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Molina‐Berenguer M, Vila‐Julià F, Pérez‐Ramos S, Salcedo‐Allende MT, Cámara Y, Torres‐Torronteras J, Martí R. Dysfunctional mitochondrial translation and combined oxidative phosphorylation deficiency in a mouse model of hepatoencephalopathy due to
Gfm1
mutations. FASEB J 2021; 36:e22091. [DOI: 10.1096/fj.202100819rrr] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Revised: 11/19/2021] [Accepted: 11/23/2021] [Indexed: 11/11/2022]
Affiliation(s)
- Miguel Molina‐Berenguer
- Research Group on Neuromuscular and Mitochondrial Diseases Vall d'Hebron Research Institute Universitat Autònoma de Barcelona Barcelona Spain
- Biomedical Network Research Centre on Rare Diseases (CIBERER) Instituto de Salud Carlos III Madrid Spain
| | - Ferran Vila‐Julià
- Research Group on Neuromuscular and Mitochondrial Diseases Vall d'Hebron Research Institute Universitat Autònoma de Barcelona Barcelona Spain
- Biomedical Network Research Centre on Rare Diseases (CIBERER) Instituto de Salud Carlos III Madrid Spain
| | - Sandra Pérez‐Ramos
- Research Group on Neuromuscular and Mitochondrial Diseases Vall d'Hebron Research Institute Universitat Autònoma de Barcelona Barcelona Spain
- Biomedical Network Research Centre on Rare Diseases (CIBERER) Instituto de Salud Carlos III Madrid Spain
| | - Maria Teresa Salcedo‐Allende
- Pathology Department Vall d'Hebron Research Institute Hospital Universitari Vall d'Hebron Universitat Autònoma de Barcelona Barcelona Spain
| | - Yolanda Cámara
- Research Group on Neuromuscular and Mitochondrial Diseases Vall d'Hebron Research Institute Universitat Autònoma de Barcelona Barcelona Spain
- Biomedical Network Research Centre on Rare Diseases (CIBERER) Instituto de Salud Carlos III Madrid Spain
| | - Javier Torres‐Torronteras
- Research Group on Neuromuscular and Mitochondrial Diseases Vall d'Hebron Research Institute Universitat Autònoma de Barcelona Barcelona Spain
- Biomedical Network Research Centre on Rare Diseases (CIBERER) Instituto de Salud Carlos III Madrid Spain
| | - Ramon Martí
- Research Group on Neuromuscular and Mitochondrial Diseases Vall d'Hebron Research Institute Universitat Autònoma de Barcelona Barcelona Spain
- Biomedical Network Research Centre on Rare Diseases (CIBERER) Instituto de Salud Carlos III Madrid Spain
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2
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Gao X, Yu X, Zhu K, Qin B, Wang W, Han P, Aleksandra Wojdyla J, Wang M, Cui S. Crystal Structure of Mycobacterium tuberculosis Elongation Factor G1. Front Mol Biosci 2021; 8:667638. [PMID: 34540889 PMCID: PMC8446442 DOI: 10.3389/fmolb.2021.667638] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2021] [Accepted: 08/19/2021] [Indexed: 11/24/2022] Open
Abstract
Mycobacterium tuberculosis (Mtb) caused an estimated 10 million cases of tuberculosis and 1.2 million deaths in 2019 globally. The increasing emergence of multidrug-resistant and extensively drug-resistant Mtb is becoming a public health threat worldwide and makes the identification of anti-Mtb drug targets urgent. Elongation factor G (EF-G) is involved in tRNA translocation on ribosomes during protein translation. Therefore, EF-G is a major focus of structural analysis and a valuable drug target of antibiotics. However, the crystal structure of Mtb EF-G1 is not yet available, and this has limited the design of inhibitors. Here, we report the crystal structure of Mtb EF-G1 in complex with GDP. The unique crystal form of the Mtb EF-G1-GDP complex provides an excellent platform for fragment-based screening using a crystallographic approach. Our findings provide a structure-based explanation for GDP recognition, and facilitate the identification of EF-G1 inhibitors with potential interest in the context of drug discovery.
