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Mattingly JM, Nguyen HA, Roy B, Fredrick K, Dunham CM. Structural analysis of noncanonical translation initiation complexes. J Biol Chem 2024:107743. [PMID: 39222680 DOI: 10.1016/j.jbc.2024.107743] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2024] [Revised: 08/14/2024] [Accepted: 08/23/2024] [Indexed: 09/04/2024] Open
Abstract
Translation initiation is a highly regulated, multi-step process which is critical for efficient and accurate protein synthesis. In bacteria, initiation begins when mRNA, initiation factors, and a dedicated initiator fMet-tRNAfMet bind the small (30S) ribosomal subunit. Specific binding of fMet-tRNAfMet in the peptidyl (P) site is mediated by the inspection of the fMet moiety by initiation factor IF2 and of three conserved G-C base pairs in the tRNA anticodon stem by the 30S head domain. Tandem A-minor interactions form between 16S ribosomal RNA nucleotides A1339 and G1338 and tRNA base pairs G30-C40 and G29-C41, respectively. Swapping the G30-C40 pair of tRNAfMet with C-G reduces discrimination against the noncanonical start codon CUG in vitro, suggesting crosstalk between gripping of the anticodon stem and recognition of the start codon. Here, we solved electron cryomicroscopy structures of E. coli 70S initiation complexes containing an fMet-tRNAfMet G30-C40 variant paired to noncanonical CUG start codon, in the presence or absence of IF2 and the non-hydrolyzable GTP analog GDPCP, alongside structures of 70S initiation complexes containing this tRNAfMet variant paired to the canonical bacterial start codons AUG, GUG, and UUG. We find that the M1 mutation weakens A-minor interactions between tRNAfMet and 16S nucleotides A1339 and G1338, with IF2 strengthening the interaction of G1338 with the tRNA minor groove. These structures suggest how even slight changes to the recognition of the fMet-tRNAfMet anticodon stem by the ribosome can impact start codon selection.
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Affiliation(s)
- Jacob M Mattingly
- Department of Chemistry, Emory University, Atlanta, GA, USA; Graduate Program in Biochemistry, Cell and Developmental Biology, Emory University, Atlanta, GA, USA
| | - Ha An Nguyen
- Department of Chemistry, Emory University, Atlanta, GA, USA
| | - Bappaditya Roy
- Department of Microbiology and Center for RNA Biology, The Ohio State University, Columbus, Ohio, USA
| | - Kurt Fredrick
- Department of Microbiology and Center for RNA Biology, The Ohio State University, Columbus, Ohio, USA
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2
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Pandiarajan I, Walunj SB, Banerjee N, Rout J, Srivastava S, Patankar S, Kaledhonkar S. Application of bio-layer interferometry for the analysis of ribosome-protein interactions. Front Mol Biosci 2024; 11:1398964. [PMID: 39148630 PMCID: PMC11325027 DOI: 10.3389/fmolb.2024.1398964] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2024] [Accepted: 07/08/2024] [Indexed: 08/17/2024] Open
Abstract
The ribosome, a ribonucleoprotein complex, performs the function of protein translation. While ribosomal RNA catalyzes polypeptide formation, several proteins assist the ribosome throughout the translation process. Studying the biochemical and kinetic properties of these proteins interacting with the ribosome is vital for elucidating their roles. Various techniques, such as zonal centrifugation, pull-down assays, dynamic light scattering (DLS), fluorescence polarization, and surface plasmon resonance (SPR) are employed for this purpose, each presenting unique advantages and limitations. We add to the repertoire of techniques by using Bio-Layer Interferometry (BLI) to examine interactions between the ribosome and translation factors. Our findings demonstrate that BLI can detect interactions of Escherichia coli ribosomes with two proteins: E. coli initiation factor 2 (IF2) and P. falciparum translation enhancing factor (PTEF). A protein (Green Fluorescent Protein; GFP) known not to bind to E. coli ribosomes, shows no binding in the BLI assay. We show that BLI could be used to study the ribosome-protein interactions as it has key advantages like label-free procedures, ease of assay performance, and ribosome sample reuse. Our results highlight the comprehensive use of BLI in studying the ribosome-protein interactions, in addition to studying protein-protein and protein-ligand interactions.
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Affiliation(s)
- Ilamathy Pandiarajan
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, India
| | - Sujata B Walunj
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, India
| | - Nirjhar Banerjee
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, India
| | - Janmejaya Rout
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, India
| | - Sanjeeva Srivastava
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, India
| | - Swati Patankar
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, India
| | - Sandip Kaledhonkar
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, India
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3
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Li L, Rybak MY, Lin J, Gagnon MG. The ribosome termination complex remodels release factor RF3 and ejects GDP. Nat Struct Mol Biol 2024:10.1038/s41594-024-01360-0. [PMID: 39030416 DOI: 10.1038/s41594-024-01360-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Accepted: 06/26/2024] [Indexed: 07/21/2024]
Abstract
Translation termination involves release factors RF1, RF2 and the GTPase RF3 that recycles RF1 and RF2 from the ribosome. RF3 dissociates from the ribosome in the GDP-bound form and must then exchange GDP for GTP. The 70S ribosome termination complex (70S-TC) accelerates GDP exchange in RF3, suggesting that the 70S-TC can function as the guanine nucleotide exchange factor for RF3. Here, we use cryogenic-electron microscopy to elucidate the mechanism of GDP dissociation from RF3 catalyzed by the Escherichia coli 70S-TC. The non-rotated ribosome bound to RF1 remodels RF3 and induces a peptide flip in the phosphate-binding loop, efficiently ejecting GDP. Binding of GTP allows RF3 to dock at the GTPase center, promoting the dissociation of RF1 from the ribosome. The structures recapitulate the functional cycle of RF3 on the ribosome and uncover the mechanism by which the 70S-TC allosterically dismantles the phosphate-binding groove in RF3, a previously overlooked function of the ribosome.
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Affiliation(s)
- Li Li
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai, China
- Center for mRNA Translational Research, Fudan University, Shanghai, China
| | - Mariia Yu Rybak
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, USA
| | - Jinzhong Lin
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai, China.
- Center for mRNA Translational Research, Fudan University, Shanghai, China.
| | - Matthieu G Gagnon
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, USA.
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, USA.
- Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, TX, USA.
- Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, TX, USA.
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4
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Wu Y, Ni MT, Wang YH, Wang C, Hou H, Zhang X, Zhou J. Structural basis of translation inhibition by a valine tRNA-derived fragment. Life Sci Alliance 2024; 7:e202302488. [PMID: 38599770 PMCID: PMC11009984 DOI: 10.26508/lsa.202302488] [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: 11/18/2023] [Revised: 03/22/2024] [Accepted: 03/22/2024] [Indexed: 04/12/2024] Open
Abstract
Translational regulation by non-coding RNAs is a mechanism commonly used by cells to fine-tune gene expression. A fragment derived from an archaeal valine tRNA (Val-tRF) has been previously identified to bind the small subunit of the ribosome and inhibit translation in Haloferax volcanii Here, we present three cryo-electron microscopy structures of Val-tRF bound to the small subunit of Sulfolobus acidocaldarius ribosomes at resolutions between 4.02 and 4.53 Å. Within these complexes, Val-tRF was observed to bind to conserved RNA-interacting sites, including the ribosomal decoding center. The binding of Val-tRF destabilizes helices h24, h44, and h45 and the anti-Shine-Dalgarno sequence of 16S rRNA. The binding position of this molecule partially overlaps with the translation initiation factor aIF1A and occludes the mRNA P-site codon. Moreover, we found that the binding of Val-tRF is associated with steric hindrance of the H69 base of 23S rRNA in the large ribosome subunit, thereby preventing 70S assembly. Our data exemplify how tRNA-derived fragments bind to ribosomes and provide new insights into the mechanisms underlying translation inhibition by Val-tRFs.
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Affiliation(s)
- Yun Wu
- Life Sciences Institute, Zhejiang University, Hangzhou, China
| | - Meng-Ting Ni
- Life Sciences Institute, Zhejiang University, Hangzhou, China
| | - Ying-Hui Wang
- Life Sciences Institute, Zhejiang University, Hangzhou, China
| | - Chen Wang
- Center for Cryo-Electron Microscopy, Zhejiang University School of Medicine, Hangzhou, China
- Department of Pathology of Sir Run Run Shaw Hospital and Department of Biophysics, Zhejiang University School of Medicine, Hangzhou, China
| | - Hai Hou
- Institute of Medical Research, Northwestern Polytechnical University, Xi'an Shaanxi, China
| | - Xing Zhang
- Center for Cryo-Electron Microscopy, Zhejiang University School of Medicine, Hangzhou, China
- Department of Pathology of Sir Run Run Shaw Hospital and Department of Biophysics, Zhejiang University School of Medicine, Hangzhou, China
| | - Jie Zhou
- Life Sciences Institute, Zhejiang University, Hangzhou, China
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5
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Seely SM, Basu RS, Gagnon MG. Mechanistic insights into the alternative ribosome recycling by HflXr. Nucleic Acids Res 2024; 52:4053-4066. [PMID: 38407413 DOI: 10.1093/nar/gkae128] [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: 11/06/2023] [Revised: 02/02/2024] [Accepted: 02/19/2024] [Indexed: 02/27/2024] Open
Abstract
During stress conditions such as heat shock and antibiotic exposure, ribosomes stall on messenger RNAs, leading to inhibition of protein synthesis. To remobilize ribosomes, bacteria use rescue factors such as HflXr, a homolog of the conserved housekeeping GTPase HflX that catalyzes the dissociation of translationally inactive ribosomes into individual subunits. Here we use time-resolved cryo-electron microscopy to elucidate the mechanism of ribosome recycling by Listeria monocytogenes HflXr. Within the 70S ribosome, HflXr displaces helix H69 of the 50S subunit and induces long-range movements of the platform domain of the 30S subunit, disrupting inter-subunit bridges B2b, B2c, B4, B7a and B7b. Our findings unveil a unique ribosome recycling strategy by HflXr which is distinct from that mediated by RRF and EF-G. The resemblance between HflXr and housekeeping HflX suggests that the alternative ribosome recycling mechanism reported here is universal in the prokaryotic kingdom.
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Affiliation(s)
- Savannah M Seely
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Ritwika S Basu
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Matthieu G Gagnon
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX 77555, USA
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX 77555, USA
- Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, TX 77555, USA
- Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, TX 77555, USA
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6
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Kazan R, Bourgeois G, Lazennec-Schurdevin C, Coureux PD, Mechulam Y, Schmitt E. Structural insights into the evolution of late steps of translation initiation in the three domains of life. Biochimie 2024; 217:31-41. [PMID: 36773835 DOI: 10.1016/j.biochi.2023.02.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Revised: 02/06/2023] [Accepted: 02/06/2023] [Indexed: 02/11/2023]
Abstract
In eukaryotes and in archaea late steps of translation initiation involve the two initiation factors e/aIF5B and e/aIF1A. These two factors are also orthologous to the bacterial IF2 and IF1 proteins, respectively. Recent cryo-EM studies showed how e/aIF5B and e/aIF1A cooperate on the small ribosomal subunit to favor the binding of the large ribosomal subunit and the formation of a ribosome competent for elongation. In this review, pioneering studies and recent biochemical and structural results providing new insights into the role of a/eIF5B in archaea and eukaryotes will be presented. Recent structures will also be compared to orthologous bacterial initiation complexes to highlight domain-specific features and the evolution of initiation mechanisms.
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Affiliation(s)
- Ramy Kazan
- Laboratoire de Biologie Structurale de la Cellule, BIOC, CNRS, Ecole polytechnique, Institut Polytechnique de Paris, 91120, Palaiseau, France
| | - Gabrielle Bourgeois
- Laboratoire de Biologie Structurale de la Cellule, BIOC, CNRS, Ecole polytechnique, Institut Polytechnique de Paris, 91120, Palaiseau, France
| | - Christine Lazennec-Schurdevin
- Laboratoire de Biologie Structurale de la Cellule, BIOC, CNRS, Ecole polytechnique, Institut Polytechnique de Paris, 91120, Palaiseau, France
| | - Pierre-Damien Coureux
- Laboratoire de Biologie Structurale de la Cellule, BIOC, CNRS, Ecole polytechnique, Institut Polytechnique de Paris, 91120, Palaiseau, France
| | - Yves Mechulam
- Laboratoire de Biologie Structurale de la Cellule, BIOC, CNRS, Ecole polytechnique, Institut Polytechnique de Paris, 91120, Palaiseau, France
| | - Emmanuelle Schmitt
- Laboratoire de Biologie Structurale de la Cellule, BIOC, CNRS, Ecole polytechnique, Institut Polytechnique de Paris, 91120, Palaiseau, France.
