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Fang N, Wu L, Duan S, Li J. The Structural and Molecular Mechanisms of Mycobacterium tuberculosis Translational Elongation Factor Proteins. Molecules 2024; 29:2058. [PMID: 38731549 PMCID: PMC11085428 DOI: 10.3390/molecules29092058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2024] [Revised: 04/19/2024] [Accepted: 04/24/2024] [Indexed: 05/13/2024] Open
Abstract
Targeting translation factor proteins holds promise for developing innovative anti-tuberculosis drugs. During protein translation, many factors cause ribosomes to stall at messenger RNA (mRNA). To maintain protein homeostasis, bacteria have evolved various ribosome rescue mechanisms, including the predominant trans-translation process, to release stalled ribosomes and remove aberrant mRNAs. The rescue systems require the participation of translation elongation factor proteins (EFs) and are essential for bacterial physiology and reproduction. However, they disappear during eukaryotic evolution, which makes the essential proteins and translation elongation factors promising antimicrobial drug targets. Here, we review the structural and molecular mechanisms of the translation elongation factors EF-Tu, EF-Ts, and EF-G, which play essential roles in the normal translation and ribosome rescue mechanisms of Mycobacterium tuberculosis (Mtb). We also briefly describe the structure-based, computer-assisted study of anti-tuberculosis drugs.
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Affiliation(s)
- Ning Fang
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Shanghai Engineering Research Center of Industrial Microorganisms, Fudan University, Shanghai 200438, China; (N.F.); (L.W.)
| | - Lingyun Wu
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Shanghai Engineering Research Center of Industrial Microorganisms, Fudan University, Shanghai 200438, China; (N.F.); (L.W.)
| | - Shuyan Duan
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Shanghai Engineering Research Center of Industrial Microorganisms, Fudan University, Shanghai 200438, China; (N.F.); (L.W.)
- College of Food Science and Pharmaceutical Engineering, Zaozhuang University, Zaozhuang 277160, China
| | - Jixi Li
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Shanghai Engineering Research Center of Industrial Microorganisms, Fudan University, Shanghai 200438, China; (N.F.); (L.W.)
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2
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Citores L, Ragucci S, Gay CC, Russo R, Chambery A, Di Maro A, Iglesias R, Ferreras JM. Edodin: A New Type of Toxin from Shiitake Mushroom ( Lentinula edodes) That Inactivates Mammalian Ribosomes. Toxins (Basel) 2024; 16:185. [PMID: 38668610 PMCID: PMC11053714 DOI: 10.3390/toxins16040185] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2024] [Revised: 04/05/2024] [Accepted: 04/08/2024] [Indexed: 04/29/2024] Open
Abstract
Ribosome-inactivating proteins (RIPs) are a group of proteins with rRNA N-glycosylase activity that irreversibly inhibit protein synthesis and consequently cause cell death. Recently, an RIP called ledodin has been found in shiitake; it is cytotoxic, strongly inhibits protein synthesis, and shows rRNA N-glycosylase activity. In this work, we isolated and characterized a 50 kDa cytotoxic protein from shiitake that we named edodin. Edodin inhibits protein synthesis in a mammalian cell-free system, but not in insect-, yeast-, and bacteria-derived systems. It exhibits rRNA N-glycosylase and DNA-nicking activities, which relate it to plant RIPs. It was also shown to be toxic to HeLa and COLO 320 cells. Its structure is not related to other RIPs found in plants, bacteria, or fungi, but, instead, it presents the characteristic structure of the fold type I of pyridoxal phosphate-dependent enzymes. Homologous sequences have been found in other fungi of the class Agaricomycetes; thus, edodin could be a new type of toxin present in many fungi, some of them edible, which makes them of great interest in health, both for their involvement in food safety and for their potential biomedical and biotechnological applications.
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Affiliation(s)
- Lucía Citores
- Department of Biochemistry and Molecular Biology and Physiology, Faculty of Sciences, University of Valladolid, E-47011 Valladolid, Spain;
| | - Sara Ragucci
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies (DiSTABiF), University of Campania ‘Luigi Vanvitelli’, Via Vivaldi 43, 81100 Caserta, Italy; (S.R.); (R.R.); (A.C.); (A.D.M.)
| | - Claudia C. Gay
- Laboratory of Protein Research, Institute of Basic and Applied Chemistry of Northeast Argentina (UNNE-CONICET), Faculty of Exact and Natural Sciences and Surveying, Av. Libertad 5470, Corrientes 3400, Argentina;
| | - Rosita Russo
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies (DiSTABiF), University of Campania ‘Luigi Vanvitelli’, Via Vivaldi 43, 81100 Caserta, Italy; (S.R.); (R.R.); (A.C.); (A.D.M.)
| | - Angela Chambery
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies (DiSTABiF), University of Campania ‘Luigi Vanvitelli’, Via Vivaldi 43, 81100 Caserta, Italy; (S.R.); (R.R.); (A.C.); (A.D.M.)
| | - Antimo Di Maro
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies (DiSTABiF), University of Campania ‘Luigi Vanvitelli’, Via Vivaldi 43, 81100 Caserta, Italy; (S.R.); (R.R.); (A.C.); (A.D.M.)
| | - Rosario Iglesias
- Department of Biochemistry and Molecular Biology and Physiology, Faculty of Sciences, University of Valladolid, E-47011 Valladolid, Spain;
| | - José M. Ferreras
- Department of Biochemistry and Molecular Biology and Physiology, Faculty of Sciences, University of Valladolid, E-47011 Valladolid, Spain;
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Chen X, Kaiser CM. AP profiling resolves co-translational folding pathway and chaperone interactions in vivo. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.01.555749. [PMID: 37693575 PMCID: PMC10491307 DOI: 10.1101/2023.09.01.555749] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/12/2023]
Abstract
Natural proteins have evolved to fold robustly along specific pathways. Folding begins during synthesis, guided by interactions of the nascent protein with the ribosome and molecular chaperones. However, the timing and progression of co-translational folding remain largely elusive, in part because the process is difficult to measure in the natural environment of the cytosol. We developed a high-throughput method to quantify co-translational folding in live cells that we term Arrest Peptide profiling (AP profiling). We employed AP profiling to delineate co-translational folding for a set of GTPase domains with very similar structures, defining how topology shapes folding pathways. Genetic ablation of major nascent chain-binding chaperones resulted in localized folding changes that suggest how functional redundancies among chaperones are achieved by distinct interactions with the nascent protein. Collectively, our studies provide a window into cellular folding pathways of complex proteins and pave the way for systematic studies on nascent protein folding at unprecedented resolution and throughput.
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Affiliation(s)
- Xiuqi Chen
- CMDB Graduate Program, Johns Hopkins University, Baltimore, MD, United States
- Department of Biology, Johns Hopkins University, Baltimore, MD, United States
- Present address: Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Delft, the Netherlands
| | - Christian M. Kaiser
- Department of Biology, Johns Hopkins University, Baltimore, MD, United States
- Department of Biophysics, Johns Hopkins University, Baltimore, MD, United States
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4
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Shanbhag C, Saraogi I. Bacterial GTPases as druggable targets to tackle antimicrobial resistance. Bioorg Med Chem Lett 2023; 87:129276. [PMID: 37030567 DOI: 10.1016/j.bmcl.2023.129276] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 04/03/2023] [Accepted: 04/04/2023] [Indexed: 04/08/2023]
Abstract
Small molecules as antibacterial agents have contributed immensely to the growth of modern medicine over the last several decades. However, the emergence of drug resistance among bacterial pathogens has undermined the effectiveness of the existing antibiotics. Thus, there is an exigency to address the antibiotic crisis by developing new antibacterial agents and identifying novel drug targets in bacteria. In this review, we summarize the importance of guanosine triphosphate hydrolyzing proteins (GTPases) as key agents for bacterial survival. We also discuss representative examples of small molecules that target bacterial GTPases as novel antibacterial agents, and highlight areas that are ripe for exploration. Given their vital roles in cell viability, virulence, and antibiotic resistance, bacterial GTPases are highly attractive antibacterial targets that will likely play a vital role in the fight against antimicrobial resistance.
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Elongation factor P modulates Acinetobacter baumannii physiology and virulence as a cyclic dimeric guanosine monophosphate effector. Proc Natl Acad Sci U S A 2022; 119:e2209838119. [PMID: 36191190 PMCID: PMC9564936 DOI: 10.1073/pnas.2209838119] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Cyclic diguanosine monophosphate (c-di-GMP) is widely used by bacteria to control biological functions in response to diverse signals or cues. A previous study showed that potential c-di-GMP metabolic enzymes play a role in the regulation of biofilm formation and motility in Acinetobacter baumannii. However, it was unclear whether and how A. baumannii cells use c-di-GMP signaling to modulate biological functions. Here, we report that c-di-GMP is an important intracellular signal in the modulation of biofilm formation, motility, and virulence in A. baumannii. The intracellular level of c-di-GMP is principally controlled by the diguanylate cyclases (DGCs) A1S_1695, A1S_2506, and A1S_3296 and the phosphodiesterase (PDE) A1S_1254. Intriguingly, we revealed that A1S_2419 (an elongation factor P [EF-P]), is a novel c-di-GMP effector in A. baumannii. Response to a c-di-GMP signal boosted A1S_2419 activity to rescue ribosomes from stalling during synthesis of proteins containing consecutive prolines and thus regulate A. baumannii physiology and pathogenesis. Our study presents a unique and widely conserved effector that controls bacterial physiology and virulence by sensing the second messenger c-di-GMP.
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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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Yanagisawa M, Asamizu S, Satoh K, Oono Y, Onaka H. Effects of carbon ion beam-induced mutagenesis for the screening of RED production-deficient mutants of Streptomyces coelicolor JCM4020. PLoS One 2022; 17:e0270379. [PMID: 35834474 PMCID: PMC9282665 DOI: 10.1371/journal.pone.0270379] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Accepted: 06/08/2022] [Indexed: 12/22/2022] Open
Abstract
Streptomyces lividans TK23 interacts with mycolic acid-containing bacteria (MACB), such as Tsukamurella pulmonis TP-B0596, and this direct cell contact activates its secondary metabolism (e.g., the production of undecylprodigiosin: RED). Here, we employed carbon (12C5+) ion beam-induced mutagenesis to investigate the signature of induced point mutations and further identify the gene(s) responsible for the production of secondary metabolites induced by T. pulmonis. We irradiated spores of the Streptomyces coelicolor strain JCM4020 with carbon ions to generate a mutant library. We screened the RED production-deficient mutants of S. coelicolor by mixing them with T. pulmonis TP-B0596 on agar plates, identifying the red/white phenotype of the growing colonies. Through this process, we selected 59 RED-deficient mutants from around 152,000 tested spores. We resequenced the genomes of 16 mutants and identified 44 point mutations, which revealed the signatures induced by 12C5+-irradiation. Via gene complementation experiments, we also revealed that two genes-glutamate synthase (gltB) and elongation factor G (fusA)-are responsible for the reduced production of RED.
