1
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Wang YH, Dai H, Zhang L, Wu Y, Wang J, Wang C, Xu CH, Hou H, Yang B, Zhu Y, Zhang X, Zhou J. Cryo-electron microscopy structure and translocation mechanism of the crenarchaeal ribosome. Nucleic Acids Res 2023; 51:8909-8924. [PMID: 37604686 PMCID: PMC10516650 DOI: 10.1093/nar/gkad661] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2022] [Revised: 06/29/2023] [Accepted: 08/02/2023] [Indexed: 08/23/2023] Open
Abstract
Archaeal ribosomes have many domain-specific features; however, our understanding of these structures is limited. We present 10 cryo-electron microscopy (cryo-EM) structures of the archaeal ribosome from crenarchaeota Sulfolobus acidocaldarius (Sac) at 2.7-5.7 Å resolution. We observed unstable conformations of H68 and h44 of ribosomal RNA (rRNA) in the subunit structures, which may interfere with subunit association. These subunit structures provided models for 12 rRNA expansion segments and 3 novel r-proteins. Furthermore, the 50S-aRF1 complex structure showed the unique domain orientation of aRF1, possibly explaining P-site transfer RNA (tRNA) release after translation termination. Sac 70S complexes were captured in seven distinct steps of the tRNA translocation reaction, confirming conserved structural features during archaeal ribosome translocation. In aEF2-engaged 70S ribosome complexes, 3D classification of cryo-EM data based on 30S head domain identified two new translocation intermediates with 30S head domain tilted 5-6° enabling its disengagement from the translocated tRNA and its release post-translocation. Additionally, we observed conformational changes to aEF2 during ribosome binding and switching from three different states. Our structural and biochemical data provide new insights into archaeal translation and ribosome translocation.
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Affiliation(s)
- Ying-Hui Wang
- Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Hong Dai
- Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Ling Zhang
- Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Yun Wu
- Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Jingfen Wang
- Center for Cryo-Electron Microscopy, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China
- Department of Pathology of Sir Run Run Shaw Hospital, and Department of Biophysics, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China
| | - Chen Wang
- Center for Cryo-Electron Microscopy, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China
- Department of Pathology of Sir Run Run Shaw Hospital, and Department of Biophysics, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China
| | - Cai-Huang Xu
- Center for Cryo-Electron Microscopy, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China
- Department of Pathology of Sir Run Run Shaw Hospital, and Department of Biophysics, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China
| | - Hai Hou
- Institute of Medical Research, Northwestern Polytechnical University, Xi’an, Shaanxi 710072, China
| | - Bing Yang
- Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Yongqun Zhu
- Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Xing Zhang
- Center for Cryo-Electron Microscopy, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China
- Department of Pathology of Sir Run Run Shaw Hospital, and Department of Biophysics, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China
| | - Jie Zhou
- Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang 310058, China
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2
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Koller TO, Morici M, Berger M, Safdari HA, Lele DS, Beckert B, Kaur KJ, Wilson DN. Structural basis for translation inhibition by the glycosylated drosocin peptide. Nat Chem Biol 2023; 19:1072-1081. [PMID: 36997646 PMCID: PMC10449632 DOI: 10.1038/s41589-023-01293-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Accepted: 02/14/2023] [Indexed: 04/07/2023]
Abstract
The proline-rich antimicrobial peptide (PrAMP) drosocin is produced by Drosophila species to combat bacterial infection. Unlike many PrAMPs, drosocin is O-glycosylated at threonine 11, a post-translation modification that enhances its antimicrobial activity. Here we demonstrate that the O-glycosylation not only influences cellular uptake of the peptide but also interacts with its intracellular target, the ribosome. Cryogenic electron microscopy structures of glycosylated drosocin on the ribosome at 2.0-2.8-Å resolution reveal that the peptide interferes with translation termination by binding within the polypeptide exit tunnel and trapping RF1 on the ribosome, reminiscent of that reported for the PrAMP apidaecin. The glycosylation of drosocin enables multiple interactions with U2609 of the 23S rRNA, leading to conformational changes that break the canonical base pair with A752. Collectively, our study reveals novel molecular insights into the interaction of O-glycosylated drosocin with the ribosome, which provide a structural basis for future development of this class of antimicrobials.
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Affiliation(s)
- Timm O Koller
- Institute for Biochemistry and Molecular Biology, University of Hamburg, Hamburg, Germany
| | - Martino Morici
- Institute for Biochemistry and Molecular Biology, University of Hamburg, Hamburg, Germany
| | - Max Berger
- Institute for Biochemistry and Molecular Biology, University of Hamburg, Hamburg, Germany
| | - Haaris A Safdari
- Institute for Biochemistry and Molecular Biology, University of Hamburg, Hamburg, Germany
| | - Deepti S Lele
- National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi, India
| | - Bertrand Beckert
- Dubochet Center for Imaging (DCI) at EPFL, EPFL SB IPHYS DCI, Lausanne, Switzerland
| | - Kanwal J Kaur
- National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi, India
| | - Daniel N Wilson
- Institute for Biochemistry and Molecular Biology, University of Hamburg, Hamburg, Germany.
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3
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González S, Ad O, Shah B, Zhang Z, Zhang X, Chatterjee A, Schepartz A. Genetic Code Expansion in the Engineered Organism Vmax X2: High Yield and Exceptional Fidelity. ACS CENTRAL SCIENCE 2021; 7:1500-1507. [PMID: 34584951 PMCID: PMC8461772 DOI: 10.1021/acscentsci.1c00499] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2021] [Indexed: 05/05/2023]
Abstract
We report that the recently introduced commercial strain of Vibrio natriegens (Vmax X2) supports robust unnatural amino acid mutagenesis, generating exceptional yields of soluble protein containing up to 5 noncanonical α-amino acids (ncAA). The isolated yields of ncAA-containing superfolder green fluorescent protein (sfGFP) expressed in Vmax X2 are up to 25-fold higher than those achieved using commercial expression strains (Top10 and BL21) and more than 10-fold higher than those achieved using two different genomically recodedEscherichia colistrains that lack endogenous UAG stop codons and release factor 1 and have been optimized for improved fitness and preferred growth temperature (C321.ΔA.opt and C321.ΔA.exp). In addition to higher yields of soluble protein, Vmax X2 cells also generate proteins with significantly lower levels of misincorporated natural α-amino acids at the UAG-programmed position, especially in cases where the ncAA is a moderate substrate for the chosen orthogonal aminoacyl tRNA synthetase (aaRS). This increase in fidelity implies that the use of Vmax X2 cells as the expression host can obviate the need for time-consuming directed evolution experiments to improve the selectivity of an aaRS toward highly desired but suboptimal ncAA substrates.
