1
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Yuce M, Ates B, Yasar NI, Sungur FA, Kurkcuoglu O. A computational workflow to determine drug candidates alternative to aminoglycosides targeting the decoding center of E. coli ribosome. J Mol Graph Model 2024; 131:108817. [PMID: 38976944 DOI: 10.1016/j.jmgm.2024.108817] [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: 03/22/2024] [Revised: 05/08/2024] [Accepted: 07/03/2024] [Indexed: 07/10/2024]
Abstract
The global antibiotic resistance problem necessitates fast and effective approaches to finding novel inhibitors to treat bacterial infections. In this study, we propose a computational workflow to identify plausible high-affinity compounds from FDA-approved, investigational, and experimental libraries for the decoding center on the small subunit 30S of the E. coli ribosome. The workflow basically consists of two molecular docking calculations on the intact 30S, followed by molecular dynamics (MD) simulations coupled with MM-GBSA calculations on a truncated ribosome structure. The parameters used in the molecular docking suits, Glide and AutoDock Vina, as well as in the MD simulations with Desmond were carefully adjusted to obtain expected interactions for the ligand-rRNA complexes. A filtering procedure was followed, considering a fingerprint based on aminoglycoside's binding site on the 30S to obtain seven hit compounds either with different clinical usages or aminoglycoside derivatives under investigation, suggested for in vitro studies. The detailed workflow developed in this study promises an effective and fast approach for the estimation of binding free energies of large protein-RNA and ligand complexes.
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Affiliation(s)
- Merve Yuce
- Istanbul Technical University, Department of Chemical Engineering, Istanbul, 34469, Turkey.
| | - Beril Ates
- Istanbul Technical University, Department of Chemical Engineering, Istanbul, 34469, Turkey.
| | - Nesrin Isil Yasar
- Istanbul Technical University, Computational Science and Engineering Division, Informatics Institute, Istanbul, 34469, Turkey.
| | - Fethiye Aylin Sungur
- Istanbul Technical University, Computational Science and Engineering Division, Informatics Institute, Istanbul, 34469, Turkey.
| | - Ozge Kurkcuoglu
- Istanbul Technical University, Department of Chemical Engineering, Istanbul, 34469, Turkey.
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2
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Alejo JL, Girodat D, Hammerling MJ, Willi JA, Jewett MC, Engelhart AE, Adamala KP. Alternate conformational trajectories in ribosome translocation. PLoS Comput Biol 2024; 20:e1012319. [PMID: 39141679 PMCID: PMC11346969 DOI: 10.1371/journal.pcbi.1012319] [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: 03/20/2024] [Revised: 08/26/2024] [Accepted: 07/12/2024] [Indexed: 08/16/2024] Open
Abstract
Translocation in protein synthesis entails the efficient and accurate movement of the mRNA-[tRNA]2 substrate through the ribosome after peptide bond formation. An essential conformational change during this process is the swiveling of the small subunit head domain about two rRNA 'hinge' elements. Using iterative selection and molecular dynamics simulations, we derive alternate hinge elements capable of translocation in vitro and in vivo and describe their effects on the conformational trajectory of the EF-G-bound, translocating ribosome. In these alternate conformational pathways, we observe a diversity of swivel kinetics, hinge motions, three-dimensional head domain trajectories and tRNA dynamics. By finding alternate conformational pathways of translocation, we identify motions and intermediates that are essential or malleable in this process. These findings highlight the plasticity of protein synthesis and provide a more thorough understanding of the available sequence and conformational landscape of a central biological process.
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Affiliation(s)
- Jose L. Alejo
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - Dylan Girodat
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, Arkansas, United States of America
| | - Michael J. Hammerling
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois, United States of America
| | - Jessica A. Willi
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois, United States of America
| | - Michael C. Jewett
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois, United States of America
- Department of Bioengineering, Stanford University, Stanford, California, United States of America
| | - Aaron E. Engelhart
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - Katarzyna P. Adamala
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, Minnesota, United States of America
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3
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Warner BR, Fredrick K. Contribution of an alternative 16S rRNA helix to biogenesis of the 30S subunit of the ribosome. RNA (NEW YORK, N.Y.) 2024; 30:770-778. [PMID: 38570183 PMCID: PMC11182017 DOI: 10.1261/rna.079960.124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Accepted: 03/23/2024] [Indexed: 04/05/2024]
Abstract
30S subunits become inactive upon exposure to low Mg2+ concentration, because of a reversible conformational change that entails nucleotides (nt) in the neck helix (h28) and 3' tail of 16S rRNA. This active-to-inactive transition involves partial unwinding of h28 and repairing of nt 921-923 with nt 1532-1534, which requires flipping of the 3' tail by ∼180°. Growing evidence suggests that immature 30S particles adopt the inactive conformation in the cell, and transition to the active state occurs at a late stage of maturation. Here, we target nucleotides that form the alternative helix (hALT) of the inactive state. Using an orthogonal ribosome system, we find that disruption of hALT decreases translation activity in the cell modestly, by approximately twofold, without compromising ribosome fidelity. Ribosomes carrying substitutions at positions 1532-1533 support the growth of Escherichia coli strain Δ7 prrn (which carries a single rRNA operon), albeit at rates 10%-20% slower than wild-type ribosomes. These mutant Δ7 prrn strains accumulate free 30S particles and precursor 17S rRNA, indicative of biogenesis defects. Analysis of purified control and mutant subunits suggests that hALT stabilizes the inactive state by 1.2 kcal/mol with little-to-no impact on the active state or the transition state of conversion.
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Affiliation(s)
- Benjamin R Warner
- Department of Microbiology and Center for RNA Biology, The Ohio State University, Columbus, Ohio 43210, USA
| | - Kurt Fredrick
- Department of Microbiology and Center for RNA Biology, The Ohio State University, Columbus, Ohio 43210, USA
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4
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Smart A, Lancaster L, Donohue JP, Niblett D, Noller H. Implication of nucleotides near the 3' end of 16S rRNA in guarding the translational reading frame. Nucleic Acids Res 2024; 52:5950-5958. [PMID: 38452198 PMCID: PMC11162774 DOI: 10.1093/nar/gkae143] [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: 10/11/2023] [Revised: 01/24/2024] [Accepted: 03/04/2024] [Indexed: 03/09/2024] Open
Abstract
Loss of the translational reading frame leads to misincorporation and premature termination, which can have lethal consequences. Based on structural evidence that A1503 of 16S rRNA intercalates between specific mRNA bases, we tested the possibility that it plays a role in maintenance of the reading frame by constructing ribosomes with an abasic nucleotide at position 1503. This was done by specific cleavage of 16S rRNA at position 1493 using the colicin E3 endonuclease and replacing the resulting 3'-terminal 49mer fragment with a synthetic oligonucleotide containing the abasic site using a novel splinted RNA ligation method. Ribosomes reconstituted from the abasic 1503 16S rRNA were highly active in protein synthesis but showed elevated levels of spontaneous frameshifting into the -1 reading frame. We then asked whether the residual frameshifting persisting in control ribosomes containing an intact A1503 is due to the absence of the N6-dimethyladenosine modifications at positions 1518 and 1519. Indeed, this frameshifting was rescued by site-specific methylation in vitro by the ksgA methylase. These findings thus implicate two different sites near the 3' end of 16S rRNA in maintenance of the translational reading frame, providing yet another example of a functional role for ribosomal RNA in protein synthesis.