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7
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Huang T, Choi J, Prabhakar A, Puglisi JD, Petrov A. Partial spontaneous intersubunit rotations in pretranslocation ribosomes. Proc Natl Acad Sci U S A 2023; 120:e2114979120. [PMID: 37801472 PMCID: PMC10576065 DOI: 10.1073/pnas.2114979120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Accepted: 08/29/2023] [Indexed: 10/08/2023] Open
Abstract
The two main steps of translation, peptidyl transfer, and translocation are accompanied by counterclockwise and clockwise rotations of the large and small ribosomal subunits with respect to each other. Upon peptidyl transfer, the small ribosomal subunit rotates counterclockwise relative to the large subunit, placing the ribosome into the rotated conformation. Simultaneously, tRNAs move into the hybrid conformation, and the L1 stalk moves inward toward the P-site tRNA. The conformational dynamics of pretranslocation ribosomes were extensively studied by ensemble and single-molecule methods. Different experimental modalities tracking ribosomal subunits, tRNAs, and the L1 stalk showed that pretranslocation ribosomes undergo spontaneous conformational transitions. Thus, peptidyl transfer unlocks the ribosome and decreases an energy barrier for the reverse ribosome rotation during translocation. However, the tracking of translation with ribosomes labeled at rRNA helices h44 and H101 showed a lack of spontaneous rotations in pretranslocation complexes. Therefore, reverse intersubunit rotations occur during EF-G catalyzed translocation. To reconcile these views, we used high-speed single-molecule microscopy to follow translation in real time. We showed spontaneous rotations in puromycin-released h44-H101 dye-labeled ribosomes. During elongation, the h44-H101 ribosomes undergo partial spontaneous rotations. Spontaneous rotations in h44-H101-labeled ribosomes are restricted prior to aminoacyl-tRNA binding. The pretranslocation h44-H101 ribosomes spontaneously exchanged between three different rotational states. This demonstrates that peptidyl transfer unlocks spontaneous rotations and pretranslocation ribosomes can adopt several thermally accessible conformations, thus supporting the Brownian model of translocation.
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Affiliation(s)
- Tianhan Huang
- Department of Biological Sciences, Auburn University, Auburn, AL36849
| | - Junhong Choi
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA94305
| | - Arjun Prabhakar
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA94305
| | - Joseph D. Puglisi
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA94305
| | - Alexey Petrov
- Department of Biological Sciences, Auburn University, Auburn, AL36849
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8
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Zafar H, Hassan AH, Demo G. Translation machinery captured in motion. WILEY INTERDISCIPLINARY REVIEWS. RNA 2023; 14:e1792. [PMID: 37132456 DOI: 10.1002/wrna.1792] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 03/14/2023] [Accepted: 04/17/2023] [Indexed: 05/04/2023]
Abstract
Translation accuracy is one of the most critical factors for protein synthesis. It is regulated by the ribosome and its dynamic behavior, along with translation factors that direct ribosome rearrangements to make translation a uniform process. Earlier structural studies of the ribosome complex with arrested translation factors laid the foundation for an understanding of ribosome dynamics and the translation process as such. Recent technological advances in time-resolved and ensemble cryo-EM have made it possible to study translation in real time at high resolution. These methods provided a detailed view of translation in bacteria for all three phases: initiation, elongation, and termination. In this review, we focus on translation factors (in some cases GTP activation) and their ability to monitor and respond to ribosome organization to enable efficient and accurate translation. This article is categorized under: Translation > Ribosome Structure/Function Translation > Mechanisms.
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Affiliation(s)
- Hassan Zafar
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Ahmed H Hassan
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Gabriel Demo
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic
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9
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Das A, Bao C, Ermolenko DN. Comparing FRET Pairs that Report on Intersubunit Rotation in Bacterial Ribosomes. J Mol Biol 2023; 435:168185. [PMID: 37348753 PMCID: PMC10528089 DOI: 10.1016/j.jmb.2023.168185] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Revised: 05/03/2023] [Accepted: 06/14/2023] [Indexed: 06/24/2023]
Abstract
Mediated by elongation factor G (EF-G), ribosome translocation along mRNA is accompanied by rotational movement between ribosomal subunits. Here, we reassess whether the intersubunit rotation requires GTP hydrolysis by EF-G or can occur spontaneously. To that end, we employ two independent FRET assays, which are based on labeling either ribosomal proteins (bS6 and bL9) or rRNAs (h44 of 16S and H101 of 23S rRNA). Both FRET pairs reveal three FRET states, corresponding to the non-rotated, rotated and semi-rotated conformations of the ribosome. Both FRET assays show that in the absence of EF-G, pre-translocation ribosomes containing deacylated P-site tRNA undergo spontaneous intersubunit rotations between non-rotated and rotated conformations. While the two FRET pairs exhibit largely similar behavior, they substantially differ in the fraction of ribosomes showing spontaneous fluctuations. Nevertheless, instead of being an invariable intrinsic property of each FRET pair, the fraction of spontaneously fluctuating molecules changes in both FRET assays depending on experimental conditions. Our results underscore importance of using multiple FRET pairs in studies of ribosome dynamics and highlight the role of thermally-driven large-scale ribosome rearrangements in translation.
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Affiliation(s)
- Ananya Das
- Department of Biochemistry & Biophysics, School of Medicine and Dentistry, and Center for RNA Biology, University of Rochester, Rochester, NY 14642, United States
| | - Chen Bao
- Department of Biochemistry & Biophysics, School of Medicine and Dentistry, and Center for RNA Biology, University of Rochester, Rochester, NY 14642, United States
| | - Dmitri N Ermolenko
- Department of Biochemistry & Biophysics, School of Medicine and Dentistry, and Center for RNA Biology, University of Rochester, Rochester, NY 14642, United States.
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10
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Li Y, Majumdar S, Treen R, Sharma MR, Corro J, Gamper HB, Manjari SR, Prusa J, Banavali NK, Stallings CL, Hou YM, Agrawal RK, Ojha AK. Starvation sensing by mycobacterial RelA/SpoT homologue through constitutive surveillance of translation. Proc Natl Acad Sci U S A 2023; 120:e2302006120. [PMID: 37216503 PMCID: PMC10235957 DOI: 10.1073/pnas.2302006120] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2023] [Accepted: 04/28/2023] [Indexed: 05/24/2023] Open
Abstract
The stringent response, which leads to persistence of nutrient-starved mycobacteria, is induced by activation of the RelA/SpoT homolog (Rsh) upon entry of a deacylated-tRNA in a translating ribosome. However, the mechanism by which Rsh identifies such ribosomes in vivo remains unclear. Here, we show that conditions inducing ribosome hibernation result in loss of intracellular Rsh in a Clp protease-dependent manner. This loss is also observed in nonstarved cells using mutations in Rsh that block its interaction with the ribosome, indicating that Rsh association with the ribosome is important for Rsh stability. The cryo-EM structure of the Rsh-bound 70S ribosome in a translation initiation complex reveals unknown interactions between the ACT domain of Rsh and components of the ribosomal L7/L12 stalk base, suggesting that the aminoacylation status of A-site tRNA is surveilled during the first cycle of elongation. Altogether, we propose a surveillance model of Rsh activation that originates from its constitutive interaction with the ribosomes entering the translation cycle.
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Affiliation(s)
- Yunlong Li
- Division of Genetics, New York State Department of Health, Wadsworth Center, Albany, NY12208
| | - Soneya Majumdar
- Division of Translational Medicine, New York State Department of Health, Wadsworth Center, Albany, NY12237
| | - Ryan Treen
- Division of Genetics, New York State Department of Health, Wadsworth Center, Albany, NY12208
- Department of Biomedical Sciences, School of Public Health, University at Albany, Albany, NY12208
| | - Manjuli R. Sharma
- Division of Translational Medicine, New York State Department of Health, Wadsworth Center, Albany, NY12237
| | - Jamie Corro
- Division of Genetics, New York State Department of Health, Wadsworth Center, Albany, NY12208
- Department of Biomedical Sciences, School of Public Health, University at Albany, Albany, NY12208
| | - Howard B. Gamper
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, PA19107
| | - Swati R. Manjari
- Division of Translational Medicine, New York State Department of Health, Wadsworth Center, Albany, NY12237
| | - Jerome Prusa
- Department of Molecular Microbiology, Washington University in St. Louis School of Medicine, St. Louis, MO63110
| | - Nilesh K. Banavali
- Division of Translational Medicine, New York State Department of Health, Wadsworth Center, Albany, NY12237
| | - Christina L. Stallings
- Department of Molecular Microbiology, Washington University in St. Louis School of Medicine, St. Louis, MO63110
| | - Ya-Ming Hou
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, PA19107
| | - Rajendra K. Agrawal
- Division of Translational Medicine, New York State Department of Health, Wadsworth Center, Albany, NY12237
- Department of Biomedical Sciences, School of Public Health, University at Albany, Albany, NY12208
| | - Anil K. Ojha
- Division of Genetics, New York State Department of Health, Wadsworth Center, Albany, NY12208
- Department of Biomedical Sciences, School of Public Health, University at Albany, Albany, NY12208
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11
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Das A, Bao C, Ermolenko DN. Comparing FRET pairs that report on intersubunit rotation in bacterial ribosomes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.09.540051. [PMID: 37214817 PMCID: PMC10197640 DOI: 10.1101/2023.05.09.540051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Mediated by elongation factor G (EF-G), ribosome translocation along mRNA is accompanied by rotational movement between ribosomal subunits. Here, we reassess whether the intersubunit rotation requires GTP hydrolysis by EF-G or can occur spontaneously. To that end, we employ two independent FRET assays, which are based on labeling either ribosomal proteins (bS6 and bL9) or rRNAs (h44 of 16S and H101 of 23S rRNA). Both FRET pairs reveal three FRET states, corresponding to the non-rotated, rotated and semi-rotated conformations of the ribosome. Both FRET assays show that in the absence of EF-G, pre-translocation ribosomes containing deacylated P-site tRNA undergo spontaneous intersubunit rotations between non-rotated and rotated conformations. While the two FRET pairs exhibit largely similar behavior, they substantially differ in the fraction of ribosomes showing spontaneous fluctuations. Nevertheless, instead of being an invariable intrinsic property of each FRET pair, the fraction of spontaneously fluctuating molecules changes in both FRET assays depending on experimental conditions. Our results underscore importance of using multiple FRET pairs in studies of ribosome dynamics and highlight the role of thermally-driven large-scale ribosome rearrangements in translation.
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12
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Hassan A, Byju S, Freitas F, Roc C, Pender N, Nguyen K, Kimbrough E, Mattingly J, Gonzalez Jr. R, de Oliveira R, Dunham C, Whitford P. Ratchet, swivel, tilt and roll: a complete description of subunit rotation in the ribosome. Nucleic Acids Res 2023; 51:919-934. [PMID: 36583339 PMCID: PMC9881166 DOI: 10.1093/nar/gkac1211] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Revised: 12/01/2022] [Accepted: 12/06/2022] [Indexed: 12/31/2022] Open
Abstract
Protein synthesis by the ribosome requires large-scale rearrangements of the 'small' subunit (SSU; ∼1 MDa), including inter- and intra-subunit rotational motions. However, with nearly 2000 structures of ribosomes and ribosomal subunits now publicly available, it is exceedingly difficult to design experiments based on analysis of all known rotation states. To overcome this, we developed an approach where the orientation of each SSU head and body is described in terms of three angular coordinates (rotation, tilt and tilt direction) and a single translation. By considering the entire RCSB PDB database, we describe 1208 fully-assembled ribosome complexes and 334 isolated small subunits, which span >50 species. This reveals aspects of subunit rearrangements that are universal, and others that are organism/domain-specific. For example, we show that tilt-like rearrangements of the SSU body (i.e. 'rolling') are pervasive in both prokaryotic and eukaryotic (cytosolic and mitochondrial) ribosomes. As another example, domain orientations associated with frameshifting in bacteria are similar to those found in eukaryotic ribosomes. Together, this study establishes a common foundation with which structural, simulation, single-molecule and biochemical efforts can more precisely interrogate the dynamics of this prototypical molecular machine.