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Affiliation(s)
| | - Omer Ad
- Department
of Chemistry, Yale University, New Haven, Connecticut 06511, United States
| | - Bhavana Shah
- Process
Development, Attribute Sciences, Amgen Inc., Thousand Oaks, California 91320, United States
| | - Zhongqi Zhang
- Process
Development, Attribute Sciences, Amgen Inc., Thousand Oaks, California 91320, United States
| | - Xizi Zhang
- Department
of Chemistry, University of California, Berkeley, California 94720, United States
| | - Abhishek Chatterjee
- Department
of Chemistry, Boston College, Chestnut Hill, Massachusetts 02467, United States
| | - Alanna Schepartz
- Department
of Chemistry, University of California, Berkeley, California 94720, United States
- Department
of Molecular and Cellular Biology, University
of California, Berkeley, California 94720, United States
- California
Institute for Quantitative Biosciences (QB3), University of California, Berkeley, California 94720, United States
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4
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Albers S, Beckert B, Matthies MC, Mandava CS, Schuster R, Seuring C, Riedner M, Sanyal S, Torda AE, Wilson DN, Ignatova Z. Repurposing tRNAs for nonsense suppression. Nat Commun 2021; 12:3850. [PMID: 34158503 PMCID: PMC8219837 DOI: 10.1038/s41467-021-24076-x] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Accepted: 06/01/2021] [Indexed: 02/06/2023] Open
Abstract
Three stop codons (UAA, UAG and UGA) terminate protein synthesis and are almost exclusively recognized by release factors. Here, we design de novo transfer RNAs (tRNAs) that efficiently decode UGA stop codons in Escherichia coli. The tRNA designs harness various functionally conserved aspects of sense-codon decoding tRNAs. Optimization within the TΨC-stem to stabilize binding to the elongation factor, displays the most potent effect in enhancing suppression activity. We determine the structure of the ribosome in a complex with the designed tRNA bound to a UGA stop codon in the A site at 2.9 Å resolution. In the context of the suppressor tRNA, the conformation of the UGA codon resembles that of a sense-codon rather than when canonical translation termination release factors are bound, suggesting conformational flexibility of the stop codons dependent on the nature of the A-site ligand. The systematic analysis, combined with structural insights, provides a rationale for targeted repurposing of tRNAs to correct devastating nonsense mutations that introduce a premature stop codon.
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Affiliation(s)
- Suki Albers
- grid.9026.d0000 0001 2287 2617Institute of Biochemistry and Molecular Biology, University of Hamburg, Hamburg, Germany
| | - Bertrand Beckert
- grid.9026.d0000 0001 2287 2617Institute of Biochemistry and Molecular Biology, University of Hamburg, Hamburg, Germany
| | - Marco C. Matthies
- grid.9026.d0000 0001 2287 2617Center for Bioinformatics, University of Hamburg, Hamburg, Germany
| | - Chandra Sekhar Mandava
- grid.8993.b0000 0004 1936 9457Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
| | - Raphael Schuster
- grid.9026.d0000 0001 2287 2617Institute of Organic Chemistry, University of Hamburg, Hamburg, Germany
| | | | - Maria Riedner
- grid.9026.d0000 0001 2287 2617Institute of Organic Chemistry, University of Hamburg, Hamburg, Germany
| | - Suparna Sanyal
- grid.8993.b0000 0004 1936 9457Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
| | - Andrew E. Torda
- grid.9026.d0000 0001 2287 2617Center for Bioinformatics, University of Hamburg, Hamburg, Germany
| | - Daniel N. Wilson
- grid.9026.d0000 0001 2287 2617Institute of Biochemistry and Molecular Biology, University of Hamburg, Hamburg, Germany
| | - Zoya Ignatova
- grid.9026.d0000 0001 2287 2617Institute of Biochemistry and Molecular Biology, University of Hamburg, Hamburg, Germany
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5
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Zhang L, Wang Y, Dai H, Zhou J. Structural and functional studies revealed key mechanisms underlying elongation step of protein translation. Acta Biochim Biophys Sin (Shanghai) 2020; 52:749-756. [PMID: 32400848 DOI: 10.1093/abbs/gmaa046] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2019] [Indexed: 11/12/2022] Open
Abstract
The ribosome is an ancient and universally conserved macromolecular machine that synthesizes proteins in all organisms. Since the discovery of the ribosome by electron microscopy in the mid-1950s, rapid progress has been made in research on it, regarding its architecture and functions. As a machine that synthesizes polypeptides, the sequential addition of amino acids to a growing polypeptide chain occurs during a phase called the elongation cycle. This is the core step of protein translation and is highly conserved between bacteria and eukarya. The elongation cycle involves codon recognition by aminoacyl tRNAs, catalysis of peptide bond formation, and the most complex operation of translation-translocation. In this review, we discuss the fundamental results from structural and functional studies over the past decades that have led to understanding of the three key questions underlying translation.
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Affiliation(s)
- Ling Zhang
- Life Sciences Institute, Zhejiang University, Hangzhou 310058, China
| | - Yinghui Wang
- Life Sciences Institute, Zhejiang University, Hangzhou 310058, China
| | - Hong Dai
- Life Sciences Institute, Zhejiang University, Hangzhou 310058, China
| | - Jie Zhou
- Life Sciences Institute, Zhejiang University, Hangzhou 310058, China
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6
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Žihala D, Eliáš M. Evolution and Unprecedented Variants of the Mitochondrial Genetic Code in a Lineage of Green Algae. Genome Biol Evol 2020; 11:2992-3007. [PMID: 31617565 PMCID: PMC6821328 DOI: 10.1093/gbe/evz210] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/17/2019] [Indexed: 12/15/2022] Open
Abstract
Mitochondria of diverse eukaryotes have evolved various departures from the standard genetic code, but the breadth of possible modifications and their phylogenetic distribution are known only incompletely. Furthermore, it is possible that some codon reassignments in previously sequenced mitogenomes have been missed, resulting in inaccurate protein sequences in databases. Here we show, considering the distribution of codons at conserved amino acid positions in mitogenome-encoded proteins, that mitochondria of the green algal order Sphaeropleales exhibit a diversity of codon reassignments, including previously missed ones and some that are unprecedented in any translation system examined so far, necessitating redefinition of existing translation tables and creating at least seven new ones. We resolve a previous controversy concerning the meaning the UAG codon in Hydrodictyaceae, which beyond any doubt encodes alanine. We further demonstrate that AGG, sometimes together with AGA, encodes alanine instead of arginine in diverse sphaeroplealeans. Further newly detected changes include Arg-to-Met reassignment of the AGG codon and Arg-to-Leu reassignment of the CGG codon in particular species. Analysis of tRNAs specified by sphaeroplealean mitogenomes provides direct support for and molecular underpinning of the proposed reassignments. Furthermore, we point to unique mutations in the mitochondrial release factor mtRF1a that correlate with changes in the use of termination codons in Sphaeropleales, including the two independent stop-to-sense UAG reassignments, the reintroduction of UGA in some Scenedesmaceae, and the sense-to-stop reassignment of UCA widespread in the group. Codon disappearance seems to be the main drive of the dynamic evolution of the mitochondrial genetic code in Sphaeropleales.
