1
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Cimicata G, Fridkin G, Bose T, Eyal Z, Halfon Y, Breiner-Goldstein E, Fox T, Zimmerman E, Bashan A, de Val N, Wlodawer A, Yonath A. Structural Studies Reveal the Role of Helix 68 in the Elongation Step of Protein Biosynthesis. mBio 2022; 13:e0030622. [PMID: 35348349 PMCID: PMC9040758 DOI: 10.1128/mbio.00306-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Accepted: 02/14/2022] [Indexed: 02/04/2023] Open
Abstract
The ribosome, a multicomponent assembly consisting of RNA and proteins, is a pivotal macromolecular machine that translates the genetic code into proteins. The large ribosomal subunit rRNA helix 68 (H68) is a key element in the protein synthesis process, as it coordinates the coupled movements of the actors involved in translocation, including the tRNAs and L1 stalk. Examination of cryo-electron microscopy (cryo-EM) structures of ribosomes incubated for various time durations at physiological temperatures led to the identification of functionally relevant H68 movements. These movements assist the transition of the L1 stalk between its open and closed states. H68 spatial flexibility and its significance to the protein synthesis process were confirmed through its effective targeting with antisense PNA oligomers. Our results suggest that H68 is actively involved in ribosome movements that are central to the elongation process. IMPORTANCE The mechanism that regulates the translocation step in ribosomes during protein synthesis is not fully understood. In this work, cryo-EM techniques used to image ribosomes from Staphylococcus aureus after incubation at physiological temperature allowed the identification of a conformation of the helix 68 that has never been observed so far. We then propose a mechanism in which such helix, switching between two different conformations, actively coordinates the translocation step, shedding light on the dynamics of ribosomal components. In addition, the relevance of helix 68 to ribosome function and its potential as an antibiotic target was proved by inhibiting Staphylococcus aureus ribosomes activity in vitro using oligomers with sequence complementarity.
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Affiliation(s)
- Giuseppe Cimicata
- Department of Chemical and Structural Biology, The Weizmann Institute of Science, Rehovot, Israel
| | - Gil Fridkin
- Department of Chemical and Structural Biology, The Weizmann Institute of Science, Rehovot, Israel
- Department of Organic Chemistry, Israel Institute for Biological Research, Ness Ziona, Israel
| | - Tanaya Bose
- Department of Chemical and Structural Biology, The Weizmann Institute of Science, Rehovot, Israel
| | - Zohar Eyal
- Department of Chemical and Structural Biology, The Weizmann Institute of Science, Rehovot, Israel
| | - Yehuda Halfon
- Department of Chemical and Structural Biology, The Weizmann Institute of Science, Rehovot, Israel
| | - Elinor Breiner-Goldstein
- Department of Chemical and Structural Biology, The Weizmann Institute of Science, Rehovot, Israel
| | - Tara Fox
- Center for Molecular Microscopy, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, Maryland, USA
| | - Ella Zimmerman
- Department of Chemical and Structural Biology, The Weizmann Institute of Science, Rehovot, Israel
| | - Anat Bashan
- Department of Chemical and Structural Biology, The Weizmann Institute of Science, Rehovot, Israel
| | - Natalia de Val
- Center for Molecular Microscopy, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, Maryland, USA
| | - Alexander Wlodawer
- Center for Structural Biology, Center for Cancer Research, National Cancer Institute, Frederick, Maryland, USA
| | - Ada Yonath
- Department of Chemical and Structural Biology, The Weizmann Institute of Science, Rehovot, Israel
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2
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Riegger RJ, Caliskan N. Thinking Outside the Frame: Impacting Genomes Capacity by Programmed Ribosomal Frameshifting. Front Mol Biosci 2022; 9:842261. [PMID: 35281266 PMCID: PMC8915115 DOI: 10.3389/fmolb.2022.842261] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Accepted: 01/26/2022] [Indexed: 01/08/2023] Open
Abstract
Translation facilitates the transfer of the genetic information stored in the genome via messenger RNAs to a functional protein and is therefore one of the most fundamental cellular processes. Programmed ribosomal frameshifting is a ubiquitous alternative translation event that is extensively used by viruses to regulate gene expression from overlapping open reading frames in a controlled manner. Recent technical advances in the translation field enabled the identification of precise mechanisms as to how and when ribosomes change the reading frame on mRNAs containing cis-acting signals. Several studies began also to illustrate that trans-acting RNA modulators can adjust the timing and efficiency of frameshifting illuminating that frameshifting can be a dynamically regulated process in cells. Here, we intend to summarize these new findings and emphasize how it fits in our current understanding of PRF mechanisms as previously described.