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Affiliation(s)
- Xiaopan Gao
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, And Center for Tuberculosis Research, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Xia Yu
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, And Center for Tuberculosis Research, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.,National Clinical Laboratory on Tuberculosis, Beijing Key Laboratory for Drug-resistant Tuberculosis Research Beijing Chest Hospital, Beijing Tuberculosis and Thoracic Tumor Institute, Capital Medical University, Beijing, China
| | - Kaixiang Zhu
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, And Center for Tuberculosis Research, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Bo Qin
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, And Center for Tuberculosis Research, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Wei Wang
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, And Center for Tuberculosis Research, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Pu Han
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | | | - Meitian Wang
- Swiss Light Source at the Paul Scherrer Institut, Villigen, Switzerland
| | - Sheng Cui
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, And Center for Tuberculosis Research, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.,Sanming Project of Medicine in Shenzhen on Construction of Novel Systematic Network Against Tuberculosis, National Clinical Research Center for Infectious Diseases, Shenzhen Third People's Hospital, Southern University of Science and Technology, Shenzhen, China
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3
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Abstract
The large ribosomal subunit has a distinct feature, the stalk, extending outside the ribosome. In bacteria it is called the L12 stalk. The base of the stalk is protein uL10 to which two or three dimers of proteins bL12 bind. In archea and eukarya P1 and P2 proteins constitute the stalk. All these extending proteins, that have a high degree of flexibility due to a hinge between their N- and C-terminal parts, are essential for proper functionalization of some of the translation factors. The role of the stalk proteins has remained enigmatic for decades but is gradually approaching an understanding. In this review we summarise the knowhow about the structure and function of the ribosomal stalk till date starting from the early phase of ribosome research.
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4
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Tanzawa T, Kato K, Girodat D, Ose T, Kumakura Y, Wieden HJ, Uchiumi T, Tanaka I, Yao M. The C-terminal helix of ribosomal P stalk recognizes a hydrophobic groove of elongation factor 2 in a novel fashion. Nucleic Acids Res 2019; 46:3232-3244. [PMID: 29471537 PMCID: PMC5887453 DOI: 10.1093/nar/gky115] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2016] [Accepted: 02/09/2018] [Indexed: 01/17/2023] Open
Abstract
Archaea and eukaryotes have ribosomal P stalks composed of anchor protein P0 and aP1 homodimers (archaea) or P1•P2 heterodimers (eukaryotes). These P stalks recruit translational GTPases to the GTPase-associated center in ribosomes to provide energy during translation. The C-terminus of the P stalk is known to selectively recognize GTPases. Here we investigated the interaction between the P stalk and elongation factor 2 by determining the structures of Pyrococcus horikoshii EF-2 (PhoEF-2) in the Apo-form, GDP-form, GMPPCP-form (GTP-form), and GMPPCP-form bound with 11 C-terminal residues of P1 (P1C11). Helical structured P1C11 binds to a hydrophobic groove between domain G and subdomain G′ of PhoEF-2, where is completely different from that of aEF-1α in terms of both position and sequence, implying that such interaction characteristic may be requested by how GTPases perform their functions on the ribosome. Combining PhoEF-2 P1-binding assays with a structural comparison of current PhoEF-2 structures and molecular dynamics model of a P1C11-bound GDP form, the conformational changes of the P1C11-binding groove in each form suggest that in response to the translation process, the groove has three states: closed, open, and release for recruiting and releasing GTPases.