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Affiliation(s)
- David Žihala
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Czech Republic.,Institute of Environmental Technologies, Faculty of Science, University of Ostrava, Czech Republic
| | - Marek Eliáš
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Czech Republic.,Institute of Environmental Technologies, Faculty of Science, University of Ostrava, Czech Republic
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7
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Release factor-dependent ribosome rescue by BrfA in the Gram-positive bacterium Bacillus subtilis. Nat Commun 2019; 10:5397. [PMID: 31776341 PMCID: PMC6881298 DOI: 10.1038/s41467-019-13408-7] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Accepted: 11/07/2019] [Indexed: 12/14/2022] Open
Abstract
Rescue of the ribosomes from dead-end translation complexes, such as those on truncated (non-stop) mRNA, is essential for the cell. Whereas bacteria use trans-translation for ribosome rescue, some Gram-negative species possess alternative and release factor (RF)-dependent rescue factors, which enable an RF to catalyze stop-codon-independent polypeptide release. We now discover that the Gram-positive Bacillus subtilis has an evolutionarily distinct ribosome rescue factor named BrfA. Genetic analysis shows that B. subtilis requires the function of either trans-translation or BrfA for growth, even in the absence of proteotoxic stresses. Biochemical and cryo-electron microscopy (cryo-EM) characterization demonstrates that BrfA binds to non-stop stalled ribosomes, recruits homologous RF2, but not RF1, and induces its transition into an open active conformation. Although BrfA is distinct from E. coli ArfA, they use convergent strategies in terms of mode of action and expression regulation, indicating that many bacteria may have evolved as yet unidentified ribosome rescue systems. In bacteria, the conserved trans-translation system serves as the primary pathway of ribosome rescue, but many species can also use alternative rescue pathways. Here the authors report that in B. subtilis, the rescue factor BrfA binds to non-stop stalled ribosomes, recruits RF2 but not RF1, and induces transition of the ribosome into an open active conformation.
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8
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Golubev AA, Validov SZ, Usachev KS, Yusupov MM. Elongation Factor P: New Mechanisms of Function and an Evolutionary Diversity of Translation Regulation. Mol Biol 2019. [DOI: 10.1134/s0026893319040034] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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9
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Graf M, Huter P, Maracci C, Peterek M, Rodnina MV, Wilson DN. Visualization of translation termination intermediates trapped by the Apidaecin 137 peptide during RF3-mediated recycling of RF1. Nat Commun 2018; 9:3053. [PMID: 30076302 PMCID: PMC6076264 DOI: 10.1038/s41467-018-05465-1] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2018] [Accepted: 07/06/2018] [Indexed: 12/20/2022] Open
Abstract
During translation termination in bacteria, the release factors RF1 and RF2 are recycled from the ribosome by RF3. While high-resolution structures of the individual termination factors on the ribosome exist, direct structural insight into how RF3 mediates dissociation of the decoding RFs has been lacking. Here we have used the Apidaecin 137 peptide to trap RF1 together with RF3 on the ribosome and visualize an ensemble of termination intermediates using cryo-electron microscopy. Binding of RF3 to the ribosome induces small subunit (SSU) rotation and swivelling of the head, yielding intermediate states with shifted P-site tRNAs and RF1 conformations. RF3 does not directly eject RF1 from the ribosome, but rather induces full rotation of the SSU that indirectly dislodges RF1 from its binding site. SSU rotation is coupled to the accommodation of the GTPase domain of RF3 on the large subunit (LSU), thereby promoting GTP hydrolysis and dissociation of RF3 from the ribosome. In bacteria, the process of translation termination is performed by three termination release factors RF1, RF2 and RF3. Here the authors provide detailed structural insights into the mechanism by which RF1 is dissociated from the ribosome by RF3 during termination.
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Affiliation(s)
- Michael Graf
- Institute for Biochemistry and Molecular Biology, University of Hamburg, Martin-Luther-King-Platz 6, 20146, Hamburg, Germany
| | - Paul Huter
- Institute for Biochemistry and Molecular Biology, University of Hamburg, Martin-Luther-King-Platz 6, 20146, Hamburg, Germany
| | - Cristina Maracci
- Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, Göttingen, 37077, Germany
| | - Miroslav Peterek
- Central European Institute of Technology (CEITEC), Masaryk University, Kamenice 5, 62500, Brno, Czech Republic
| | - Marina V Rodnina
- Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, Göttingen, 37077, Germany
| | - Daniel N Wilson
- Institute for Biochemistry and Molecular Biology, University of Hamburg, Martin-Luther-King-Platz 6, 20146, Hamburg, Germany.
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10
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Abstract
Codon usage depends on mutation bias, tRNA-mediated selection, and the need for high efficiency and accuracy in translation. One codon in a synonymous codon family is often strongly over-used, especially in highly expressed genes, which often leads to a high dN/dS ratio because dS is very small. Many different codon usage indices have been proposed to measure codon usage and codon adaptation. Sense codon could be misread by release factors and stop codons misread by tRNAs, which also contribute to codon usage in rare cases. This chapter outlines the conceptual framework on codon evolution, illustrates codon-specific and gene-specific codon usage indices, and presents their applications. A new index for codon adaptation that accounts for background mutation bias (Index of Translation Elongation) is presented and contrasted with codon adaptation index (CAI) which does not consider background mutation bias. They are used to re-analyze data from a recent paper claiming that translation elongation efficiency matters little in protein production. The reanalysis disproves the claim.
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11
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Casy W, Prater AR, Cornish PV. Operative Binding of Class I Release Factors and YaeJ Stabilizes the Ribosome in the Nonrotated State. Biochemistry 2018; 57:1954-1966. [PMID: 29499110 DOI: 10.1021/acs.biochem.7b00824] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
During translation, the small subunit of the ribosome rotates with respect to the large subunit primarily between two states as mRNA is being translated into a protein. At the termination of bacterial translation, class I release factors (RFs) bind to a stop codon in the A-site and catalyze the release of the peptide chain from the ribosome. Periodically, mRNA is truncated prematurely, and the translating ribosome stalls at the end of the mRNA forming a nonstop complex requiring one of several ribosome rescue factors to intervene. One factor, YaeJ, is structurally homologous with the catalytic region of RFs but differs by binding to the ribosome directly through its C-terminal tail. Structures of the ribosome show that the ribosome adopts the nonrotated state conformation when these factors are bound. However, these studies do not elucidate the influence of binding to cognate or noncognate codons on the dynamics of intersubunit rotation. Here, we investigate the effects of wild-type and mutant forms of RF1, RF2, and YaeJ binding on ribosome intersubunit rotation using single-molecule Förster resonance energy transfer. We show that both RF1 binding and RF2 binding are sufficient to shift the population of posthydrolysis ribosome complexes from primarily the rotated to the nonrotated state only when a cognate stop codon is present in the A-site. Similarly, YaeJ binding stabilizes nonstop ribosomal complexes in the nonrotated state. Along with previous studies, these results are consistent with the idea that directed conformational changes and binding of subsequent factors to the ribosome are requisite for efficient termination and ribosome recycling.
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Affiliation(s)
- Widler Casy
- Department of Biochemistry , University of Missouri , Columbia , Missouri 65211 , United States
| | - Austin R Prater
- Department of Biochemistry , University of Missouri , Columbia , Missouri 65211 , United States
| | - Peter V Cornish
- Department of Biochemistry , University of Missouri , Columbia , Missouri 65211 , United States
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12
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Pierson WE, Hoffer ED, Keedy HE, Simms CL, Dunham CM, Zaher HS. Uniformity of Peptide Release Is Maintained by Methylation of Release Factors. Cell Rep 2017; 17:11-18. [PMID: 27681416 DOI: 10.1016/j.celrep.2016.08.085] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2016] [Revised: 06/30/2016] [Accepted: 08/24/2016] [Indexed: 10/20/2022] Open
Abstract
Termination of protein synthesis on the ribosome is catalyzed by release factors (RFs), which share a conserved glycine-glycine-glutamine (GGQ) motif. The glutamine residue is methylated in vivo, but a mechanistic understanding of its contribution to hydrolysis is lacking. Here, we show that the modification, apart from increasing the overall rate of termination on all dipeptides, substantially increases the rate of peptide release on a subset of amino acids. In the presence of unmethylated RFs, we measure rates of hydrolysis that are exceptionally slow on proline and glycine residues and approximately two orders of magnitude faster in the presence of the methylated factors. Structures of 70S ribosomes bound to methylated RF1 and RF2 reveal that the glutamine side-chain methylation packs against 23S rRNA nucleotide 2451, stabilizing the GGQ motif and placing the side-chain amide of the glutamine toward tRNA. These data provide a framework for understanding how release factor modifications impact termination.