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Affiliation(s)
- Ricarda J. Riegger
- Helmholtz Centre for Infection Research (HZI), Helmholtz Institute for RNA-Based Infection Research (HIRI), Würzburg, Germany
- Graduate School of Life Sciences (GSLS), University of Würzburg, Würzburg, Germany
| | - Neva Caliskan
- Helmholtz Centre for Infection Research (HZI), Helmholtz Institute for RNA-Based Infection Research (HIRI), Würzburg, Germany
- Medical Faculty, University of Würzburg, Würzburg, Germany
- *Correspondence: Neva Caliskan,
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3
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Xu B, Liu L, Song G. Functions and Regulation of Translation Elongation Factors. Front Mol Biosci 2022; 8:816398. [PMID: 35127825 PMCID: PMC8807479 DOI: 10.3389/fmolb.2021.816398] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Accepted: 12/20/2021] [Indexed: 12/18/2022] Open
Abstract
Translation elongation is a key step of protein synthesis, during which the nascent polypeptide chain extends by one amino acid residue during one elongation cycle. More and more data revealed that the elongation is a key regulatory node for translational control in health and disease. During elongation, elongation factor Tu (EF-Tu, eEF1A in eukaryotes) is used to deliver aminoacyl-tRNA (aa-tRNA) to the A-site of the ribosome, and elongation factor G (EF-G, EF2 in eukaryotes and archaea) is used to facilitate the translocation of the tRNA2-mRNA complex on the ribosome. Other elongation factors, such as EF-Ts/eEF1B, EF-P/eIF5A, EF4, eEF3, SelB/EFsec, TetO/Tet(M), RelA and BipA, have been found to affect the overall rate of elongation. Here, we made a systematic review on the canonical and non-canonical functions and regulation of these elongation factors. In particular, we discussed the close link between translational factors and human diseases, and clarified how post-translational modifications control the activity of translational factors in tumors.
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Affiliation(s)
- Benjin Xu
- Department of Medical Laboratory Science, Fenyang College, Shanxi Medical University, Fenyang, China
- *Correspondence: Benjin Xu, ; Guangtao Song,
| | - Ling Liu
- Department of Medical Laboratory Science, Fenyang College, Shanxi Medical University, Fenyang, China
| | - Guangtao Song
- Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- *Correspondence: Benjin Xu, ; Guangtao Song,
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4
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Dila G, Ripp R, Mayer C, Poch O, Michel CJ, Thompson JD. Circular code motifs in the ribosome: a missing link in the evolution of translation? RNA (NEW YORK, N.Y.) 2019; 25:1714-1730. [PMID: 31506380 PMCID: PMC6859856 DOI: 10.1261/rna.072074.119] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2019] [Accepted: 09/06/2019] [Indexed: 05/29/2023]
Abstract
The origin of the genetic code remains enigmatic five decades after it was elucidated, although there is growing evidence that the code coevolved progressively with the ribosome. A number of primordial codes were proposed as ancestors of the modern genetic code, including comma-free codes such as the RRY, RNY, or GNC codes (R = G or A, Y = C or T, N = any nucleotide), and the X circular code, an error-correcting code that also allows identification and maintenance of the reading frame. It was demonstrated previously that motifs of the X circular code are significantly enriched in the protein-coding genes of most organisms, from bacteria to eukaryotes. Here, we show that imprints of this code also exist in the ribosomal RNA (rRNA). In a large-scale study involving 133 organisms representative of the three domains of life, we identified 32 universal X motifs that are conserved in the rRNA of >90% of the organisms. Intriguingly, most of the universal X motifs are located in rRNA regions involved in important ribosome functions, notably in the peptidyl transferase center and the decoding center that form the original "proto-ribosome." Building on the existing accretion models for ribosome evolution, we propose that error-correcting circular codes represented an important step in the emergence of the modern genetic code. Thus, circular codes would have allowed the simultaneous coding of amino acids and synchronization of the reading frame in primitive translation systems, prior to the emergence of more sophisticated start codon recognition and translation initiation mechanisms.