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Affiliation(s)
- Masaomi Yanagisawa
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo, Tokyo, Japan
| | - Shumpei Asamizu
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo, Tokyo, Japan
- Collaborative Research Institute for Innovative Microbiology (CRIIM), The University of Tokyo, Bunkyo, Tokyo, Japan
- * E-mail: (SA); (HO)
| | - Katsuya Satoh
- Department of Radiation-Applied Biology Research, Takasaki Advanced Radiation Research Institute, Quantum Beam Science Research Directorate, National Institutes for Quantum Science and Technology, Takasaki, Gunma, Japan
| | - Yutaka Oono
- Department of Radiation-Applied Biology Research, Takasaki Advanced Radiation Research Institute, Quantum Beam Science Research Directorate, National Institutes for Quantum Science and Technology, Takasaki, Gunma, Japan
| | - Hiroyasu Onaka
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo, Tokyo, Japan
- Collaborative Research Institute for Innovative Microbiology (CRIIM), The University of Tokyo, Bunkyo, Tokyo, Japan
- * E-mail: (SA); (HO)
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Górka S, Kubiak D, Ciesińska M, Niedojadło K, Tyburski J, Niedojadło J. Function of Cajal Bodies in Nuclear RNA Retention in A. thaliana Leaves Subjected to Hypoxia. Int J Mol Sci 2022; 23:ijms23147568. [PMID: 35886915 PMCID: PMC9321658 DOI: 10.3390/ijms23147568] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Revised: 06/27/2022] [Accepted: 06/28/2022] [Indexed: 11/29/2022] Open
Abstract
Retention of RNA in the nucleus precisely regulates the time and rate of translation and controls transcriptional bursts that can generate profound variability in mRNA levels among identical cells in tissues. In this study, we investigated the function of Cajal bodies (CBs) in RNA retention in A. thaliana leaf nuclei during hypoxia stress was investigated. It was observed that in ncb-1 mutants with a complete absence of CBs, the accumulation of poly(A+) RNA in the leaf nuclei was lower than that in wt under stress. Moreover, unlike in root cells, CBs store less RNA, and RNA retention in the nuclei is much less intense. Our results reveal that the function of CBs in the accumulation of RNA in nuclei under stress depends on the plant organ. Additionally, in ncb-1, retention of introns of mRNA RPB1 (largest subunit of RNA polymerase II) mRNA was observed. However, this isoform is highly accumulated in the nucleus. It thus follows that intron retention in transcripts is more important than CBs for the accumulation of RNA in nuclei. Accumulated mRNAs with introns in the nucleus could escape transcript degradation by NMD (nonsense-mediated mRNA decay). From non-fully spliced mRNAs in ncb-1 nuclei, whose levels increase during hypoxia, introns are removed during reoxygenation. Then, the mRNA is transferred to the cytoplasm, and the RPB1 protein is translated. Despite the accumulation of isoforms in nuclei with retention of introns in reoxygenation, ncb-1 coped much worse with long hypoxia, and manifested faster yellowing and shrinkage of leaves.
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Affiliation(s)
- Sylwia Górka
- Department of Cellular and Molecular Biology, Nicolaus Copernicus University, Lwowska 1, 87-100 Toruń, Poland; (S.G.); (D.K.); (M.C.); (K.N.)
- Centre For Modern Interdisciplinary Technologies, Nicolaus Copernicus University, Wileńska 4, 87-100 Toruń, Poland
| | - Dawid Kubiak
- Department of Cellular and Molecular Biology, Nicolaus Copernicus University, Lwowska 1, 87-100 Toruń, Poland; (S.G.); (D.K.); (M.C.); (K.N.)
- Centre For Modern Interdisciplinary Technologies, Nicolaus Copernicus University, Wileńska 4, 87-100 Toruń, Poland
| | - Małgorzata Ciesińska
- Department of Cellular and Molecular Biology, Nicolaus Copernicus University, Lwowska 1, 87-100 Toruń, Poland; (S.G.); (D.K.); (M.C.); (K.N.)
| | - Katarzyna Niedojadło
- Department of Cellular and Molecular Biology, Nicolaus Copernicus University, Lwowska 1, 87-100 Toruń, Poland; (S.G.); (D.K.); (M.C.); (K.N.)
- Centre For Modern Interdisciplinary Technologies, Nicolaus Copernicus University, Wileńska 4, 87-100 Toruń, Poland
| | - Jarosław Tyburski
- Chair of Plant Physiology and Biotechnology, Nicolaus Copernicus University, Lwowska 1, 87-100 Toruń, Poland;
| | - Janusz Niedojadło
- Department of Cellular and Molecular Biology, Nicolaus Copernicus University, Lwowska 1, 87-100 Toruń, Poland; (S.G.); (D.K.); (M.C.); (K.N.)
- Centre For Modern Interdisciplinary Technologies, Nicolaus Copernicus University, Wileńska 4, 87-100 Toruń, Poland
- Correspondence:
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Lan T, Xiong W, Chen X, Mo B, Tang G. Plant cytoplasmic ribosomal proteins: an update on classification, nomenclature, evolution and resources. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 110:292-318. [PMID: 35000252 DOI: 10.1111/tpj.15667] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2021] [Revised: 12/23/2021] [Accepted: 01/02/2022] [Indexed: 06/14/2023]
Abstract
Standardized naming systems are essential to integrate and unify distinct research fields, and to link multi-species data within and across kingdoms. We conducted a comprehensive survey of cytoplasmic ribosomal proteins (CRPs) in the dicot model Arabidopsis thaliana and the monocot model rice, noting that the standardized naming system has not been widely adopted in the plant community. We generated a database linking the old classical names to their updated and compliant names. We also explored the sequences, molecular evolution, and structural and functional characteristics of all plant CRP families, emphasizing evolutionarily conserved and plant-specific features through cross-kingdom comparisons. Unlike fungal CRP paralogs that were mainly created by whole-genome duplication (WGD) or retroposition under a concerted evolution mode, plant CRP genes evolved primarily through both WGD and tandem duplications in a rapid birth-and-death process. We also provide a web-based resource (http://www.plantcrp.cn/) with the aim of sharing the latest knowledge on plant CRPs and facilitating the continued development of a standardized framework across the entire community.
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Affiliation(s)
- Ting Lan
- Guangdong Provincial Key Laboratory for Plant Epigenetics, Longhua Bioindustry and Innovation Research Institute, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518060, China
- Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Optoelectronic Engineering, Shenzhen University, Shenzhen, 518060, China
| | - Wei Xiong
- Guangdong Provincial Key Laboratory for Plant Epigenetics, Longhua Bioindustry and Innovation Research Institute, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518060, China
| | - Xuemei Chen
- Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, 92521, CA, USA
| | - Beixin Mo
- Guangdong Provincial Key Laboratory for Plant Epigenetics, Longhua Bioindustry and Innovation Research Institute, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518060, China
| | - Guiliang Tang
- Department of Biological Sciences, Life Science and Technology Institute, Michigan Technological University, Houghton, 49931, MI, USA
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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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Ong JS, Liu YW, Liong MT, Choi SB, Tsai YC, Low WY. Molecular evolutionary and 3D protein structural analyses of Lactobacillus fermentum elongation factor Tu, a novel brain health promoting factor. Genomics 2020; 112:3915-3924. [PMID: 32629096 DOI: 10.1016/j.ygeno.2020.06.052] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Revised: 06/29/2020] [Accepted: 06/30/2020] [Indexed: 12/17/2022]
Abstract
The role of microbiota in gut-brain communication has led to the development of probiotics promoting brain health. Here we report a genomic study of a Lactobacillus fermentum PS150 and its patented bioactive protein, elongation factor Tu (EF-Tu), which is associated with cognitive improvement in rats. The L. fermentum PS150 circular chromosome is 2,238,401 bp and it consists of 2281 genes. Chromosome comparisons with other L. fermentum strains highlighted a cluster of glycosyltransferases as potential candidate probiotic factors besides EF-Tu. Molecular evolutionary analyses on EF-Tu genes (tuf) in 235 bacteria species revealed one to three copies of the gene per genome. Seven tuf pseudogenes were found and three species only possessed pseudogenes, which is an unprecedented finding. Protein variability analysis of EF-Tu showed five highly variable residues (40 K, 41G, 42 L, 44 K, and 46E) on the protein surface, which warrant further investigation regarding their potential roles as binding sites.
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Affiliation(s)
- Jia Sin Ong
- Bioprocess Technology, School of Industrial Technology, Universiti Sains Malaysia, 11800 Penang, Malaysia
| | - Yen-Wenn Liu
- Institute of Biochemistry and Molecular Biology, National Yang-Ming University, Taipei 11221, Taiwan
| | - Min-Tze Liong
- Bioprocess Technology, School of Industrial Technology, Universiti Sains Malaysia, 11800 Penang, Malaysia
| | - Sy Bing Choi
- School of Data Sciences, Perdana University, Jalan MAEPS Perdana, 43400 Serdang, Selangor, Malaysia
| | - Ying-Chieh Tsai
- Institute of Biochemistry and Molecular Biology, National Yang-Ming University, Taipei 11221, Taiwan.
| | - Wai Yee Low
- School of Data Sciences, Perdana University, Jalan MAEPS Perdana, 43400 Serdang, Selangor, Malaysia; The Davies Research Centre, School of Animal and Veterinary Sciences, University of Adelaide, Roseworthy, SA 5371, Australia.
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Abstract
Large proteins composed of multiple domains are abundant in all proteomes, but their folding and structural dynamics remain poorly understood. Using single-molecule force spectroscopy, we have defined how stabilizing interfaces among the domains of elongation factor G (EF-G) shape its folding pathway. Contrary to the expectation that multidomain proteins fold sequentially as they emerge from the ribosome, we find that folding cannot be completed until the full protein has been synthesized. This posttranslational folding mechanism results in a propensity for misfolding. It is dictated by an energetic coupling among domains that enables conformational flexibility crucial for EF-G function. EF-G thus provides an example of how distinct biological ends—robust folding and functionally important flexibility—come into conflict during protein biogenesis. Large proteins with multiple domains are thought to fold cotranslationally to minimize interdomain misfolding. Once folded, domains interact with each other through the formation of extensive interfaces that are important for protein stability and function. However, multidomain protein folding and the energetics of domain interactions remain poorly understood. In elongation factor G (EF-G), a highly conserved protein composed of 5 domains, the 2 N-terminal domains form a stably structured unit cotranslationally. Using single-molecule optical tweezers, we have defined the steps leading to fully folded EF-G. We find that the central domain III of EF-G is highly dynamic and does not fold upon emerging from the ribosome. Surprisingly, a large interface with the N-terminal domains does not contribute to the stability of domain III. Instead, it requires interactions with its folded C-terminal neighbors to be stably structured. Because of the directionality of protein synthesis, this energetic dependency of domain III on its C-terminal neighbors disrupts cotranslational folding and imposes a posttranslational mechanism on the folding of the C-terminal part of EF-G. As a consequence, unfolded domains accumulate during synthesis, leading to the extensive population of misfolded species that interfere with productive folding. Domain III flexibility enables large-scale conformational transitions that are part of the EF-G functional cycle during ribosome translocation. Our results suggest that energetic tuning of domain stabilities, which is likely crucial for EF-G function, complicates the folding of this large multidomain protein.