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Affiliation(s)
- William E Pierson
- Department of Biology, Washington University in St. Louis, Campus Box 1137, 1 Brookings Drive, St. Louis, MO 63130, USA
| | - Eric D Hoffer
- Biochemistry, Cell and Developmental Biology Graduate Program, Emory University School of Medicine, 1510 Clifton Road NE, Room G223, Atlanta, GA 30322, USA; Department of Biochemistry, Emory University School of Medicine, 1510 Clifton Road NE, Room G223, Atlanta, GA 30322, USA
| | - Hannah E Keedy
- Department of Biology, Washington University in St. Louis, Campus Box 1137, 1 Brookings Drive, St. Louis, MO 63130, USA
| | - Carrie L Simms
- Department of Biology, Washington University in St. Louis, Campus Box 1137, 1 Brookings Drive, St. Louis, MO 63130, USA
| | - Christine M Dunham
- Department of Biochemistry, Emory University School of Medicine, 1510 Clifton Road NE, Room G223, Atlanta, GA 30322, USA.
| | - Hani S Zaher
- Department of Biology, Washington University in St. Louis, Campus Box 1137, 1 Brookings Drive, St. Louis, MO 63130, USA.
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13
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Huter P, Arenz S, Bock LV, Graf M, Frister JO, Heuer A, Peil L, Starosta AL, Wohlgemuth I, Peske F, Nováček J, Berninghausen O, Grubmüller H, Tenson T, Beckmann R, Rodnina MV, Vaiana AC, Wilson DN. Structural Basis for Polyproline-Mediated Ribosome Stalling and Rescue by the Translation Elongation Factor EF-P. Mol Cell 2017; 68:515-527.e6. [PMID: 29100052 DOI: 10.1016/j.molcel.2017.10.014] [Citation(s) in RCA: 91] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Revised: 09/29/2017] [Accepted: 10/11/2017] [Indexed: 12/15/2022]
Abstract
Ribosomes synthesizing proteins containing consecutive proline residues become stalled and require rescue via the action of uniquely modified translation elongation factors, EF-P in bacteria, or archaeal/eukaryotic a/eIF5A. To date, no structures exist of EF-P or eIF5A in complex with translating ribosomes stalled at polyproline stretches, and thus structural insight into how EF-P/eIF5A rescue these arrested ribosomes has been lacking. Here we present cryo-EM structures of ribosomes stalled on proline stretches, without and with modified EF-P. The structures suggest that the favored conformation of the polyproline-containing nascent chain is incompatible with the peptide exit tunnel of the ribosome and leads to destabilization of the peptidyl-tRNA. Binding of EF-P stabilizes the P-site tRNA, particularly via interactions between its modification and the CCA end, thereby enforcing an alternative conformation of the polyproline-containing nascent chain, which allows a favorable substrate geometry for peptide bond formation.
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Affiliation(s)
- Paul Huter
- Gene Center, Department for Biochemistry and Center for integrated Protein Science Munich (CiPSM), University of Munich, Feodor-Lynenstr. 25, 81377 Munich, Germany
| | - Stefan Arenz
- Gene Center, Department for Biochemistry and Center for integrated Protein Science Munich (CiPSM), University of Munich, Feodor-Lynenstr. 25, 81377 Munich, Germany
| | - Lars V Bock
- Department of Theoretical and Computational Biophysics, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, Göttingen 37077, Germany
| | - Michael Graf
- Gene Center, Department for Biochemistry and Center for integrated Protein Science Munich (CiPSM), University of Munich, Feodor-Lynenstr. 25, 81377 Munich, Germany
| | - Jan Ole Frister
- Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Andre Heuer
- Gene Center, Department for Biochemistry and Center for integrated Protein Science Munich (CiPSM), University of Munich, Feodor-Lynenstr. 25, 81377 Munich, Germany
| | - Lauri Peil
- University of Tartu, Institute of Technology, Nooruse 1, 50411 Tartu, Estonia
| | - Agata L Starosta
- Gene Center, Department for Biochemistry and Center for integrated Protein Science Munich (CiPSM), University of Munich, Feodor-Lynenstr. 25, 81377 Munich, Germany
| | - Ingo Wohlgemuth
- Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Frank Peske
- Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Jiří Nováček
- Central European Institute of Technology (CEITEC), Masaryk University, Kamenice 5, 62500 Brno, Czech Republic
| | - Otto Berninghausen
- Gene Center, Department for Biochemistry and Center for integrated Protein Science Munich (CiPSM), University of Munich, Feodor-Lynenstr. 25, 81377 Munich, Germany
| | - Helmut Grubmüller
- Department of Theoretical and Computational Biophysics, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, Göttingen 37077, Germany
| | - Tanel Tenson
- University of Tartu, Institute of Technology, Nooruse 1, 50411 Tartu, Estonia
| | - Roland Beckmann
- Gene Center, Department for Biochemistry and Center for integrated Protein Science Munich (CiPSM), University of Munich, Feodor-Lynenstr. 25, 81377 Munich, Germany
| | - Marina V Rodnina
- Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Andrea C Vaiana
- Department of Theoretical and Computational Biophysics, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, Göttingen 37077, Germany
| | - Daniel N Wilson
- Gene Center, Department for Biochemistry and Center for integrated Protein Science Munich (CiPSM), University of Munich, Feodor-Lynenstr. 25, 81377 Munich, Germany; Institute for Biochemistry and Molecular Biology, University of Hamburg, Martin-Luther-King-Platz 6, 20146 Hamburg, Germany.
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14
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Kumar A, Basu D, Satpati P. Structure-Based Energetics of Stop Codon Recognition by Eukaryotic Release Factor. J Chem Inf Model 2017; 57:2321-2328. [PMID: 28825483 DOI: 10.1021/acs.jcim.7b00340] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
In translation termination, the eukaryotic release factor (eRF1) recognizes mRNA stop codons (UAA, UAG, or UGA) in a ribosomal A site and triggers release of the nascent polypeptide chain from P-site tRNA. eRF1 is highly selective for U in the first position and a combination of purines (except two consecutive guanines, i.e., GG) in the second and third positions. Eukaryotes decode all three stop codons with a single release factor eRF1, instead of two (RF1 and RF2), in bacteria. Furthermore, unlike bacterial RF1/RF2, eRF1 stabilizes the compact U-turn mRNA configuration in the ribosomal A site by accommodating four nucleotides instead of three. Despite the available cryo-EM structures (resolution ∼3.5-3.8 Å), the energetic principle for eRF1 selectivity toward a stop codon remains a fundamentally unsolved problem. Using cryo-EM structures of eukaryotic translation termination complexes as templates, we carried out molecular dynamics free energy simulations of cognate and near-cognate complexes to quantitatively address the energetics of stop codon recognition by eRF1. Our results suggest that eRF1 has a higher discriminatory power against sense codons, compared to that reported earlier for RF1/RF2. The compact mRNA formed specific intra-mRNA interactions, which itself contributed to stop codon specificity. Furthermore, the specificity is enhanced by the loss of protein-mRNA interactions and, most importantly, by desolvation of the incorrect codons in the near-cognate complexes. Our work provides a clue to how eRF1 discriminates between cognate and near-cognate codons during protein synthesis.