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Affiliation(s)
- Takehito Tanzawa
- Graduate School of Life Science, Hokkaido University, Sapporo, Hokkaido 060-0810, Japan
| | - Koji Kato
- Graduate School of Life Science, Hokkaido University, Sapporo, Hokkaido 060-0810, Japan.,Faculty of Advanced Life Science, Hokkaido University, Sapporo, Hokkaido 060-0810, Japan
| | - Dylan Girodat
- Alberta RNA Research and Training Institute, Department of Chemistry and Biochemistry, University of Lethbridge, Lethbridge AB T1K 3M4, Canada
| | - Toyoyuki Ose
- Graduate School of Life Science, Hokkaido University, Sapporo, Hokkaido 060-0810, Japan.,Faculty of Advanced Life Science, Hokkaido University, Sapporo, Hokkaido 060-0810, Japan
| | - Yuki Kumakura
- Graduate School of Life Science, Hokkaido University, Sapporo, Hokkaido 060-0810, Japan
| | - Hans-Joachim Wieden
- Alberta RNA Research and Training Institute, Department of Chemistry and Biochemistry, University of Lethbridge, Lethbridge AB T1K 3M4, Canada
| | - Toshio Uchiumi
- Department of Biology, Faculty of Science, Niigata University, 8050 Ikarashi 2-no-cho, Nishi-ku, Niigata 950-2181, Japan
| | - Isao Tanaka
- Faculty of Advanced Life Science, Hokkaido University, Sapporo, Hokkaido 060-0810, Japan
| | - Min Yao
- Graduate School of Life Science, Hokkaido University, Sapporo, Hokkaido 060-0810, Japan.,Faculty of Advanced Life Science, Hokkaido University, Sapporo, Hokkaido 060-0810, Japan
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5
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Macé K, Giudice E, Chat S, Gillet R. The structure of an elongation factor G-ribosome complex captured in the absence of inhibitors. Nucleic Acids Res 2019; 46:3211-3217. [PMID: 29408956 PMCID: PMC5887593 DOI: 10.1093/nar/gky081] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2017] [Accepted: 01/27/2018] [Indexed: 12/25/2022] Open
Abstract
During translation’s elongation cycle, elongation factor G (EF-G) promotes messenger and transfer RNA translocation through the ribosome. Until now, the structures reported for EF-G–ribosome complexes have been obtained by trapping EF-G in the ribosome. These results were based on use of non-hydrolyzable guanosine 5′-triphosphate (GTP) analogs, specific inhibitors or a mutated EF-G form. Here, we present the first cryo-electron microscopy structure of EF-G bound to ribosome in the absence of an inhibitor. The structure reveals a natural conformation of EF-G·GDP in the ribosome, with a previously unseen conformation of its third domain. These data show how EF-G must affect translocation, and suggest the molecular mechanism by which fusidic acid antibiotic prevents the release of EF-G after GTP hydrolysis.
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Affiliation(s)
- Kevin Macé
- Univ. Rennes, CNRS, Institut de Génétique et de Développement de Rennes (IGDR), UMR6290, F35000 Rennes, France
| | - Emmanuel Giudice
- Univ. Rennes, CNRS, Institut de Génétique et de Développement de Rennes (IGDR), UMR6290, F35000 Rennes, France
| | - Sophie Chat
- Univ. Rennes, CNRS, Institut de Génétique et de Développement de Rennes (IGDR), UMR6290, F35000 Rennes, France
| | - Reynald Gillet
- Univ. Rennes, CNRS, Institut de Génétique et de Développement de Rennes (IGDR), UMR6290, F35000 Rennes, France
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6
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Ero R, Kumar V, Chen Y, Gao YG. Similarity and diversity of translational GTPase factors EF-G, EF4, and BipA: From structure to function. RNA Biol 2016; 13:1258-1273. [PMID: 27325008 PMCID: PMC5207388 DOI: 10.1080/15476286.2016.1201627] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
EF-G, EF4, and BipA are members of the translation factor family of GTPases with a common ribosome binding mode and GTPase activation mechanism. However, topological variations of shared as well as unique domains ensure different roles played by these proteins during translation. Recent X-ray crystallography and cryo-electron microscopy studies have revealed the structural basis for the involvement of EF-G domain IV in securing the movement of tRNAs and mRNA during translocation as well as revealing how the unique C-terminal domains of EF4 and BipA interact with the ribosome and tRNAs contributing to the regulation of translation under certain conditions. EF-G, EF-4, and BipA are intriguing examples of structural variations on a common theme that results in diverse behavior and function. Structural studies of translational GTPase factors have been greatly facilitated by the use of antibiotics, which have revealed their mechanism of action.
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Affiliation(s)
- Rya Ero
- a School of Biological Sciences , Nanyang Technological University , Singapore
| | - Veerendra Kumar
- a School of Biological Sciences , Nanyang Technological University , Singapore.,b Institute of Molecular and Cell Biology, A*STAR , Singapore
| | - Yun Chen
- a School of Biological Sciences , Nanyang Technological University , Singapore
| | - Yong-Gui Gao
- a School of Biological Sciences , Nanyang Technological University , Singapore.,b Institute of Molecular and Cell Biology, A*STAR , Singapore
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7
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Feng S, Chen Y, Gao YG. Crystal structure of 70S ribosome with both cognate tRNAs in the E and P sites representing an authentic elongation complex. PLoS One 2013; 8:e58829. [PMID: 23527033 PMCID: PMC3602588 DOI: 10.1371/journal.pone.0058829] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2012] [Accepted: 02/07/2013] [Indexed: 11/18/2022] Open
Abstract
During the translation cycle, a cognate deacylated tRNA can only move together with the codon into the E site. We here present the first structure of a cognate tRNA bound to the ribosomal E site resulting from translocation by EF-G, in which an entire L1 stalk (L1 protein and L1 rRNA) interacts with E-site tRNA (E-tRNA), representing an authentic ribosome elongation complex. Our results revealed that the Watson-Crick base pairing is formed at the first and second codon-anticodon positions in the E site in the ribosome elongation complex, whereas the codon-anticodon interaction in the third position is indirect. Analysis of the observed conformations of mRNA and E-tRNA suggests that the ribosome intrinsically has the potential to form codon-anticodon interaction in the E site, independently of the mRNA configuration. We also present a detailed description of the biologically relevant position of the entire L1 stalk and its interacting cognate E-tRNA, which provides a better understanding of the structural basis for translation elongation. Furthermore, to gain insight into translocation, we report the positioning of protein L6 contacting EF-G, as well as the conformational change of the C-terminal tail of protein S13 in the decoding center.