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Yatoo MI, Parray OR, Bhat RA, Nazir QU, Haq AU, Malik HU, Fazilli MUR, Gopalakrishnan A, Bashir ST, Tiwari R, Khurana SK, Chaicumpa W, Dhama K. Novel Candidates for Vaccine Development Against Mycoplasma Capricolum Subspecies Capripneumoniae (Mccp)-Current Knowledge and Future Prospects. Vaccines (Basel) 2019; 7:E71. [PMID: 31340571 PMCID: PMC6789616 DOI: 10.3390/vaccines7030071] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Revised: 07/05/2019] [Accepted: 07/12/2019] [Indexed: 02/06/2023] Open
Abstract
Exploration of novel candidates for vaccine development against Mycoplasma capricolum subspecies capripneumoniae (Mccp), the causative agent of contagious caprine pleuropneumonia (CCPP), has recently gained immense importance due to both the increased number of outbreaks and the alarming risk of transboundary spread of disease. Treatment by antibiotics as the only therapeutic strategy is not a viable option due to pathogen persistence, economic issues, and concerns of antibiotic resistance. Therefore, prophylactics or vaccines are becoming important under the current scenario. For quite some time inactivated, killed, or attenuated vaccines proved to be beneficial and provided good immunity up to a year. However, their adverse effects and requirement for larger doses led to the need for production of large quantities of Mccp. This is challenging because the required culture medium is costly and Mycoplasma growth is fastidious and slow. Furthermore, quality control is always an issue with such vaccines. Currently, novel candidate antigens including capsular polysaccharides (CPS), proteins, enzymes, and genes are being evaluated for potential use as vaccines. These have shown potential immunogenicity with promising results in eliciting protective immune responses. Being easy to produce, specific, effective and free from side effects, these novel vaccine candidates can revolutionize vaccination against CCPP. Use of novel proteomic approaches, including sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE), two-dimensional gel electrophoresis, immunoblotting, matrix-assisted laser desorption/ionization-time-of-flight (MALDI-TOF) mass spectrometry, tandem mass spectroscopy, fast protein liquid chromatography (FPLC), bioinformatics, computerized simulation and genomic approaches, including multilocus sequence analysis, next-generation sequencing, basic local alignment search tool (BLAST), gene expression, and recombinant expression, will further enable recognition of ideal antigenic proteins and virulence genes with vaccination potential.
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Affiliation(s)
- Mohd Iqbal Yatoo
- Mycoplasma Laboratory, Division of Veterinary Clinical Complex, Faculty of Veterinary Sciences and Animal Husbandry, Jammu and Kashmir, Srinagar 190006, India.
| | - Oveas Raffiq Parray
- Mycoplasma Laboratory, Division of Veterinary Clinical Complex, Faculty of Veterinary Sciences and Animal Husbandry, Jammu and Kashmir, Srinagar 190006, India
| | - Riyaz Ahmed Bhat
- Mycoplasma Laboratory, Division of Veterinary Clinical Complex, Faculty of Veterinary Sciences and Animal Husbandry, Jammu and Kashmir, Srinagar 190006, India
| | - Qurat Un Nazir
- Mycoplasma Laboratory, Division of Veterinary Clinical Complex, Faculty of Veterinary Sciences and Animal Husbandry, Jammu and Kashmir, Srinagar 190006, India
| | - Abrar Ul Haq
- Mycoplasma Laboratory, Division of Veterinary Clinical Complex, Faculty of Veterinary Sciences and Animal Husbandry, Jammu and Kashmir, Srinagar 190006, India
| | - Hamid Ullah Malik
- Mycoplasma Laboratory, Division of Veterinary Clinical Complex, Faculty of Veterinary Sciences and Animal Husbandry, Jammu and Kashmir, Srinagar 190006, India
| | - Mujeeb Ur Rehman Fazilli
- Mycoplasma Laboratory, Division of Veterinary Clinical Complex, Faculty of Veterinary Sciences and Animal Husbandry, Jammu and Kashmir, Srinagar 190006, India
| | - Arumugam Gopalakrishnan
- Department of Veterinary Clinical Medicine, Madras Veterinary College, Tamilnadu Veterinary and Animal Sciences University, Vepery 600007, India
| | - Shah Tauseef Bashir
- Department of Molecular and Integrative Physiology, University of Illinois, Urbana-Champaign, Urbana, IL 61801, USA
| | - Ruchi Tiwari
- Department of Veterinary Microbiology and Immunology, College of Veterinary Sciences, Deen Dayal Upadhayay Pashu Chikitsa Vigyan Vishwavidyalay Evum Go-Anusandhan Sansthan (DUVASU), Mathura 281001, India
| | - Sandip Kumar Khurana
- ICAR-Central Institute for Research on Buffaloes, Sirsa Road, Hisar 125001, India
| | - Wanpen Chaicumpa
- Center of Research Excellence on Therapeutic Proteins and Antibody Engineering, Department of Parasitology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand
| | - Kuldeep Dhama
- Division of Pathology, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, India.
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14
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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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15
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Li G, Qin Y. Mitochondrial translation factor EF4 regulates oxidative phosphorylation complexes and the production of ROS. Free Radic Res 2019; 52:1250-1255. [PMID: 30693836 DOI: 10.1080/10715762.2018.1479063] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Mitochondrial translation system executes the biosynthesis of mitochondrial DNA encoded polypeptides that are the core subunits of oxidative phosphorylation complexes. Recently, we reported that elongation factor 4 (EF4) is a key quality control factor in bacterial and mitochondrial translation regulating tRNA translocation and modulating cellular responses via a direct cross-talk with cytoplasmic translation machinery. Here, we made a brief review on mtEF4-regulated mitochondrial translation, respiratory chain biogenesis and the production of reactive oxygen species (ROS). We will discuss the influence of mtEF4 on the electron transport chain, especially at respiratory chain complex IV, which could result in cytochrome c peroxidase formation, electron leakage from electron transport chain and ROS increase.
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Affiliation(s)
- Guichen Li
- a Key Laboratory of RNA Biology , Institute of Biophysics, Chinese Academy of Sciences , Chaoyang District , Beijing , China
| | - Yan Qin
- a Key Laboratory of RNA Biology , Institute of Biophysics, Chinese Academy of Sciences , Chaoyang District , Beijing , China.,b University of Chinese Academy of Sciences , Beijing , China
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16
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The Origin and Evolution of Release Factors: Implications for Translation Termination, Ribosome Rescue, and Quality Control Pathways. Int J Mol Sci 2019; 20:ijms20081981. [PMID: 31018531 PMCID: PMC6514570 DOI: 10.3390/ijms20081981] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Revised: 04/18/2019] [Accepted: 04/18/2019] [Indexed: 01/26/2023] Open
Abstract
The evolution of release factors catalyzing the hydrolysis of the final peptidyl-tRNA bond and the release of the polypeptide from the ribosome has been a longstanding paradox. While the components of the translation apparatus are generally well-conserved across extant life, structurally unrelated release factor peptidyl hydrolases (RF-PHs) emerged in the stems of the bacterial and archaeo-eukaryotic lineages. We analyze the diversification of RF-PH domains within the broader evolutionary framework of the translation apparatus. Thus, we reconstruct the possible state of translation termination in the Last Universal Common Ancestor with possible tRNA-like terminators. Further, evolutionary trajectories of the several auxiliary release factors in ribosome quality control (RQC) and rescue pathways point to multiple independent solutions to this problem and frequent transfers between superkingdoms including the recently characterized ArfT, which is more widely distributed across life than previously appreciated. The eukaryotic RQC system was pieced together from components with disparate provenance, which include the long-sought-after Vms1/ANKZF1 RF-PH of bacterial origin. We also uncover an under-appreciated evolutionary driver of innovation in rescue pathways: effectors deployed in biological conflicts that target the ribosome. At least three rescue pathways (centered on the prfH/RFH, baeRF-1, and C12orf65 RF-PH domains), were likely innovated in response to such conflicts.
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17
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Lu J, Cui L, Lin S, Hao L, Cao N, Yi J, Liu X, Lu L, Kang Q. Short communication: Global transcriptome analysis of Lactococcus lactis ssp. lactis in response to gradient freezing. J Dairy Sci 2019; 102:3933-3938. [PMID: 30852017 DOI: 10.3168/jds.2018-15972] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2018] [Accepted: 01/07/2019] [Indexed: 11/19/2022]
Abstract
Lactic acid bacteria are often preserved as starter cultures by freezing to extend shelf stability as well as maintain cell viability and acidification activity. Previous studies showed that the endocyte extracted from gradient-freezing pretreated cells could act as lyoprotectant in the lyophilization process of Lactococcus lactis ssp. lactis. In this study, the molecular mechanisms of L. lactis in response to gradient freezing exposure are described using high-throughput sequencing. Nineteen of 56 genes were upregulated after gradient freezing, whereas 37 genes were downregulated. Further validation results of quantitative real-time PCR experiments were consistent with the RNA sequencing. Gene Ontology (http://www.geneontology.org/) enrichment and Kyoto Encyclopedia of Genes and Genomes (KEGG; https://www.genome.jp/kegg/) pathway were used to analyze the differentially expressed genes. Several pathways, such as glutathione metabolism, ATP-binding cassette transport, metabolism of cell wall and cell membrane components, and stress response-related pathways, were affected by gradient freezing. Six genes relevant to freezing stress response were selected for quantitative real-time PCR, including 3 upregulated genes (hisK, eutD, dukA) and 3 downregulated genes (als, yedF, pepN). The Gene Ontology enrichment and KEGG pathway analyses showed these genes may influence stress response-related pathways, improving the survival of the L. lactis under freezing stress. The identification of these genes deepened an understanding about their response under freezing stress, helping us find potential genes or pathways related to gradient freezing for further research on lyoprotectants.
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Affiliation(s)
- Jike Lu
- School of Life Sciences, Zhengzhou University, Zhengzhou, Henan 450001, China.
| | - Lianming Cui
- School of Life Sciences, Zhengzhou University, Zhengzhou, Henan 450001, China
| | - Songyang Lin
- School of Life Sciences, Zhengzhou University, Zhengzhou, Henan 450001, China
| | - Limin Hao
- The Quartermaster Equipment Institute, Academy of Military Sciences PLA China, Beijing 100010, China
| | - Nana Cao
- School of Life Sciences, Zhengzhou University, Zhengzhou, Henan 450001, China
| | - Juanjuan Yi
- School of Life Sciences, Zhengzhou University, Zhengzhou, Henan 450001, China
| | - Xin Liu
- School of Life Sciences, Zhengzhou University, Zhengzhou, Henan 450001, China
| | - Laizheng Lu
- Zhengzhou Mindtek Biotechnology Co. Ltd., Zhengzhou, Henan 450001, China
| | - Qiaozhen Kang
- School of Life Sciences, Zhengzhou University, Zhengzhou, Henan 450001, China.
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18
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Kürkçüoğlu Ö. Exploring allosteric communication in multiple states of the bacterial ribosome using residue network analysis. Turk J Biol 2018; 42:392-404. [PMID: 30930623 PMCID: PMC6438126 DOI: 10.3906/biy-1802-77] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Antibiotic resistance is one of the most important problems of our era and hence the discovery of new effective therapeutics is urgent. At this point, studying the allosteric communication pathways in the bacterial ribosome and revealing allosteric sites/residues is critical for designing new inhibitors or repurposing readily approved drugs for this enormous machine. To shed light onto molecular details of the allosteric mechanisms, here we construct residue networks of the bacterial ribosomal complex at four different states of translation by using an effective description of the intermolecular interactions. Centrality analysis of these networks highlights the functional roles of structural components and critical residues on the ribosomal complex. High betweenness scores reveal pathways of residues connecting numerous sites on the structure. Interestingly, these pathways assemble highly conserved residues, drug binding sites, and known allosterically linked regions on the same structure. This study proposes a new residue-level model to test how distant sites on the molecular machine may be linked through hub residues that are critically located on the contact topology to inherently form communication pathways. Findings also indicate intersubunit bridges B1b, B3, B5, B7, and B8 as critical targets to design novel antibiotics.