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Affiliation(s)
- Amit Kumar
- Department of Biosciences and Bioengineering, Indian Institute of Technology, Guwahati , Guwahati 781039, Assam, India
| | - Debadrita Basu
- Department of Biosciences and Bioengineering, Indian Institute of Technology, Guwahati , Guwahati 781039, Assam, India
| | - Priyadarshi Satpati
- Department of Biosciences and Bioengineering, Indian Institute of Technology, Guwahati , Guwahati 781039, Assam, India
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15
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Huter P, Müller C, Arenz S, Beckert B, Wilson DN. Structural Basis for Ribosome Rescue in Bacteria. Trends Biochem Sci 2017. [PMID: 28629612 DOI: 10.1016/j.tibs.2017.05.009] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Ribosomes that translate mRNAs lacking stop codons become stalled at the 3' end of the mRNA. Recycling of these stalled ribosomes is essential for cell viability. In bacteria three ribosome rescue systems have been identified so far, with the most ubiquitous and best characterized being the trans-translation system mediated by transfer-messenger RNA (tmRNA) and small protein B (SmpB). The two additional rescue systems present in some bacteria employ alternative rescue factor (Arf) A and release factor (RF) 2 or ArfB. Recent structures have revealed how ArfA mediates ribosome rescue by recruiting the canonical termination factor RF2 to ribosomes stalled on truncated mRNAs. This now provides us with the opportunity to compare and contrast the available structures of all three bacterial ribosome rescue systems.
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Affiliation(s)
- Paul Huter
- Gene Center, Department of Biochemistry and Center for Integrated Protein Science Munich (CiPSM), Feodor-Lynenstr. 25, 81377 München, Germany
| | - Claudia Müller
- Gene Center, Department of Biochemistry and Center for Integrated Protein Science Munich (CiPSM), Feodor-Lynenstr. 25, 81377 München, Germany
| | - Stefan Arenz
- Gene Center, Department of Biochemistry and Center for Integrated Protein Science Munich (CiPSM), Feodor-Lynenstr. 25, 81377 München, Germany
| | - Bertrand Beckert
- Gene Center, Department of Biochemistry and Center for Integrated Protein Science Munich (CiPSM), Feodor-Lynenstr. 25, 81377 München, Germany; Institute for Biochemistry and Molecular Biology, University of Hamburg, Martin-Luther-King-Platz 6, 20146 Hamburg, Germany
| | - Daniel N Wilson
- Gene Center, Department of Biochemistry and Center for Integrated Protein Science Munich (CiPSM), Feodor-Lynenstr. 25, 81377 München, Germany; Institute for Biochemistry and Molecular Biology, University of Hamburg, Martin-Luther-King-Platz 6, 20146 Hamburg, Germany.
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16
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Baggett NE, Zhang Y, Gross CA. Global analysis of translation termination in E. coli. PLoS Genet 2017; 13:e1006676. [PMID: 28301469 PMCID: PMC5373646 DOI: 10.1371/journal.pgen.1006676] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2016] [Revised: 03/30/2017] [Accepted: 03/08/2017] [Indexed: 01/01/2023] Open
Abstract
Terminating protein translation accurately and efficiently is critical for both protein fidelity and ribosome recycling for continued translation. The three bacterial release factors (RFs) play key roles: RF1 and 2 recognize stop codons and terminate translation; and RF3 promotes disassociation of bound release factors. Probing release factors mutations with reporter constructs containing programmed frameshifting sequences or premature stop codons had revealed a propensity for readthrough or frameshifting at these specific sites, but their effects on translation genome-wide have not been examined. We performed ribosome profiling on a set of isogenic strains with well-characterized release factor mutations to determine how they alter translation globally. Consistent with their known defects, strains with increasingly severe release factor defects exhibit increasingly severe accumulation of ribosomes over stop codons, indicative of an increased duration of the termination/release phase of translation. Release factor mutant strains also exhibit increased occupancy in the region following the stop codon at a significant number of genes. Our global analysis revealed that, as expected, translation termination is generally efficient and accurate, but that at a significant number of genes (≥ 50) the ribosome signature after the stop codon is suggestive of translation past the stop codon. Even native E. coli K-12 exhibits the ribosome signature suggestive of protein extension, especially at UGA codons, which rely exclusively on the reduced function RF2 variant of the K-12 strain for termination. Deletion of RF3 increases the severity of the defect. We unambiguously demonstrate readthrough and frameshifting protein extensions and their further accumulation in mutant strains for a few select cases. In addition to enhancing recoding, ribosome accumulation over stop codons disrupts attenuation control of biosynthetic operons, and may alter expression of some overlapping genes. Together, these functional alterations may either augment the protein repertoire or produce deleterious proteins. Proteins are the cellular workhorses, performing essentially all of the functions required for cell and organismal survival. But, it takes a great deal of energy to make proteins, making it critical that proteins are made accurately and in the proper time frame. After a ribosome synthesizes a protein, release factors catalyze the accurate and timely release of the finished protein from the ribosome, a process called termination. Ribosomes are then recycled and start the next protein. We utilized ribosome profiling, a method that allows us to follow the position of every ribosome that is making a protein, to globally investigate and strengthen insights on termination fidelity for cells with and without mutant release factors. We find that as we decrease release factor function, the time to terminate/release a protein increases across the genome. We observe that the accuracy of terminating a protein at the correct place decreases on a global scale. Using this metric we identify genes with inherently low termination efficiency and confirm two novel events resulting in extended protein products. In addition we find that beyond disrupting accurate protein synthesis, release factor mutations can alter expression of genes involved in the production of key amino acids.
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Affiliation(s)
- Natalie E. Baggett
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, California, United States of America
| | - Yan Zhang
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, California, United States of America
| | - Carol A. Gross
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, California, United States of America
- Department of Cell and Tissue Biology, University of California, San Francisco, San Francisco, California, United States of America
- California Institute of Quantitative Biology, University of California, San Francisco, San Francisco, California, United States of America
- * E-mail:
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17
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Huter P, Müller C, Beckert B, Arenz S, Berninghausen O, Beckmann R, Wilson DN. Structural basis for ArfA-RF2-mediated translation termination on mRNAs lacking stop codons. Nature 2016; 541:546-549. [PMID: 27906161 DOI: 10.1038/nature20821] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2016] [Accepted: 11/25/2016] [Indexed: 11/09/2022]
Abstract
In bacteria, ribosomes stalled on truncated mRNAs that lack a stop codon are rescued by the transfer-messenger RNA (tmRNA), alternative rescue factor A (ArfA) or ArfB systems. Although tmRNA-ribosome and ArfB-ribosome structures have been determined, how ArfA recognizes the presence of truncated mRNAs and recruits the canonical termination release factor RF2 to rescue the stalled ribosomes is unclear. Here we present a cryo-electron microscopy reconstruction of the Escherichia coli 70S ribosome stalled on a truncated mRNA in the presence of ArfA and RF2. The structure shows that the C terminus of ArfA binds within the mRNA entry channel on the small ribosomal subunit, and explains how ArfA distinguishes between ribosomes that bear truncated or full-length mRNAs. The N terminus of ArfA establishes several interactions with the decoding domain of RF2, and this finding illustrates how ArfA recruits RF2 to the stalled ribosome. Furthermore, ArfA is shown to stabilize a unique conformation of the switch loop of RF2, which mimics the canonical translation termination state by directing the catalytically important GGQ motif within domain 3 of RF2 towards the peptidyl-transferase centre of the ribosome. Thus, our structure reveals not only how ArfA recruits RF2 to the ribosome but also how it promotes an active conformation of RF2 to enable translation termination in the absence of a stop codon.