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Affiliation(s)
- Gopal Dila
- Department of Computer Science, ICube, CNRS, University of Strasbourg, Strasbourg 67000, France
| | - Raymond Ripp
- Department of Computer Science, ICube, CNRS, University of Strasbourg, Strasbourg 67000, France
| | - Claudine Mayer
- Department of Computer Science, ICube, CNRS, University of Strasbourg, Strasbourg 67000, France
- Unité de Microbiologie Structurale, Institut Pasteur, CNRS, 75724 Paris Cedex 15, France
- Université Paris Diderot, Sorbonne Paris Cité, 75724 Paris Cedex 15, France
| | - Olivier Poch
- Department of Computer Science, ICube, CNRS, University of Strasbourg, Strasbourg 67000, France
| | - Christian J Michel
- Department of Computer Science, ICube, CNRS, University of Strasbourg, Strasbourg 67000, France
| | - Julie D Thompson
- Department of Computer Science, ICube, CNRS, University of Strasbourg, Strasbourg 67000, France
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5
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Yin H, Gavriliuc M, Lin R, Xu S, Wang Y. Modulation and Visualization of EF-G Power Stroke During Ribosomal Translocation. Chembiochem 2019; 20:2927-2935. [PMID: 31194278 PMCID: PMC6888950 DOI: 10.1002/cbic.201900276] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Indexed: 11/30/2022]
Abstract
During ribosome translocation, the elongation factor EF‐G undergoes large conformational change while maintaining its contact with the moving tRNA. We previously measured a power stroke accompanying EF‐G catalysis, which was consistent with structural studies. However, the role of power stroke in translocation fidelity remains unclear. Here, we report quantitative measurements of the power strokes of structurally modified EF‐Gs by using two different techniques and reveal the correlation between power stroke and translocation efficiency and fidelity. We discovered that the reduced power stroke only lowered the percentage of translocation but did not introduce translocation error. The established force ‐structure–function correlation for EF‐G indicates that power stroke drives ribosomal translocation, but the mRNA reading frame is probably maintained by ribosome itself. Furthermore, the microscope detection method reported here can be simply implemented for other biochemical applications.
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Affiliation(s)
- Heng Yin
- Department of Chemistry, University of Houston, Houston, TX, 77204, USA
| | - Miriam Gavriliuc
- Department of Biology and Biochemistry, University of Houston, Houston, TX, 77204, USA
| | - Ran Lin
- Department of Biology and Biochemistry, University of Houston, Houston, TX, 77204, USA
| | - Shoujun Xu
- Department of Chemistry, University of Houston, Houston, TX, 77204, USA
| | - Yuhong Wang
- Department of Biology and Biochemistry, University of Houston, Houston, TX, 77204, USA
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6
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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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7
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Dao EH, Poitevin F, Sierra RG, Gati C, Rao Y, Ciftci HI, Akşit F, McGurk A, Obrinski T, Mgbam P, Hayes B, De Lichtenberg C, Pardo-Avila F, Corsepius N, Zhang L, Seaberg MH, Hunter MS, Liang M, Koglin JE, Wakatsuki S, Demirci H. Structure of the 30S ribosomal decoding complex at ambient temperature. RNA (NEW YORK, N.Y.) 2018; 24:1667-1676. [PMID: 30139800 PMCID: PMC6239188 DOI: 10.1261/rna.067660.118] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Accepted: 08/14/2018] [Indexed: 05/29/2023]
Abstract
The ribosome translates nucleotide sequences of messenger RNA to proteins through selection of cognate transfer RNA according to the genetic code. To date, structural studies of ribosomal decoding complexes yielding high-resolution data have predominantly relied on experiments performed at cryogenic temperatures. New light sources like the X-ray free electron laser (XFEL) have enabled data collection from macromolecular crystals at ambient temperature. Here, we report an X-ray crystal structure of the Thermus thermophilus 30S ribosomal subunit decoding complex to 3.45 Å resolution using data obtained at ambient temperature at the Linac Coherent Light Source (LCLS). We find that this ambient-temperature structure is largely consistent with existing cryogenic-temperature crystal structures, with key residues of the decoding complex exhibiting similar conformations, including adenosine residues 1492 and 1493. Minor variations were observed, namely an alternate conformation of cytosine 1397 near the mRNA channel and the A-site. Our serial crystallography experiment illustrates the amenability of ribosomal microcrystals to routine structural studies at ambient temperature, thus overcoming a long-standing experimental limitation to structural studies of RNA and RNA-protein complexes at near-physiological temperatures.