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Affiliation(s)
- Özge Kürkçüoğlu
- Department of Chemical Engineering, Faculty of Chemical-Metallurgical Engineering, İstanbul Technical University , İstanbul , Turkey
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19
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Wan J, Gao X, Mao Y, Zhang X, Qian SB. A Coding Sequence-Embedded Principle Governs Translational Reading Frame Fidelity. RESEARCH (WASHINGTON, D.C.) 2018; 2018:7089174. [PMID: 31549036 PMCID: PMC6750092 DOI: 10.1155/2018/7089174] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/28/2018] [Accepted: 08/28/2018] [Indexed: 06/10/2023]
Abstract
Upon initiation at a start codon, the ribosome must maintain the correct reading frame for hundreds of codons in order to produce functional proteins. While some sequence elements are able to trigger programmed ribosomal frameshifting (PRF), very little is known about how the ribosome normally prevents spontaneous frameshift errors that can have dire consequences if uncorrected. Using high resolution ribosome profiling data sets, we discovered that the translating ribosome uses the 3' end of 18S rRNA to scan the AUG-like codons after the decoding process. The postdecoding mRNA:rRNA interaction not only contributes to predominant translational pausing, but also provides a retrospective mechanism to safeguard the ribosome in the correct reading frame. Partially eliminating the AUG-like "sticky" codons in the reporter message leads to increased +1 frameshift errors. Remarkably, mutating the highly conserved CAU triplet of 18S rRNA globally changes the codon "stickiness". Further supporting the role of "sticky" sequences in reading frame maintenance, the codon composition of open reading frames is highly optimized across eukaryotic genomes. These results suggest an important layer of information embedded within the protein-coding sequences that instructs the ribosome to ensure reading frame fidelity during translation.
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Affiliation(s)
- Ji Wan
- Division of Nutritional Sciences, Cornell University, Ithaca, NY 14853, USA
| | - Xiangwei Gao
- Division of Nutritional Sciences, Cornell University, Ithaca, NY 14853, USA
| | - Yuanhui Mao
- Division of Nutritional Sciences, Cornell University, Ithaca, NY 14853, USA
| | - Xingqian Zhang
- Division of Nutritional Sciences, Cornell University, Ithaca, NY 14853, USA
| | - Shu-Bing Qian
- Division of Nutritional Sciences, Cornell University, Ithaca, NY 14853, USA
- Graduate Programs in Genetics Genomics and Development, Biochemistry Molecular and Cellular Biology, Cornell University, Ithaca, NY 14853, USA
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20
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Susorov D, Zakharov N, Shuvalova E, Ivanov A, Egorova T, Shuvalov A, Shatsky IN, Alkalaeva E. Eukaryotic translation elongation factor 2 (eEF2) catalyzes reverse translocation of the eukaryotic ribosome. J Biol Chem 2018; 293:5220-5229. [PMID: 29453282 DOI: 10.1074/jbc.ra117.000761] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Revised: 01/22/2018] [Indexed: 01/10/2023] Open
Abstract
During protein synthesis, a ribosome moves along the mRNA template and, using aminoacyl-tRNAs, decodes the template nucleotide triplets to assemble a protein amino acid sequence. This movement is accompanied by shifting of mRNA-tRNA complexes within the ribosome in a process called translocation. In living cells, this process proceeds in a unidirectional manner, bringing the ribosome to the 3' end of mRNA, and is catalyzed by the GTPase translation elongation factor 2 (EF-G in prokaryotes and eEF2 in eukaryotes). Interestingly, the possibility of spontaneous backward translocation has been shown in vitro for bacterial ribosomes, suggesting a potential reversibility of this reaction. However, this possibility has not yet been tested for eukaryotic ribosomes. Here, using a reconstituted mammalian translation system, we show that the eukaryotic elongation factor eEF2 catalyzes ribosomal reverse translocation at one mRNA triplet. We found that this process requires a cognate tRNA in the ribosomal E-site and cannot occur spontaneously without eEF2. The efficiency of this reaction depended on the concentrations of eEF2 and cognate tRNAs and increased in the presence of nonhydrolyzable GTP analogues. Of note, ADP-ribosylation of eEF2 domain IV blocked reverse translocation, suggesting a crucial role of interactions of this domain with the ribosome for the catalysis of the reaction. In summary, our findings indicate that eEF2 is able to induce ribosomal translocation in forward and backward directions, highlighting the universal mechanism of tRNA-mRNA movements within the ribosome.
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Affiliation(s)
- Denis Susorov
- From the Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia.,the Faculty of Bioengineering and Bioinformatics, M. V. Lomonosov Moscow State University, Moscow 119234, Russia
| | - Nikita Zakharov
- the Department of Biological and Medical Physics, Moscow Institute of Physics and Technology, Dolgoprudny, Russia 141700
| | - Ekaterina Shuvalova
- From the Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia
| | - Alexander Ivanov
- From the Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia.,the Faculty of Bioengineering and Bioinformatics, M. V. Lomonosov Moscow State University, Moscow 119234, Russia
| | - Tatiana Egorova
- From the Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia.,the Pirogov Russian National Research Medical University, Moscow 117997, Russia, and
| | - Alexey Shuvalov
- From the Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia
| | - Ivan N Shatsky
- the Belozersky Institute of Physico-Chemical Biology, Moscow State University, Moscow 119992, Russia
| | - Elena Alkalaeva
- From the Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia,
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21
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Parks MM, Kurylo CM, Dass RA, Bojmar L, Lyden D, Vincent CT, Blanchard SC. Variant ribosomal RNA alleles are conserved and exhibit tissue-specific expression. SCIENCE ADVANCES 2018; 4:eaao0665. [PMID: 29503865 PMCID: PMC5829973 DOI: 10.1126/sciadv.aao0665] [Citation(s) in RCA: 130] [Impact Index Per Article: 21.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2017] [Accepted: 01/08/2018] [Indexed: 05/25/2023]
Abstract
The ribosome, the integration point for protein synthesis in the cell, is conventionally considered a homogeneous molecular assembly that only passively contributes to gene expression. Yet, epigenetic features of the ribosomal DNA (rDNA) operon and changes in the ribosome's molecular composition have been associated with disease phenotypes, suggesting that the ribosome itself may possess inherent regulatory capacity. Analyzing whole-genome sequencing data from the 1000 Genomes Project and the Mouse Genomes Project, we find that rDNA copy number varies widely across individuals, and we identify pervasive intra- and interindividual nucleotide variation in the 5S, 5.8S, 18S, and 28S ribosomal RNA (rRNA) genes of both human and mouse. Conserved rRNA sequence heterogeneities map to functional centers of the assembled ribosome, variant rRNA alleles exhibit tissue-specific expression, and ribosomes bearing variant rRNA alleles are present in the actively translating ribosome pool. These findings provide a critical framework for exploring the possibility that the expression of genomically encoded variant rRNA alleles gives rise to physically and functionally heterogeneous ribosomes that contribute to mammalian physiology and human disease.
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Affiliation(s)
- Matthew M. Parks
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY 10065, USA
| | - Chad M. Kurylo
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY 10065, USA
| | - Randall A. Dass
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY 10065, USA
| | - Linda Bojmar
- Children’s Cancer and Blood Foundation Laboratories, Departments of Pediatrics, and Cell and Developmental Biology, Drukier Institute for Children’s Health, Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10065, USA
- Department of Surgery, County Council of Östergötland, and Department of Clinical and Experimental Medicine, Faculty of Health Sciences, Linköping University, 58185 Linköping, Sweden
- Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden
| | - David Lyden
- Children’s Cancer and Blood Foundation Laboratories, Departments of Pediatrics, and Cell and Developmental Biology, Drukier Institute for Children’s Health, Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10065, USA
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - C. Theresa Vincent
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY 10065, USA
- Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden
| | - Scott C. Blanchard
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY 10065, USA
- Tri-Institutional Training Program in Chemical Biology, Weill Cornell Medicine, New York, NY 10065, USA
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22
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A genetic system for targeted mutations to disrupt and restore genes in the obligate bacterium, Ehrlichia chaffeensis. Sci Rep 2017; 7:15801. [PMID: 29150636 PMCID: PMC5693922 DOI: 10.1038/s41598-017-16023-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2017] [Accepted: 10/02/2017] [Indexed: 11/17/2022] Open
Abstract
Obligate intracellular bacteria (obligates) belonging to Rickettsiales and Chlamydiales cause diseases in hundreds of millions of people worldwide and in many animal species. Lack of an efficient system for targeted mutagenesis in obligates remains a major impediment in understanding microbial pathogenesis. Challenges in creating targeted mutations may be attributed to essential nature of majority of the genes and intracellular replication dependence. Despite success in generating random mutations, a method that works well in creating mutations in specific genes of interest followed by complementation remains problematic for obligates and is a highly sought-after goal. We describe protocols to generate stable targeted mutations by allelic exchange in Ehrlichia chaffeensis, an obligate intracellular tick-borne bacterium responsible for human monocytic ehrlichiosis. Targeted mutations in E. chaffeensis were created to disrupt two genes, and also to restore one gene by another allelic exchange mutation leading to the restoration of transcription and protein expression from the inactivated gene and the recovered organisms also express mCherry, which distinguishes from the wild type. We expect that the methods developed are broadly applicable to other obligates, particularly to rickettsial pathogens, to routinely perform targeted mutations to enable studies focused on protein structure-function analyses, host-pathogen interactions and in developing vaccines.
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23
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Joazeiro CAP. Ribosomal Stalling During Translation: Providing Substrates for Ribosome-Associated Protein Quality Control. Annu Rev Cell Dev Biol 2017; 33:343-368. [PMID: 28715909 DOI: 10.1146/annurev-cellbio-111315-125249] [Citation(s) in RCA: 136] [Impact Index Per Article: 19.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Cells of all organisms survey problems during translation elongation, which may happen as a consequence of mRNA aberrations, inefficient decoding, or other sources. In eukaryotes, ribosome-associated quality control (RQC) senses elongation-stalled ribosomes and promotes dissociation of ribosomal subunits. This so-called ribosomal rescue releases the mRNA for degradation and allows 40S subunits to be recycled for new rounds of translation. However, the nascent polypeptide chains remain linked to tRNA and associated with the rescued 60S subunits. As a final critical step in this pathway, the Ltn1/Listerin E3 ligase subunit of the RQC complex (RQCc) ubiquitylates the nascent chain, which promotes clearance of the 60S subunit while simultaneously marking the nascent chain for elimination. Here we review the ribosomal stalling and rescue steps upstream of the RQCc, where one witnesses intersection with cellular machineries implicated in translation elongation, translation termination, ribosomal subunit recycling, and mRNA quality control. We emphasize both recent progress and future directions in this area, as well as examples linking ribosomal rescue with the production of Ltn1-RQCc substrates.