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Affiliation(s)
- Asem Hassan
- Department of Physics, Northeastern University, Dana Research Center 111, 360 Huntington Ave, Boston, MA 02115, USA
- Center for Theoretical Biological Physics, Northeastern University, 360 Huntington Ave, Boston, MA 02115, USA
| | - Sandra Byju
- Department of Physics, Northeastern University, Dana Research Center 111, 360 Huntington Ave, Boston, MA 02115, USA
- Center for Theoretical Biological Physics, Northeastern University, 360 Huntington Ave, Boston, MA 02115, USA
| | - Frederico Campos Freitas
- Laboratório de Biofísica Teórica, Departamento de Física, Instituto de Ciências Exatas, Naturais e Educação, Universidade Federal do Triângulo Mineiro, Uberaba, MG 38064-200, Brazil
| | - Claude Roc
- Department of Physics, Northeastern University, Dana Research Center 111, 360 Huntington Ave, Boston, MA 02115, USA
| | - Nisaa Pender
- Department of Physics, Northeastern University, Dana Research Center 111, 360 Huntington Ave, Boston, MA 02115, USA
| | - Kien Nguyen
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - Evelyn M Kimbrough
- Department of Biochemistry, Emory University, Rollins Research Center 4027, 1510 Clifton Rd NE, Atlanta, GA 30322, USA
- Department of Chemistry, Emory University, 1515 Dickey Dr, Atlanta, GA 30322, USA
| | - Jacob M Mattingly
- Department of Biochemistry, Emory University, Rollins Research Center 4027, 1510 Clifton Rd NE, Atlanta, GA 30322, USA
| | | | - Ronaldo Junio de Oliveira
- Laboratório de Biofísica Teórica, Departamento de Física, Instituto de Ciências Exatas, Naturais e Educação, Universidade Federal do Triângulo Mineiro, Uberaba, MG 38064-200, Brazil
| | - Christine M Dunham
- Department of Biochemistry, Emory University, Rollins Research Center 4027, 1510 Clifton Rd NE, Atlanta, GA 30322, USA
| | - Paul C Whitford
- Department of Physics, Northeastern University, Dana Research Center 111, 360 Huntington Ave, Boston, MA 02115, USA
- Center for Theoretical Biological Physics, Northeastern University, 360 Huntington Ave, Boston, MA 02115, USA
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13
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Singh J, Mishra RK, Ayyub SA, Hussain T, Varshney U. The initiation factor 3 (IF3) residues interacting with initiator tRNA elbow modulate the fidelity of translation initiation and growth fitness in Escherichia coli. Nucleic Acids Res 2022; 50:11712-11726. [PMID: 36399509 PMCID: PMC9723500 DOI: 10.1093/nar/gkac1053] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Revised: 10/18/2022] [Accepted: 10/24/2022] [Indexed: 11/19/2022] Open
Abstract
Initiation factor 3 (IF3) regulates the fidelity of bacterial translation initiation by debarring the use of non-canonical start codons or non-initiator tRNAs and prevents premature docking of the 50S ribosomal subunit to the 30S pre-initiation complex (PIC). The C-terminal domain (CTD) of IF3 can carry out most of the known functions of IF3 and sustain Escherichia coli growth. However, the roles of the N-terminal domain (NTD) have remained unclear. We hypothesized that the interaction between NTD and initiator tRNAfMet (i-tRNA) is essential to coordinate the movement of the two domains during the initiation pathway to ensure fidelity of the process. Here, using atomistic molecular dynamics (MD) simulation, we show that R25A/Q33A/R66A mutations do not impact NTD structure but disrupt its interaction with i-tRNA. These NTD residues modulate the fidelity of translation initiation and are crucial for bacterial growth. Our observations also implicate the role of these interactions in the subunit dissociation activity of CTD of IF3. Overall, the study shows that the interactions between NTD of IF3 and i-tRNA are crucial for coupling the movements of NTD and CTD of IF3 during the initiation pathway and in imparting growth fitness to E. coli.
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Affiliation(s)
| | | | - Shreya Ahana Ayyub
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore 560012, India
| | - Tanweer Hussain
- Correspondence may also be addressed to Tanweer Hussain. Tel: +91 80 22933262;
| | - Umesh Varshney
- To whom correspondence should be addressed. Tel: +91 80 22932686;
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14
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Fer E, McGrath KM, Guy L, Hockenberry AJ, Kaçar B. Early divergence of translation initiation and elongation factors. Protein Sci 2022; 31:e4393. [PMID: 36250475 PMCID: PMC9601768 DOI: 10.1002/pro.4393] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Revised: 07/05/2022] [Accepted: 07/11/2022] [Indexed: 11/18/2022]
Abstract
Protein translation is a foundational attribute of all living cells. The translation function carried out by the ribosome critically depends on an assortment of protein interaction partners, collectively referred to as the translation machinery. Various studies suggest that the diversification of the translation machinery occurred prior to the last universal common ancestor, yet it is unclear whether the predecessors of the extant translation machinery factors were functionally distinct from their modern counterparts. Here we reconstructed the shared ancestral trajectory and subsequent evolution of essential translation factor GTPases, elongation factor EF-Tu (aEF-1A/eEF-1A), and initiation factor IF2 (aIF5B/eIF5B). Based upon their similar functions and structural homologies, it has been proposed that EF-Tu and IF2 emerged from an ancient common ancestor. We generated the phylogenetic tree of IF2 and EF-Tu proteins and reconstructed ancestral sequences corresponding to the deepest nodes in their shared evolutionary history, including the last common IF2 and EF-Tu ancestor. By identifying the residue and domain substitutions, as well as structural changes along the phylogenetic history, we developed an evolutionary scenario for the origins, divergence and functional refinement of EF-Tu and IF2 proteins. Our analyses suggest that the common ancestor of IF2 and EF-Tu was an IF2-like GTPase protein. Given the central importance of the translation machinery to all cellular life, its earliest evolutionary constraints and trajectories are key to characterizing the universal constraints and capabilities of cellular evolution.
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Affiliation(s)
- Evrim Fer
- Department of BacteriologyUniversity of Wisconsin‐MadisonMadisonWisconsinUSA
- Microbiology Doctoral Training ProgramUniversity of Wisconsin‐MadisonMadisonWisconsinUSA
- NASA Center for Early Life and EvolutionUniversity of Wisconsin‐MadisonMadisonWisconsinUSA
| | - Kaitlyn M. McGrath
- Department of BacteriologyUniversity of Wisconsin‐MadisonMadisonWisconsinUSA
- NASA Center for Early Life and EvolutionUniversity of Wisconsin‐MadisonMadisonWisconsinUSA
- Department of Molecular and Cellular BiologyUniversity of ArizonaTucsonArizonaUSA
| | - Lionel Guy
- Department of Medical Biochemistry and Microbiology, Science for Life LaboratoryUppsala UniversityUppsalaSweden
| | - Adam J. Hockenberry
- Department of Integrative BiologyThe University of Texas at AustinAustinTexasUSA
| | - Betül Kaçar
- Department of BacteriologyUniversity of Wisconsin‐MadisonMadisonWisconsinUSA
- NASA Center for Early Life and EvolutionUniversity of Wisconsin‐MadisonMadisonWisconsinUSA
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15
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Lapointe CP, Grosely R, Sokabe M, Alvarado C, Wang J, Montabana E, Villa N, Shin BS, Dever TE, Fraser CS, Fernández IS, Puglisi JD. eIF5B and eIF1A reorient initiator tRNA to allow ribosomal subunit joining. Nature 2022; 607:185-190. [PMID: 35732735 PMCID: PMC9728550 DOI: 10.1038/s41586-022-04858-z] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Accepted: 05/11/2022] [Indexed: 01/03/2023]
Abstract
Translation initiation defines the identity and quantity of a synthesized protein. The process is dysregulated in many human diseases1,2. A key commitment step is when the ribosomal subunits join at a translation start site on a messenger RNA to form a functional ribosome. Here, we combined single-molecule spectroscopy and structural methods using an in vitro reconstituted system to examine how the human ribosomal subunits join. Single-molecule fluorescence revealed when the universally conserved eukaryotic initiation factors eIF1A and eIF5B associate with and depart from initiation complexes. Guided by single-molecule dynamics, we visualized initiation complexes that contained both eIF1A and eIF5B using single-particle cryo-electron microscopy. The resulting structure revealed how eukaryote-specific contacts between the two proteins remodel the initiation complex to orient the initiator aminoacyl-tRNA in a conformation compatible with ribosomal subunit joining. Collectively, our findings provide a quantitative and architectural framework for the molecular choreography orchestrated by eIF1A and eIF5B during translation initiation in humans.
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Affiliation(s)
- Christopher P Lapointe
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Rosslyn Grosely
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Masaaki Sokabe
- Department of Molecular and Cellular Biology College of Biological Sciences, University of California, Davis, CA, USA
| | - Carlos Alvarado
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Jinfan Wang
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Elizabeth Montabana
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Nancy Villa
- Department of Molecular and Cellular Biology College of Biological Sciences, University of California, Davis, CA, USA
| | - Byung-Sik Shin
- Section on Protein Biosynthesis, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Thomas E Dever
- Section on Protein Biosynthesis, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Christopher S Fraser
- Department of Molecular and Cellular Biology College of Biological Sciences, University of California, Davis, CA, USA
| | - Israel S Fernández
- Department of Structural Biology, St Jude Children's Research Hospital, Memphis, TN, USA.
| | - Joseph D Puglisi
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA.
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16
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Kazan R, Bourgeois G, Lazennec-Schurdevin C, Larquet E, Mechulam Y, Coureux PD, Schmitt E. Role of aIF5B in archaeal translation initiation. Nucleic Acids Res 2022; 50:6532-6548. [PMID: 35694843 PMCID: PMC9226500 DOI: 10.1093/nar/gkac490] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Revised: 05/20/2022] [Accepted: 05/25/2022] [Indexed: 01/22/2023] Open
Abstract
In eukaryotes and in archaea late steps of translation initiation involve the two initiation factors e/aIF5B and e/aIF1A. In eukaryotes, the role of eIF5B in ribosomal subunit joining is established and structural data showing eIF5B bound to the full ribosome were obtained. To achieve its function, eIF5B collaborates with eIF1A. However, structural data illustrating how these two factors interact on the small ribosomal subunit have long been awaited. The role of the archaeal counterparts, aIF5B and aIF1A, remains to be extensively addressed. Here, we study the late steps of Pyrococcus abyssi translation initiation. Using in vitro reconstituted initiation complexes and light scattering, we show that aIF5B bound to GTP accelerates subunit joining without the need for GTP hydrolysis. We report the crystallographic structures of aIF5B bound to GDP and GTP and analyze domain movements associated to these two nucleotide states. Finally, we present the cryo-EM structure of an initiation complex containing 30S bound to mRNA, Met-tRNAiMet, aIF5B and aIF1A at 2.7 Å resolution. Structural data shows how archaeal 5B and 1A factors cooperate to induce a conformation of the initiator tRNA favorable to subunit joining. Archaeal and eukaryotic features of late steps of translation initiation are discussed.
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Affiliation(s)
- Ramy Kazan
- Laboratoire de Biologie Structurale de la Cellule, BIOC, Ecole polytechnique, CNRS, Institut Polytechnique de Paris, 91128 Palaiseau cedex, France
| | - Gabrielle Bourgeois
- Laboratoire de Biologie Structurale de la Cellule, BIOC, Ecole polytechnique, CNRS, Institut Polytechnique de Paris, 91128 Palaiseau cedex, France
| | - Christine Lazennec-Schurdevin
- Laboratoire de Biologie Structurale de la Cellule, BIOC, Ecole polytechnique, CNRS, Institut Polytechnique de Paris, 91128 Palaiseau cedex, France
| | - Eric Larquet
- Laboratoire de Physique de la Matière Condensée, PMC, Ecole polytechnique, CNRS, Institut Polytechnique de Paris, 91128 Palaiseau cedex, France
| | - Yves Mechulam
- Laboratoire de Biologie Structurale de la Cellule, BIOC, Ecole polytechnique, CNRS, Institut Polytechnique de Paris, 91128 Palaiseau cedex, France
| | - Pierre-Damien Coureux
- Laboratoire de Biologie Structurale de la Cellule, BIOC, Ecole polytechnique, CNRS, Institut Polytechnique de Paris, 91128 Palaiseau cedex, France
| | - Emmanuelle Schmitt
- Laboratoire de Biologie Structurale de la Cellule, BIOC, Ecole polytechnique, CNRS, Institut Polytechnique de Paris, 91128 Palaiseau cedex, France
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17
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Basu RS, Sherman MB, Gagnon MG. Compact IF2 allows initiator tRNA accommodation into the P site and gates the ribosome to elongation. Nat Commun 2022; 13:3388. [PMID: 35697706 PMCID: PMC9192638 DOI: 10.1038/s41467-022-31129-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Accepted: 06/02/2022] [Indexed: 11/09/2022] Open
Abstract
During translation initiation, initiation factor 2 (IF2) holds initiator transfer RNA (fMet-tRNAifMet) in a specific orientation in the peptidyl (P) site of the ribosome. Upon subunit joining IF2 hydrolyzes GTP and, concomitant with inorganic phosphate (Pi) release, changes conformation facilitating fMet-tRNAifMet accommodation into the P site and transition of the 70 S ribosome initiation complex (70S-IC) to an elongation-competent ribosome. The mechanism by which IF2 separates from initiator tRNA at the end of translation initiation remains elusive. Here, we report cryo-electron microscopy (cryo-EM) structures of the 70S-IC from Pseudomonas aeruginosa bound to compact IF2-GDP and initiator tRNA. Relative to GTP-bound IF2, rotation of the switch 2 α-helix in the G-domain bound to GDP unlocks a cascade of large-domain movements in IF2 that propagate to the distal tRNA-binding domain C2. The C2-domain relocates 35 angstroms away from tRNA, explaining how IF2 makes way for fMet-tRNAifMet accommodation into the P site. Our findings provide the basis by which IF2 gates the ribosome to the elongation phase.
