTu in patient fibroblasts were reduced by 75% and 60%, respectively, and the amounts of assembled complexes I, IV, and V were reduced by 35%-91% compared with the amounts in controls. These phenotypes and the translation defect were rescued by retroviral expression of either EFTs or EFTu. These data clearly establish mutant EFTs as the cause of disease in these patients. The fact that the same mutation is associated with distinct clinical phenotypes suggests the presence of genetic modifiers of the mitochondrial translation apparatus.
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Affiliation(s)
- Jan A M Smeitink
- Nijmegen Centre for Mitochondrial Disorders, Department of Pediatrics, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands.
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Sakurai M, Watanabe YI, Watanabe K, Ohtsuki T. A protein extension to shorten RNA: elongated elongation factor-Tu recognizes the D-arm of T-armless tRNAs in nematode mitochondria. Biochem J 2006; 399:249-56. [PMID: 16859488 PMCID: PMC1609916 DOI: 10.1042/bj20060781] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Nematode mitochondria possess extremely truncated tRNAs. Of 22 tRNAs, 20 lack the entire T-arm. The T-arm is necessary for the binding of canonical tRNAs and EF (elongation factor)-Tu (thermo-unstable). The nematode mitochondrial translation system employs two different EF-Tu factors named EF-Tu1 and EF-Tu2. Our previous study showed that nematode Caenorhabditis elegans EF-Tu1 binds specifically to T-armless tRNA. C. elegans EF-Tu1 has a 57-amino acid C-terminal extension that is absent from canonical EF-Tu, and the T-arm-binding residues of canonical EF-Tu are not conserved. In this study, the recognition mechanism of T-armless tRNA by EF-Tu1 was investigated. Both modification interference assays and primer extension analysis of cross-linked ternary complexes revealed that EF-Tu1 interacts not only with the tRNA acceptor stem but also with the D-arm. This is the first example of an EF-Tu recognizing the D-arm of a tRNA. The binding activity of EF-Tu1 was impaired by deletion of only 14 residues from the C-terminus, indicating that the C-terminus of EF-Tu1 is required for its binding to T-armless tRNA. These results suggest that C. elegans EF-Tu1 recognizes the D-arm instead of the T-arm by a mechanism involving its C-terminal region. This study sheds light on the co-evolution of RNA and RNA-binding proteins in nematode mitochondria.
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Affiliation(s)
- Masayuki Sakurai
- *Department of Integrated Biosciences, Graduate School of Frontier Sciences, University of Tokyo, Kashiwa, Chiba 277-8562, Japan
- †Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Yoh-ichi Watanabe
- ‡Department of Biomedical Chemistry, Graduate School of Medicine, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Kimitsuna Watanabe
- *Department of Integrated Biosciences, Graduate School of Frontier Sciences, University of Tokyo, Kashiwa, Chiba 277-8562, Japan
| | - Takashi Ohtsuki
- *Department of Integrated Biosciences, Graduate School of Frontier Sciences, University of Tokyo, Kashiwa, Chiba 277-8562, Japan
- To whom correspondence should be addressed (email ). Present address: Department of Bioscience and Biotechnology, Okayama University, 3-1-1 Tsushimanaka, Okayama 700-8530, Japan
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Dahl LD, Wieden HJ, Rodnina MV, Knudsen CR. The importance of P-loop and domain movements in EF-Tu for guanine nucleotide exchange. J Biol Chem 2006; 281:21139-21146. [PMID: 16717093 DOI: 10.1074/jbc.m602068200] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Elongation factor Ts (EF-Ts) is the guanine nucleotide exchange factor for elongation factor Tu (EF-Tu). An important feature of the nucleotide exchange is the structural rearrangement of EF-Tu in the EF-Tu.EF-Ts complex caused by insertion of Phe-81 of EF-Ts between His-84 and His-118 of EF-Tu. In this study, the contribution of His-118 to nucleotide release was studied by pre-steady state kinetic analysis of nucleotide exchange in EF-Tu mutants in which His-118 was replaced by Ala or Glu. Intrinsic as well as EF-Ts-catalyzed release of GDP/GTP was affected by the mutations, resulting in an approximately 10-fold faster spontaneous nucleotide release and a 10-50-fold slower EF-Ts-catalyzed nucleotide release. The effects are attributed to the interference of the mutations with the EF-Ts-induced movements of the P-loop of EF-Tu and changes at the domain 1/3 interface, leading to the release of the beta-phosphate group of GTP/GDP. The K(d) for GTP is increased by more than 40 times when His-118 is replaced with Glu, which may explain the inhibition by His-118 mutations of aminoacyl-tRNA binding to EF-Tu. The mutations had no effect on EF-Tu-dependent delivery of aminoacyl-tRNA to the ribosome.