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Affiliation(s)
- Claudio A P Joazeiro
- ZMBH, University of Heidelberg, 69120 Heidelberg, Germany; .,The Scripps Research Institute, La Jolla, California 92037
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24
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Lilleorg S, Reier K, Remme J, Liiv A. The Intersubunit Bridge B1b of the Bacterial Ribosome Facilitates Initiation of Protein Synthesis and Maintenance of Translational Fidelity. J Mol Biol 2017; 429:1067-1080. [PMID: 28238762 DOI: 10.1016/j.jmb.2017.02.015] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2016] [Revised: 02/10/2017] [Accepted: 02/17/2017] [Indexed: 10/20/2022]
Abstract
In bacteria, ribosomal subunits are connected via 12 intersubunit bridges involving RNA-RNA, RNA-protein, and protein-protein interactions. The only protein-protein bridge in the ribosome is ribosomal intersubunit bridge 1b (B1b), which is mainly formed by the bacterial protein L31 (bL31) and connects the head domain of 30S subunit and the central protuberance of the 50S subunit. It is known to be the most dynamic intersubunit bridge. Here, we have evaluated the role of bL31 and thereby the bridge B1b in the working cycle of the ribosome. First, bL31-deficient ribosomes are severely compromised in their ability to ensure translational fidelity particularly in reading frame maintenance in vivo. Second, in the absence of bL31, the rate of initiation is significantly reduced both in vivo and in vitro. Third, polysome profile and subunit reassociation assays demonstrate that bL31 is important for stabilizing subunit joining in vivo and in vitro. Together, our results demonstrate that bL31 is important for determining translational fidelity and stabilizing subunit association. We conclude that the only protein-protein intersubunit bridge of the bacterial ribosome facilitates translation initiation and is essential for maintaining the reading frame of mRNA translation.
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Affiliation(s)
- Silva Lilleorg
- Institute of Molecular and Cell Biology, University of Tartu, Riia street 23B, Tartu 51010, Estonia
| | - Kaspar Reier
- Institute of Molecular and Cell Biology, University of Tartu, Riia street 23B, Tartu 51010, Estonia
| | - Jaanus Remme
- Institute of Molecular and Cell Biology, University of Tartu, Riia street 23B, Tartu 51010, Estonia
| | - Aivar Liiv
- Institute of Molecular and Cell Biology, University of Tartu, Riia street 23B, Tartu 51010, Estonia.
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25
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Mg2+ regulates transcription of mgtA in Salmonella Typhimurium via translation of proline codons during synthesis of the MgtL peptide. Proc Natl Acad Sci U S A 2016; 113:15096-15101. [PMID: 27849575 DOI: 10.1073/pnas.1612268113] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
In Salmonella enterica serovar Typhimurium, Mg2+ limitation induces transcription of the mgtA Mg2+ transport gene, but the mechanism involved is unclear. The 5' leader of the mgtA mRNA contains a 17-codon, proline-rich ORF, mgtL, whose translation regulates the transcription of mgtA [Park S-Y et al. (2010) Cell 142:737-748]. Rapid translation of mgtL promotes formation of a secondary structure in the mgtA mRNA that permits termination of transcription by the Rho protein upstream of mgtA, whereas slow or incomplete translation of mgtL generates a different structure that blocks termination. We identified the following mutations that conferred high-level transcription of mgtA at high [Mg2+]: (i) a base-pair change that introduced an additional proline codon into mgtL, generating three consecutive proline codons; (ii) lesions in rpmA and rpmE, which encode ribosomal proteins L27 and L31, respectively; (iii) deletion of efp, which encodes elongation factor EF-P that assists the translation of proline codons; and (iv) a heat-sensitive mutation in trmD, whose product catalyzes the m1G37 methylation of tRNAPro Furthermore, substitution of three of the four proline codons in mgtL rendered mgtA uninducible. We hypothesize that the proline codons present an impediment to the translation of mgtL, which can be alleviated by high [Mg2+] exerted on component(s) of the translation machinery, such as EF-P, TrmD, or a ribosomal factor. Inadequate [Mg2+] precludes this alleviation, making mgtL translation inefficient and thereby permitting mgtA transcription. These findings are a significant step toward defining the target of Mg2+ in the regulation of mgtA transcription.
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Cao X, Qin Y. Mitochondrial translation factors reflect coordination between organelles and cytoplasmic translation via mTOR signaling: Implication in disease. Free Radic Biol Med 2016; 100:231-237. [PMID: 27101739 DOI: 10.1016/j.freeradbiomed.2016.04.010] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/18/2016] [Revised: 04/11/2016] [Accepted: 04/13/2016] [Indexed: 12/24/2022]
Abstract
Mitochondria are semi-autonomous organelle possessing their own translation machinery to biosynthesize mitochondrial DNA (mtDNA)-encoded polypeptides, which are the core subunits of oxidative phosphorylation (OXPHOS) complexes. Mitochondrial translation elongation factor 4 (mtEF4) is a key quality control factor in mitochondrial translation (mt-translation) that regulates mitochondrial tRNA translocation and modulates cellular responses by influencing cytoplasmic translation (ct-translation). In addition to mtEF4, mt-translational activators, mitochondrial microRNAs (mitomiRs), and MITRAC have been reported recently as crucial mt-translation regulators. Here, we focus on the novel ways how these factors regulate mt-translation, discuss the main cellular response of mammalian target of rapamycin (mTOR) signalling upon mt-translation defects, and summarize the related human diseases.
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Affiliation(s)
- Xintao Cao
- Key Laboratory of RNA Biology, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Chaoyang District, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yan Qin
- Key Laboratory of RNA Biology, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Chaoyang District, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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Avilamycin and evernimicin induce structural changes in rProteins uL16 and CTC that enhance the inhibition of A-site tRNA binding. Proc Natl Acad Sci U S A 2016; 113:E6796-E6805. [PMID: 27791159 DOI: 10.1073/pnas.1614297113] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Two structurally unique ribosomal antibiotics belonging to the orthosomycin family, avilamycin and evernimicin, possess activity against Enterococci, Staphylococci, and Streptococci, and other Gram-positive bacteria. Here, we describe the high-resolution crystal structures of the eubacterial large ribosomal subunit in complex with them. Their extended binding sites span the A-tRNA entrance corridor, thus inhibiting protein biosynthesis by blocking the binding site of the A-tRNA elbow, a mechanism not shared with other known antibiotics. Along with using the ribosomal components that bind and discriminate the A-tRNA-namely, ribosomal RNA (rRNA) helices H89, H91, and ribosomal proteins (rProtein) uL16-these structures revealed novel interactions with domain 2 of the CTC protein, a feature typical to various Gram-positive bacteria. Furthermore, analysis of these structures explained how single nucleotide mutations and methylations in helices H89 and H91 confer resistance to orthosomycins and revealed the sequence variations in 23S rRNA nucleotides alongside the difference in the lengths of the eukaryotic and prokaryotic α1 helix of protein uL16 that play a key role in the selectivity of those drugs. The accurate interpretation of the crystal structures that could be performed beyond that recently reported in cryo-EM models provide structural insights that may be useful for the design of novel pathogen-specific antibiotics, and for improving the potency of orthosomycins. Because both drugs are extensively metabolized in vivo, their environmental toxicity is very low, thus placing them at the frontline of drugs with reduced ecological hazards.
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Song G, Qin Y. EF4 reveals the energy barrier for tRNA back-translocation in the peptidyl transferase center. RNA Biol 2016; 13:934-939. [DOI: 10.1080/15476286.2016.1215795] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
Affiliation(s)
- Guangtao Song
- Key Laboratory of RNA Biology, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Chaoyang District, Beijing, China
| | - Yan Qin
- Key Laboratory of RNA Biology, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Chaoyang District, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
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Melnikov S, Mailliot J, Shin BS, Rigger L, Yusupova G, Micura R, Dever TE, Yusupov M. Crystal Structure of Hypusine-Containing Translation Factor eIF5A Bound to a Rotated Eukaryotic Ribosome. J Mol Biol 2016; 428:3570-3576. [PMID: 27196944 PMCID: PMC5408928 DOI: 10.1016/j.jmb.2016.05.011] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2016] [Revised: 05/04/2016] [Accepted: 05/07/2016] [Indexed: 10/21/2022]
Abstract
Eukaryotic translation initiation factor eIF5A promotes protein synthesis by resolving polyproline-induced ribosomal stalling. Here, we report a 3.25-Å resolution crystal structure of eIF5A bound to the yeast 80S ribosome. The structure reveals a previously unseen conformation of an eIF5A-ribosome complex and highlights a possible functional link between conformational changes of the ribosome during protein synthesis and the eIF5A-ribosome association.
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Affiliation(s)
- Sergey Melnikov
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS UMR7104, INSERM U964, 1 rue Laurent Fries, 67404 Illkirch-Graffenstaden, France
- Université de Strasbourg, 4 Rue Blaise Pascal, 67081 Strasbourg, France
| | - Justine Mailliot
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS UMR7104, INSERM U964, 1 rue Laurent Fries, 67404 Illkirch-Graffenstaden, France
- Université de Strasbourg, 4 Rue Blaise Pascal, 67081 Strasbourg, France
| | - Byung-Sik Shin
- Laboratory of Gene Regulation and Development, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Lukas Rigger
- Institute of Organic Chemistry, Leopold Franzens University, Innrain 80/82, A-6020, Innsbruck, Austria
| | - Gulnara Yusupova
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS UMR7104, INSERM U964, 1 rue Laurent Fries, 67404 Illkirch-Graffenstaden, France
- Université de Strasbourg, 4 Rue Blaise Pascal, 67081 Strasbourg, France
| | - Ronald Micura
- Institute of Organic Chemistry, Leopold Franzens University, Innrain 80/82, A-6020, Innsbruck, Austria
| | - Thomas E. Dever
- Laboratory of Gene Regulation and Development, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Marat Yusupov
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS UMR7104, INSERM U964, 1 rue Laurent Fries, 67404 Illkirch-Graffenstaden, France
- Université de Strasbourg, 4 Rue Blaise Pascal, 67081 Strasbourg, France
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Arenz S, Wilson DN. Bacterial Protein Synthesis as a Target for Antibiotic Inhibition. Cold Spring Harb Perspect Med 2016; 6:cshperspect.a025361. [PMID: 27481773 DOI: 10.1101/cshperspect.a025361] [Citation(s) in RCA: 74] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Protein synthesis occurs on macromolecular machines, called ribosomes. Bacterial ribosomes and the translational machinery represent one of the major targets for antibiotics in the cell. Therefore, structural and biochemical investigations into ribosome-targeting antibiotics provide not only insight into the mechanism of action and resistance of antibiotics, but also insight into the fundamental process of protein synthesis. This review summarizes the recent advances in our understanding of protein synthesis, particularly with respect to X-ray and cryoelectron microscopy (cryo-EM) structures of ribosome complexes, and highlights the different steps of translation that are targeted by the diverse array of known antibiotics. Such findings will be important for the ongoing development of novel and improved antimicrobial agents to combat the rapid emergence of multidrug resistant pathogenic bacteria.