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Affiliation(s)
- Alexandria Smart
- Center for Molecular Biology of RNA and Department of Molecular, Cell and Developmental Biology, University of California at Santa Cruz, Santa Cruz, CA, USA
| | - Laura Lancaster
- Center for Molecular Biology of RNA and Department of Molecular, Cell and Developmental Biology, University of California at Santa Cruz, Santa Cruz, CA, USA
| | - John Paul Donohue
- Center for Molecular Biology of RNA and Department of Molecular, Cell and Developmental Biology, University of California at Santa Cruz, Santa Cruz, CA, USA
| | - Dustin Niblett
- Center for Molecular Biology of RNA and Department of Molecular, Cell and Developmental Biology, University of California at Santa Cruz, Santa Cruz, CA, USA
| | - Harry F Noller
- Center for Molecular Biology of RNA and Department of Molecular, Cell and Developmental Biology, University of California at Santa Cruz, Santa Cruz, CA, USA
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5
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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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6
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Chowdhury AR, Sapkota D, Girodat D. Conformational changes of ribosomes during translation elongation resolved by molecular dynamics simulations. Curr Opin Struct Biol 2024; 86:102804. [PMID: 38569462 DOI: 10.1016/j.sbi.2024.102804] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Revised: 02/06/2024] [Accepted: 03/04/2024] [Indexed: 04/05/2024]
Abstract
Molecular dynamics simulations have emerged as a powerful set of tools to unravel the intricate dynamics of ribosomes during protein synthesis. Recent advancements in this field have enabled simulations to delve deep into the conformational rearrangements of ribosomes and associated factors, providing invaluable insights into the intricacies of translation. Emphasis on simulations has recently been on translation elongation, such as tRNA selection, translocation, and ribosomal head-swivel motions. These studies have offered crucial structural interpretations of how genetic information is faithfully translated into proteins. This review outlines recent discoveries concerning ribosome conformational changes occurring during translation elongation, as elucidated through molecular dynamics simulations.
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Affiliation(s)
- Anuradha Rai Chowdhury
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, AR, 72701, USA. https://twitter.com/atomcellplankl
| | - Divya Sapkota
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, AR, 72701, USA; Cell and Molecular Biology Program, University of Arkansas, Fayetteville, AR, 72701, USA
| | - Dylan Girodat
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, AR, 72701, USA.
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7
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Gerovac M, Chihara K, Wicke L, Böttcher B, Lavigne R, Vogel J. Phage proteins target and co-opt host ribosomes immediately upon infection. Nat Microbiol 2024; 9:787-800. [PMID: 38443577 PMCID: PMC10914614 DOI: 10.1038/s41564-024-01616-x] [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: 09/04/2023] [Accepted: 01/19/2024] [Indexed: 03/07/2024]
Abstract
Bacteriophages must seize control of the host gene expression machinery to replicate. To bypass bacterial anti-phage defence systems, this host takeover occurs immediately upon infection. A general understanding of phage mechanisms for immediate targeting of host transcription and translation processes is lacking. Here we introduce an integrative high-throughput approach to uncover phage-encoded proteins that target the gene expression machinery of Pseudomonas aeruginosa immediately upon infection with the jumbo phage ΦKZ. By integrating biochemical, genetic and structural analyses, we identify an abundant and conserved phage factor ΦKZ014 that targets the large ribosomal subunit by binding the 5S ribosomal RNA, and rapidly promotes replication in several clinical isolates. ΦKZ014 is among the earliest ΦKZ proteins expressed after infection and remains bound to ribosomes during the entire translation cycle. Our study provides a strategy to decipher molecular components of phage-mediated host takeover and argues that phage genomes represent an untapped discovery space for proteins that modulate the host gene expression machinery.
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Affiliation(s)
- Milan Gerovac
- Institute for Molecular Infection Biology (IMIB), University of Würzburg, Würzburg, Germany
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), Würzburg, Germany
| | - Kotaro Chihara
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), Würzburg, Germany
| | - Laura Wicke
- Laboratory of Gene Technology, KU Leuven, Leuven, Belgium
| | - Bettina Böttcher
- Biocenter and Rudolf Virchow Center for Integrative and Translational Bioimaging, University of Würzburg, Würzburg, Germany
| | - Rob Lavigne
- Laboratory of Gene Technology, KU Leuven, Leuven, Belgium
| | - Jörg Vogel
- Institute for Molecular Infection Biology (IMIB), University of Würzburg, Würzburg, Germany.
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), Würzburg, Germany.
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8
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Kravchenko OV, Baymukhametov TN, Afonina ZA, Vassilenko KS. High-Resolution Structure and Internal Mobility of a Plant 40S Ribosomal Subunit. Int J Mol Sci 2023; 24:17453. [PMID: 38139282 PMCID: PMC10743738 DOI: 10.3390/ijms242417453] [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: 11/23/2023] [Revised: 12/08/2023] [Accepted: 12/12/2023] [Indexed: 12/24/2023] Open
Abstract
Ribosome is a major part of the protein synthesis machinery, and analysis of its structure is of paramount importance. However, the structure of ribosomes from only a limited number of organisms has been resolved to date; it especially concerns plant ribosomes and ribosomal subunits. Here, we report a high-resolution cryo-electron microscopy reconstruction of the small subunit of the Triticum aestivum (common wheat) cytoplasmic ribosome. A detailed atomic model was built that includes the majority of the rRNA and some of the protein modifications. The analysis of the obtained data revealed structural peculiarities of the 40S subunit in the monocot plant ribosome. We applied the 3D Flexible Refinement approach to analyze the internal mobility of the 40S subunit and succeeded in decomposing it into four major motions, describing rotations of the head domain and a shift in the massive rRNA expansion segment. It was shown that these motions are almost uncorrelated and that the 40S subunit is flexible enough to spontaneously adopt any conformation it takes as a part of a translating ribosome or ribosomal complex. Here, we introduce the first high-resolution structure of an isolated plant 40S subunit and the first quantitative analysis of the flexibility of small ribosomal subunits, hoping that it will help in studying various aspects of ribosome functioning.
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Affiliation(s)
- Olesya V. Kravchenko
- Institute of Protein Research, Russian Academy of Sciences, 142290 Pushchino, Russia; (O.V.K.)
| | - Timur N. Baymukhametov
- National Research Center, “Kurchatov Institute”, Akademika Kurchatova pl. 1, 123182 Moscow, Russia;
| | - Zhanna A. Afonina
- Institute of Protein Research, Russian Academy of Sciences, 142290 Pushchino, Russia; (O.V.K.)
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9
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Poulis P, Peske F, Rodnina MV. The many faces of ribosome translocation along the mRNA: reading frame maintenance, ribosome frameshifting and translational bypassing. Biol Chem 2023; 404:755-767. [PMID: 37077160 DOI: 10.1515/hsz-2023-0142] [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: 02/21/2023] [Accepted: 03/22/2023] [Indexed: 04/21/2023]
Abstract
In each round of translation elongation, the ribosome translocates along the mRNA by precisely one codon. Translocation is promoted by elongation factor G (EF-G) in bacteria (eEF2 in eukaryotes) and entails a number of precisely-timed large-scale structural rearrangements. As a rule, the movements of the ribosome, tRNAs, mRNA and EF-G are orchestrated to maintain the exact codon-wise step size. However, signals in the mRNA, as well as environmental cues, can change the timing and dynamics of the key rearrangements leading to recoding of the mRNA into production of trans-frame peptides from the same mRNA. In this review, we discuss recent advances on the mechanics of translocation and reading frame maintenance. Furthermore, we describe the mechanisms and biological relevance of non-canonical translocation pathways, such as hungry and programmed frameshifting and translational bypassing, and their link to disease and infection.