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Affiliation(s)
- Louise D Dahl
- Department of Molecular Biology, Aarhus University, Gustav Wieds Vej 10C, DK-8000 Århus C, Denmark
| | - Hans-Joachim Wieden
- Institute of Physical Biochemistry, University of Witten/Herdecke, Stockumer Strasse 10, D-58448 Witten, Germany
| | - Marina V Rodnina
- Institute of Physical Biochemistry, University of Witten/Herdecke, Stockumer Strasse 10, D-58448 Witten, Germany
| | - Charlotte R Knudsen
- Department of Molecular Biology, Aarhus University, Gustav Wieds Vej 10C, DK-8000 Århus C, Denmark.
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Zipfel C, Kunze G, Chinchilla D, Caniard A, Jones JDG, Boller T, Felix G. Perception of the bacterial PAMP EF-Tu by the receptor EFR restricts Agrobacterium-mediated transformation. Cell 2006; 125:749-60. [PMID: 16713565 DOI: 10.1016/j.cell.2006.03.037] [Citation(s) in RCA: 1167] [Impact Index Per Article: 64.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2005] [Revised: 02/11/2006] [Accepted: 03/16/2006] [Indexed: 01/09/2023]
Abstract
Higher eukaryotes sense microbes through the perception of pathogen-associated molecular patterns (PAMPs). Arabidopsis plants detect a variety of PAMPs including conserved domains of bacterial flagellin and of bacterial EF-Tu. Here, we show that flagellin and EF-Tu activate a common set of signaling events and defense responses but without clear synergistic effects. Treatment with either PAMP results in increased binding sites for both PAMPs. We used this finding in a targeted reverse-genetic approach to identify a receptor kinase essential for EF-Tu perception, which we called EFR. Nicotiana benthamiana, a plant unable to perceive EF-Tu, acquires EF-Tu binding sites and responsiveness upon transient expression of EFR. Arabidopsis efr mutants show enhanced susceptibility to the bacterium Agrobacterium tumefaciens, as revealed by a higher efficiency of T-DNA transformation. These results demonstrate that EFR is the EF-Tu receptor and that plant defense responses induced by PAMPs such as EF-Tu reduce transformation by Agrobacterium.
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Affiliation(s)
- Cyril Zipfel
- Botanical Institute, Zurich-Basel Plant Science Centre, University of Basel, Hebelstrasse 1, CH-4056 Basel, Switzerland.
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Yatime L, Mechulam Y, Blanquet S, Schmitt E. Structural switch of the gamma subunit in an archaeal aIF2 alpha gamma heterodimer. Structure 2006; 14:119-28. [PMID: 16407071 DOI: 10.1016/j.str.2005.09.020] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2005] [Revised: 09/23/2005] [Accepted: 09/23/2005] [Indexed: 11/25/2022]
Abstract
Eukaryotic and archaeal initiation factors 2 (e/aIF2) are heterotrimeric proteins (alphabetagamma) supplying the small subunit of the ribosome with methionylated initiator tRNA. This study reports the crystallographic structure of an aIF2alphagamma heterodimer from Sulfolobus solfataricus bound to Gpp(NH)p-Mg(2+). aIF2gamma is in a closed conformation with the G domain packed on domains II and III. The C-terminal domain of aIF2alpha interacts with domain II of aIF2gamma. Conformations of the two switch regions involved in GTP binding are similar to those encountered in an EF1A:GTP:Phe-tRNA(Phe) complex. Comparison with the EF1A structure suggests that only the gamma subunit of the aIF2alphagamma heterodimer contacts tRNA. Because the alpha subunit markedly reinforces the affinity of tRNA for the gamma subunit, a contribution of the alpha subunit to the switch movements observed in the gamma structure is considered.
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Affiliation(s)
- Laure Yatime
- Laboratoire de Biochimie, Unité Mixte de Recherche 7654, CNRS-Ecole Polytechnique, F-91128 Palaiseau cedex, France
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