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Affiliation(s)
- Ritwika S Basu
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, 77555, USA
| | - Michael B Sherman
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, 77555, USA
- Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, TX, 77555, USA
| | - Matthieu G Gagnon
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, 77555, USA.
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, 77555, USA.
- Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, TX, 77555, USA.
- Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, TX, 77555, USA.
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18
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Seely SM, Gagnon MG. Mechanisms of ribosome recycling in bacteria and mitochondria: a structural perspective. RNA Biol 2022; 19:662-677. [PMID: 35485608 PMCID: PMC9067457 DOI: 10.1080/15476286.2022.2067712] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022] Open
Abstract
In all living cells, the ribosome translates the genetic information carried by messenger RNAs (mRNAs) into proteins. The process of ribosome recycling, a key step during protein synthesis that ensures ribosomal subunits remain available for new rounds of translation, has been largely overlooked. Despite being essential to the survival of the cell, several mechanistic aspects of ribosome recycling remain unclear. In eubacteria and mitochondria, recycling of the ribosome into subunits requires the concerted action of the ribosome recycling factor (RRF) and elongation factor G (EF-G). Recently, the conserved protein HflX was identified in bacteria as an alternative factor that recycles the ribosome under stress growth conditions. The homologue of HflX, the GTP-binding protein 6 (GTPBP6), has a dual role in mitochondrial translation by facilitating ribosome recycling and biogenesis. In this review, mechanisms of ribosome recycling in eubacteria and mitochondria are described based on structural studies of ribosome complexes.
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Affiliation(s)
- Savannah M Seely
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX 77555-1019, USA
| | - Matthieu G Gagnon
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX 77555-1019, USA.,Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX 77555-1019, USA.,Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, TX 77555-1019, USA.,Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, Texas 77555, USA
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19
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Abstract
Accurate protein synthesis (translation) relies on translation factors that rectify ribosome fluctuations into a unidirectional process. Understanding this process requires structural characterization of the ribosome and translation-factor dynamics. In the 2000s, crystallographic studies determined high-resolution structures of ribosomes stalled with translation factors, providing a starting point for visualizing translation. Recent progress in single-particle cryogenic electron microscopy (cryo-EM) has enabled near-atomic resolution of numerous structures sampled in heterogeneous complexes (ensembles). Ensemble and time-resolved cryo-EM have now revealed unprecedented views of ribosome transitions in the three principal stages of translation: initiation, elongation, and termination. This review focuses on how translation factors help achieve high accuracy and efficiency of translation by monitoring distinct ribosome conformations and by differentially shifting the equilibria of ribosome rearrangements for cognate and near-cognate substrates. Expected final online publication date for the Annual Review of Biochemistry, Volume 91 is June 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Andrei A Korostelev
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA;
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20
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Cabrera-Orefice A, Potter A, Evers F, Hevler JF, Guerrero-Castillo S. Complexome Profiling-Exploring Mitochondrial Protein Complexes in Health and Disease. Front Cell Dev Biol 2022; 9:796128. [PMID: 35096826 PMCID: PMC8790184 DOI: 10.3389/fcell.2021.796128] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Accepted: 12/08/2021] [Indexed: 12/14/2022] Open
Abstract
Complexome profiling (CP) is a state-of-the-art approach that combines separation of native proteins by electrophoresis, size exclusion chromatography or density gradient centrifugation with tandem mass spectrometry identification and quantification. Resulting data are computationally clustered to visualize the inventory, abundance and arrangement of multiprotein complexes in a biological sample. Since its formal introduction a decade ago, this method has been mostly applied to explore not only the composition and abundance of mitochondrial oxidative phosphorylation (OXPHOS) complexes in several species but also to identify novel protein interactors involved in their assembly, maintenance and functions. Besides, complexome profiling has been utilized to study the dynamics of OXPHOS complexes, as well as the impact of an increasing number of mutations leading to mitochondrial disorders or rearrangements of the whole mitochondrial complexome. Here, we summarize the major findings obtained by this approach; emphasize its advantages and current limitations; discuss multiple examples on how this tool could be applied to further investigate pathophysiological mechanisms and comment on the latest advances and opportunity areas to keep developing this methodology.
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Affiliation(s)
- Alfredo Cabrera-Orefice
- Center for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, Netherlands
| | - Alisa Potter
- Department of Pediatrics, Radboud Center for Mitochondrial Medicine, Radboud University Medical Center, Nijmegen, Netherlands
| | - Felix Evers
- Department of Medical Microbiology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, Netherlands
| | - Johannes F Hevler
- Biomolecular Mass Spectrometry and Proteomics, University of Utrecht, Utrecht, Netherlands.,Bijvoet Center for Biomolecular Research, University of Utrecht, Utrecht, Netherlands.,Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Utrecht, Netherlands.,Netherlands Proteomics Center, Utrecht, Netherlands
| | - Sergio Guerrero-Castillo
- University Children's Research@Kinder-UKE, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
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21
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Tomsic J, Caserta E, Pon CL, Gualerzi CO. Weakening the IF2-fMet-tRNA Interaction Suppresses the Lethal Phenotype Caused by GTPase Inactivation. Int J Mol Sci 2021; 22:ijms222413238. [PMID: 34948034 PMCID: PMC8709274 DOI: 10.3390/ijms222413238] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2021] [Revised: 12/07/2021] [Accepted: 12/07/2021] [Indexed: 01/12/2023] Open
Abstract
Substitution of the conserved Histidine 448 present in one of the three consensus elements characterizing the guanosine nucleotide binding domain (IF2 G2) of Escherichia coli translation initiation factor IF2 resulted in impaired ribosome-dependent GTPase activity which prevented IF2 dissociation from the ribosome, caused a severe protein synthesis inhibition, and yielded a dominant lethal phenotype. A reduced IF2 affinity for the ribosome was previously shown to suppress this lethality. Here, we demonstrate that also a reduced IF2 affinity for fMet-tRNA can suppress this dominant lethal phenotype and allows IF2 to support faithful translation in the complete absence of GTP hydrolysis. These results strengthen the premise that the conformational changes of ribosome, IF2, and fMet-tRNA occurring during the late stages of translation initiation are thermally driven and that the energy generated by IF2-dependent GTP hydrolysis is not required for successful translation initiation and that the dissociation of the interaction between IF2 C2 and the acceptor end of fMet-tRNA, which represents the last tie anchoring the factor to the ribosome before the formation of an elongation-competent 70S complex, is rate limiting for both the adjustment of fMet-tRNA in a productive P site and the IF2 release from the ribosome.
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Affiliation(s)
- Jerneja Tomsic
- Laboratory of Genetics, Department of Bioscience and Biotechnology, University of Camerino, 62032 Camerino, Italy; (J.T.); (E.C.); (C.L.P.)
- City of Hope Comprehensive Cancer Center, Duarte, CA 91010, USA
| | - Enrico Caserta
- Laboratory of Genetics, Department of Bioscience and Biotechnology, University of Camerino, 62032 Camerino, Italy; (J.T.); (E.C.); (C.L.P.)
- City of Hope Comprehensive Cancer Center, Duarte, CA 91010, USA
| | - Cynthia L. Pon
- Laboratory of Genetics, Department of Bioscience and Biotechnology, University of Camerino, 62032 Camerino, Italy; (J.T.); (E.C.); (C.L.P.)
| | - Claudio O. Gualerzi
- Laboratory of Genetics, Department of Bioscience and Biotechnology, University of Camerino, 62032 Camerino, Italy; (J.T.); (E.C.); (C.L.P.)
- Correspondence: ; Tel.: +39-3391602957
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22
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Protein Synthesis in the Developing Neocortex at Near-Atomic Resolution Reveals Ebp1-Mediated Neuronal Proteostasis at the 60S Tunnel Exit. Mol Cell 2020; 81:304-322.e16. [PMID: 33357414 DOI: 10.1016/j.molcel.2020.11.037] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Revised: 09/04/2020] [Accepted: 11/19/2020] [Indexed: 02/07/2023]
Abstract
Protein synthesis must be finely tuned in the developing nervous system as the final essential step of gene expression. This study investigates the architecture of ribosomes from the neocortex during neurogenesis, revealing Ebp1 as a high-occupancy 60S peptide tunnel exit (TE) factor during protein synthesis at near-atomic resolution by cryoelectron microscopy (cryo-EM). Ribosome profiling demonstrated Ebp1-60S binding is highest during start codon initiation and N-terminal peptide elongation, regulating ribosome occupancy of these codons. Membrane-targeting domains emerging from the 60S tunnel, which recruit SRP/Sec61 to the shared binding site, displace Ebp1. Ebp1 is particularly abundant in the early-born neural stem cell (NSC) lineage and regulates neuronal morphology. Ebp1 especially impacts the synthesis of membrane-targeted cell adhesion molecules (CAMs), measured by pulsed stable isotope labeling by amino acids in cell culture (pSILAC)/bioorthogonal noncanonical amino acid tagging (BONCAT) mass spectrometry (MS). Therefore, Ebp1 is a central component of protein synthesis, and the ribosome TE is a focal point of gene expression control in the molecular specification of neuronal morphology during development.
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23
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Wang J, Wang J, Shin BS, Kim JR, Dever TE, Puglisi JD, Fernández IS. Structural basis for the transition from translation initiation to elongation by an 80S-eIF5B complex. Nat Commun 2020; 11:5003. [PMID: 33024099 PMCID: PMC7538418 DOI: 10.1038/s41467-020-18829-3] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2020] [Accepted: 09/16/2020] [Indexed: 11/09/2022] Open
Abstract
Recognition of a start codon by the initiator aminoacyl-tRNA determines the reading frame of messenger RNA (mRNA) translation by the ribosome. In eukaryotes, the GTPase eIF5B collaborates in the correct positioning of the initiator Met-tRNAiMet on the ribosome in the later stages of translation initiation, gating entrance into elongation. Leveraging the long residence time of eIF5B on the ribosome recently identified by single-molecule fluorescence measurements, we determine the cryoEM structure of the naturally long-lived ribosome complex with eIF5B and Met-tRNAiMet immediately before transition into elongation. The structure uncovers an unexpected, eukaryotic specific and dynamic fidelity checkpoint implemented by eIF5B in concert with components of the large ribosomal subunit.
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Affiliation(s)
- Jinfan Wang
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Jing Wang
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York City, NY, USA
| | - Byung-Sik Shin
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, Bethesda, MD, USA
| | - Joo-Ran Kim
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, Bethesda, MD, USA
| | - Thomas E Dever
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, Bethesda, MD, USA.
| | - Joseph D Puglisi
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA.
| | - Israel S Fernández
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York City, NY, USA.
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24
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Tharp JM, Krahn N, Varshney U, Söll D. Hijacking Translation Initiation for Synthetic Biology. Chembiochem 2020; 21:1387-1396. [PMID: 32023356 PMCID: PMC7237318 DOI: 10.1002/cbic.202000017] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Indexed: 12/17/2022]
Abstract
Genetic code expansion (GCE) has revolutionized the field of protein chemistry. Over the past several decades more than 150 different noncanonical amino acids (ncAAs) have been co-translationally installed into proteins within various host organisms. The vast majority of these ncAAs have been incorporated between the start and stop codons within an open reading frame. This requires that the ncAA be able to form a peptide bond at the α-amine, limiting the types of molecules that can be genetically encoded. In contrast, the α-amine of the initiating amino acid is not required for peptide bond formation. Therefore, including the initiator position in GCE allows for co-translational insertion of more diverse molecules that are modified, or completely lacking an α-amine. This review explores various methods which have been used to initiate protein synthesis with diverse molecules both in vitro and in vivo.