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Affiliation(s)
- Panagiotis Poulis
- Department of Physical Biochemistry, Max Planck Institute for Multidisciplinary Sciences, Am Fassberg 11, D-37077 Göttingen, Germany
| | - Frank Peske
- Department of Physical Biochemistry, Max Planck Institute for Multidisciplinary Sciences, Am Fassberg 11, D-37077 Göttingen, Germany
| | - Marina V Rodnina
- Department of Physical Biochemistry, Max Planck Institute for Multidisciplinary Sciences, Am Fassberg 11, D-37077 Göttingen, Germany
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10
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Yu T, Jiang J, Yu Q, Li X, Zeng F. Structural Insights into the Distortion of the Ribosomal Small Subunit at Different Magnesium Concentrations. Biomolecules 2023; 13:biom13030566. [PMID: 36979501 PMCID: PMC10046523 DOI: 10.3390/biom13030566] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2023] [Revised: 03/15/2023] [Accepted: 03/17/2023] [Indexed: 03/30/2023] Open
Abstract
Magnesium ions are abundant and play indispensable functions in the ribosome. A decrease in Mg2+ concentration causes 70S ribosome dissociation and subsequent unfolding. Structural distortion at low Mg2+ concentrations has been observed in an immature pre50S, while the structural changes in mature subunits have not yet been studied. Here, we purified the 30S subunits of E. coli cells under various Mg2+ concentrations and analyzed their structural distortion by cryo-electron microscopy. Upon systematically interrogating the structural heterogeneity within the 1 mM Mg2+ dataset, we observed 30S particles with different levels of structural distortion in the decoding center, h17, and the 30S head. Our model showed that, when the Mg2+ concentration decreases, the decoding center distorts, starting from h44 and followed by the shifting of h18 and h27, as well as the dissociation of ribosomal protein S12. Mg2+ deficiency also eliminates the interactions between h17, h10, h15, and S16, resulting in the movement of h17 towards the tip of h6. More flexible structures were observed in the 30S head and platform, showing high variability in these regions. In summary, the structures resolved here showed several prominent distortion events in the decoding center and h17. The requirement for Mg2+ in ribosomes suggests that the conformational changes reported here are likely shared due to a lack of cellular Mg2+ in all domains of life.
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Affiliation(s)
- Ting Yu
- Department of Systems Biology, School of Life Sciences, Southern University of Science and Technology, No. 1088 Xueyuan Avenue, Shenzhen 518055, China
| | - Junyi Jiang
- Department of Systems Biology, School of Life Sciences, Southern University of Science and Technology, No. 1088 Xueyuan Avenue, Shenzhen 518055, China
| | - Qianxi Yu
- Department of Systems Biology, School of Life Sciences, Southern University of Science and Technology, No. 1088 Xueyuan Avenue, Shenzhen 518055, China
| | - Xin Li
- Department of Systems Biology, School of Life Sciences, Southern University of Science and Technology, No. 1088 Xueyuan Avenue, Shenzhen 518055, China
| | - Fuxing Zeng
- Department of Systems Biology, School of Life Sciences, Southern University of Science and Technology, No. 1088 Xueyuan Avenue, Shenzhen 518055, China
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11
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D'Urso G, Guyomar C, Chat S, Giudice E, Gillet R. Insights into the ribosomal trans-translation rescue system: lessons from recent structural studies. FEBS J 2023; 290:1461-1472. [PMID: 35015931 DOI: 10.1111/febs.16349] [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: 10/06/2021] [Revised: 12/27/2021] [Accepted: 01/10/2022] [Indexed: 11/29/2022]
Abstract
The arrest of protein synthesis caused when ribosomes stall on an mRNA lacking a stop codon is a deadly risk for all cells. In bacteria, this situation is remedied by the trans-translation quality control system. Trans-translation occurs because of the synergistic action of two main partners, transfer-messenger RNA (tmRNA) and small protein B (SmpB). These act in complex to monitor protein synthesis, intervening when necessary to rescue stalled ribosomes. During this process, incomplete nascent peptides are tagged for destruction, problematic mRNAs are degraded and the previously stalled ribosomes are recycled. In this 'Structural Snapshot' article, we describe the mechanism at the molecular level, a view updated after the most recent structural studies using cryo-electron microscopy.
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Affiliation(s)
- Gaetano D'Urso
- Institut de Génétique et Développement de Rennes (IGDR), CNRS, Univ. Rennes, France
| | - Charlotte Guyomar
- Institut de Génétique et Développement de Rennes (IGDR), CNRS, Univ. Rennes, France
| | - Sophie Chat
- Institut de Génétique et Développement de Rennes (IGDR), CNRS, Univ. Rennes, France
| | - Emmanuel Giudice
- Institut de Génétique et Développement de Rennes (IGDR), CNRS, Univ. Rennes, France
| | - Reynald Gillet
- Institut de Génétique et Développement de Rennes (IGDR), CNRS, Univ. Rennes, France
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12
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Parker MD, Karbstein K. Quality control ensures fidelity in ribosome assembly and cellular health. J Cell Biol 2023; 222:213871. [PMID: 36790396 PMCID: PMC9960125 DOI: 10.1083/jcb.202209115] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Revised: 01/09/2023] [Accepted: 02/02/2023] [Indexed: 02/16/2023] Open
Abstract
The coordinated integration of ribosomal RNA and protein into two functional ribosomal subunits is safeguarded by quality control checkpoints that ensure ribosomes are correctly assembled and functional before they engage in translation. Quality control is critical in maintaining the integrity of ribosomes and necessary to support healthy cell growth and prevent diseases associated with mistakes in ribosome assembly. Its importance is demonstrated by the finding that bypassing quality control leads to misassembled, malfunctioning ribosomes with altered translation fidelity, which change gene expression and disrupt protein homeostasis. In this review, we outline our understanding of quality control within ribosome synthesis and how failure to enforce quality control contributes to human disease. We first provide a definition of quality control to guide our investigation, briefly present the main assembly steps, and then examine stages of assembly that test ribosome function, establish a pass-fail system to evaluate these functions, and contribute to altered ribosome performance when bypassed, and are thus considered "quality control."
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Affiliation(s)
- Melissa D. Parker
- The Skaggs Graduate School of Chemical and Biological Sciences, The Scripps Research Institute, La Jolla, CA, USA,University of Florida—Scripps Biomedical Research, Jupiter, FL, USA
| | - Katrin Karbstein
- The Skaggs Graduate School of Chemical and Biological Sciences, The Scripps Research Institute, La Jolla, CA, USA,University of Florida—Scripps Biomedical Research, Jupiter, FL, USA,Howard Hughes Medical Institute Faculty Scholar, Howard Hughes Medical Institute, Chevy Chase, MD, USA,Correspondence to Katrin Karbstein:
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13
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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 2022; 51:919-934. [PMID: 36583339 PMCID: PMC9881166 DOI: 10.1093/nar/gkac1211] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [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)
| | | | | | - 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
- To whom correspondence should be addressed. Tel: +1 617 373 2952;
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14
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Nishima W, Girodat D, Holm M, Rundlet EJ, Alejo JL, Fischer K, Blanchard SC, Sanbonmatsu KY. Hyper-swivel head domain motions are required for complete mRNA-tRNA translocation and ribosome resetting. Nucleic Acids Res 2022; 50:8302-8320. [PMID: 35808938 DOI: 10.1093/nar/gkac597] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Revised: 06/15/2022] [Accepted: 07/05/2022] [Indexed: 11/14/2022] Open
Abstract
Translocation of messenger RNA (mRNA) and transfer RNA (tRNA) substrates through the ribosome during protein synthesis, an exemplar of directional molecular movement in biology, entails a complex interplay of conformational, compositional, and chemical changes. The molecular determinants of early translocation steps have been investigated rigorously. However, the elements enabling the ribosome to complete translocation and reset for subsequent protein synthesis reactions remain poorly understood. Here, we have combined molecular simulations with single-molecule fluorescence resonance energy transfer imaging to gain insights into the rate-limiting events of the translocation mechanism. We find that diffusive motions of the ribosomal small subunit head domain to hyper-swivelled positions, governed by universally conserved rRNA, can maneuver the mRNA and tRNAs to their fully translocated positions. Subsequent engagement of peptidyl-tRNA and disengagement of deacyl-tRNA from mRNA, within their respective small subunit binding sites, facilitate the ribosome resetting mechanism after translocation has occurred to enable protein synthesis to resume.