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Affiliation(s)
- Paul Huter
- Gene Center, Department of Biochemistry and Center for integrated Protein Science Munich (CiPSM), Ludwig-Maximilians-Universität München, Feodor-Lynen-Strasse 25, 81377 Munich, Germany
| | - Claudia Müller
- Gene Center, Department of Biochemistry and Center for integrated Protein Science Munich (CiPSM), Ludwig-Maximilians-Universität München, Feodor-Lynen-Strasse 25, 81377 Munich, Germany
| | - Bertrand Beckert
- Gene Center, Department of Biochemistry and Center for integrated Protein Science Munich (CiPSM), Ludwig-Maximilians-Universität München, Feodor-Lynen-Strasse 25, 81377 Munich, Germany.,Institute for Biochemistry and Molecular Biology, University of Hamburg, Martin-Luther-King-Pl. 6, 20146 Hamburg, Germany
| | - Stefan Arenz
- Gene Center, Department of Biochemistry and Center for integrated Protein Science Munich (CiPSM), Ludwig-Maximilians-Universität München, Feodor-Lynen-Strasse 25, 81377 Munich, Germany
| | - Otto Berninghausen
- Gene Center, Department of Biochemistry and Center for integrated Protein Science Munich (CiPSM), Ludwig-Maximilians-Universität München, Feodor-Lynen-Strasse 25, 81377 Munich, Germany
| | - Roland Beckmann
- Gene Center, Department of Biochemistry and Center for integrated Protein Science Munich (CiPSM), Ludwig-Maximilians-Universität München, Feodor-Lynen-Strasse 25, 81377 Munich, Germany
| | - Daniel N Wilson
- Gene Center, Department of Biochemistry and Center for integrated Protein Science Munich (CiPSM), Ludwig-Maximilians-Universität München, Feodor-Lynen-Strasse 25, 81377 Munich, Germany.,Institute for Biochemistry and Molecular Biology, University of Hamburg, Martin-Luther-King-Pl. 6, 20146 Hamburg, Germany
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18
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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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19
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Katz A, Elgamal S, Rajkovic A, Ibba M. Non-canonical roles of tRNAs and tRNA mimics in bacterial cell biology. Mol Microbiol 2016; 101:545-58. [PMID: 27169680 DOI: 10.1111/mmi.13419] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/09/2016] [Indexed: 12/27/2022]
Abstract
Transfer RNAs (tRNAs) are the macromolecules that transfer activated amino acids from aminoacyl-tRNA synthetases to the ribosome, where they are used for the mRNA guided synthesis of proteins. Transfer RNAs are ancient molecules, perhaps even predating the existence of the translation machinery. Albeit old, these molecules are tremendously conserved, a characteristic that is well illustrated by the fact that some bacterial tRNAs are efficient and specific substrates of eukaryotic aminoacyl-tRNA synthetases and ribosomes. Considering their ancient origin and high structural conservation, it is not surprising that tRNAs have been hijacked during evolution for functions outside of translation. These roles beyond translation include synthetic, regulatory and information functions within the cell. Here we provide an overview of the non-canonical roles of tRNAs and their mimics in bacteria, and discuss some of the common themes that arise when comparing these different functions.
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Affiliation(s)
- Assaf Katz
- Programa de Biología Celular y Molecular, ICBM, Facultad de Medicina, Universidad de Chile, Santiago, 8380453, Chile
| | - Sara Elgamal
- Department of Microbiology and The Center for RNA Biology, Ohio State University, Columbus, Ohio, 43210, USA
| | - Andrei Rajkovic
- Department of Microbiology and The Center for RNA Biology, Ohio State University, Columbus, Ohio, 43210, USA
| | - Michael Ibba
- Department of Microbiology and The Center for RNA Biology, Ohio State University, Columbus, Ohio, 43210, USA
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20
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Steinchen W, Bange G. The magic dance of the alarmones (p)ppGpp. Mol Microbiol 2016; 101:531-44. [PMID: 27149325 DOI: 10.1111/mmi.13412] [Citation(s) in RCA: 129] [Impact Index Per Article: 16.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/02/2016] [Indexed: 11/26/2022]
Abstract
The alarmones (p)ppGpp are important second messengers that orchestrate pleiotropic adaptations of bacteria and plant chloroplasts in response to starvation and stress. Here, we review our structural and mechanistic knowledge on (p)ppGpp metabolism including their synthesis, degradation and interconversion by a highly diverse set of enzymes. Increasing structural information shows how (p)ppGpp interacts with an incredibly diverse set of different targets that are essential for replication, transcription, translation, ribosome assembly and metabolism. This raises the question how the chemically rather simple (p)ppGpp is able to interact with these different targets? Structural analysis shows that the diversity of (p)ppGpp interaction with cellular targets critically relies on the conformational flexibility of the 3' and 5' phosphate moieties allowing alarmones to efficiently modulate the activity of target structures in a broad concentration range. Current approaches in the design of (p)ppGpp-analogs as future antibiotics might be aided by the comprehension of conformational flexibility exhibited by the magic dancers (p)ppGpp.
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Affiliation(s)
- Wieland Steinchen
- Department of Chemistry, LOEWE Center for Synthetic Microbiology (Synmikro), Philipps University Marburg, Hans-Meerwein-Strasse, Marburg, 35043, Germany
| | - Gert Bange
- Department of Chemistry, LOEWE Center for Synthetic Microbiology (Synmikro), Philipps University Marburg, Hans-Meerwein-Strasse, Marburg, 35043, Germany
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21
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Matheisl S, Berninghausen O, Becker T, Beckmann R. Structure of a human translation termination complex. Nucleic Acids Res 2015; 43:8615-26. [PMID: 26384426 PMCID: PMC4605324 DOI: 10.1093/nar/gkv909] [Citation(s) in RCA: 85] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2015] [Accepted: 08/12/2015] [Indexed: 12/02/2022] Open
Abstract
In contrast to bacteria that have two release factors, RF1 and RF2, eukaryotes only possess one unrelated release factor eRF1, which recognizes all three stop codons of the mRNA and hydrolyses the peptidyl-tRNA bond. While the molecular basis for bacterial termination has been elucidated, high-resolution structures of eukaryotic termination complexes have been lacking. Here we present a 3.8 Å structure of a human translation termination complex with eRF1 decoding a UAA(A) stop codon. The complex was formed using the human cytomegalovirus (hCMV) stalling peptide, which perturbs the peptidyltransferase center (PTC) to silence the hydrolysis activity of eRF1. Moreover, unlike sense codons or bacterial stop codons, the UAA stop codon adopts a U-turn-like conformation within a pocket formed by eRF1 and the ribosome. Inducing the U-turn conformation for stop codon recognition rationalizes how decoding by eRF1 includes monitoring geometry in order to discriminate against sense codons.