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Affiliation(s)
- Jeffery M Tharp
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06520, USA
| | - Natalie Krahn
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06520, USA
| | - Umesh Varshney
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, 560012, India
| | - Dieter Söll
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06520, USA
- Department of Chemistry, Yale University, New Haven, CT, 06520, USA
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25
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Electrostatics of Prokaryotic Ribosome and Its Biological Implication. Biophys J 2020; 118:1205-1212. [PMID: 32023436 DOI: 10.1016/j.bpj.2020.01.014] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2019] [Revised: 12/26/2019] [Accepted: 01/09/2020] [Indexed: 12/19/2022] Open
Abstract
Ribosomes are essential machines for protein synthesis in cells. Their structures are very complex but conserved in different species. Because most parts of a ribosome are composed of negatively charged RNAs, its electrostatics should play a fundamental role in the realization of its functions. However, a complete picture of the electrostatics of ribosomes is still absent at present. Here, assisted by the latest version of DelPhi (version 8.4), we illustrate a picture of the electrostatics of a prokaryotic ribosome as well as its molecular chaperones. The revealed electrostatics features are consistent with available experimental data as well as the functions of the ribosome and its molecular chaperones and provides a basis for further studying the mechanism underlying these functions.
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26
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Tomsic J, Smorlesi A, Caserta E, Giuliodori AM, Pon CL, Gualerzi CO. Disparate Phenotypes Resulting from Mutations of a Single Histidine in Switch II of Geobacillus stearothermophilus Translation Initiation Factor IF2. Int J Mol Sci 2020; 21:ijms21030735. [PMID: 31979156 PMCID: PMC7037019 DOI: 10.3390/ijms21030735] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2019] [Revised: 01/20/2020] [Accepted: 01/20/2020] [Indexed: 11/16/2022] Open
Abstract
The conserved Histidine 301 in switch II of Geobacillus stearothermophilus IF2 G2 domain was substituted with Ser, Gln, Arg, Leu and Tyr to generate mutants displaying different phenotypes. Overexpression of IF2H301S, IF2H301L and IF2H301Y in cells expressing wtIF2, unlike IF2H301Q and IF2H301R, caused a dominant lethal phenotype, inhibiting in vivo translation and drastically reducing cell viability. All mutants bound GTP but, except for IF2H301Q, were inactive in ribosome-dependent GTPase for different reasons. All mutants promoted 30S initiation complex (30S IC) formation with wild type (wt) efficiency but upon 30S IC association with the 50S subunit, the fMet-tRNA reacted with puromycin to different extents depending upon the IF2 mutant present in the complex (wtIF2 ≥ to IF2H301Q > IF2H301R >>> IF2H301S, IF2H301L and IF2H301Y) whereas only fMet-tRNA 30S-bound with IF2H301Q retained some ability to form initiation dipeptide fMet-Phe. Unlike wtIF2, all mutants, regardless of their ability to hydrolyze GTP, displayed higher affinity for the ribosome and failed to dissociate from the ribosomes upon 50S docking to 30S IC. We conclude that different amino acids substitutions of His301 cause different structural alterations of the factor, resulting in disparate phenotypes with no direct correlation existing between GTPase inactivation and IF2 failure to dissociate from ribosomes.
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27
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Long-range interdomain communications in eIF5B regulate GTP hydrolysis and translation initiation. Proc Natl Acad Sci U S A 2020; 117:1429-1437. [PMID: 31900355 PMCID: PMC6983393 DOI: 10.1073/pnas.1916436117] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Translation is a key regulatory step in the control of gene expression. The first stage of translation, initiation, establishes the foundation for the sequential synthesis of a protein. In eukaryotes, 2 GTP-regulated checkpoints ensure the efficiency and fidelity of translation initiation. The GTPase eIF5B is responsible for the correct functioning of the second checkpoint. Molecular interactions of eIF5B with other correctly assembled components on the ribosome lead to GTP hydrolysis that allows the machinery of protein production to transition from initiation into elongation. Here, we show how a highly conserved stretch of residues in eIF5B, identified using electron cryomicroscopy, coordinates the gating into elongation, underscoring the importance of modular architecture in translation factors to sense and communicate ribosomal states. Translation initiation controls protein synthesis by regulating the delivery of the first aminoacyl-tRNA to messenger RNAs (mRNAs). In eukaryotes, initiation is sophisticated, requiring dozens of protein factors and 2 GTP-regulated steps. The GTPase eIF5B gates progression to elongation during the second GTP-regulated step. Using electron cryomicroscopy (cryo-EM), we imaged an in vitro initiation reaction which is set up with purified yeast components and designed to stall with eIF5B and a nonhydrolyzable GTP analog. A high-resolution reconstruction of a “dead-end” intermediate at 3.6 Å allowed us to visualize eIF5B in its ribosome-bound conformation. We identified a stretch of residues in eIF5B, located close to the γ-phosphate of GTP and centered around the universally conserved tyrosine 837 (Saccharomyces cerevisiae numbering), that contacts the catalytic histidine of eIF5B (H480). Site-directed mutagenesis confirmed the essential role that these residues play in regulating ribosome binding, GTP hydrolysis, and translation initiation both in vitro and in vivo. Our results illustrate how eIF5B transmits the presence of a properly delivered initiator aminoacyl-tRNA at the P site to the distant GTPase center through interdomain communications and underscore the importance of the multidomain architecture in translation factors to sense and communicate ribosomal states.
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28
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Structural basis for ribosome recycling by RRF and tRNA. Nat Struct Mol Biol 2019; 27:25-32. [PMID: 31873307 DOI: 10.1038/s41594-019-0350-7] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Accepted: 11/12/2019] [Indexed: 11/08/2022]
Abstract
The bacterial ribosome is recycled into subunits by two conserved proteins, elongation factor G (EF-G) and the ribosome recycling factor (RRF). The molecular basis for ribosome recycling by RRF and EF-G remains unclear. Here, we report the crystal structure of a posttermination Thermus thermophilus 70S ribosome complexed with EF-G, RRF and two transfer RNAs at a resolution of 3.5 Å. The deacylated tRNA in the peptidyl (P) site moves into a previously unsuspected state of binding (peptidyl/recycling, p/R) that is analogous to that seen during initiation. The terminal end of the p/R-tRNA forms nonfavorable contacts with the 50S subunit while RRF wedges next to central inter-subunit bridges, illuminating the active roles of tRNA and RRF in dissociation of ribosomal subunits. The structure uncovers a missing snapshot of tRNA as it transits between the P and exit (E) sites, providing insights into the mechanisms of ribosome recycling and tRNA translocation.
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29
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Halfon Y, Jimenez-Fernandez A, La Rosa R, Espinosa Portero R, Krogh Johansen H, Matzov D, Eyal Z, Bashan A, Zimmerman E, Belousoff M, Molin S, Yonath A. Structure of Pseudomonas aeruginosa ribosomes from an aminoglycoside-resistant clinical isolate. Proc Natl Acad Sci U S A 2019; 116:22275-22281. [PMID: 31611393 PMCID: PMC6825255 DOI: 10.1073/pnas.1909831116] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Resistance to antibiotics has become a major threat to modern medicine. The ribosome plays a fundamental role in cell vitality by the translation of the genetic code into proteins; hence, it is a major target for clinically useful antibiotics. We report here the cryo-electron microscopy structures of the ribosome of a pathogenic aminoglycoside (AG)-resistant Pseudomonas aeruginosa strain, as well as of a nonresistance strain isolated from a cystic fibrosis patient. The structural studies disclosed defective ribosome complex formation due to a conformational change of rRNA helix H69, an essential intersubunit bridge, and a secondary binding site of the AGs. In addition, a stable conformation of nucleotides A1486 and A1487, pointing into helix h44, is created compared to a non-AG-bound ribosome. We suggest that altering the conformations of ribosomal protein uL6 and rRNA helix H69, which interact with initiation-factor IF2, interferes with proper protein synthesis initiation.
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Affiliation(s)
- Yehuda Halfon
- Department of Structural Biology, The Weizmann Institute of Science, 7610001 Rehovot, Israel
| | - Alicia Jimenez-Fernandez
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - Ruggero La Rosa
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - Rocio Espinosa Portero
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - Helle Krogh Johansen
- Department of Clinical Microbiology, Rigshospitalet, 2100 Copenhagen, Denmark
- Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, 1165 Copenhagen, Denmark
| | - Donna Matzov
- Department of Structural Biology, The Weizmann Institute of Science, 7610001 Rehovot, Israel
| | - Zohar Eyal
- Department of Structural Biology, The Weizmann Institute of Science, 7610001 Rehovot, Israel
| | - Anat Bashan
- Department of Structural Biology, The Weizmann Institute of Science, 7610001 Rehovot, Israel
| | - Ella Zimmerman
- Department of Structural Biology, The Weizmann Institute of Science, 7610001 Rehovot, Israel
| | - Matthew Belousoff
- Biomedicine Discovery Institute, Department of Microbiology, Monash University, 3800 Clayton, VIC, Australia
| | - Søren Molin
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark;
| | - Ada Yonath
- Department of Structural Biology, The Weizmann Institute of Science, 7610001 Rehovot, Israel;
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30
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Kaledhonkar S, Fu Z, Caban K, Li W, Chen B, Sun M, Gonzalez RL, Frank J. Late steps in bacterial translation initiation visualized using time-resolved cryo-EM. Nature 2019; 570:400-404. [PMID: 31108498 PMCID: PMC7060745 DOI: 10.1038/s41586-019-1249-5] [Citation(s) in RCA: 79] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Accepted: 05/08/2019] [Indexed: 12/02/2022]
Abstract
The initiation of bacterial translation involves the tightly regulated joining of the 50S ribosomal subunit to an initiator transfer RNA (fMet-tRNAfMet)-containing 30S ribosomal initiation complex to form a 70S initiation complex, which subsequently matures into a 70S elongation-competent complex. Rapid and accurate formation of the 70S initiation complex is promoted by initiation factors, which must dissociate from the 30S initiation complex before the resulting 70S elongation-competent complex can begin the elongation of translation1. Although comparisons of the structures of the 30S2-5 and 70S4,6-8 initiation complexes have revealed that the ribosome, initiation factors and fMet-tRNAfMet can acquire different conformations in these complexes, the timing of conformational changes during formation of the 70S initiation complex, the structures of any intermediates formed during these rearrangements, and the contributions that these dynamics might make to the mechanism and regulation of initiation remain unknown. Moreover, the absence of a structure of the 70S elongation-competent complex formed via an initiation-factor-catalysed reaction has precluded an understanding of the rearrangements to the ribosome, initiation factors and fMet-tRNAfMet that occur during maturation of a 70S initiation complex into a 70S elongation-competent complex. Here, using time-resolved cryogenic electron microscopy9, we report the near-atomic-resolution view of how a time-ordered series of conformational changes drive and regulate subunit joining, initiation factor dissociation and fMet-tRNAfMet positioning during formation of the 70S elongation-competent complex. Our results demonstrate the power of time-resolved cryogenic electron microscopy to determine how a time-ordered series of conformational changes contribute to the mechanism and regulation of one of the most fundamental processes in biology.
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MESH Headings
- Cryoelectron Microscopy
- Escherichia coli/chemistry
- Escherichia coli/metabolism
- Escherichia coli/ultrastructure
- Peptide Chain Elongation, Translational
- Peptide Chain Initiation, Translational
- Protein Conformation
- Ribosome Subunits, Large, Bacterial/metabolism
- Ribosome Subunits, Large, Bacterial/ultrastructure
- Ribosome Subunits, Small, Bacterial/metabolism
- Ribosome Subunits, Small, Bacterial/ultrastructure
- Ribosomes/chemistry
- Ribosomes/metabolism
- Ribosomes/ultrastructure
- Time Factors
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Affiliation(s)
- Sandip Kaledhonkar
- Department of Biochemistry & Molecular Biophysics, Columbia University, New York, NY, USA
| | - Ziao Fu
- Integrated Program in Cellular, Molecular and Biophysical Studies, Columbia University, College of Physicians and Surgeons, New York, NY, USA
| | - Kelvin Caban
- Department of Chemistry, Columbia University, New York, NY, USA
| | - Wen Li
- Department of Biochemistry & Molecular Biophysics, Columbia University, New York, NY, USA
| | - Bo Chen
- Department of Biochemistry & Molecular Biophysics, Columbia University, New York, NY, USA
| | - Ming Sun
- Department of Biological Sciences, Columbia University, New York, NY, USA
| | - Ruben L Gonzalez
- Department of Chemistry, Columbia University, New York, NY, USA.
| | - Joachim Frank
- Department of Biochemistry & Molecular Biophysics, Columbia University, New York, NY, USA.
- Department of Biological Sciences, Columbia University, New York, NY, USA.