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Affiliation(s)
- Shu Feng
- School of Biological Science, Nanyang Technological University, Singapore
| | - Yun Chen
- School of Biological Science, Nanyang Technological University, Singapore
| | - Yong-Gui Gao
- School of Biological Science, Nanyang Technological University, Singapore
- Institute of Molecular and Cell Biology, Proteos, Singapore
- MRC Laboratory of Molecular Biology, Cambridge, United Kingdom
- * E-mail:
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8
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Baba K, Tumuraya K, Tanaka I, Yao M, Uchiumi T. Molecular dissection of the silkworm ribosomal stalk complex: the role of multiple copies of the stalk proteins. Nucleic Acids Res 2013; 41:3635-43. [PMID: 23376928 PMCID: PMC3616719 DOI: 10.1093/nar/gkt044] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
In animal ribosomes, two stalk proteins P1 and P2 form a heterodimer, and the two dimers, with the anchor protein P0, constitute a pentameric complex crucial for recruitment of translational GTPase factors to the ribosome. To investigate the functional contribution of each copy of the stalk proteins, we constructed P0 mutants, in which one of the two C-terminal helices, namely helix I (N-terminal side) or helix II (C-terminal side) were unable to bind the P1–P2 dimer. We also constructed ‘one-C-terminal domain (CTD) stalk dimers’, P1–P2ΔC and P1ΔC–P2, composed of intact P1/P2 monomer and a CTD-truncated partner. Through combinations of P0 and P1–P2 variants, various complexes were reconstituted and their function tested in eEF-2-dependent GTPase and eEF-1α/eEF-2-dependent polyphenylalanine synthesis assays in vitro. Double/single-CTD dimers bound to helix I showed higher activity than that bound to helix II. Despite low polypeptide synthetic activity by a single one-CTD dimer, its binding to both helices considerably increased activity, suggesting that two stalk dimers cooperate, particularly in polypeptide synthesis. This promotion of activity by two stalk dimers was lost upon mutation of the conserved YPT sequence connecting the two helices of P0, suggesting a role for this sequence in cooperativity of two stalk dimers.
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Affiliation(s)
- Kentaro Baba
- Department of Biology, Faculty of Science, Niigata University, Nishi-ku, Ikarashi-2, Niigata 950-2181, Japan
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9
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Galmiche L, Serre V, Beinat M, Zossou R, Assouline Z, Lebre AS, Chretien F, Shenhav R, Zeharia A, Saada A, Vedrenne V, Boddaert N, de Lonlay P, Rio M, Munnich A, Rötig A. Toward genotype phenotype correlations in GFM1 mutations. Mitochondrion 2012; 12:242-7. [DOI: 10.1016/j.mito.2011.09.007] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2011] [Revised: 09/07/2011] [Accepted: 09/16/2011] [Indexed: 10/17/2022]
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10
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Seshadri A, Samhita L, Gaur R, Malshetty V, Varshney U. Analysis of the fusA2 locus encoding EFG2 in Mycobacterium smegmatis. Tuberculosis (Edinb) 2011; 89:453-64. [PMID: 19595631 DOI: 10.1016/j.tube.2009.06.003] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2009] [Revised: 06/01/2009] [Accepted: 06/05/2009] [Indexed: 11/25/2022]
Abstract
The translation elongation factor G (EFG) is encoded by the fusA gene. Several bacteria possess a second fusA-like locus, fusA2 which encodes EFG2. A comparison of EFG and EFG2 from various bacteria reveals that EFG2 preserves domain organization and maintains significant sequence homology with EFG, suggesting that EFG2 may function as an elongation factor. However, with the single exception of a recent study on Thermus thermophilus EFG2, this class of EFG-like factors has not been investigated. Here, we have characterized EFG2 (MSMEG_6535) from Mycobacterium smegmatis. Expression of EFG2 was detected in stationary phase cultures of M. smegmatis (Msm). Our in vitro studies show that while MsmEFG2 binds guanine nucleotides, it lacks the ribosome-dependent GTPase activity characteristic of EFGs. Furthermore, unlike MsmEFG (MSMEG_1400), MsmEFG2 failed to rescue an E. coli strain harboring a temperature-sensitive allele of EFG, for its growth at the non-permissive temperature. Subsequent experiments showed that the fusA2 gene could be disrupted in M. smegmatis mc(2)155 with Kan(R) marker. The M. smegmatis fusA2::kan strain was viable and showed growth kinetics similar to that of the parent strain (wild-type for fusA2). However, in the growth competition assays, the disruption of fusA2 was found to confer a fitness disadvantage to M. smegmatis, raising the possibility that EFG2 is of some physiological relevance to mycobacteria.