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Affiliation(s)
- Stefan Arenz
- Center for Integrated Protein Science Munich (CiPSM), University of Munich, 81377 Munich, Germany
| | - Daniel N Wilson
- Center for Integrated Protein Science Munich (CiPSM), University of Munich, 81377 Munich, Germany Gene Center and Department for Biochemistry, University of Munich, 81377 Munich, Germany
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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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Kumar V, Ero R, Ahmed T, Goh KJ, Zhan Y, Bhushan S, Gao YG. Structure of the GTP Form of Elongation Factor 4 (EF4) Bound to the Ribosome. J Biol Chem 2016; 291:12943-50. [PMID: 27137929 DOI: 10.1074/jbc.m116.725945] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2016] [Indexed: 11/06/2022] Open
Abstract
Elongation factor 4 (EF4) is a member of the family of ribosome-dependent translational GTPase factors, along with elongation factor G and BPI-inducible protein A. Although EF4 is highly conserved in bacterial, mitochondrial, and chloroplast genomes, its exact biological function remains controversial. Here we present the cryo-EM reconstitution of the GTP form of EF4 bound to the ribosome with P and E site tRNAs at 3.8-Å resolution. Interestingly, our structure reveals an unrotated ribosome rather than a clockwise-rotated ribosome, as observed in the presence of EF4-GDP and P site tRNA. In addition, we also observed a counterclockwise-rotated form of the above complex at 5.7-Å resolution. Taken together, our results shed light on the interactions formed between EF4, the ribosome, and the P site tRNA and illuminate the GTPase activation mechanism at previously unresolved detail.
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Affiliation(s)
- Veerendra Kumar
- From the Institute of Molecular and Cell Biology, The Agency for Science, Technology and Research (A*STAR), 61 Biopolis Drive, 138673 Singapore, the School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, 637551 Singapore, and
| | - Rya Ero
- the School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, 637551 Singapore, and
| | - Tofayel Ahmed
- the School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, 637551 Singapore, and
| | - Kwok Jian Goh
- the School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, 637551 Singapore, and
| | - Yin Zhan
- the School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, 637551 Singapore, and
| | - Shashi Bhushan
- the School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, 637551 Singapore, and the Institute of Structural Biology, Nanyang Technological University, 636921 Singapore
| | - Yong-Gui Gao
- From the Institute of Molecular and Cell Biology, The Agency for Science, Technology and Research (A*STAR), 61 Biopolis Drive, 138673 Singapore, the School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, 637551 Singapore, and the Institute of Structural Biology, Nanyang Technological University, 636921 Singapore
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33
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Step back for seminal translation. Nat Struct Mol Biol 2016; 23:362-3. [DOI: 10.1038/nsmb.3217] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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34
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Mammalian elongation factor 4 regulates mitochondrial translation essential for spermatogenesis. Nat Struct Mol Biol 2016; 23:441-9. [DOI: 10.1038/nsmb.3206] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2015] [Accepted: 03/17/2016] [Indexed: 11/08/2022]
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35
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Nguyen K, Whitford PC. Steric interactions lead to collective tilting motion in the ribosome during mRNA-tRNA translocation. Nat Commun 2016; 7:10586. [PMID: 26838673 PMCID: PMC4742886 DOI: 10.1038/ncomms10586] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2015] [Accepted: 12/31/2015] [Indexed: 12/01/2022] Open
Abstract
Translocation of mRNA and tRNA through the ribosome is associated with large-scale rearrangements of the head domain in the 30S ribosomal subunit. To elucidate the relationship between 30S head dynamics and mRNA–tRNA displacement, we apply molecular dynamics simulations using an all-atom structure-based model. Here we provide a statistical analysis of 250 spontaneous transitions between the A/P–P/E and P/P–E/E ensembles. Consistent with structural studies, the ribosome samples a chimeric ap/P–pe/E intermediate, where the 30S head is rotated ∼18°. It then transiently populates a previously unreported intermediate ensemble, which is characterized by a ∼10° tilt of the head. To identify the origins of head tilting, we analyse 781 additional simulations in which specific steric features are perturbed. These calculations show that head tilting may be attributed to specific steric interactions between tRNA and the 30S subunit (PE loop and protein S13). Taken together, this study demonstrates how molecular structure can give rise to large-scale collective rearrangements. During protein elongation, the translocation of mRNA and tRNA molecules across the 30S ribosomal subunit is associated with large-scale motions of the 30S head domain. Here the authors carry out MD simulations to probe the associated steric interactions and identify novel tilting motions during the late stages of translocation.
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Affiliation(s)
- Kien Nguyen
- Department of Physics, Northeastern University, Dana Research Center 111, 360 Huntington Avenue, Boston, Massachusetts 02115, USA
| | - Paul C Whitford
- Department of Physics, Northeastern University, Dana Research Center 111, 360 Huntington Avenue, Boston, Massachusetts 02115, USA
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EF4 disengages the peptidyl-tRNA CCA end and facilitates back-translocation on the 70S ribosome. Nat Struct Mol Biol 2016; 23:125-31. [PMID: 26809121 DOI: 10.1038/nsmb.3160] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2015] [Accepted: 12/11/2015] [Indexed: 11/08/2022]
Abstract
EF4 catalyzes tRNA back-translocation through an unknown mechanism. We report cryo-EM structures of Escherichia coli EF4 in post- and pretranslocational ribosomes (Post- and Pre-EF4) at 3.7- and 3.2-Å resolution, respectively. In Post-EF4, peptidyl-tRNA occupies the peptidyl (P) site, but the interaction between its CCA end and the P loop is disrupted. In Pre-EF4, the peptidyl-tRNA assumes a unique position near the aminoacyl (A) site, denoted the A site/EF4 bound (A/4) site, with a large displacement at its acceptor arm. Mutagenesis analyses suggest that a specific region in the EF4 C-terminal domain (CTD) interferes with base-pairing between the peptidyl-tRNA 3'-CCA and the P loop, whereas the EF4 CTD enhances peptidyl-tRNA interaction at the A/4 site. Therefore, EF4 induces back-translocation by disengaging the tRNA's CCA end from the peptidyl transferase center of the translating ribosome.
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Koch M, Clementi N, Rusca N, Vögele P, Erlacher M, Polacek N. The integrity of the G2421-C2395 base pair in the ribosomal E-site is crucial for protein synthesis. RNA Biol 2015; 12:70-81. [PMID: 25826414 PMCID: PMC4615901 DOI: 10.1080/15476286.2015.1017218] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
During the elongation cycle of protein biosynthesis, tRNAs traverse through the ribosome by consecutive binding to the 3 ribosomal binding sites (A-, P-, and E- sites). While the ribosomal A- and P-sites have been functionally well characterized in the past, the contribution of the E-site to protein biosynthesis is still poorly understood in molecular terms. Previous studies suggested an important functional interaction of the terminal residue A76 of E-tRNA with the nucleobase of the universally conserved 23S rRNA residue C2394. Using an atomic mutagenesis approach to introduce non-natural nucleoside analogs into the 23S rRNA, we could show that removal of the nucleobase or the ribose 2'-OH at C2394 had no effect on protein synthesis. On the other hand, our data disclose the importance of the highly conserved E-site base pair G2421-C2395 for effective translation. Ribosomes with a disrupted G2421-C2395 base pair are defective in tRNA binding to the E-site. This results in an impaired translation of genuine mRNAs, while homo-polymeric templates are not affected. Cumulatively our data emphasize the importance of E-site tRNA occupancy and in particular the intactness of the 23S rRNA base pair G2421-C2395 for productive protein biosynthesis.
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Affiliation(s)
- Miriam Koch
- a Department of Chemistry and Biochemistry; University of Bern ; Bern , Switzerland
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Clancy E, Higgins O, Forrest MS, Boo TW, Cormican M, Barry T, Piepenburg O, Smith TJ. Development of a rapid recombinase polymerase amplification assay for the detection of Streptococcus pneumoniae in whole blood. BMC Infect Dis 2015; 15:481. [PMID: 26515409 PMCID: PMC4625855 DOI: 10.1186/s12879-015-1212-5] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2015] [Accepted: 10/13/2015] [Indexed: 01/02/2023] Open
Abstract
Background Streptococcus pneumoniae is an important cause of microbial disease in humans. The introduction of multivalent vaccines has coincided with a dramatic decrease in the number of pneumococcal-related deaths. In spite of this, at a global level, pneumococcal infection remains an important cause of death among children under 5 years of age and in adults 65 years of age or older. In order to properly manage patients and control the spread of infection, a rapid and highly sensitive diagnostic method is needed for routine implementation, especially in resource-limited regions where pneumococcal disease is most prevalent. Methods Using the gene encoding leader peptidase A as a molecular diagnostics target, a real-time RPA assay was designed and optimised for the detection of S. pneumoniae in whole blood. The performance of the assay was compared to real-time PCR in terms of its analytical limit of detection and specificity. The inhibitory effect of human genomic DNA on amplification was investigated. The potential clinical utility of the assay was investigated using a small number of clinical samples. Results The RPA assay has a limit of detection equivalent to PCR (4.0 and 5.1 genome equivalents per reaction, respectively) and was capable of detecting the equivalent of <1 colony forming unit of S. pneumoniae when spiked into human whole blood. The RPA assay was 100 % inclusive (38/38 laboratory reference strains and 19/19 invasive clinical isolates) and 100 % exclusive; differentiating strains of S. pneumoniae species from other viridans group streptococci, including S. pseudopneumoniae. When applied to the analysis of a small number (n = 11) of clinical samples (blood culture positive for S. pneumoniae), the RPA assay was demonstrated to be both rapid and sensitive. Conclusions The RPA assay developed in this work is shown to be as sensitive and as specific as PCR. In terms of reaction kinetics, the RPA assay is shown to exceed those of the PCR, with the RPA running to completion in 20 minutes and capable generating a positive signal in as little as 6 minutes. This work represents a potentially suitable assay for application in point-of-care settings.
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Affiliation(s)
- Eoin Clancy
- Molecular Diagnostics Research Group, School of Natural Sciences, National University of Ireland, Galway, Ireland. .,Biomedical Diagnostics Institute Programme, National Centre for Biomedical Engineering Science, National University of Ireland, Galway, Ireland.
| | - Owen Higgins
- Molecular Diagnostics Research Group, School of Natural Sciences, National University of Ireland, Galway, Ireland. .,Biomedical Diagnostics Institute Programme, National Centre for Biomedical Engineering Science, National University of Ireland, Galway, Ireland.
| | | | - Teck Wee Boo
- Biomedical Diagnostics Institute Programme, National Centre for Biomedical Engineering Science, National University of Ireland, Galway, Ireland. .,School of Medicine, National University of Ireland , Galway, Ireland.
| | - Martin Cormican
- Biomedical Diagnostics Institute Programme, National Centre for Biomedical Engineering Science, National University of Ireland, Galway, Ireland. .,School of Medicine, National University of Ireland , Galway, Ireland.
| | - Thomas Barry
- Biomedical Diagnostics Institute Programme, National Centre for Biomedical Engineering Science, National University of Ireland, Galway, Ireland. .,Nucleic Acids Diagnostics Research Laboratory, Microbiology, School of Natural Sciences, National University of Ireland, Galway, Ireland.
| | | | - Terry J Smith
- Molecular Diagnostics Research Group, School of Natural Sciences, National University of Ireland, Galway, Ireland. .,Biomedical Diagnostics Institute Programme, National Centre for Biomedical Engineering Science, National University of Ireland, Galway, Ireland.