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Affiliation(s)
- Wataru Nishima
- Theoretical Biology and Biophysics, Theoretical Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
- New Mexico Consortium, Los Alamos, NM 87544, USA
| | - Dylan Girodat
- Theoretical Biology and Biophysics, Theoretical Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
- New Mexico Consortium, Los Alamos, NM 87544, USA
| | - Mikael Holm
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Emily J Rundlet
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
- Tri-Institutional PhD Program in Chemical Biology, Weill Cornell Medicine, New York, NY 10021, USA
| | - Jose L Alejo
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, MN 55455, USA
| | - Kara Fischer
- New Mexico Consortium, Los Alamos, NM 87544, USA
| | - Scott C Blanchard
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Karissa Y Sanbonmatsu
- Theoretical Biology and Biophysics, Theoretical Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
- New Mexico Consortium, Los Alamos, NM 87544, USA
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15
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Noller HF, Donohue JP, Gutell RR. The universally conserved nucleotides of the small subunit ribosomal RNAs. RNA (NEW YORK, N.Y.) 2022; 28:623-644. [PMID: 35115361 PMCID: PMC9014874 DOI: 10.1261/rna.079019.121] [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] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Accepted: 01/19/2022] [Indexed: 05/03/2023]
Abstract
The ribosomal RNAs, along with their substrates the transfer RNAs, contain the most highly conserved nucleotides in all of biology. We have assembled a database containing structure-based alignments of sequences of the small-subunit rRNAs from organisms that span the entire phylogenetic spectrum, to identify the nucleotides that are universally conserved. In its simplest (bacterial and archaeal) forms, the small-subunit rRNA has ∼1500 nt, of which we identify 140 that are absolutely invariant among the 1961 species in our alignment. We examine the positions and detailed structural and functional interactions of these universal nucleotides in the context of a half century of biochemical and genetic studies and high-resolution structures of ribosome functional complexes. The vast majority of these nucleotides are exposed on the subunit interface surface of the small subunit, where the functional processes of the ribosome take place. However, only 40 of them have been directly implicated in specific ribosomal functions, such as contacting the tRNAs, mRNA, or translation factors. The roles of many other invariant nucleotides may serve to constrain the positions and orientations of those nucleotides that are directly involved in function. Yet others can be rationalized by participation in unusual noncanonical tertiary structures that may uniquely allow correct folding of the rRNA to form a functional ribosome. However, there remain at least 50 nt whose universal conservation is not obvious, serving as a metric for the incompleteness of our understanding of ribosome structure and function.
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Affiliation(s)
- Harry F Noller
- Center for Molecular Biology of RNA, Department of Molecular, Cell and Developmental Biology, University of California at Santa Cruz, Santa Cruz, California 95064, USA
| | - John Paul Donohue
- Center for Molecular Biology of RNA, Department of Molecular, Cell and Developmental Biology, University of California at Santa Cruz, Santa Cruz, California 95064, USA
| | - Robin R Gutell
- Department of Integrative Biology, University of Texas at Austin, Austin, Texas 78712, USA
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16
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Gamper H, Masuda I, Hou YM. Genome Expansion by tRNA +1 Frameshifting at Quadruplet Codons. J Mol Biol 2022; 434:167440. [PMID: 34995554 PMCID: PMC9643101 DOI: 10.1016/j.jmb.2021.167440] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2021] [Revised: 12/27/2021] [Accepted: 12/30/2021] [Indexed: 11/29/2022]
Abstract
Inducing tRNA +1 frameshifting to read a quadruplet codon has the potential to incorporate a non-canonical amino acid (ncAA) into the polypeptide chain. While this strategy is attractive for genome expansion in biotechnology and bioengineering endeavors, improving the yield is hampered by a lack of understanding of where the shift can occur in an elongation cycle of protein synthesis. Lacking a clear answer to this question, current efforts have focused on designing +1-frameshifting tRNAs with an extra nucleotide inserted to the anticodon loop for pairing with a quadruplet codon in the aminoacyl-tRNA binding (A) site of the ribosome. However, the designed and evolved +1-frameshifting tRNAs vary broadly in achieving successful genome expansion. Here we summarize recent work on +1-frameshifting tRNAs. We suggest that, rather than engineering the quadruplet anticodon-codon pairing scheme at the ribosome A site, efforts should be made to engineer the pairing scheme at steps after the A site, including the step of the subsequent translocation and the step that stabilizes the pairing scheme in the +1-frame in the peptidyl-tRNA binding (P) site.
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Affiliation(s)
- Howard Gamper
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, USA
| | - Isao Masuda
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, USA
| | - Ya-Ming Hou
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, USA.
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17
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Tirumalai MR, Rivas M, Tran Q, Fox GE. The Peptidyl Transferase Center: a Window to the Past. Microbiol Mol Biol Rev 2021; 85:e0010421. [PMID: 34756086 PMCID: PMC8579967 DOI: 10.1128/mmbr.00104-21] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
In his 2001 article, "Translation: in retrospect and prospect," the late Carl Woese made a prescient observation that there was a need for the then-current view of translation to be "reformulated to become an all-embracing perspective about which 21st century Biology can develop" (RNA 7:1055-1067, 2001, https://doi.org/10.1017/s1355838201010615). The quest to decipher the origins of life and the road to the genetic code are both inextricably linked with the history of the ribosome. After over 60 years of research, significant progress in our understanding of how ribosomes work has been made. Particularly attractive is a model in which the ribosome may facilitate an ∼180° rotation of the CCA end of the tRNA from the A-site to the P-site while the acceptor stem of the tRNA would then undergo a translation from the A-site to the P-site. However, the central question of how the ribosome originated remains unresolved. Along the path from a primitive RNA world or an RNA-peptide world to a proto-ribosome world, the advent of the peptidyl transferase activity would have been a seminal event. This functionality is now housed within a local region of the large-subunit (LSU) rRNA, namely, the peptidyl transferase center (PTC). The PTC is responsible for peptide bond formation during protein synthesis and is usually considered to be the oldest part of the modern ribosome. What is frequently overlooked is that by examining the origins of the PTC itself, one is likely going back even further in time. In this regard, it has been proposed that the modern PTC originated from the association of two smaller RNAs that were once independent and now comprise a pseudosymmetric region in the modern PTC. Could such an association have survived? Recent studies have shown that the extant PTC is largely depleted of ribosomal protein interactions. It is other elements like metallic ion coordination and nonstandard base/base interactions that would have had to stabilize the association of RNAs. Here, we present a detailed review of the literature focused on the nature of the extant PTC and its proposed ancestor, the proto-ribosome.