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Affiliation(s)
- E Han Dao
- Stanford PULSE Institute, SLAC National Laboratory, Menlo Park, California 94025, USA
| | - Frédéric Poitevin
- Stanford PULSE Institute, SLAC National Laboratory, Menlo Park, California 94025, USA
- Department of Structural Biology, Stanford University, Palo Alto, California 94305, USA
| | - Raymond G Sierra
- Stanford PULSE Institute, SLAC National Laboratory, Menlo Park, California 94025, USA
- Linac Coherent Light Source, SLAC National Laboratory, Menlo Park, California 94025, USA
| | - Cornelius Gati
- Department of Structural Biology, Stanford University, Palo Alto, California 94305, USA
- Biosciences Division, SLAC National Laboratory, Menlo Park, California 94025, USA
| | - Yashas Rao
- Stanford PULSE Institute, SLAC National Laboratory, Menlo Park, California 94025, USA
- Linac Coherent Light Source, SLAC National Laboratory, Menlo Park, California 94025, USA
| | - Halil Ibrahim Ciftci
- Stanford PULSE Institute, SLAC National Laboratory, Menlo Park, California 94025, USA
| | - Fulya Akşit
- Stanford PULSE Institute, SLAC National Laboratory, Menlo Park, California 94025, USA
| | - Alex McGurk
- Linac Coherent Light Source, SLAC National Laboratory, Menlo Park, California 94025, USA
| | - Trevor Obrinski
- Linac Coherent Light Source, SLAC National Laboratory, Menlo Park, California 94025, USA
| | - Paul Mgbam
- Linac Coherent Light Source, SLAC National Laboratory, Menlo Park, California 94025, USA
| | - Brandon Hayes
- Linac Coherent Light Source, SLAC National Laboratory, Menlo Park, California 94025, USA
| | - Casper De Lichtenberg
- Institutionen för Kemi, Kemiskt Biologiskt Centrum, Umeå Universitet, SE-901 87 Umeå, Sweden
| | - Fatima Pardo-Avila
- Department of Structural Biology, Stanford University, Palo Alto, California 94305, USA
| | - Nicholas Corsepius
- Department of Structural Biology, Stanford University, Palo Alto, California 94305, USA
| | - Lindsey Zhang
- Linac Coherent Light Source, SLAC National Laboratory, Menlo Park, California 94025, USA
| | - Matthew H Seaberg
- Linac Coherent Light Source, SLAC National Laboratory, Menlo Park, California 94025, USA
| | - Mark S Hunter
- Linac Coherent Light Source, SLAC National Laboratory, Menlo Park, California 94025, USA
| | - Mengling Liang
- Linac Coherent Light Source, SLAC National Laboratory, Menlo Park, California 94025, USA
| | - Jason E Koglin
- Linac Coherent Light Source, SLAC National Laboratory, Menlo Park, California 94025, USA
| | - Soichi Wakatsuki
- Department of Structural Biology, Stanford University, Palo Alto, California 94305, USA
- Biosciences Division, SLAC National Laboratory, Menlo Park, California 94025, USA
| | - Hasan Demirci
- Stanford PULSE Institute, SLAC National Laboratory, Menlo Park, California 94025, USA
- Department of Structural Biology, Stanford University, Palo Alto, California 94305, USA
- Biosciences Division, SLAC National Laboratory, Menlo Park, California 94025, USA
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8
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Pellegrino S, Demeshkina N, Mancera-Martinez E, Melnikov S, Simonetti A, Myasnikov A, Yusupov M, Yusupova G, Hashem Y. Structural Insights into the Role of Diphthamide on Elongation Factor 2 in mRNA Reading-Frame Maintenance. J Mol Biol 2018; 430:2677-2687. [PMID: 29886014 DOI: 10.1016/j.jmb.2018.06.006] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Revised: 05/11/2018] [Accepted: 06/04/2018] [Indexed: 01/27/2023]
Abstract
One of the most critical steps of protein biosynthesis is the coupled movement of mRNA, which encodes genetic information, with tRNAs on the ribosome. In eukaryotes, this process is catalyzed by a conserved G-protein, the elongation factor 2 (eEF2), which carries a unique post-translational modification, called diphthamide, found in all eukaryotic species. Here we present near-atomic resolution cryo-electron microscopy structures of yeast 80S ribosome complexes containing mRNA, tRNA and eEF2 trapped in different GTP-hydrolysis states which provide further structural insights into the role of diphthamide in the mechanism of translation fidelity in eukaryotes.