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Zhang D, Yan K, Zhang Y, Liu G, Cao X, Song G, Xie Q, Gao N, Qin Y. New insights into the enzymatic role of EF-G in ribosome recycling. Nucleic Acids Res 2015; 43:10525-33. [PMID: 26432831 PMCID: PMC4666400 DOI: 10.1093/nar/gkv995] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2015] [Accepted: 09/19/2015] [Indexed: 12/30/2022] Open
Abstract
During translation, elongation factor G (EF-G) plays a catalytic role in tRNA translocation and a facilitative role in ribosome recycling. By stabilizing the rotated ribosome and interacting with ribosome recycling factor (RRF), EF-G was hypothesized to induce the domain rotations of RRF, which subsequently performs the function of splitting the major intersubunit bridges and thus separates the ribosome into subunits for recycling. Here, with systematic mutagenesis, FRET analysis and cryo-EM single particle approach, we analyzed the interplay between EF-G/RRF and post termination complex (PoTC). Our data reveal that the two conserved loops (loop I and II) at the tip region of EF-G domain IV possess distinct roles in tRNA translocation and ribosome recycling. Specifically, loop II might be directly involved in disrupting the main intersubunit bridge B2a between helix 44 (h44 from the 30S subunit) and helix 69 (H69 from the 50S subunit) in PoTC. Therefore, our data suggest a new ribosome recycling mechanism which requires an active involvement of EF-G. In addition to supporting RRF, EF-G plays an enzymatic role in destabilizing B2a via its loop II.
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Affiliation(s)
- Dejiu Zhang
- Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China University of Chinese Academy of Sciences, Beijing 100049, China
| | - Kaige Yan
- Ministry of Education Key Laboratory of Protein Sciences, Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Yiwei Zhang
- Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Guangqiao Liu
- Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Xintao Cao
- Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China University of Chinese Academy of Sciences, Beijing 100049, China
| | - Guangtao Song
- Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Qiang Xie
- College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Ning Gao
- Ministry of Education Key Laboratory of Protein Sciences, Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Yan Qin
- Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China University of Chinese Academy of Sciences, Beijing 100049, China
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Koripella RK, Holm M, Dourado D, Mandava CS, Flores S, Sanyal S. A conserved histidine in switch-II of EF-G moderates release of inorganic phosphate. Sci Rep 2015; 5:12970. [PMID: 26264741 PMCID: PMC4532990 DOI: 10.1038/srep12970] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2015] [Accepted: 07/13/2015] [Indexed: 01/13/2023] Open
Abstract
Elongation factor G (EF-G), a translational GTPase responsible for tRNA-mRNA translocation possesses a conserved histidine (H91 in Escherichia coli) at the apex of switch-II, which has been implicated in GTPase activation and GTP hydrolysis. While H91A, H91R and H91E mutants showed different degrees of defect in ribosome associated GTP hydrolysis, H91Q behaved like the WT. However, all these mutants, including H91Q, are much more defective in inorganic phosphate (Pi) release, thereby suggesting that H91 facilitates Pi release. In crystal structures of the ribosome bound EF-G•GTP a tight coupling between H91 and the γ-phosphate of GTP can be seen. Following GTP hydrolysis, H91 flips ~140° in the opposite direction, probably with Pi still coupled to it. This, we suggest, promotes Pi to detach from GDP and reach the inter-domain space of EF-G, which constitutes an exit path for the Pi. Molecular dynamics simulations are consistent with this hypothesis and demonstrate a vital role of an Mg2+ ion in the process.
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Affiliation(s)
- Ravi Kiran Koripella
- Department of Cell and Molecular Biology, Uppsala University, Box-596, BMC, 75124, Uppsala, Sweden
| | - Mikael Holm
- Department of Cell and Molecular Biology, Uppsala University, Box-596, BMC, 75124, Uppsala, Sweden
| | - Daniel Dourado
- Department of Cell and Molecular Biology, Uppsala University, Box-596, BMC, 75124, Uppsala, Sweden
| | - Chandra Sekhar Mandava
- Department of Cell and Molecular Biology, Uppsala University, Box-596, BMC, 75124, Uppsala, Sweden
| | - Samuel Flores
- Department of Cell and Molecular Biology, Uppsala University, Box-596, BMC, 75124, Uppsala, Sweden
| | - Suparna Sanyal
- Department of Cell and Molecular Biology, Uppsala University, Box-596, BMC, 75124, Uppsala, Sweden
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Achenbach J, Jahnz M, Bethge L, Paal K, Jung M, Schuster M, Albrecht R, Jarosch F, Nierhaus KH, Klussmann S. Outwitting EF-Tu and the ribosome: translation with d-amino acids. Nucleic Acids Res 2015; 43:5687-98. [PMID: 26026160 PMCID: PMC4499158 DOI: 10.1093/nar/gkv566] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2015] [Accepted: 05/18/2015] [Indexed: 01/09/2023] Open
Abstract
Key components of the translational apparatus, i.e. ribosomes, elongation factor EF-Tu and most aminoacyl-tRNA synthetases, are stereoselective and prevent incorporation of d-amino acids (d-aa) into polypeptides. The rare appearance of d-aa in natural polypeptides arises from post-translational modifications or non-ribosomal synthesis. We introduce an in vitro translation system that enables single incorporation of 17 out of 18 tested d-aa into a polypeptide; incorporation of two or three successive d-aa was also observed in several cases. The system consists of wild-type components and d-aa are introduced via artificially charged, unmodified tRNAGly that was selected according to the rules of ‘thermodynamic compensation’. The results reveal an unexpected plasticity of the ribosomal peptidyltransferase center and thus shed new light on the mechanism of chiral discrimination during translation. Furthermore, ribosomal incorporation of d-aa into polypeptides may greatly expand the armamentarium of in vitro translation towards the identification of peptides and proteins with new properties and functions.
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Affiliation(s)
- John Achenbach
- NOXXON Pharma AG, Max-Dohrn-Strasse 8-10, 10589 Berlin, Germany
| | - Michael Jahnz
- NOXXON Pharma AG, Max-Dohrn-Strasse 8-10, 10589 Berlin, Germany
| | - Lucas Bethge
- NOXXON Pharma AG, Max-Dohrn-Strasse 8-10, 10589 Berlin, Germany
| | - Krisztina Paal
- NOXXON Pharma AG, Max-Dohrn-Strasse 8-10, 10589 Berlin, Germany
| | - Maria Jung
- NOXXON Pharma AG, Max-Dohrn-Strasse 8-10, 10589 Berlin, Germany
| | - Maja Schuster
- NOXXON Pharma AG, Max-Dohrn-Strasse 8-10, 10589 Berlin, Germany
| | - Renate Albrecht
- Institut für Medizinische Physik und Biophysik, Charité - Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany
| | - Florian Jarosch
- NOXXON Pharma AG, Max-Dohrn-Strasse 8-10, 10589 Berlin, Germany
| | - Knud H Nierhaus
- Institut für Medizinische Physik und Biophysik, Charité - Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany
| | - Sven Klussmann
- NOXXON Pharma AG, Max-Dohrn-Strasse 8-10, 10589 Berlin, Germany
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43
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Carvalho ATP, Szeler K, Vavitsas K, Åqvist J, Kamerlin SCL. Modeling the mechanisms of biological GTP hydrolysis. Arch Biochem Biophys 2015; 582:80-90. [PMID: 25731854 DOI: 10.1016/j.abb.2015.02.027] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2015] [Revised: 02/19/2015] [Accepted: 02/21/2015] [Indexed: 01/11/2023]
Abstract
Enzymes that hydrolyze GTP are currently in the spotlight, due to their molecular switch mechanism that controls many cellular processes. One of the best-known classes of these enzymes are small GTPases such as members of the Ras superfamily, which catalyze the hydrolysis of the γ-phosphate bond in GTP. In addition, the availability of an increasing number of crystal structures of translational GTPases such as EF-Tu and EF-G have made it possible to probe the molecular details of GTP hydrolysis on the ribosome. However, despite a wealth of biochemical, structural and computational data, the way in which GTP hydrolysis is activated and regulated is still a controversial topic and well-designed simulations can play an important role in resolving and rationalizing the experimental data. In this review, we discuss the contributions of computational biology to our understanding of GTP hydrolysis on the ribosome and in small GTPases.
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Affiliation(s)
- Alexandra T P Carvalho
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, BMC Box 596, SE-751 24 Uppsala, Sweden
| | - Klaudia Szeler
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, BMC Box 596, SE-751 24 Uppsala, Sweden
| | - Konstantinos Vavitsas
- Copenhagen Plant Science Centre (CPSC), Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg C, Denmark
| | - Johan Åqvist
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, BMC Box 596, SE-751 24 Uppsala, Sweden
| | - Shina C L Kamerlin
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, BMC Box 596, SE-751 24 Uppsala, Sweden.
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44
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Åqvist J, Kamerlin SCL. The conformation of a catalytic loop is central to GTPase activity on the ribosome. Biochemistry 2014; 54:546-56. [PMID: 25515218 DOI: 10.1021/bi501373g] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The translational GTPases hydrolyze GTP on the ribosome at several stages of the protein synthesis cycle. Because of the strong conservation of their catalytic center, these enzymes are expected to operate through a universal hydrolysis mechanism, in which a critical histidine residue together with the sarcin-ricin loop of the large ribosomal subunit is necessary for GTPase activation. Here we examine different possible pathways for GTP hydrolysis by EF-Tu through extensive computer simulations. We show that a conformational change of the peptide plane preceding this histidine has a decisive effect on the energetics of the reaction. This transition was predicted earlier by us and has recently been confirmed experimentally. It is found to promote early proton transfer from water to the γ-phosphate group of GTP, followed by nucleophilic attack by hydroxide ion. The calculated reaction energetics is in good agreement with available kinetic data, for both wild-type and mutant versions of EF-Tu, and indicates that the latter may enforce a change in mechanism toward more concerted pathways.
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Affiliation(s)
- Johan Åqvist
- Department of Cell & Molecular Biology, Uppsala University, Biomedical Center , Box 596, SE-751 24 Uppsala, Sweden
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45
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Abstract
Ribosomal elongation factor 4 (EF4) is highly conserved among bacteria, mitochondria, and chloroplasts. However, the EF4-encoding gene, lepA, is nonessential and its deficiency shows no growth or fitness defect. In purified systems, EF4 back-translocates stalled, posttranslational ribosomes for efficient protein synthesis; consequently, EF4 has a protective role during moderate stress. We were surprised to find that EF4 also has a detrimental role during severe stress: deletion of lepA increased Escherichia coli survival following treatment with several antimicrobials. EF4 contributed to stress-mediated lethality through reactive oxygen species (ROS) because (i) the protective effect of a ΔlepA mutation against lethal antimicrobials was eliminated by anaerobic growth or by agents that block hydroxyl radical accumulation and (ii) the ΔlepA mutation decreased ROS levels stimulated by antimicrobial stress. Epistasis experiments showed that EF4 functions in the same genetic pathway as the MazF toxin, a stress response factor implicated in ROS-mediated cell death. The detrimental action of EF4 required transfer-messenger RNA (tmRNA, which tags truncated proteins for degradation and is known to be inhibited by EF4) and the ClpP protease. Inhibition of a protective, tmRNA/ClpP-mediated degradative activity would allow truncated proteins to indirectly perturb the respiratory chain and thereby provide a potential link between EF4 and ROS. The connection among EF4, MazF, tmRNA, and ROS expands a pathway leading from harsh stress to bacterial self-destruction. The destructive aspect of EF4 plus the protective properties described previously make EF4 a bifunctional factor in a stress response that promotes survival or death, depending on the severity of stress. Translation elongation factor 4 (EF4) is one of the most conserved proteins in nature, but it is dispensable. Lack of strong phenotypes for its genetic knockout has made EF4 an enigma. Recent biochemical work has demonstrated that mild stress may stall ribosomes and that EF4 can reposition stalled ribosomes to resume proper translation. Thus, EF4 protects cells from moderate stress. Here we report that EF4 is paradoxically harmful during severe stress, such as that caused by antimicrobial treatment. EF4 acts in a pathway that leads to excessive accumulation of reactive oxygen species (ROS), thereby participating in a bacterial self-destruction that occurs when cells cannot effectively repair stress-mediated damage. Thus, EF4 has two opposing functions—at low-to-moderate levels of stress, the protein is protective by allowing stress-paused translation to resume; at high-levels of stress, EF4 helps bacteria self-destruct. These data support the existence of a bacterial live-or-die response to stress.