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31
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Abstract
Ribosomes are biological nanomachine that synthesise all proteins within a cell. It took decades to reveal the architecture of this essential cellular component. To understand the structure -function relationship of this nanomachine needed the utilisisation of different biochemical, biophysical and structural techniques. Structural studies combined with mutagenesis of the different ribosomal complexes comprising various RNAs and proteins enabled us to understand how this machine works inside a cell. Nowadays quite a number of ribosomal structures were published that confirmed biochemical studies on particular steps of protein synthesis by the ribosome . Four major steps were identified: initiation , elongation, termination and recycling. These steps lead us to the important question how the ribosome function can be regulated. Advances in technology for cryo electron microscopy: sample preparations, image recording, developments in algorithms for image analysis and processing significantly helped in revelation of structural details of the ribosome . We now have a library of ribosome structures from prokaryotes to eukaryotes that enable us to understand the complex mechanics of this nanomachine. As this structural library continues to grow, we gradually improve our understanding of this process and how it can be regulated and how the specific ribosomes can be stalled or activated, or completely disabled. This article provides a comprehensive overview of ribosomal structures that represent structural snapshots of the ribosome at its different functional states. Better understanding rises more particular questions that have to be addressed by determination structures of more complexes.Synopsis: Structural biology of the ribosome.
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Affiliation(s)
- Abid Javed
- Institute of Structural and Molecular Biology, Department of Biological Sciences, Birkbeck College, Malet Street, London, WC1E 7HX, UK
| | - Elena V Orlova
- Institute of Structural and Molecular Biology, Department of Biological Sciences, Birkbeck College, Malet Street, London, WC1E 7HX, UK.
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32
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Welty R, Pabit SA, Katz AM, Calvey GD, Pollack L, Hall KB. Divalent ions tune the kinetics of a bacterial GTPase center rRNA folding transition from secondary to tertiary structure. RNA (NEW YORK, N.Y.) 2018; 24:1828-1838. [PMID: 30254137 PMCID: PMC6239185 DOI: 10.1261/rna.068361.118] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Accepted: 09/20/2018] [Indexed: 05/22/2023]
Abstract
Folding of an RNA from secondary to tertiary structure often depends on divalent ions for efficient electrostatic charge screening (nonspecific association) or binding (specific association). To measure how different divalent cations modify folding kinetics of the 60 nucleotide Ecoli rRNA GTPase center, we combined stopped-flow fluorescence in the presence of Mg2+, Ca2+, or Sr2+ together with time-resolved small angle X-ray scattering (SAXS) in the presence of Mg2+ to observe the folding process. Immediately upon addition of each divalent ion, the RNA undergoes a transition from an extended state with secondary structure to a more compact structure. Subsequently, specific divalent ions modulate populations of intermediates in conformational ensembles along the folding pathway with transition times longer than 10 msec. Rate constants for the five folding transitions act on timescales from submillisecond to tens of seconds. The sensitivity of RNA tertiary structure to divalent cation identity affects all but the fastest events in RNA folding, and allowed us to identify those states that prefer Mg2+ The GTPase center RNA appears to have optimized its folding trajectory to specifically utilize this most abundant intracellular divalent ion.
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Affiliation(s)
- Robb Welty
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri 63110, USA
| | - Suzette A Pabit
- School of Applied and Engineering Physics, Cornell University, Ithaca, New York 14853, USA
| | - Andrea M Katz
- School of Applied and Engineering Physics, Cornell University, Ithaca, New York 14853, USA
| | - George D Calvey
- School of Applied and Engineering Physics, Cornell University, Ithaca, New York 14853, USA
| | - Lois Pollack
- School of Applied and Engineering Physics, Cornell University, Ithaca, New York 14853, USA
| | - Kathleen B Hall
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri 63110, USA
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33
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Kim E, Kim JH, Seo K, Hong KY, An SWA, Kwon J, Lee SJV, Jang SK. eIF2A, an initiator tRNA carrier refractory to eIF2α kinases, functions synergistically with eIF5B. Cell Mol Life Sci 2018; 75:4287-4300. [PMID: 30019215 PMCID: PMC6208778 DOI: 10.1007/s00018-018-2870-4] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Revised: 06/26/2018] [Accepted: 07/04/2018] [Indexed: 12/12/2022]
Abstract
The initiator tRNA (Met-tRNA i Met ) at the P site of the small ribosomal subunit plays an important role in the recognition of an mRNA start codon. In bacteria, the initiator tRNA carrier, IF2, facilitates the positioning of Met-tRNA i Met on the small ribosomal subunit. Eukarya contain the Met-tRNA i Met carrier, eIF2 (unrelated to IF2), whose carrier activity is inhibited under stress conditions by the phosphorylation of its α-subunit by stress-activated eIF2α kinases. The stress-resistant initiator tRNA carrier, eIF2A, was recently uncovered and shown to load Met-tRNA i Met on the 40S ribosomal subunit associated with a stress-resistant mRNA under stress conditions. Here, we report that eIF2A interacts and functionally cooperates with eIF5B (a homolog of IF2), and we describe the functional domains of eIF2A that are required for its binding of Met-tRNA i Met , eIF5B, and a stress-resistant mRNA. The results indicate that the eukaryotic eIF5B-eIF2A complex functionally mimics the bacterial IF2 containing ribosome-, GTP-, and initiator tRNA-binding domains in a single polypeptide.
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Affiliation(s)
- Eunah Kim
- PBC, Department of Life Sciences, Pohang University of Science and Technology, Cheongam-ro 77, Nam-gu, Pohang-si, Gyeongsangbuk-do, 37673, Republic of Korea
| | - Joon Hyun Kim
- PBC, Department of Life Sciences, Pohang University of Science and Technology, Cheongam-ro 77, Nam-gu, Pohang-si, Gyeongsangbuk-do, 37673, Republic of Korea
| | - Keunhee Seo
- PBC, Department of Life Sciences, Pohang University of Science and Technology, Cheongam-ro 77, Nam-gu, Pohang-si, Gyeongsangbuk-do, 37673, Republic of Korea
| | - Ka Young Hong
- PBC, Department of Life Sciences, Pohang University of Science and Technology, Cheongam-ro 77, Nam-gu, Pohang-si, Gyeongsangbuk-do, 37673, Republic of Korea
| | - Seon Woo A An
- PBC, Department of Life Sciences, Pohang University of Science and Technology, Cheongam-ro 77, Nam-gu, Pohang-si, Gyeongsangbuk-do, 37673, Republic of Korea
| | - Junyoung Kwon
- PBC, Department of Life Sciences, Pohang University of Science and Technology, Cheongam-ro 77, Nam-gu, Pohang-si, Gyeongsangbuk-do, 37673, Republic of Korea
| | - Seung-Jae V Lee
- PBC, Department of Life Sciences, Pohang University of Science and Technology, Cheongam-ro 77, Nam-gu, Pohang-si, Gyeongsangbuk-do, 37673, Republic of Korea
- School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology, Cheongam-ro 77, Nam-gu, Pohang-si, Gyeongsangbuk-do, 37673, Republic of Korea
| | - Sung Key Jang
- PBC, Department of Life Sciences, Pohang University of Science and Technology, Cheongam-ro 77, Nam-gu, Pohang-si, Gyeongsangbuk-do, 37673, Republic of Korea.
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34
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Abstract
This review summarizes our current understanding of translation in prokaryotes, focusing on the mechanistic and structural aspects of each phase of translation: initiation, elongation, termination, and ribosome recycling. The assembly of the initiation complex provides multiple checkpoints for messenger RNA (mRNA) and start-site selection. Correct codon-anticodon interaction during the decoding phase of elongation results in major conformational changes of the small ribosomal subunit and shapes the reaction pathway of guanosine triphosphate (GTP) hydrolysis. The ribosome orchestrates proton transfer during peptide bond formation, but requires the help of elongation factor P (EF-P) when two or more consecutive Pro residues are to be incorporated. Understanding the choreography of transfer RNA (tRNA) and mRNA movements during translocation helps to place the available structures of translocation intermediates onto the time axis of the reaction pathway. The nascent protein begins to fold cotranslationally, in the constrained space of the polypeptide exit tunnel of the ribosome. When a stop codon is reached at the end of the coding sequence, the ribosome, assisted by termination factors, hydrolyzes the ester bond of the peptidyl-tRNA, thereby releasing the nascent protein. Following termination, the ribosome is dissociated into subunits and recycled into another round of initiation. At each step of translation, the ribosome undergoes dynamic fluctuations between different conformation states. The aim of this article is to show the link between ribosome structure, dynamics, and function.
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Affiliation(s)
- Marina V Rodnina
- Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, Goettingen 37077, Germany
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35
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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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36
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Tiemann JK, Rose AS, Ismer J, Darvish MD, Hilal T, Spahn CM, Hildebrand PW. FragFit: a web-application for interactive modeling of protein segments into cryo-EM density maps. Nucleic Acids Res 2018; 46:W310-W314. [PMID: 29788317 PMCID: PMC6030921 DOI: 10.1093/nar/gky424] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Accepted: 05/10/2018] [Indexed: 11/20/2022] Open
Abstract
Cryo-electron microscopy (cryo-EM) is a standard method to determine the three-dimensional structures of molecular complexes. However, easy to use tools for modeling of protein segments into cryo-EM maps are sparse. Here, we present the FragFit web-application, a web server for interactive modeling of segments of up to 35 amino acids length into cryo-EM density maps. The fragments are provided by a regularly updated database containing at the moment about 1 billion entries extracted from PDB structures and can be readily integrated into a protein structure. Fragments are selected based on geometric criteria, sequence similarity and fit into a given cryo-EM density map. Web-based molecular visualization with the NGL Viewer allows interactive selection of fragments. The FragFit web-application, accessible at http://proteinformatics.de/FragFit, is free and open to all users, without any login requirements.
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Affiliation(s)
- Johanna Ks Tiemann
- Institute of Medical Physics and Biophysics, Charité University Medicine Berlin, Berlin 10117, Germany.,Institute of Medical Physics and Biophysics, Medical University Leipzig, Leipzig, Sachsen 04107, Germany
| | - Alexander S Rose
- Institute of Medical Physics and Biophysics, Charité University Medicine Berlin, Berlin 10117, Germany
| | - Jochen Ismer
- Institute of Medical Physics and Biophysics, Charité University Medicine Berlin, Berlin 10117, Germany
| | - Mitra D Darvish
- Institute of Medical Physics and Biophysics, Charité University Medicine Berlin, Berlin 10117, Germany
| | - Tarek Hilal
- Institute of Medical Physics and Biophysics, Charité University Medicine Berlin, Berlin 10117, Germany
| | - Christian Mt Spahn
- Institute of Medical Physics and Biophysics, Charité University Medicine Berlin, Berlin 10117, Germany
| | - Peter W Hildebrand
- Institute of Medical Physics and Biophysics, Charité University Medicine Berlin, Berlin 10117, Germany.,Institute of Medical Physics and Biophysics, Medical University Leipzig, Leipzig, Sachsen 04107, Germany
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37
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Structural Visualization of the Formation and Activation of the 50S Ribosomal Subunit during In Vitro Reconstitution. Mol Cell 2018; 70:881-893.e3. [DOI: 10.1016/j.molcel.2018.05.003] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2017] [Revised: 02/27/2018] [Accepted: 05/01/2018] [Indexed: 01/07/2023]
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38
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Complementary charge-based interaction between the ribosomal-stalk protein L7/12 and IF2 is the key to rapid subunit association. Proc Natl Acad Sci U S A 2018; 115:4649-4654. [PMID: 29686090 DOI: 10.1073/pnas.1802001115] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
The interaction between the ribosomal-stalk protein L7/12 (L12) and initiation factor 2 (IF2) is essential for rapid subunit association, but the underlying mechanism is unknown. Here, we have characterized the L12-IF2 interaction on Escherichia coli ribosomes using site-directed mutagenesis, fast kinetics, and molecular dynamics (MD) simulations. Fifteen individual point mutations were introduced into the C-terminal domain of L12 (L12-CTD) at helices 4 and 5, which constitute the common interaction site for translational GTPases. In parallel, 15 point mutations were also introduced into IF2 between the G4 and G5 motifs, which we hypothesized as the potential L12 interaction sites. The L12 and IF2 mutants were tested in ribosomal subunit association assay in a stopped-flow instrument. Those amino acids that caused defective subunit association upon substitution were identified as the molecular determinants of L12-IF2 interaction. Further, MD simulations of IF2 docked onto the L12-CTD pinpointed the exact interacting partners-all of which were positively charged on L12 and negatively charged on IF2, connected by salt bridges. Lastly, we tested two pairs of charge-reversed mutants of L12 and IF2, which significantly restored the yield and the rate of formation of the 70S initiation complex. We conclude that complementary charge-based interaction between L12-CTD and IF2 is the key for fast subunit association. Considering the homology of the G domain, similar mechanisms may apply for L12 interactions with other translational GTPases.