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Affiliation(s)
- Anuradha Seshadri
- Department of Microbiology and Cell Biology, Indian Institute of Science, CNR Rao Circle, Bangalore 560012, India
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11
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Smits P, Antonicka H, van Hasselt PM, Weraarpachai W, Haller W, Schreurs M, Venselaar H, Rodenburg RJ, Smeitink JA, van den Heuvel LP. Mutation in subdomain G' of mitochondrial elongation factor G1 is associated with combined OXPHOS deficiency in fibroblasts but not in muscle. Eur J Hum Genet 2010; 19:275-9. [PMID: 21119709 DOI: 10.1038/ejhg.2010.208] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
The mitochondrial translation system is responsible for the synthesis of 13 proteins required for oxidative phosphorylation (OXPHOS), the major energy-generating process of our cells. Mitochondrial translation is controlled by various nuclear encoded proteins. In 27 patients with combined OXPHOS deficiencies, in whom complex II (the only complex that is entirely encoded by the nuclear DNA) showed normal activities, and mutations in the mitochondrial genome as well as polymerase gamma were excluded, we screened all mitochondrial translation factors for mutations. Here, we report a mutation in mitochondrial elongation factor G1 (GFM1) in a patient affected by severe, rapidly progressive mitochondrial encephalopathy. This mutation is predicted to result in an Arg250Trp substitution in subdomain G' of the elongation factor G1 protein and is presumed to hamper ribosome-dependent GTP hydrolysis. Strikingly, the decrease in enzyme activities of complex I, III and IV detected in patient fibroblasts was not found in muscle tissue. The OXPHOS system defects and the impairment in mitochondrial translation in fibroblasts were rescued by overexpressing wild-type GFM1, establishing the GFM1 defect as the cause of the fatal mitochondrial disease. Furthermore, this study evinces the importance of a thorough diagnostic biochemical analysis of both muscle tissue and fibroblasts in patients suspected to suffer from a mitochondrial disorder, as enzyme deficiencies can be selectively expressed.
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Affiliation(s)
- Paulien Smits
- Department of Pediatrics, Nijmegen Center for Mitochondrial Disorders, Radboud University Nijmegen Medical Center, Nijmegen, The Netherlands
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12
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Translational defects in a mutant deficient in YajL, the bacterial homolog of the parkinsonism-associated protein DJ-1. J Bacteriol 2010; 192:6302-6. [PMID: 20889753 DOI: 10.1128/jb.01077-10] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We report here that YajL is associated with ribosomes and interacts with many ribosomal proteins and that a yajL mutant of Escherichia coli displays decreased translation accuracy, as well as increased dissociation of 70S ribosomes into 50S and 30S subunits after oxidative stress.