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46
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Balakrishnan R, Oman K, Shoji S, Bundschuh R, Fredrick K. The conserved GTPase LepA contributes mainly to translation initiation in Escherichia coli. Nucleic Acids Res 2014; 42:13370-83. [PMID: 25378333 PMCID: PMC4245954 DOI: 10.1093/nar/gku1098] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
LepA is a paralog of EF-G found in all bacteria. Deletion of lepA confers no obvious growth defect in Escherichia coli, and the physiological role of LepA remains unknown. Here, we identify nine strains (ΔdksA, ΔmolR1, ΔrsgA, ΔtatB, ΔtonB, ΔtolR, ΔubiF, ΔubiG or ΔubiH) in which ΔlepA confers a synthetic growth phenotype. These strains are compromised for gene regulation, ribosome assembly, transport and/or respiration, indicating that LepA contributes to these functions in some way. We also use ribosome profiling to deduce the effects of LepA on translation. We find that loss of LepA alters the average ribosome density (ARD) for hundreds of mRNA coding regions in the cell, substantially reducing ARD in many cases. By contrast, only subtle and codon-specific changes in ribosome distribution along mRNA are seen. These data suggest that LepA contributes mainly to the initiation phase of translation. Consistent with this interpretation, the effect of LepA on ARD is related to the sequence of the Shine–Dalgarno region. Global perturbation of gene expression in the ΔlepA mutant likely explains most of its phenotypes.
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Affiliation(s)
- Rohan Balakrishnan
- Ohio State Biochemistry Program, The Ohio State University, Columbus, OH 43210, USA Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA
| | - Kenji Oman
- Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA Department of Physics, The Ohio State University, Columbus, OH 43210, USA
| | - Shinichiro Shoji
- Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA
| | - Ralf Bundschuh
- Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA Department of Physics, The Ohio State University, Columbus, OH 43210, USA
| | - Kurt Fredrick
- Ohio State Biochemistry Program, The Ohio State University, Columbus, OH 43210, USA Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA
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Polikanov YS, Osterman IA, Szal T, Tashlitsky VN, Serebryakova MV, Kusochek P, Bulkley D, Malanicheva IA, Efimenko TA, Efremenkova OV, Konevega AL, Shaw KJ, Bogdanov AA, Rodnina MV, Dontsova OA, Mankin AS, Steitz TA, Sergiev PV. Amicoumacin a inhibits translation by stabilizing mRNA interaction with the ribosome. Mol Cell 2014; 56:531-40. [PMID: 25306919 DOI: 10.1016/j.molcel.2014.09.020] [Citation(s) in RCA: 63] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2014] [Revised: 08/18/2014] [Accepted: 09/18/2014] [Indexed: 11/26/2022]
Abstract
We demonstrate that the antibiotic amicoumacin A (AMI) is a potent inhibitor of protein synthesis. Resistance mutations in helix 24 of the 16S rRNA mapped the AMI binding site to the small ribosomal subunit. The crystal structure of bacterial ribosome in complex with AMI solved at 2.4 Å resolution revealed that the antibiotic makes contacts with universally conserved nucleotides of 16S rRNA in the E site and the mRNA backbone. Simultaneous interactions of AMI with 16S rRNA and mRNA and the in vivo experimental evidence suggest that it may inhibit the progression of the ribosome along mRNA. Consistent with this proposal, binding of AMI interferes with translocation in vitro. The inhibitory action of AMI can be partly compensated by mutations in the translation elongation factor G.
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Affiliation(s)
- Yury S Polikanov
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA; Howard Hughes Medical Institute, Yale University, New Haven, CT 06520, USA
| | - Ilya A Osterman
- Lomonosov Moscow State University, Department of Chemistry and A.N. Belozersky Institute of Physico-Chemical Biology, 119992 Moscow, Russia
| | - Teresa Szal
- Center for Pharmaceutical Biotechnology, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Vadim N Tashlitsky
- Lomonosov Moscow State University, Department of Chemistry and A.N. Belozersky Institute of Physico-Chemical Biology, 119992 Moscow, Russia
| | - Marina V Serebryakova
- Lomonosov Moscow State University, Department of Chemistry and A.N. Belozersky Institute of Physico-Chemical Biology, 119992 Moscow, Russia
| | - Pavel Kusochek
- Lomonosov Moscow State University, Department of Chemistry and A.N. Belozersky Institute of Physico-Chemical Biology, 119992 Moscow, Russia
| | - David Bulkley
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
| | - Irina A Malanicheva
- G.F. Gause Institute of New Antibiotics, Russian Academy of Medical Sciences, 119867 Moscow, Russia
| | - Tatyana A Efimenko
- G.F. Gause Institute of New Antibiotics, Russian Academy of Medical Sciences, 119867 Moscow, Russia
| | - Olga V Efremenkova
- G.F. Gause Institute of New Antibiotics, Russian Academy of Medical Sciences, 119867 Moscow, Russia
| | - Andrey L Konevega
- B.P. Konstantinov Petersburg Nuclear Physics Institute, 188300 Gatchina, Russia; Saint Petersburg State Polytechnical University, Polytechnicheskaya 29, 195251 Saint Petersburg, Russia
| | - Karen J Shaw
- Hearts Consulting Group, San Diego, CA 92127, USA
| | - Alexey A Bogdanov
- Lomonosov Moscow State University, Department of Chemistry and A.N. Belozersky Institute of Physico-Chemical Biology, 119992 Moscow, Russia
| | - Marina V Rodnina
- Max Planck Institute for Biophysical Chemistry, 37077 Gottingen, Germany
| | - Olga A Dontsova
- Lomonosov Moscow State University, Department of Chemistry and A.N. Belozersky Institute of Physico-Chemical Biology, 119992 Moscow, Russia
| | - Alexander S Mankin
- Center for Pharmaceutical Biotechnology, University of Illinois at Chicago, Chicago, IL 60607, USA.
| | - Thomas A Steitz
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA; Howard Hughes Medical Institute, Yale University, New Haven, CT 06520, USA.
| | - Petr V Sergiev
- Lomonosov Moscow State University, Department of Chemistry and A.N. Belozersky Institute of Physico-Chemical Biology, 119992 Moscow, Russia.
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48
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Starosta AL, Lassak J, Jung K, Wilson DN. The bacterial translation stress response. FEMS Microbiol Rev 2014; 38:1172-201. [PMID: 25135187 DOI: 10.1111/1574-6976.12083] [Citation(s) in RCA: 134] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2014] [Revised: 07/18/2014] [Accepted: 08/07/2014] [Indexed: 11/30/2022] Open
Abstract
Throughout their life, bacteria need to sense and respond to environmental stress. Thus, such stress responses can require dramatic cellular reprogramming, both at the transcriptional as well as the translational level. This review focuses on the protein factors that interact with the bacterial translational apparatus to respond to and cope with different types of environmental stress. For example, the stringent factor RelA interacts with the ribosome to generate ppGpp under nutrient deprivation, whereas a variety of factors have been identified that bind to the ribosome under unfavorable growth conditions to shut-down (RelE, pY, RMF, HPF and EttA) or re-program (MazF, EF4 and BipA) translation. Additional factors have been identified that rescue ribosomes stalled due to stress-induced mRNA truncation (tmRNA, ArfA, ArfB), translation of unfavorable protein sequences (EF-P), heat shock-induced subunit dissociation (Hsp15), or antibiotic inhibition (TetM, FusB). Understanding the mechanism of how the bacterial cell responds to stress will not only provide fundamental insight into translation regulation, but will also be an important step to identifying new targets for the development of novel antimicrobial agents.
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Affiliation(s)
- Agata L Starosta
- Gene Center, Department for Biochemistry, Ludwig-Maximilians-Universität München, Munich, Germany; Center for integrated Protein Science Munich (CiPSM), Ludwig-Maximilians-Universität München, Munich, Germany
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49
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EF-G catalyzes tRNA translocation by disrupting interactions between decoding center and codon-anticodon duplex. Nat Struct Mol Biol 2014; 21:817-24. [PMID: 25108354 DOI: 10.1038/nsmb.2869] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2013] [Accepted: 07/11/2014] [Indexed: 02/01/2023]
Abstract
During translation, elongation factor G (EF-G) catalyzes the translocation of tRNA2-mRNA inside the ribosome. Translocation is coupled to a cycle of conformational rearrangements of the ribosomal machinery, and how EF-G initiates translocation remains unresolved. Here we performed systematic mutagenesis of Escherichia coli EF-G and analyzed inhibitory single-site mutants of EF-G that preserved pretranslocation (Pre)-state ribosomes with tRNAs in A/P and P/E sites (Pre-EF-G). Our results suggest that the interactions between the decoding center and the codon-anticodon duplex constitute the barrier for translocation. Catalysis of translocation by EF-G involves the factor's highly conserved loops I and II at the tip of domain IV, which disrupt the hydrogen bonds between the decoding center and the duplex to release the latter, hence inducing subsequent translocation events, namely 30S head swiveling and tRNA2-mRNA movement on the 30S subunit.
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50
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Gagnon MG, Lin J, Bulkley D, Steitz TA. Crystal structure of elongation factor 4 bound to a clockwise ratcheted ribosome. Science 2014; 345:684-7. [PMID: 25104389 PMCID: PMC9153294 DOI: 10.1126/science.1253525] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Elongation factor 4 (EF4/LepA) is a highly conserved guanosine triphosphatase translation factor. It was shown to promote back-translocation of tRNAs on posttranslocational ribosome complexes and to compete with elongation factor G for interaction with pretranslocational ribosomes, inhibiting the elongation phase of protein synthesis. Here, we report a crystal structure of EF4-guanosine diphosphate bound to the Thermus thermophilus ribosome with a P-site tRNA at 2.9 angstroms resolution. The C-terminal domain of EF4 reaches into the peptidyl transferase center and interacts with the acceptor stem of the peptidyl-tRNA in the P site. The ribosome is in an unusual state of ratcheting with the 30S subunit rotated clockwise relative to the 50S subunit, resulting in a remodeled decoding center. The structure is consistent with EF4 functioning either as a back-translocase or a ribosome sequester.
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Affiliation(s)
- Matthieu G Gagnon
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520-8114, USA. Howard Hughes Medical Institute, Yale University, New Haven, CT 06520-8114, USA
| | - Jinzhong Lin
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520-8114, USA
| | - David Bulkley
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520-8114, USA. Department of Chemistry, Yale University, New Haven, CT 06520-8107, USA
| | - Thomas A Steitz
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520-8114, USA. Howard Hughes Medical Institute, Yale University, New Haven, CT 06520-8114, USA. Department of Chemistry, Yale University, New Haven, CT 06520-8107, USA.
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