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Affiliation(s)
- Madhan R. Tirumalai
- Department of Biology and Biochemistry, University of Houston, Houston, Texas, USA
| | - Mario Rivas
- Department of Biology and Biochemistry, University of Houston, Houston, Texas, USA
| | - Quyen Tran
- Department of Biology and Biochemistry, University of Houston, Houston, Texas, USA
| | - George E. Fox
- Department of Biology and Biochemistry, University of Houston, Houston, Texas, USA
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18
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Bao C, Ermolenko DN. Ribosome as a Translocase and Helicase. BIOCHEMISTRY (MOSCOW) 2021; 86:992-1002. [PMID: 34488575 PMCID: PMC8294220 DOI: 10.1134/s0006297921080095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
During protein synthesis, ribosome moves along mRNA to decode one codon after the other. Ribosome translocation is induced by a universally conserved protein, elongation factor G (EF-G) in bacteria and elongation factor 2 (EF-2) in eukaryotes. EF-G-induced translocation results in unwinding of the intramolecular secondary structures of mRNA by three base pairs at a time that renders the translating ribosome a processive helicase. Professor Alexander Sergeevich Spirin has made numerous seminal contributions to understanding the molecular mechanism of translocation. Here, we review Spirin's insights into the ribosomal translocation and recent advances in the field that stemmed from Spirin's pioneering work. We also discuss key remaining challenges in studies of translocase and helicase activities of the ribosome.
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Affiliation(s)
- Chen Bao
- Department of Biochemistry & Biophysics, School of Medicine and Dentistry and Center for RNA Biology, University of Rochester, Rochester, NY, USA.
| | - Dmitri N Ermolenko
- Department of Biochemistry & Biophysics, School of Medicine and Dentistry and Center for RNA Biology, University of Rochester, Rochester, NY, USA.
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19
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Belardinelli R, Sharma H, Peske F, Rodnina MV. Perturbation of ribosomal subunit dynamics by inhibitors of tRNA translocation. RNA (NEW YORK, N.Y.) 2021; 27:981-990. [PMID: 34117118 PMCID: PMC8370747 DOI: 10.1261/rna.078758.121] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Accepted: 06/03/2021] [Indexed: 05/02/2023]
Abstract
Many antibiotics that bind to the ribosome inhibit translation by blocking the movement of tRNAs and mRNA or interfering with ribosome dynamics, which impairs the formation of essential translocation intermediates. Here we show how translocation inhibitors viomycin (Vio), neomycin (Neo), paromomycin (Par), kanamycin (Kan), spectinomycin (Spc), hygromycin B (HygB), and streptomycin (Str, an antibiotic that does not inhibit tRNA movement), affect principal motions of the small ribosomal subunits (SSU) during EF-G-promoted translocation. Using ensemble kinetics, we studied the SSU body domain rotation and SSU head domain swiveling in real time. We show that although antibiotics binding to the ribosome can favor a particular ribosome conformation in the absence of EF-G, their kinetic effect on the EF-G-induced transition to the rotated/swiveled state of the SSU is moderate. The antibiotics mostly inhibit backward movements of the SSU body and/or the head domains. Vio, Spc, and high concentrations of Neo completely inhibit the backward movements of the SSU body and head domain. Kan, Par, HygB, and low concentrations of Neo slow down both movements, but their sequence and coordination are retained. Finally, Str has very little effect on the backward rotation of the SSU body domain, but retards the SSU head movement. The data underscore the importance of ribosome dynamics for tRNA-mRNA translocation and provide new insights into the mechanism of antibiotic action.
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Affiliation(s)
- Riccardo Belardinelli
- Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, Göttingen 37077, Germany
| | - Heena Sharma
- Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, Göttingen 37077, Germany
| | - Frank Peske
- Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, Göttingen 37077, Germany
| | - Marina V Rodnina
- Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, Göttingen 37077, Germany
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20
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Structures of tmRNA and SmpB as they transit through the ribosome. Nat Commun 2021; 12:4909. [PMID: 34389707 PMCID: PMC8363625 DOI: 10.1038/s41467-021-24881-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Accepted: 07/13/2021] [Indexed: 01/01/2023] Open
Abstract
In bacteria, trans-translation is the main rescue system, freeing ribosomes stalled on defective messenger RNAs. This mechanism is driven by small protein B (SmpB) and transfer-messenger RNA (tmRNA), a hybrid RNA known to have both a tRNA-like and an mRNA-like domain. Here we present four cryo-EM structures of the ribosome during trans-translation at resolutions from 3.0 to 3.4 Å. These include the high-resolution structure of the whole pre-accommodated state, as well as structures of the accommodated state, the translocated state, and a translocation intermediate. Together, they shed light on the movements of the tmRNA-SmpB complex in the ribosome, from its delivery by the elongation factor EF-Tu to its passage through the ribosomal A and P sites after the opening of the B1 bridges. Additionally, we describe the interactions between the tmRNA-SmpB complex and the ribosome. These explain why the process does not interfere with canonical translation.
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21
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A Phylogenetic Approach to Structural Variation in Organization of Nuclear Group I Introns and Their Ribozymes. Noncoding RNA 2021; 7:ncrna7030043. [PMID: 34449660 PMCID: PMC8395846 DOI: 10.3390/ncrna7030043] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Revised: 07/16/2021] [Accepted: 07/21/2021] [Indexed: 01/22/2023] Open
Abstract
Nuclear group I introns are restricted to the ribosomal DNA locus where they interrupt genes for small subunit and large subunit ribosomal RNAs at conserved sites in some eukaryotic microorganisms. Here, the myxomycete protists are a frequent source of nuclear group I introns due to their unique life strategy and a billion years of separate evolution. The ribosomal DNA of the myxomycete Mucilago crustacea was investigated and found to contain seven group I introns, including a direct repeat-containing intron at insertion site S1389 in the small subunit ribosomal RNA gene. We collected, analyzed, and compared 72 S1389 group IC1 introns representing diverse myxomycete taxa. The consensus secondary structure revealed a conserved ribozyme core, but with surprising sequence variations in the guanosine binding site in segment P7. Some S1389 introns harbored large extension sequences in the peripheral region of segment P9 containing direct repeat arrays. These repeats contained up to 52 copies of a putative internal guide sequence motif. Other S1389 introns harbored homing endonuclease genes in segment P1 encoding His-Cys proteins. Homing endonuclease genes were further interrupted by small spliceosomal introns that have to be removed in order to generate the open reading frames. Phylogenetic analyses of S1389 intron and host gene indicated both vertical and horizontal intron transfer during evolution, and revealed sporadic appearances of direct repeats, homing endonuclease genes, and guanosine binding site variants among the myxomycete taxa.
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22
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Chang KC, Wen JD. Programmed -1 ribosomal frameshifting from the perspective of the conformational dynamics of mRNA and ribosomes. Comput Struct Biotechnol J 2021; 19:3580-3588. [PMID: 34257837 PMCID: PMC8246090 DOI: 10.1016/j.csbj.2021.06.015] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Revised: 06/11/2021] [Accepted: 06/12/2021] [Indexed: 11/01/2022] Open
Abstract
Programmed -1 ribosomal frameshifting (-1 PRF) is a translation mechanism that regulates the relative expression level of two proteins encoded on the same messenger RNA (mRNA). This regulation is commonly used by viruses such as coronaviruses and retroviruses but rarely by host human cells, and for this reason, it has long been considered as a therapeutic target for antiviral drug development. Understanding the molecular mechanism of -1 PRF is one step toward this goal. Minus-one PRF occurs with a certain efficiency when translating ribosomes encounter the specialized mRNA signal consisting of the frameshifting site and a downstream stimulatory structure, which impedes translocation of the ribosome. The impeded ribosome can still undergo profound conformational changes to proceed with translocation; however, some of these changes may be unique and essential to frameshifting. In addition, most stimulatory structures exhibit conformational dynamics and sufficient mechanical strength, which, when under the action of ribosomes, may in turn further promote -1 PRF efficiency. In this review, we discuss how the dynamic features of ribosomes and mRNA stimulatory structures may influence the occurrence of -1 PRF and propose a hypothetical frameshifting model that recapitulates the role of conformational dynamics.