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Affiliation(s)
- Simone Pellegrino
- Department of Integrated Structural Biology, Institute of Genetics and Molecular and Cellular Biology, CNRS UMR710, INSERM U964, University of Strasbourg, Strasbourg 67000, France
| | - Natalia Demeshkina
- Department of Integrated Structural Biology, Institute of Genetics and Molecular and Cellular Biology, CNRS UMR710, INSERM U964, University of Strasbourg, Strasbourg 67000, France
| | - Eder Mancera-Martinez
- Architecture and Reactivity of RNA, University of Strasbourg, Institute of Molecular and Cellular Biology of the CNRS UPR9002, Strasbourg 67084, France
| | - Sergey Melnikov
- Department of Integrated Structural Biology, Institute of Genetics and Molecular and Cellular Biology, CNRS UMR710, INSERM U964, University of Strasbourg, Strasbourg 67000, France
| | - Angelita Simonetti
- Architecture and Reactivity of RNA, University of Strasbourg, Institute of Molecular and Cellular Biology of the CNRS UPR9002, Strasbourg 67084, France
| | - Alexander Myasnikov
- Department of Integrated Structural Biology, Institute of Genetics and Molecular and Cellular Biology, CNRS UMR710, INSERM U964, University of Strasbourg, Strasbourg 67000, France
| | - Marat Yusupov
- Department of Integrated Structural Biology, Institute of Genetics and Molecular and Cellular Biology, CNRS UMR710, INSERM U964, University of Strasbourg, Strasbourg 67000, France; Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan 420008, Russia.
| | - Gulnara Yusupova
- Department of Integrated Structural Biology, Institute of Genetics and Molecular and Cellular Biology, CNRS UMR710, INSERM U964, University of Strasbourg, Strasbourg 67000, France.
| | - Yaser Hashem
- ARNA, U1212 Université de Bordeaux, Institut Européen de Chimie et de Biologie (IECB) Inserm, Pessac 33600, France.
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9
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Hentschel J, Burnside C, Mignot I, Leibundgut M, Boehringer D, Ban N. The Complete Structure of the Mycobacterium smegmatis 70S Ribosome. Cell Rep 2018; 20:149-160. [PMID: 28683309 DOI: 10.1016/j.celrep.2017.06.029] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2017] [Revised: 06/03/2017] [Accepted: 06/10/2017] [Indexed: 11/24/2022] Open
Abstract
The ribosome carries out the synthesis of proteins in every living cell. It consequently represents a frontline target in anti-microbial therapy. Tuberculosis ranks among the leading causes of death worldwide, due in large part to the combination of difficult-to-treat latency and antibiotic resistance. Here, we present the 3.3-Å cryo-EM structure of the 70S ribosome of Mycobacterium smegmatis, a close relative to the human pathogen Mycobacterium tuberculosis. The structure reveals two additional ribosomal proteins and localizes them to the vicinity of drug-target sites in both the catalytic center and the decoding site of the ribosome. Furthermore, we visualized actinobacterium-specific rRNA and protein expansions that extensively remodel the ribosomal surface with implications for polysome organization. Our results provide a foundation for understanding the idiosyncrasies of mycobacterial translation and reveal atomic details of the structure that will facilitate the design of anti-tubercular therapeutics.