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39
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Zeng F, Jin H. Conformation of methylated GGQ in the Peptidyl Transferase Center during Translation Termination. Sci Rep 2018; 8:2349. [PMID: 29403017 PMCID: PMC5799190 DOI: 10.1038/s41598-018-20107-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Accepted: 01/12/2018] [Indexed: 11/24/2022] Open
Abstract
The universally conserved Gly-Gly-Gln (GGQ) tripeptide in release factors or release factor-like surveillance proteins is required to catalyze the release of nascent peptide in the ribosome. The glutamine of the GGQ is methylated post-translationally at the N5 position in vivo; this covalent modification is essential for optimal cell growth and efficient translation termination. However, the precise conformation of the methylated-GGQ tripeptide in the ribosome remains unknown. Using cryoEM and X-ray crystallography, we report the conformation of methylated-GGQ in the peptidyl transferase center of the ribosome during canonical translational termination and co-translation quality control. It has been suggested that the GGQ motif arose independently through convergent evolution among otherwise unrelated proteins that catalyze peptide release. The requirement for this tripeptide in the highly conserved peptidyl transferase center suggests that the conformation reported here is likely shared during termination of protein synthesis in all domains of life.
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Affiliation(s)
- Fuxing Zeng
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, USA
| | - Hong Jin
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, USA. .,Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, USA.
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40
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Gibbs MR, Fredrick K. Roles of elusive translational GTPases come to light and inform on the process of ribosome biogenesis in bacteria. Mol Microbiol 2017; 107:445-454. [PMID: 29235176 DOI: 10.1111/mmi.13895] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2017] [Revised: 12/07/2017] [Accepted: 12/08/2017] [Indexed: 12/25/2022]
Abstract
Protein synthesis relies on several translational GTPases (trGTPases), related proteins that couple the hydrolysis of GTP to specific molecular events on the ribosome. Most bacterial trGTPases, including IF2, EF-Tu, EF-G and RF3, play well-known roles in translation. The cellular functions of LepA (also termed EF4) and BipA (also termed TypA), conversely, have remained enigmatic. Recent studies provide compelling in vivo evidence that LepA and BipA function in biogenesis of the 30S and 50S subunit respectively. These findings have important implications for ribosome biogenesis in bacteria. Because the GTPase activity of each of these proteins depends on interactions with both ribosomal subunits, some portion of 30S and 50S assembly must occur in the context of the 70S ribosome. In this review, we introduce the trGTPases of bacteria, describe the new functional data on LepA and BipA, and discuss the how these findings shape our current view of ribosome biogenesis in bacteria.
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Affiliation(s)
- Michelle R Gibbs
- Department of Microbiology and Center for RNA Biology, The Ohio State University, 484 W. 12th Ave, Columbus, OH 43210, USA
| | - Kurt Fredrick
- Department of Microbiology and Center for RNA Biology, The Ohio State University, 484 W. 12th Ave, Columbus, OH 43210, USA
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41
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Abstract
During protein synthesis, the ribosome simultaneously binds up to three different transfer RNA (tRNA) molecules. Among the three tRNA binding sites, the regulatory role of the exit (E) site, where deacylated tRNA spontaneously dissociates from the translational complex, has remained elusive. Here we use two donor-quencher pairs to observe and correlate both the conformation of ribosomes and tRNAs as well as tRNA occupancy. Our results reveal a partially rotated state of the ribosome wherein all three tRNA sites are occupied during translation elongation. The appearance and lifetime of this state depend on the E-site tRNA dissociation kinetics, which may vary among tRNA species and depends on temperature and ionic strength. The 3-tRNA partially rotated state is not a proper substrate for elongation factor G (EF-G), thus inhibiting translocation until the E-site tRNA dissociates. Our result presents two parallel kinetic pathways during translation elongation, underscoring the ability of E-site codons to modulate the dynamics of protein synthesis.
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42
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Caban K, Pavlov M, Ehrenberg M, Gonzalez RL. A conformational switch in initiation factor 2 controls the fidelity of translation initiation in bacteria. Nat Commun 2017; 8:1475. [PMID: 29133802 PMCID: PMC5684235 DOI: 10.1038/s41467-017-01492-6] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2017] [Accepted: 09/21/2017] [Indexed: 11/09/2022] Open
Abstract
Initiation factor (IF) 2 controls the fidelity of translation initiation by selectively increasing the rate of 50S ribosomal subunit joining to 30S initiation complexes (ICs) that carry an N-formyl-methionyl-tRNA (fMet-tRNAfMet). Previous studies suggest that rapid 50S subunit joining involves a GTP- and fMet-tRNAfMet-dependent "activation" of IF2, but a lack of data on the structure and conformational dynamics of 30S IC-bound IF2 has precluded a mechanistic understanding of this process. Here, using an IF2-tRNA single-molecule fluorescence resonance energy transfer signal, we directly observe the conformational switch that is associated with IF2 activation within 30S ICs that lack IF3. Based on these results, we propose a model of IF2 activation that reveals how GTP, fMet-tRNAfMet, and specific structural elements of IF2 drive and regulate this conformational switch. Notably, we find that domain III of IF2 plays a pivotal, allosteric, role in IF2 activation, suggesting that this domain can be targeted for the development of novel antibiotics.
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Affiliation(s)
- Kelvin Caban
- Department of Chemistry, Columbia University, 3000 Broadway, MC3126, New York, NY, 10027, USA
| | - Michael Pavlov
- Department of Cell and Molecular Biology, BMC, Uppsala University, Husargatan 3, Uppsala, 751 24, Sweden
| | - Måns Ehrenberg
- Department of Cell and Molecular Biology, BMC, Uppsala University, Husargatan 3, Uppsala, 751 24, Sweden
| | - Ruben L Gonzalez
- Department of Chemistry, Columbia University, 3000 Broadway, MC3126, New York, NY, 10027, USA.
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43
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Ismer J, Rose AS, Tiemann JKS, Hildebrand PW. A fragment based method for modeling of protein segments into cryo-EM density maps. BMC Bioinformatics 2017; 18:475. [PMID: 29132296 PMCID: PMC5683378 DOI: 10.1186/s12859-017-1904-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2017] [Accepted: 11/01/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Single-particle analysis of electron cryo-microscopy (cryo-EM) is a key technology for elucidation of macromolecular structures. Recent technical advances in hardware and software developments significantly enhanced the resolution of cryo-EM density maps and broadened the applicability and the circle of users. To facilitate modeling of macromolecules into cryo-EM density maps, fast and easy to use methods for modeling are now demanded. RESULTS Here we investigated and benchmarked the suitability of a classical and well established fragment-based approach for modeling of segments into cryo-EM density maps (termed FragFit). FragFit uses a hierarchical strategy to select fragments from a pre-calculated set of billions of fragments derived from structures deposited in the Protein Data Bank, based on sequence similarly, fit of stem atoms and fit to a cryo-EM density map. The user only has to specify the sequence of the segment and the number of the N- and C-terminal stem-residues in the protein. Using a representative data set of protein structures, we show that protein segments can be accurately modeled into cryo-EM density maps of different resolution by FragFit. Prediction quality depends on segment length, the type of secondary structure of the segment and local quality of the map. CONCLUSION Fast and automated calculation of FragFit renders it applicable for implementation of interactive web-applications e.g. to model missing segments, flexible protein parts or hinge-regions into cryo-EM density maps.
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Affiliation(s)
- Jochen Ismer
- Institute of Medical Physics and Biophysics, University Medicine Berlin, Charitéplatz 1, 10117, Berlin, Germany
| | - Alexander S Rose
- Institute of Medical Physics and Biophysics, University Medicine Berlin, Charitéplatz 1, 10117, Berlin, Germany.,RCSB Protein Data Bank, San Diego Supercomputer Center, University of California, San Diego, CA, 92093-0743, USA
| | - Johanna K S Tiemann
- Institute of Medical Physics and Biophysics, University Medicine Berlin, Charitéplatz 1, 10117, Berlin, Germany.,Institute of Medical Physics and Biophysics, University Leipzig, Härtelstraße 16-18, 04107, Leipzig, Germany
| | - Peter W Hildebrand
- Institute of Medical Physics and Biophysics, University Medicine Berlin, Charitéplatz 1, 10117, Berlin, Germany. .,Institute of Medical Physics and Biophysics, University Leipzig, Härtelstraße 16-18, 04107, Leipzig, Germany.
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44
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Yang K, Chang JY, Cui Z, Li X, Meng R, Duan L, Thongchol J, Jakana J, Huwe CM, Sacchettini JC, Zhang J. Structural insights into species-specific features of the ribosome from the human pathogen Mycobacterium tuberculosis. Nucleic Acids Res 2017; 45:10884-10894. [PMID: 28977617 PMCID: PMC5737476 DOI: 10.1093/nar/gkx785] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2017] [Accepted: 08/26/2017] [Indexed: 12/11/2022] Open
Abstract
Ribosomes from Mycobacterium tuberculosis (Mtb) possess species-specific ribosomal RNA (rRNA) expansion segments and ribosomal proteins (rProtein). Here, we present the near-atomic structures of the Mtb 50S ribosomal subunit and the complete Mtb 70S ribosome, solved by cryo-electron microscopy. Upon joining of the large and small ribosomal subunits, a 100-nt long expansion segment of the Mtb 23S rRNA, named H54a or the ‘handle’, switches interactions from with rRNA helix H68 and rProtein uL2 to with rProtein bS6, forming a new intersubunit bridge ‘B9’. In Mtb 70S, bridge B9 is mostly maintained, leading to correlated motions among the handle, the L1 stalk and the small subunit in the rotated and non-rotated states. Two new protein densities were discovered near the decoding center and the peptidyl transferase center, respectively. These results provide a structural basis for studying translation in Mtb as well as developing new tuberculosis drugs.
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Affiliation(s)
- Kailu Yang
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA
| | - Jeng-Yih Chang
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA
| | - Zhicheng Cui
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA
| | - Xiaojun Li
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA
| | - Ran Meng
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA
| | - Lijun Duan
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA
| | - Jirapat Thongchol
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA
| | - Joanita Jakana
- National Center for Macromolecular Imaging, Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Christoph M Huwe
- Bayer AG Pharmaceuticals, Global External Innovation & Alliances, 13342 Berlin, Germany
| | - James C Sacchettini
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA
| | - Junjie Zhang
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA
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45
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López-Alonso JP, Fabbretti A, Kaminishi T, Iturrioz I, Brandi L, Gil-Carton D, Gualerzi CO, Fucini P, Connell SR. Structure of a 30S pre-initiation complex stalled by GE81112 reveals structural parallels in bacterial and eukaryotic protein synthesis initiation pathways. Nucleic Acids Res 2017; 45:2179-2187. [PMID: 27986852 PMCID: PMC5389724 DOI: 10.1093/nar/gkw1251] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2016] [Accepted: 12/13/2016] [Indexed: 12/28/2022] Open
Abstract
In bacteria, the start site and the reading frame of the messenger RNA are selected by the small ribosomal subunit (30S) when the start codon, typically an AUG, is decoded in the P-site by the initiator tRNA in a process guided and controlled by three initiation factors. This process can be efficiently inhibited by GE81112, a natural tetrapeptide antibiotic that is highly specific toward bacteria. Here GE81112 was used to stabilize the 30S pre-initiation complex and obtain its structure by cryo-electron microscopy. The results obtained reveal the occurrence of changes in both the ribosome conformation and initiator tRNA position that may play a critical role in controlling translational fidelity. Furthermore, the structure highlights similarities with the early steps of initiation in eukaryotes suggesting that shared structural features guide initiation in all kingdoms of life.