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Affiliation(s)
- Kai-Chun Chang
- Department of Bioengineering and Therapeutic Sciences, Schools of Medicine and Pharmacy, University of California, San Francisco, CA 94158, United States
| | - Jin-Der Wen
- Institute of Molecular and Cellular Biology, National Taiwan University, Taipei 10617, Taiwan
- Genome and Systems Biology Degree Program, National Taiwan University and Academia Sinica, Taipei 10617, Taiwan
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23
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Freitas FC, Fuchs G, de Oliveira RJ, Whitford PC. The dynamics of subunit rotation in a eukaryotic ribosome. BIOPHYSICA 2021; 1:204-221. [PMID: 37484008 PMCID: PMC10361705 DOI: 10.3390/biophysica1020016] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 07/25/2023]
Abstract
Protein synthesis by the ribosome is coordinated by an intricate series of large-scale conformational rearrangements. Structural studies can provide information about long-lived states, however biological kinetics are controlled by the intervening free-energy barriers. While there has been progress describing the energy landscapes of bacterial ribosomes, very little is known about the energetics of large-scale rearrangements in eukaryotic systems. To address this topic, we constructed an all-atom model with simplified energetics and performed simulations of subunit rotation in the yeast ribosome. In these simulations, the small subunit (SSU; ~1MDa) undergoes spontaneous and reversible rotations (~8°). By enabling the simulation of this rearrangement under equilibrium conditions, these calculations provide initial insights into the molecular factors that control dynamics in eukaryotic ribosomes. Through this, we are able to identify specific inter-subunit interactions that have a pronounced influence on the rate-limiting free-energy barrier. We also show that, as a result of changes in molecular flexibility, the thermodynamic balance between the rotated and unrotated states is temperature-dependent. This effect may be interpreted in terms of differential molecular flexibility within the rotated and unrotated states. Together, these calculations provide a foundation, upon which the field may begin to dissect the energetics of these complex molecular machines.
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Affiliation(s)
- Frederico Campos Freitas
- Laboratório de Biofísica Teórica, Departamento de Física, Instituto de Ciências Exatas, Naturais e Educação, Universidade Federal do Triângulo Mineiro, Uberaba, MG, Brazil
| | - Gabriele Fuchs
- Department of Biological Sciences, The RNA Institute, University at Albany 1400 Washington Ave, Albany, NY,12222
| | - 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, Brazil
| | - Paul Charles Whitford
- Department of Physics, Northeastern University, 360 Huntington Ave, Boston, MA 02115
- Center for Theoretical Biological Physics, Northeastern University, 360 Huntington Ave, Boston, MA 02115
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24
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Schedlbauer A, Iturrioz I, Ochoa-Lizarralde B, Diercks T, López-Alonso JP, Lavin JL, Kaminishi T, Çapuni R, Dhimole N, de Astigarraga E, Gil-Carton D, Fucini P, Connell SR. A conserved rRNA switch is central to decoding site maturation on the small ribosomal subunit. SCIENCE ADVANCES 2021; 7:7/23/eabf7547. [PMID: 34088665 PMCID: PMC8177701 DOI: 10.1126/sciadv.abf7547] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Accepted: 04/20/2021] [Indexed: 05/03/2023]
Abstract
While a structural description of the molecular mechanisms guiding ribosome assembly in eukaryotic systems is emerging, bacteria use an unrelated core set of assembly factors for which high-resolution structural information is still missing. To address this, we used single-particle cryo-electron microscopy to visualize the effects of bacterial ribosome assembly factors RimP, RbfA, RsmA, and RsgA on the conformational landscape of the 30S ribosomal subunit and obtained eight snapshots representing late steps in the folding of the decoding center. Analysis of these structures identifies a conserved secondary structure switch in the 16S ribosomal RNA central to decoding site maturation and suggests both a sequential order of action and molecular mechanisms for the assembly factors in coordinating and controlling this switch. Structural and mechanistic parallels between bacterial and eukaryotic systems indicate common folding features inherent to all ribosomes.
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Affiliation(s)
- Andreas Schedlbauer
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 801A, 48160 Derio, Spain
| | - Idoia Iturrioz
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 801A, 48160 Derio, Spain
| | - Borja Ochoa-Lizarralde
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 801A, 48160 Derio, Spain
| | - Tammo Diercks
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 801A, 48160 Derio, Spain
| | - Jorge Pedro López-Alonso
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 801A, 48160 Derio, Spain
| | | | - Tatsuya Kaminishi
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 801A, 48160 Derio, Spain
- Department of Genetics, Graduate School of Medicine, Osaka University, Japan
| | - Retina Çapuni
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 801A, 48160 Derio, Spain
| | - Neha Dhimole
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 801A, 48160 Derio, Spain
| | - Elisa de Astigarraga
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 801A, 48160 Derio, Spain
| | - David Gil-Carton
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 801A, 48160 Derio, Spain
| | - Paola Fucini
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 801A, 48160 Derio, Spain.
- IKERBASQUE, Basque Foundation for Science, 48013 Bilbao, Spain
| | - Sean R Connell
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 801A, 48160 Derio, Spain.
- IKERBASQUE, Basque Foundation for Science, 48013 Bilbao, Spain
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25
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Plassart L, Shayan R, Montellese C, Rinaldi D, Larburu N, Pichereaux C, Froment C, Lebaron S, O'Donohue MF, Kutay U, Marcoux J, Gleizes PE, Plisson-Chastang C. The final step of 40S ribosomal subunit maturation is controlled by a dual key lock. eLife 2021; 10:61254. [PMID: 33908345 PMCID: PMC8112863 DOI: 10.7554/elife.61254] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Accepted: 04/19/2021] [Indexed: 12/31/2022] Open
Abstract
Preventing premature interaction of pre-ribosomes with the translation apparatus is essential for translational accuracy. Hence, the final maturation step releasing functional 40S ribosomal subunits, namely processing of the 18S ribosomal RNA 3' end, is safeguarded by the protein DIM2, which both interacts with the endoribonuclease NOB1 and masks the rRNA cleavage site. To elucidate the control mechanism that unlocks NOB1 activity, we performed cryo-electron microscopy analysis of late human pre-40S particles purified using a catalytically inactive form of the ATPase RIO1. These structures, together with in vivo and in vitro functional analyses, support a model in which ATP-loaded RIO1 cooperates with ribosomal protein RPS26/eS26 to displace DIM2 from the 18S rRNA 3' end, thereby triggering final cleavage by NOB1; release of ADP then leads to RIO1 dissociation from the 40S subunit. This dual key lock mechanism requiring RIO1 and RPS26 guarantees the precise timing of pre-40S particle conversion into translation-competent ribosomal subunits.