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Affiliation(s)
- Jendrik Hentschel
- Institute of Molecular Biology and Biophysics, Eidgenössische Technische Hochschule (ETH) Zürich, Otto-Stern-Weg 5, Zürich 8093, Switzerland
| | - Chloe Burnside
- Institute of Molecular Biology and Biophysics, Eidgenössische Technische Hochschule (ETH) Zürich, Otto-Stern-Weg 5, Zürich 8093, Switzerland
| | - Ingrid Mignot
- Institute of Molecular Biology and Biophysics, Eidgenössische Technische Hochschule (ETH) Zürich, Otto-Stern-Weg 5, Zürich 8093, Switzerland
| | - Marc Leibundgut
- Institute of Molecular Biology and Biophysics, Eidgenössische Technische Hochschule (ETH) Zürich, Otto-Stern-Weg 5, Zürich 8093, Switzerland
| | - Daniel Boehringer
- Institute of Molecular Biology and Biophysics, Eidgenössische Technische Hochschule (ETH) Zürich, Otto-Stern-Weg 5, Zürich 8093, Switzerland
| | - Nenad Ban
- Institute of Molecular Biology and Biophysics, Eidgenössische Technische Hochschule (ETH) Zürich, Otto-Stern-Weg 5, Zürich 8093, Switzerland.
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10
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Ribosome structural dynamics in translocation: yet another functional role for ribosomal RNA. Q Rev Biophys 2017; 50:e12. [DOI: 10.1017/s0033583517000117] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
AbstractRibosomes are remarkable ribonucleoprotein complexes that are responsible for protein synthesis in all forms of life. They polymerize polypeptide chains programmed by nucleotide sequences in messenger RNA in a mechanism mediated by transfer RNA. One of the most challenging problems in the ribosome field is to understand the mechanism of coupled translocation of mRNA and tRNA during the elongation phase of protein synthesis. In recent years, the results of structural, biophysical and biochemical studies have provided extensive evidence that translocation is based on the structural dynamics of the ribosome itself. Detailed structural analysis has shown that ribosome dynamics, like aminoacyl-tRNA selection and catalysis of peptide bond formation, is made possible by the properties of ribosomal RNA.
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11
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Recurring RNA structural motifs underlie the mechanics of L1 stalk movement. Nat Commun 2017; 8:14285. [PMID: 28176782 PMCID: PMC5309774 DOI: 10.1038/ncomms14285] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2016] [Accepted: 12/15/2016] [Indexed: 01/19/2023] Open
Abstract
The L1 stalk of the large ribosomal subunit undergoes large-scale movements coupled to the translocation of deacylated tRNA during protein synthesis. We use quantitative comparative structural analysis to localize the origins of L1 stalk movement and to understand its dynamic interactions with tRNA and other structural elements of the ribosome. Besides its stacking interactions with the tRNA elbow, stalk movement is directly linked to intersubunit rotation, rotation of the 30S head domain and contact of the acceptor arm of deacylated tRNA with helix 68 of 23S rRNA. Movement originates from pivoting at stacked non-canonical base pairs in a Family A three-way junction and bending in an internal G-U-rich zone. Use of these same motifs as hinge points to enable such dynamic events as rotation of the 30S subunit head domain and in flexing of the anticodon arm of tRNA suggests that they represent general strategies for movement of functional RNAs. Translocation of the tRNA on the ribosome is associated with large-scale molecular movements of the ribosomal L1 stalk. Here the authors identify the key determinants that allow these dramatic movements, and suggest they represent general strategies used to enable large-scale motions in functional RNAs.