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13
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Intramolecular movements in EF-G, trapped at different stages in its GTP hydrolytic cycle, probed by FRET. J Mol Biol 2010; 397:1245-60. [PMID: 20219471 DOI: 10.1016/j.jmb.2010.02.039] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2009] [Revised: 02/19/2010] [Accepted: 02/22/2010] [Indexed: 11/24/2022]
Abstract
Elongation factor G (EF-G) is one of several GTP hydrolytic proteins (GTPases) that cycles repeatedly on and off the ribosome during protein synthesis in bacterial cells. In the functional cycle of EF-G, hydrolysis of guanosine 5'-triphosphate (GTP) is coupled to tRNA-mRNA translocation in ribosomes. GTP hydrolysis induces conformational rearrangements in two switch elements in the G domain of EF-G and other GTPases. These switch elements are thought to initiate the cascade of events that lead to translocation and EF-G cycling between ribosomes. To further define the coupling mechanism, we developed a new fluorescent approach that can detect intramolecular movements in EF-G. We attached a fluorescent probe to the switch I element (sw1) of Escherichia coli EF-G. We monitored the position of the sw1 probe, relative to another fluorescent probe anchored to the GTP substrate or product, by measuring the distance-dependent, Förster resonance energy transfer between the two probes. By analyzing EF-G trapped at five different functional states in its cycle, we could infer the cyclical movements of sw1 within EF-G. Our results provide evidence for conformational changes in sw1, which help to drive the unidirectional EF-G cycle during protein synthesis. More generally, our approach might also serve to define the conformational dynamics of other GTPases with their cellular receptors.
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14
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Ticu C, Nechifor R, Nguyen B, Desrosiers M, Wilson KS. Conformational changes in switch I of EF-G drive its directional cycling on and off the ribosome. EMBO J 2009; 28:2053-65. [PMID: 19536129 DOI: 10.1038/emboj.2009.169] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2009] [Accepted: 05/26/2009] [Indexed: 11/09/2022] Open
Abstract
We have trapped elongation factor G (EF-G) from Escherichia coli in six, functionally defined states, representing intermediates in its unidirectional catalytic cycle, which couples GTP hydrolysis to tRNA-mRNA translocation in the ribosome. By probing EF-G with trypsin in each state, we identified a substantial conformational change involving its conserved switch I (sw1) element, which contacts the GTP substrate. By attaching FeBABE (a hydroxyl radical generating probe) to sw1, we could monitor sw1 movement (by approximately 20 A), relative to the 70S ribosome, during the EF-G cycle. In free EF-G, sw1 is disordered, particularly in GDP-bound and nucleotide-free states. On EF-G*GTP binding to the ribosome, sw1 becomes structured and tucked inside the ribosome, thereby locking GTP onto EF-G. After hydrolysis and translocation, sw1 flips out from the ribosome, greatly accelerating release of GDP and EF-G from the ribosome. Collectively, our results support a central role of sw1 in driving the EF-G cycle during protein synthesis.
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Affiliation(s)
- Cristina Ticu
- Department of Biochemistry, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, Canada T6G 2H7
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15
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Jin Lee Y. Mass spectrometric analysis of cross-linking sites for the structure of proteins and protein complexes. MOLECULAR BIOSYSTEMS 2008; 4:816-23. [DOI: 10.1039/b801810c] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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16
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Abstract
In the elongation cycle of translation, translocation is the process that advances the mRNA-tRNA moiety on the ribosome, to allow the next codon to move into the decoding center. New results obtained by cryoelectron microscopy, interpreted in the light of x-ray structures and kinetic data, allow us to develop a model of the molecular events during translocation.
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17
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Nechifor R, Murataliev M, Wilson KS. Functional interactions between the G' subdomain of bacterial translation factor EF-G and ribosomal protein L7/L12. J Biol Chem 2007; 282:36998-7005. [PMID: 17932030 DOI: 10.1074/jbc.m707179200] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Protein L7/L12 of the bacterial ribosome plays an important role in activating the GTP hydrolytic activity of elongation factor G (EF-G), which promotes ribosomal translocation during protein synthesis. Previously, we cross-linked L7/L12 from two residues (209 and 231) flanking alpha-helix AG' in the G' subdomain of Escherichia coli EF-G. Here we report kinetic studies on the functional effects of mutating three neighboring glutamic acid residues (224, 228, and 231) to lysine, either singly or in combination. Two single mutations (E224K and E228K), both within helix AG', caused large defects in GTP hydrolysis and smaller defects in ribosomal translocation. Removal of L7/L12 from the ribosome strongly reduced the activities of wild type EF-G but had no effect on the activities of the E224K and E228K mutants. Together, these results provide evidence for functionally important interactions between helix AG' of EF-G and L7/L12 of the ribosome.
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Affiliation(s)
- Roxana Nechifor
- Department of Biochemistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
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