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Affiliation(s)
- Laura Plassart
- Molecular, Cellular and Developmental Biology department (MCD), Centre de Biologie Integrative (CBI), University of Toulouse, CNRS, UPS, Toulouse, France
| | - Ramtin Shayan
- Molecular, Cellular and Developmental Biology department (MCD), Centre de Biologie Integrative (CBI), University of Toulouse, CNRS, UPS, Toulouse, France
| | | | - Dana Rinaldi
- Molecular, Cellular and Developmental Biology department (MCD), Centre de Biologie Integrative (CBI), University of Toulouse, CNRS, UPS, Toulouse, France
| | - Natacha Larburu
- Molecular, Cellular and Developmental Biology department (MCD), Centre de Biologie Integrative (CBI), University of Toulouse, CNRS, UPS, Toulouse, France
| | - Carole Pichereaux
- Institut de Pharmacologie et Biologie Structurale, Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Carine Froment
- Institut de Pharmacologie et Biologie Structurale, Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Simon Lebaron
- Molecular, Cellular and Developmental Biology department (MCD), Centre de Biologie Integrative (CBI), University of Toulouse, CNRS, UPS, Toulouse, France
| | - Marie-Françoise O'Donohue
- Molecular, Cellular and Developmental Biology department (MCD), Centre de Biologie Integrative (CBI), University of Toulouse, CNRS, UPS, Toulouse, France
| | - Ulrike Kutay
- Institut für Biochemie, ETH Zürich, Zurich, Switzerland
| | - Julien Marcoux
- Institut de Pharmacologie et Biologie Structurale, Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Pierre-Emmanuel Gleizes
- Molecular, Cellular and Developmental Biology department (MCD), Centre de Biologie Integrative (CBI), University of Toulouse, CNRS, UPS, Toulouse, France
| | - Celia Plisson-Chastang
- Molecular, Cellular and Developmental Biology department (MCD), Centre de Biologie Integrative (CBI), University of Toulouse, CNRS, UPS, Toulouse, France
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26
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Li Y, Koripella RK, Sharma MR, Lee RE, Agrawal RK, Ojha AK. Replacement of S14 Protein in Ribosomes of Zinc-Starved Mycobacteria Reduces Spectinamide Sensitivity. Antimicrob Agents Chemother 2021; 65:e01833-20. [PMID: 33361293 PMCID: PMC8092523 DOI: 10.1128/aac.01833-20] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Accepted: 12/13/2020] [Indexed: 11/20/2022] Open
Abstract
Zinc is an essential micronutrient for mycobacteria, and its depletion induces multiple adaptive changes in cellular physiology, the most remarkable of which are remodeling and hibernation of ribosomes. Ribosome remodeling, induced upon relatively moderate depletion of zinc, involves replacement of multiple ribosomal proteins containing the zinc-binding CXXC motif (called C+ r proteins) by their motif-free C- paralogs. Severe zinc depletion induces binding of mycobacterial protein Y (Mpy) to the 70S C- ribosome, thereby stabilizing the ribosome in an inactive state that is also resistant to kanamycin and streptomycin. Because the Mpy binding region on the ribosome is proximal to the binding pocket of spectinamides (Spa), the preclinical drug candidates for tuberculosis, we addressed the impact of remodeling and hibernation of ribosomes on Spa sensitivity. We report here that while Mpy binding has no significant effect on Spa sensitivity to the ribosome, replacement of S14C+ with its C- counterpart reduces the binding affinity of the drug by ∼2-fold, causing increased Spa tolerance in Mycobacterium smegmatis and Mycobacterium tuberculosis cells harboring the C- ribosome. The altered interaction between Spa and ribosomes likely results from new contact points for D67 and R83 residues of S14C- with U1138 and C1184 of 16S rRNA helix 34, respectively. Given that M. tuberculosis induces ribosome remodeling during progression from the acute to chronic phase of lung infection, our findings highlight new considerations in the development of Spa as effective drugs against tuberculosis.
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Affiliation(s)
- Yunlong Li
- Division of Genetics, Wadsworth Center, New York State Department of Health, Albany, New York, USA
| | - Ravi K Koripella
- Division of Translational Medicine, Wadsworth Center, New York State Department of Health, Albany, New York, USA
| | - Manjuli R Sharma
- Division of Translational Medicine, Wadsworth Center, New York State Department of Health, Albany, New York, USA
| | - Richard E Lee
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Rajendra K Agrawal
- Division of Translational Medicine, Wadsworth Center, New York State Department of Health, Albany, New York, USA
- Department of Biomedical Sciences, University at Albany, Albany, New York, USA
| | - Anil K Ojha
- Division of Genetics, Wadsworth Center, New York State Department of Health, Albany, New York, USA
- Department of Biomedical Sciences, University at Albany, Albany, New York, USA
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27
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Gamper H, Li H, Masuda I, Miklos Robkis D, Christian T, Conn AB, Blaha G, Petersson EJ, Gonzalez RL, Hou YM. Insights into genome recoding from the mechanism of a classic +1-frameshifting tRNA. Nat Commun 2021; 12:328. [PMID: 33436566 PMCID: PMC7803779 DOI: 10.1038/s41467-020-20373-z] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Accepted: 11/30/2020] [Indexed: 12/18/2022] Open
Abstract
While genome recoding using quadruplet codons to incorporate non-proteinogenic amino acids is attractive for biotechnology and bioengineering purposes, the mechanism through which such codons are translated is poorly understood. Here we investigate translation of quadruplet codons by a +1-frameshifting tRNA, SufB2, that contains an extra nucleotide in its anticodon loop. Natural post-transcriptional modification of SufB2 in cells prevents it from frameshifting using a quadruplet-pairing mechanism such that it preferentially employs a triplet-slippage mechanism. We show that SufB2 uses triplet anticodon-codon pairing in the 0-frame to initially decode the quadruplet codon, but subsequently shifts to the +1-frame during tRNA-mRNA translocation. SufB2 frameshifting involves perturbation of an essential ribosome conformational change that facilitates tRNA-mRNA movements at a late stage of the translocation reaction. Our results provide a molecular mechanism for SufB2-induced +1 frameshifting and suggest that engineering of a specific ribosome conformational change can improve the efficiency of genome recoding. Genome recoding with quadruplet codons requires a +1-frameshift-suppressor tRNA able to insert an amino acid at quadruplet codons of interest. Here the authors identify the mechanisms resulting in +1 frameshifting and the steps of the elongation cycle in which it occurs.
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Affiliation(s)
- Howard Gamper
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, PA, 19107, USA
| | - Haixing Li
- Department of Chemistry, Columbia University, New York, NY, 10027, USA
| | - Isao Masuda
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, PA, 19107, USA
| | - D Miklos Robkis
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Thomas Christian
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, PA, 19107, USA
| | - Adam B Conn
- Department of Biochemistry, University of California, Riverside, CA, 92521, USA
| | - Gregor Blaha
- Department of Biochemistry, University of California, Riverside, CA, 92521, USA
| | - E James Petersson
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Ruben L Gonzalez
- Department of Chemistry, Columbia University, New York, NY, 10027, USA.
| | - Ya-Ming Hou
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, PA, 19107, USA.
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28
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Schäkermann S, Wüllner D, Yayci A, Emili A, Bandow JE. Applicability of Chromatographic Co-Elution for Antibiotic Target Identification. Proteomics 2020; 21:e2000038. [PMID: 32951352 DOI: 10.1002/pmic.202000038] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Revised: 09/09/2020] [Indexed: 11/07/2022]
Abstract
Identification of the molecular target is a crucial step in evaluating novel antibiotics. To support target identification, a label-free method based on chromatographic co-elution has previously been developed. Target identification by chromatographic coelution (TICC) exploits the alteration of the elution profile of target-bound drug versus free drug in ion exchange (IEX) chromatography to identify potential target proteins from elution fractions. The applicability of TICC for antibiotic research is investigated by evaluating which proteins, that is, putative targets, can be monitored in Bacillus subtilis. Coelution of components of known protein complexes provides a read-out for how well the native state of proteins is conserved during chromatography. Rifampicin, which targets RNA polymerase, is used in a proof-of-concept study.