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12
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Jiang N, Hu L, Liu C, Gao X, Zheng S. 60S ribosomal protein L35 regulates β-casein translational elongation and secretion in bovine mammary epithelial cells. Arch Biochem Biophys 2015; 583:130-9. [PMID: 26297660 DOI: 10.1016/j.abb.2015.08.006] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2015] [Revised: 08/13/2015] [Accepted: 08/16/2015] [Indexed: 11/18/2022]
Abstract
60S ribosomal protein L35 (RPL35) is an important component of the 60S ribosomal subunit and has a role in protein translation and endoplasmic reticulum (ER) docking. However, few studies have investigated RPL35 in eukaryotes and much remains to be learned. Here, we analyzed the function of RPL35 in β-casein (CSN2) synthesis and secretion in bovine mammary epithelial cells (BMECs). We found that methionine (Met) could promote the expressions of CSN2 and RPL35. Analysis of overexpression and inhibition of RPL35 confirmed that it could mediate the Met signal and regulate CSN2 expression. The mechanism of CSN2 regulation by RPL35 was analyzed by coimmunoprecipitation (Co-IP), colocalization, fluorescence resonance energy transfer (FRET) and gene mutation. We found that RPL35 could control ribosome translational elongation during synthesis of CSN2 by interacting with eukaryotic translational elongation factor 2 (eEF2), and that eEF2 was the signaling molecule downstream of RPL35 controlling this process. RPL35 could also control the secretion of CSN2 by locating it to the ER. Taken together, these results revealed that, RPL35 was an important positive regulatory factor involving in the Met-mediated regulation of CSN2 translational elongation and secretion.
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Affiliation(s)
- Nan Jiang
- College of Life Science and Technology, Dalian University, Dalian Economic Technological Development Zone, Liaoning, 116622, China; The Laboratory of Pathophysiology in College of Veterinary Medicine, Northeast Agricultura University, Xiangfang District, Harbin, 150030, China.
| | - Lijun Hu
- The Laboratory of Pathophysiology in College of Veterinary Medicine, Northeast Agricultura University, Xiangfang District, Harbin, 150030, China.
| | - Chaonan Liu
- The Laboratory of Pathophysiology in College of Veterinary Medicine, Northeast Agricultura University, Xiangfang District, Harbin, 150030, China.
| | - Xueli Gao
- The Laboratory of Pathophysiology in College of Veterinary Medicine, Northeast Agricultura University, Xiangfang District, Harbin, 150030, China.
| | - Shimin Zheng
- The Laboratory of Pathophysiology in College of Veterinary Medicine, Northeast Agricultura University, Xiangfang District, Harbin, 150030, China.
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Caetano-Anollés G, Caetano-Anollés D. Computing the origin and evolution of the ribosome from its structure - Uncovering processes of macromolecular accretion benefiting synthetic biology. Comput Struct Biotechnol J 2015; 13:427-47. [PMID: 27096056 PMCID: PMC4823900 DOI: 10.1016/j.csbj.2015.07.003] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2015] [Revised: 07/16/2015] [Accepted: 07/19/2015] [Indexed: 12/11/2022] Open
Abstract
Accretion occurs pervasively in nature at widely different timeframes. The process also manifests in the evolution of macromolecules. Here we review recent computational and structural biology studies of evolutionary accretion that make use of the ideographic (historical, retrodictive) and nomothetic (universal, predictive) scientific frameworks. Computational studies uncover explicit timelines of accretion of structural parts in molecular repertoires and molecules. Phylogenetic trees of protein structural domains and proteomes and their molecular functions were built from a genomic census of millions of encoded proteins and associated terminal Gene Ontology terms. Trees reveal a ‘metabolic-first’ origin of proteins, the late development of translation, and a patchwork distribution of proteins in biological networks mediated by molecular recruitment. Similarly, the natural history of ancient RNA molecules inferred from trees of molecular substructures built from a census of molecular features shows patchwork-like accretion patterns. Ideographic analyses of ribosomal history uncover the early appearance of structures supporting mRNA decoding and tRNA translocation, the coevolution of ribosomal proteins and RNA, and a first evolutionary transition that brings ribosomal subunits together into a processive protein biosynthetic complex. Nomothetic structural biology studies of tertiary interactions and ancient insertions in rRNA complement these findings, once concentric layering assumptions are removed. Patterns of coaxial helical stacking reveal a frustrated dynamics of outward and inward ribosomal growth possibly mediated by structural grafting. The early rise of the ribosomal ‘turnstile’ suggests an evolutionary transition in natural biological computation. Results make explicit the need to understand processes of molecular growth and information transfer of macromolecules.