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Affiliation(s)
- Sarah Matheisl
- Gene Center and Center for integrated Protein Science Munich, Department of Biochemistry, Feodor-Lynen-Str. 25, University of Munich, 81377 Munich, Germany
| | - Otto Berninghausen
- Gene Center and Center for integrated Protein Science Munich, Department of Biochemistry, Feodor-Lynen-Str. 25, University of Munich, 81377 Munich, Germany
| | - Thomas Becker
- Gene Center and Center for integrated Protein Science Munich, Department of Biochemistry, Feodor-Lynen-Str. 25, University of Munich, 81377 Munich, Germany
| | - Roland Beckmann
- Gene Center and Center for integrated Protein Science Munich, Department of Biochemistry, Feodor-Lynen-Str. 25, University of Munich, 81377 Munich, Germany
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22
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Kowalinski E, Schuller A, Green R, Conti E. Saccharomyces cerevisiae Ski7 Is a GTP-Binding Protein Adopting the Characteristic Conformation of Active Translational GTPases. Structure 2015; 23:1336-43. [PMID: 26051716 PMCID: PMC4509514 DOI: 10.1016/j.str.2015.04.018] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2015] [Revised: 04/29/2015] [Accepted: 04/29/2015] [Indexed: 01/04/2023]
Abstract
Ski7 is a cofactor of the cytoplasmic exosome in budding yeast, functioning in both mRNA turnover and non-stop decay (NSD), a surveillance pathway that degrades faulty mRNAs lacking a stop codon. The C-terminal region of Ski7 (Ski7C) shares overall sequence similarity with the translational GTPase (trGTPase) Hbs1, but whether Ski7 has retained the properties of a trGTPase is unclear. Here, we report the high-resolution structures of Ski7C bound to either intact guanosine triphosphate (GTP) or guanosine diphosphate-Pi. The individual domains of Ski7C adopt the conformation characteristic of active trGTPases. Furthermore, the nucleotide-binding site of Ski7C shares similar features compared with active trGTPases, notably the presence of a characteristic monovalent cation. However, a suboptimal polar residue at the putative catalytic site and an unusual polar residue that interacts with the γ-phosphate of GTP distinguish Ski7 from other trGTPases, suggesting it might function rather as a GTP-binding protein than as a GTP-hydrolyzing enzyme.
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Affiliation(s)
- Eva Kowalinski
- Department of Structural Cell Biology Department, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Anthony Schuller
- Howard Hughes Medical Institute, Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Rachel Green
- Howard Hughes Medical Institute, Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Elena Conti
- Department of Structural Cell Biology Department, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany.
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23
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Structural Insights into tRNA Dynamics on the Ribosome. Int J Mol Sci 2015; 16:9866-95. [PMID: 25941930 PMCID: PMC4463622 DOI: 10.3390/ijms16059866] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2015] [Revised: 04/21/2015] [Accepted: 04/22/2015] [Indexed: 11/17/2022] Open
Abstract
High-resolution structures at different stages, as well as biochemical, single molecule and computational approaches have highlighted the elasticity of tRNA molecules when bound to the ribosome. It is well acknowledged that the inherent structural flexibility of the tRNA lies at the heart of the protein synthesis process. Here, we review the recent advances and describe considerations that the conformational changes of the tRNA molecules offer about the mechanisms grounded in translation.
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24
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Blanchet S, Rowe M, Von der Haar T, Fabret C, Demais S, Howard MJ, Namy O. New insights into stop codon recognition by eRF1. Nucleic Acids Res 2015; 43:3298-308. [PMID: 25735746 PMCID: PMC4381064 DOI: 10.1093/nar/gkv154] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2015] [Accepted: 02/17/2015] [Indexed: 11/25/2022] Open
Abstract
In eukaryotes, translation termination is performed by eRF1, which recognizes stop codons via its N-terminal domain. Many previous studies based on point mutagenesis, cross-linking experiments or eRF1 chimeras have investigated the mechanism by which the stop signal is decoded by eRF1. Conserved motifs, such as GTS and YxCxxxF, were found to be important for termination efficiency, but the recognition mechanism remains unclear. We characterized a region of the eRF1 N-terminal domain, the P1 pocket, that we had previously shown to be involved in termination efficiency. We performed alanine scanning mutagenesis of this region, and we quantified in vivo readthrough efficiency for each alanine mutant. We identified two residues, arginine 65 and lysine 109, as critical for recognition of the three stop codons. We also demonstrated a role for the serine 33 and serine 70 residues in UGA decoding in vivo. NMR analysis of the alanine mutants revealed that the correct conformation of this region was controlled by the YxCxxxF motif. By combining our genetic data with a structural analysis of eRF1 mutants, we were able to formulate a new model in which the stop codon interacts with eRF1 through the P1 pocket.
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Affiliation(s)
- Sandra Blanchet
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Batiment 400, 91400 Orsay, France
| | - Michelle Rowe
- School of Biosciences, University of Kent, Canterbury, Kent, CT2 7NJ, UK
| | | | - Céline Fabret
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Batiment 400, 91400 Orsay, France
| | - Stéphane Demais
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Batiment 400, 91400 Orsay, France
| | - Mark J Howard
- School of Biosciences, University of Kent, Canterbury, Kent, CT2 7NJ, UK
| | - Olivier Namy
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Batiment 400, 91400 Orsay, France
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25
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Petropoulos AD, McDonald ME, Green R, Zaher HS. Distinct roles for release factor 1 and release factor 2 in translational quality control. J Biol Chem 2014; 289:17589-96. [PMID: 24798339 DOI: 10.1074/jbc.m114.564989] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
In bacteria, stop codons are recognized by two similar class 1 release factors, release factor 1 (RF1) and release factor 2 (RF2). Normally, during termination, the class 2 release factor 3 (RF3), a GTPase, functions downstream of peptide release where it accelerates the dissociation of RF1/RF2 prior to ribosome recycling. In addition to their canonical function in termination, both classes of release factor are also involved in a post peptidyl transfer quality control (post PT QC) mechanism where the termination factors recognize mismatched (i.e. error-containing) ribosome complexes and promote premature termination. Here, using a well defined in vitro system, we explored the role of release factors in canonical termination and post PT QC. As reported previously, during canonical termination, RF1 and RF2 recognize stop codons in a similar manner, and RF3 accelerates their rate of dissociation. During post PT QC, only RF2 (and not RF1) effectively binds to mismatched ribosome complexes; and whereas the addition of RF3 to RF2 increased its rate of release on mismatched complexes, the addition of RF3 to RF1 inhibited its rate of release but increased the rate of peptidyl-tRNA dissociation. Our data strongly suggest that RF2, in addition to its primary role in peptide release, functions as the principle factor for post PT QC.