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Affiliation(s)
- Jorge P López-Alonso
- Structural Biology Unit, CIC bioGUNE, Parque Tecnológico de Bizkaia, 48160 Derio, Bizkaia, Spain
| | - Attilio Fabbretti
- Laboratory of Genetics, University of Camerino, 62032 Camerino, Italy
| | - Tatsuya Kaminishi
- Structural Biology Unit, CIC bioGUNE, Parque Tecnológico de Bizkaia, 48160 Derio, Bizkaia, Spain
| | - Idoia Iturrioz
- Structural Biology Unit, CIC bioGUNE, Parque Tecnológico de Bizkaia, 48160 Derio, Bizkaia, Spain
| | - Letizia Brandi
- Laboratory of Genetics, University of Camerino, 62032 Camerino, Italy
| | - David Gil-Carton
- Structural Biology Unit, CIC bioGUNE, Parque Tecnológico de Bizkaia, 48160 Derio, Bizkaia, Spain
| | | | - Paola Fucini
- Structural Biology Unit, CIC bioGUNE, Parque Tecnológico de Bizkaia, 48160 Derio, Bizkaia, Spain.,IKERBASQUE, Basque Foundation for Science, 48013 Bilbao, Spain
| | - Sean R Connell
- Structural Biology Unit, CIC bioGUNE, Parque Tecnológico de Bizkaia, 48160 Derio, Bizkaia, Spain.,IKERBASQUE, Basque Foundation for Science, 48013 Bilbao, Spain
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46
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von Loeffelholz O, Natchiar SK, Djabeur N, Myasnikov AG, Kratzat H, Ménétret JF, Hazemann I, Klaholz BP. Focused classification and refinement in high-resolution cryo-EM structural analysis of ribosome complexes. Curr Opin Struct Biol 2017; 46:140-148. [PMID: 28850874 DOI: 10.1016/j.sbi.2017.07.007] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2017] [Revised: 07/23/2017] [Accepted: 07/27/2017] [Indexed: 11/17/2022]
Abstract
Cryo electron microscopy (cryo-EM) historically has had a strong impact on the structural and mechanistic analysis of protein synthesis by the prokaryotic and eukaryotic ribosomes. Vice versa, studying ribosomes has helped moving forwards many methodological aspects in single particle cryo-EM, at the level of automated data collection and image processing including advanced techniques for particle sorting to address structural and compositional heterogeneity. Here we review some of the latest ribosome structures, where cryo-EM allowed gaining unprecedented insights based on 3D structure sorting with focused classification and refinement methods helping to reach local resolution levels better than 3Å. Such high-resolution features now enable the analysis of drug interactions with RNA and protein side-chains including even the visualization of chemical modifications of the ribosomal RNA. These advances represent a major breakthrough in structural biology and show the strong potential of cryo-EM beyond the ribosome field including for structure-based drug design.
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Affiliation(s)
- Ottilie von Loeffelholz
- Centre for Integrative Biology (CBI), Department of Integrated Structural Biology, IGBMC (Institute of Genetics and of Molecular and Cellular Biology), 1 rue Laurent Fries, Illkirch, France; Centre National de la Recherche Scientifique (CNRS) UMR 7104, Illkirch, France; Institut National de la Santé et de la Recherche Médicale (INSERM) U964, Illkirch, France; Université de Strasbourg, Strasbourg, France
| | - S Kundhavai Natchiar
- Centre for Integrative Biology (CBI), Department of Integrated Structural Biology, IGBMC (Institute of Genetics and of Molecular and Cellular Biology), 1 rue Laurent Fries, Illkirch, France; Centre National de la Recherche Scientifique (CNRS) UMR 7104, Illkirch, France; Institut National de la Santé et de la Recherche Médicale (INSERM) U964, Illkirch, France; Université de Strasbourg, Strasbourg, France
| | - Nadia Djabeur
- Centre for Integrative Biology (CBI), Department of Integrated Structural Biology, IGBMC (Institute of Genetics and of Molecular and Cellular Biology), 1 rue Laurent Fries, Illkirch, France; Centre National de la Recherche Scientifique (CNRS) UMR 7104, Illkirch, France; Institut National de la Santé et de la Recherche Médicale (INSERM) U964, Illkirch, France; Université de Strasbourg, Strasbourg, France
| | - Alexander G Myasnikov
- Centre for Integrative Biology (CBI), Department of Integrated Structural Biology, IGBMC (Institute of Genetics and of Molecular and Cellular Biology), 1 rue Laurent Fries, Illkirch, France; Centre National de la Recherche Scientifique (CNRS) UMR 7104, Illkirch, France; Institut National de la Santé et de la Recherche Médicale (INSERM) U964, Illkirch, France; Université de Strasbourg, Strasbourg, France
| | - Hanna Kratzat
- Centre for Integrative Biology (CBI), Department of Integrated Structural Biology, IGBMC (Institute of Genetics and of Molecular and Cellular Biology), 1 rue Laurent Fries, Illkirch, France; Centre National de la Recherche Scientifique (CNRS) UMR 7104, Illkirch, France; Institut National de la Santé et de la Recherche Médicale (INSERM) U964, Illkirch, France; Université de Strasbourg, Strasbourg, France
| | - Jean-François Ménétret
- Centre for Integrative Biology (CBI), Department of Integrated Structural Biology, IGBMC (Institute of Genetics and of Molecular and Cellular Biology), 1 rue Laurent Fries, Illkirch, France; Centre National de la Recherche Scientifique (CNRS) UMR 7104, Illkirch, France; Institut National de la Santé et de la Recherche Médicale (INSERM) U964, Illkirch, France; Université de Strasbourg, Strasbourg, France
| | - Isabelle Hazemann
- Centre for Integrative Biology (CBI), Department of Integrated Structural Biology, IGBMC (Institute of Genetics and of Molecular and Cellular Biology), 1 rue Laurent Fries, Illkirch, France; Centre National de la Recherche Scientifique (CNRS) UMR 7104, Illkirch, France; Institut National de la Santé et de la Recherche Médicale (INSERM) U964, Illkirch, France; Université de Strasbourg, Strasbourg, France
| | - Bruno P Klaholz
- Centre for Integrative Biology (CBI), Department of Integrated Structural Biology, IGBMC (Institute of Genetics and of Molecular and Cellular Biology), 1 rue Laurent Fries, Illkirch, France; Centre National de la Recherche Scientifique (CNRS) UMR 7104, Illkirch, France; Institut National de la Santé et de la Recherche Médicale (INSERM) U964, Illkirch, France; Université de Strasbourg, Strasbourg, France. mailto:
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47
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Carlson MA, Haddad BG, Weis AJ, Blackwood CS, Shelton CD, Wuerth ME, Walter JD, Spiegel PC. Ribosomal protein L7/L12 is required for GTPase translation factors EF-G, RF3, and IF2 to bind in their GTP state to 70S ribosomes. FEBS J 2017; 284:1631-1643. [PMID: 28342293 DOI: 10.1111/febs.14067] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2017] [Revised: 03/06/2017] [Accepted: 03/22/2017] [Indexed: 12/01/2022]
Abstract
Ribosomal protein L7/L12 is associated with translation initiation, elongation, and termination by the 70S ribosome. The guanosine 5' triphosphate hydrolase (GTPase) activity of elongation factor G (EF-G) requires the presence of L7/L12, which is critical for ribosomal translocation. Here, we have developed new methods for the complete depletion of L7/L12 from Escherichia coli 70S ribosomes to analyze the effect of L7/L12 on the activities of the GTPase factors EF-G, RF3, IF2, and LepA. Upon removal of L7/L12 from ribosomes, the GTPase activities of EF-G, RF3, and IF2 decreased to basal levels, while the activity of LepA decreased marginally. Upon reconstitution of ribosomes with recombinant L12, the GTPase activities of all GTPases returned to full activity. Moreover, ribosome binding assays indicated that EF-G, RF3, and IF2 require L7/L12 for stable binding in the GTP state, and LepA retained > 50% binding. Lastly, an EF-G∆G' truncation mutant possessed ribosome-dependent GTPase activity, which was insensitive to L7/L12. Our results indicate that L7/L12 is required for stable binding of ribosome-dependent GTPases that harbor direct interactions to the L7/L12 C-terminal domains, either through a G' domain (EF-G, RF3) or a unique N-terminal domain (IF2). Furthermore, we hypothesize this interaction is concomitant with counterclockwise ribosomal intersubunit rotation, which is required for translocation, initiation, and post-termination.
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Affiliation(s)
- Markus A Carlson
- Department of Chemistry, Western Washington University, Bellingham, WA, USA
| | - Bassam G Haddad
- Department of Chemistry, Western Washington University, Bellingham, WA, USA
| | - Amanda J Weis
- Department of Chemistry, Western Washington University, Bellingham, WA, USA
| | - Colby S Blackwood
- Department of Chemistry, Western Washington University, Bellingham, WA, USA
| | | | - Michelle E Wuerth
- Department of Chemistry, Western Washington University, Bellingham, WA, USA
| | - Justin D Walter
- Department of Chemistry, Western Washington University, Bellingham, WA, USA
| | - Paul Clint Spiegel
- Department of Chemistry, Western Washington University, Bellingham, WA, USA
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48
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Jurėnas D, Chatterjee S, Konijnenberg A, Sobott F, Droogmans L, Garcia-Pino A, Van Melderen L. AtaT blocks translation initiation by N-acetylation of the initiator tRNAfMet. Nat Chem Biol 2017; 13:640-646. [DOI: 10.1038/nchembio.2346] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2016] [Accepted: 01/12/2017] [Indexed: 11/09/2022]
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49
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Zeng F, Chen Y, Remis J, Shekhar M, Phillips JC, Tajkhorshid E, Jin H. Structural basis of co-translational quality control by ArfA and RF2 bound to ribosome. Nature 2017; 541:554-557. [PMID: 28077875 DOI: 10.1038/nature21053] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2016] [Accepted: 12/14/2016] [Indexed: 01/26/2023]
Abstract
Quality control mechanisms intervene appropriately when defective translation events occur, in order to preserve the integrity of protein synthesis. Rescue of ribosomes translating on messenger RNAs that lack stop codons is one of the co-translational quality control pathways. In many bacteria, ArfA recognizes stalled ribosomes and recruits the release factor RF2, which catalyses the termination of protein synthesis. Although an induced-fit mechanism of nonstop mRNA surveillance mediated by ArfA and RF2 has been reported, the molecular interaction between ArfA and RF2 in the ribosome that is responsible for the mechanism is unknown. Here we report an electron cryo-microscopy structure of ArfA and RF2 in complex with the 70S ribosome bound to a nonstop mRNA. The structure, which is consistent with our kinetic and biochemical data, reveals the molecular interactions that enable ArfA to specifically recruit RF2, not RF1, into the ribosome and to enable RF2 to release the truncated protein product in this co-translational quality control pathway. The positively charged C-terminal domain of ArfA anchors in the mRNA entry channel of the ribosome. Furthermore, binding of ArfA and RF2 induces conformational changes in the ribosomal decoding centre that are similar to those seen in other protein-involved decoding processes. Specific interactions between residues in the N-terminal domain of ArfA and RF2 help RF2 to adopt a catalytically competent conformation for peptide release. Our findings provide a framework for understanding recognition of the translational state of the ribosome by new proteins, and expand our knowledge of the decoding potential of the ribosome.
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Affiliation(s)
- Fuxing Zeng
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Yanbo Chen
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Jonathan Remis
- Department of Molecular Biosciences, Northwestern University, Evanston, Illinois 60208-3500, USA
| | - Mrinal Shekhar
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA.,Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - James C Phillips
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Emad Tajkhorshid
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA.,Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA.,Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Hong Jin
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA.,Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
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50
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Hussain T, Llácer JL, Wimberly BT, Kieft JS, Ramakrishnan V. Large-Scale Movements of IF3 and tRNA during Bacterial Translation Initiation. Cell 2016; 167:133-144.e13. [PMID: 27662086 PMCID: PMC5037330 DOI: 10.1016/j.cell.2016.08.074] [Citation(s) in RCA: 106] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2016] [Revised: 08/04/2016] [Accepted: 08/23/2016] [Indexed: 11/19/2022]
Abstract
In bacterial translational initiation, three initiation factors (IFs 1–3) enable the selection of initiator tRNA and the start codon in the P site of the 30S ribosomal subunit. Here, we report 11 single-particle cryo-electron microscopy (cryoEM) reconstructions of the complex of bacterial 30S subunit with initiator tRNA, mRNA, and IFs 1–3, representing different steps along the initiation pathway. IF1 provides key anchoring points for IF2 and IF3, thereby enhancing their activities. IF2 positions a domain in an extended conformation appropriate for capturing the formylmethionyl moiety charged on tRNA. IF3 and tRNA undergo large conformational changes to facilitate the accommodation of the formylmethionyl-tRNA (fMet-tRNAfMet) into the P site for start codon recognition. Structures of the 30S ribosomal subunit with initiation factors, tRNA and mRNA IF3 helps to position the correct start codon in the P site before binding of tRNA Large-scale conformational changes of IF3 and tRNA are observed IF3 movements facilitate the accommodation of initiator tRNA in P site
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Affiliation(s)
| | - Jose L Llácer
- MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, UK
| | - Brian T Wimberly
- MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, UK; Department of Biochemistry and Molecular Genetics, University of Colorado Denver School of Medicine, Aurora, CO 80045, USA
| | - Jeffrey S Kieft
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver School of Medicine, Aurora, CO 80045, USA; RNA BioScience Initiative, University of Colorado Denver School of Medicine, Aurora, CO 80045, USA
| | - V Ramakrishnan
- MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, UK.
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