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Affiliation(s)
- Gustavo Caetano-Anollés
- Evolutionary Bioinformatics Laboratory, Department of Crop Sciences, University of Illinois at Urbana-Champaign, 1101W. Peabody Drive, Urbana, IL 61801, USA; C.R. Woese Institute for Genomic Biology, University of Illinois, Urbana, IL 61801, USA
| | - Derek Caetano-Anollés
- C.R. Woese Institute for Genomic Biology, University of Illinois, Urbana, IL 61801, USA
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Caetano-Anollés D, Caetano-Anollés G. Ribosomal accretion, apriorism and the phylogenetic method: a response to Petrov and Williams. Front Genet 2015; 6:194. [PMID: 26082795 PMCID: PMC4451634 DOI: 10.3389/fgene.2015.00194] [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] [Received: 04/29/2015] [Accepted: 05/14/2015] [Indexed: 12/21/2022] Open
Abstract
Historical (ideographic) and non-historical (nomothetic) studies of ribosomal accretion appear to arrive at diametrically opposite conclusions. Phylogenetic analysis of thousands of RNA molecules and protein structures in hundreds of genomes supports the structural origin of the ribosome in RNA decoding and ribosomal mechanics. Predictions from extant features in a handful of rRNA structural models of the large ribosomal subunit support its origin in protein biosynthesis. In recent correspondence, one of us reported that correcting dismissals of conflicting data and avoiding unwarranted assumptions of the nomothetic method reconciled conclusions. In response, Petrov and Williams dismissed our arguments claiming we did not understand their algorithmic model of ribosomal apical growth. Instead, they controverted the historical approach. Here we show that their objections to the phylogenetic method are unjustified, that their algorithm subjectively guarantees back-in-time molecular deconstructions toward the protein biosynthetic core, and that processes of ribosomal growth are much more complex. We prompt abandoning apriorism, decreasing ad hoc hypotheses and integrating historical and non-historical scientific methods.
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Affiliation(s)
- Derek Caetano-Anollés
- Carl R. Woese Institute for Genomic Biology, University of Illinois, Urbana, IL, USA
| | - Gustavo Caetano-Anollés
- Carl R. Woese Institute for Genomic Biology, University of Illinois, Urbana, IL, USA
- Evolutionary Bioinformatics Laboratory, Department of Crop Sciences, University of Illinois, Urbana, IL, USA
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Role of a ribosomal RNA phosphate oxygen during the EF-G-triggered GTP hydrolysis. Proc Natl Acad Sci U S A 2015; 112:E2561-8. [PMID: 25941362 DOI: 10.1073/pnas.1505231112] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Elongation factor-catalyzed GTP hydrolysis is a key reaction during the ribosomal elongation cycle. Recent crystal structures of G proteins, such as elongation factor G (EF-G) bound to the ribosome, as well as many biochemical studies, provide evidence that the direct interaction of translational GTPases (trGTPases) with the sarcin-ricin loop (SRL) of ribosomal RNA (rRNA) is pivotal for hydrolysis. However, the precise mechanism remains elusive and is intensively debated. Based on the close proximity of the phosphate oxygen of A2662 of the SRL to the supposedly catalytic histidine of EF-G (His87), we probed this interaction by an atomic mutagenesis approach. We individually replaced either of the two nonbridging phosphate oxygens at A2662 with a methyl group by the introduction of a methylphosphonate instead of the natural phosphate in fully functional, reconstituted bacterial ribosomes. Our major finding was that only one of the two resulting diastereomers, the SP methylphosphonate, was compatible with efficient GTPase activation on EF-G. The same trend was observed for a second trGTPase, namely EF4 (LepA). In addition, we provide evidence that the negative charge of the A2662 phosphate group must be retained for uncompromised activity in GTP hydrolysis. In summary, our data strongly corroborate that the nonbridging proSP phosphate oxygen at the A2662 of the SRL is critically involved in the activation of GTP hydrolysis. A mechanistic scenario is supported in which positioning of the catalytically active, protonated His87 through electrostatic interactions with the A2662 phosphate group and H-bond networks are key features of ribosome-triggered activation of trGTPases.
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