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Affiliation(s)
- Alexandros D Petropoulos
- From the Howard Hughes Medical Institute, Department of Molecular Biology and Genetics, The Johns Hopkins University School of Medicine, Baltimore, Maryland 21205 and
| | - Megan E McDonald
- From the Howard Hughes Medical Institute, Department of Molecular Biology and Genetics, The Johns Hopkins University School of Medicine, Baltimore, Maryland 21205 and
| | - Rachel Green
- From the Howard Hughes Medical Institute, Department of Molecular Biology and Genetics, The Johns Hopkins University School of Medicine, Baltimore, Maryland 21205 and
| | - Hani S Zaher
- the Department of Biology, Washington University in St. Louis, St. Louis, Missouri 63130
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26
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Koutmou KS, McDonald ME, Brunelle JL, Green R. RF3:GTP promotes rapid dissociation of the class 1 termination factor. RNA (NEW YORK, N.Y.) 2014; 20:609-620. [PMID: 24667215 PMCID: PMC3988563 DOI: 10.1261/rna.042523.113] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2013] [Accepted: 01/24/2014] [Indexed: 05/29/2023]
Abstract
Translation termination is promoted by class 1 and class 2 release factors in all domains of life. While the role of the bacterial class 1 factors, RF1 and RF2, in translation termination is well understood, the precise contribution of the bacterial class 2 release factor, RF3, to this process remains less clear. Here, we use a combination of binding assays and pre-steady state kinetics to provide a kinetic and thermodynamic framework for understanding the role of the translational GTPase RF3 in bacterial translation termination. First, we find that GDP and GTP have similar affinities for RF3 and that, on average, the t1/2 for nucleotide dissociation from the protein is 1-2 min. We further show that RF3:GDPNP, but not RF3:GDP, tightly associates with the ribosome pre- and post-termination complexes. Finally, we use stopped-flow fluorescence to demonstrate that RF3:GTP enhances RF1 dissociation rates by over 500-fold, providing the first direct observation of this step. Importantly, catalytically inactive variants of RF1 are not rapidly dissociated from the ribosome by RF3:GTP, arguing that a rotated state of the ribosome must be sampled for this step to efficiently occur. Together, these data define a more precise role for RF3 in translation termination and provide insights into the function of this family of translational GTPases.
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Affiliation(s)
- Kristin S. Koutmou
- Howard Hughes Medical Institute, Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
| | - Megan E. McDonald
- Howard Hughes Medical Institute, Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
| | - Julie L. Brunelle
- Howard Hughes Medical Institute, Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
| | - Rachel Green
- Howard Hughes Medical Institute, Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
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27
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Kobayashi K, Ishitani R, Nureki O. Recent structural studies on Dom34/aPelota and Hbs1/aEF1α: important factors for solving general problems of ribosomal stall in translation. Biophysics (Nagoya-shi) 2013; 9:131-40. [PMID: 27493551 PMCID: PMC4629679 DOI: 10.2142/biophysics.9.131] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2013] [Accepted: 08/12/2013] [Indexed: 12/01/2022] Open
Abstract
In the translation process, translating ribosomes usually move on an mRNA until they reach the stop codon. However, when ribosomes translate an aberrant mRNA, they stall. Then, ribosomes are rescued from the aberrant mRNA, and the aberrant mRNA is subsequently degraded. In eukaryotes, Pelota (Dom34 in yeast) and Hbs1 are responsible for solving general problems of ribosomal stall in translation. In archaea, aPelota and aEF1α, homologous to Pelota and Hbs1, respectively, are considered to be involved in that process. In recent years, great progress has been made in determining structures of Dom34/aPelota and Hbs1/aEF1α. In this review, we focus on the functional roles of Dom34/aPelota and Hbs1/aEF1α in ribosome rescue, based on recent structural studies of them. We will also present questions to be answered by future work.
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Affiliation(s)
- Kan Kobayashi
- Department of Biophysics and Biochemistry, Graduate School of Science, The University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan
| | - Ryuichiro Ishitani
- Department of Biophysics and Biochemistry, Graduate School of Science, The University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan
| | - Osamu Nureki
- Department of Biophysics and Biochemistry, Graduate School of Science, The University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan
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28
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Blasticidin S inhibits translation by trapping deformed tRNA on the ribosome. Proc Natl Acad Sci U S A 2013; 110:12283-8. [PMID: 23824292 DOI: 10.1073/pnas.1304922110] [Citation(s) in RCA: 72] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The antibiotic blasticidin S (BlaS) is a potent inhibitor of protein synthesis in bacteria and eukaryotes. We have determined a 3.4-Å crystal structure of BlaS bound to a 70S⋅tRNA ribosome complex and performed biochemical and single-molecule FRET experiments to determine the mechanism of action of the antibiotic. We find that BlaS enhances tRNA binding to the P site of the large ribosomal subunit and slows down spontaneous intersubunit rotation in pretranslocation ribosomes. However, the antibiotic has negligible effect on elongation factor G catalyzed translocation of tRNA and mRNA. The crystal structure of the antibiotic-ribosome complex reveals that BlaS impedes protein synthesis through a unique mechanism by bending the 3' terminus of the P-site tRNA toward the A site of the large ribosomal subunit. Biochemical experiments demonstrate that stabilization of the deformed conformation of the P-site tRNA by BlaS strongly inhibits peptidyl-tRNA hydrolysis by release factors and, to a lesser extent, peptide bond formation.
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29
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Santos N, Zhu J, Donohue JP, Korostelev AA, Noller HF. Crystal structure of the 70S ribosome bound with the Q253P mutant form of release factor RF2. Structure 2013; 21:1258-63. [PMID: 23769667 DOI: 10.1016/j.str.2013.04.028] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2013] [Revised: 03/26/2013] [Accepted: 04/26/2013] [Indexed: 11/25/2022]
Abstract
Bacterial translation termination is mediated by release factors RF1 and RF2, which recognize stop codons and catalyze hydrolysis of the peptidyl-tRNA ester bond. The catalytic mechanism has been debated. We proposed that the backbone amide NH group, rather than the side chain, of the glutamine of the universally conserved GGQ motif participates in catalysis by H-bonding to the tetrahedral transition-state intermediate and by product stabilization. This was supported by complete loss of RF1 catalytic activity when glutamine is replaced by proline, the only residue that lacks a backbone NH group. Here, we present the 3.4 Å crystal structure of the ribosome complex containing the RF2 Q253P mutant and find that its fold, including the GGP sequence, is virtually identical to that of wild-type RF2. This rules out proline-induced misfolding and further supports the proposal that catalytic activity requires interaction of the Gln-253 backbone amide with the 3' end of peptidyl-tRNA.
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Affiliation(s)
- Natalia Santos
- Center for Molecular Biology of RNA and Department of Molecular, Cell and Developmental Biology, University of California at Santa Cruz, Santa Cruz, CA 95064, USA
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30
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Rodnina MV. The ribosome as a versatile catalyst: reactions at the peptidyl transferase center. Curr Opin Struct Biol 2013; 23:595-602. [PMID: 23711800 DOI: 10.1016/j.sbi.2013.04.012] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2013] [Accepted: 04/10/2013] [Indexed: 11/29/2022]
Abstract
In all contemporary organisms, the active site of the ribosome--the peptidyl transferase center--catalyzes two distinct reactions, peptide bond formation between peptidyl-tRNA and aminoacyl-tRNA as well as the hydrolysis of peptidyl-tRNA with the help of a release factor. However, when provided with appropriate substrates, ribosomes can also catalyze a broad range of other chemical reaction, which provides the basis for orthogonal translation and synthesis of alloproteins from unnatural building blocks. Advances in understanding the mechanisms of the two ubiquitous reactions, the peptide bond formation and peptide release, provide insights into the versatility of the active site of the ribosome. Release factors 1 and 2 and elongation factor P are auxiliary factors that augment the intrinsic catalytic activity of the ribosome in special cases.
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Affiliation(s)
- Marina V Rodnina
- Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, 37077 Goettingen, Germany.
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