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Affiliation(s)
- Sina Schäkermann
- Applied Microbiology, Faculty of Biology and Biotechnology, Ruhr-Universität Bochum, 44801, Bochum, Germany
| | - Dominik Wüllner
- Applied Microbiology, Faculty of Biology and Biotechnology, Ruhr-Universität Bochum, 44801, Bochum, Germany
| | - Abdulkadir Yayci
- Applied Microbiology, Faculty of Biology and Biotechnology, Ruhr-Universität Bochum, 44801, Bochum, Germany
| | - Andrew Emili
- Center for Network Systems Biology, Boston University School of Medicine, Boston, MA, 02215, USA
| | - Julia Elisabeth Bandow
- Applied Microbiology, Faculty of Biology and Biotechnology, Ruhr-Universität Bochum, 44801, Bochum, Germany
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29
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Hoffer ED, Hong S, Sunita S, Maehigashi T, Gonzalez RL, Whitford PC, Dunham CM. Structural insights into mRNA reading frame regulation by tRNA modification and slippery codon-anticodon pairing. eLife 2020; 9:51898. [PMID: 33016876 PMCID: PMC7577736 DOI: 10.7554/elife.51898] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Accepted: 10/02/2020] [Indexed: 01/10/2023] Open
Abstract
Modifications in the tRNA anticodon loop, adjacent to the three-nucleotide anticodon, influence translation fidelity by stabilizing the tRNA to allow for accurate reading of the mRNA genetic code. One example is the N1-methylguanosine modification at guanine nucleotide 37 (m1G37) located in the anticodon loop andimmediately adjacent to the anticodon nucleotides 34, 35, 36. The absence of m1G37 in tRNAPro causes +1 frameshifting on polynucleotide, slippery codons. Here, we report structures of the bacterial ribosome containing tRNAPro bound to either cognate or slippery codons to determine how the m1G37 modification prevents mRNA frameshifting. The structures reveal that certain codon–anticodon contexts and the lack of m1G37 destabilize interactions of tRNAPro with the P site of the ribosome, causing large conformational changes typically only seen during EF-G-mediated translocation of the mRNA-tRNA pairs. These studies provide molecular insights into how m1G37 stabilizes the interactions of tRNAPro with the ribosome in the context of a slippery mRNA codon.
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Affiliation(s)
- Eric D Hoffer
- Department of Biochemistry, Emory University School of Medicine, Atlanta, United States
| | - Samuel Hong
- Department of Biochemistry, Emory University School of Medicine, Atlanta, United States
| | - S Sunita
- Department of Biochemistry, Emory University School of Medicine, Atlanta, United States
| | - Tatsuya Maehigashi
- Department of Biochemistry, Emory University School of Medicine, Atlanta, United States
| | - Ruben L Gonzalez
- Department of Chemistry, Columbia University, New York, United States
| | - Paul C Whitford
- Department of Physics, Northeastern University, Boston, United States
| | - Christine M Dunham
- Department of Biochemistry, Emory University School of Medicine, Atlanta, United States
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30
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Murphy EL, Singh KV, Avila B, Kleffmann T, Gregory ST, Murray BE, Krause KL, Khayat R, Jogl G. Cryo-electron microscopy structure of the 70S ribosome from Enterococcus faecalis. Sci Rep 2020; 10:16301. [PMID: 33004869 PMCID: PMC7530986 DOI: 10.1038/s41598-020-73199-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Accepted: 09/11/2020] [Indexed: 01/21/2023] Open
Abstract
Enterococcus faecalis is a gram-positive organism responsible for serious infections in humans, but as with many bacterial pathogens, resistance has rendered a number of commonly used antibiotics ineffective. Here, we report the cryo-EM structure of the E. faecalis 70S ribosome to a global resolution of 2.8 Å. Structural differences are clustered in peripheral and solvent exposed regions when compared with Escherichia coli, whereas functional centres, including antibiotic binding sites, are similar to other bacterial ribosomes. Comparison of intersubunit conformations among five classes obtained after three-dimensional classification identifies several rotated states. Large ribosomal subunit protein bL31, which forms intersubunit bridges to the small ribosomal subunit, assumes different conformations in the five classes, revealing how contacts to the small subunit are maintained throughout intersubunit rotation. A tRNA observed in one of the five classes is positioned in a chimeric pe/E position in a rotated ribosomal state. The 70S ribosome structure of E. faecalis now extends our knowledge of bacterial ribosome structures and may serve as a basis for the development of novel antibiotic compounds effective against this pathogen.
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Affiliation(s)
- Eileen L. Murphy
- grid.40263.330000 0004 1936 9094Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, RI 02912 USA
| | - Kavindra V. Singh
- grid.267308.80000 0000 9206 2401Division of Infectious Diseases, Department of Internal Medicine, University of Texas Health Science Center, Houston, TX 77030 USA ,grid.267308.80000 0000 9206 2401Center for Antimicrobial Resistance and Microbial Genomics, University of Texas Health Science Center, Houston, TX 77030 USA
| | - Bryant Avila
- grid.254250.40000 0001 2264 7145Department of Chemistry and Biochemistry, The City College of New York, New York, NY 10031 USA
| | - Torsten Kleffmann
- grid.29980.3a0000 0004 1936 7830Department of Biochemistry, University of Otago, Dunedin, 9054 New Zealand
| | - Steven T. Gregory
- grid.20431.340000 0004 0416 2242Department of Cell and Molecular Biology, The University of Rhode Island, Kingston, RI 02881 USA
| | - Barbara E. Murray
- grid.267308.80000 0000 9206 2401Division of Infectious Diseases, Department of Internal Medicine, University of Texas Health Science Center, Houston, TX 77030 USA ,grid.267308.80000 0000 9206 2401Center for Antimicrobial Resistance and Microbial Genomics, University of Texas Health Science Center, Houston, TX 77030 USA ,grid.267308.80000 0000 9206 2401Department of Microbiology and Molecular Genetics, University of Texas Health Science Center, Houston, TX 77030 USA
| | - Kurt L. Krause
- grid.29980.3a0000 0004 1936 7830Department of Biochemistry, University of Otago, Dunedin, 9054 New Zealand
| | - Reza Khayat
- grid.254250.40000 0001 2264 7145Department of Chemistry and Biochemistry, The City College of New York, New York, NY 10031 USA
| | - Gerwald Jogl
- grid.40263.330000 0004 1936 9094Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, RI 02912 USA
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31
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Nicholson D, Edwards TA, O'Neill AJ, Ranson NA. Structure of the 70S Ribosome from the Human Pathogen Acinetobacter baumannii in Complex with Clinically Relevant Antibiotics. Structure 2020; 28:1087-1100.e3. [PMID: 32857965 PMCID: PMC7546915 DOI: 10.1016/j.str.2020.08.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Revised: 07/06/2020] [Accepted: 08/07/2020] [Indexed: 12/19/2022]
Abstract
Acinetobacter baumannii is a Gram-negative bacterium primarily associated with hospital-acquired, often multidrug-resistant (MDR) infections. The ribosome-targeting antibiotics amikacin and tigecycline are among the limited arsenal of drugs available for treatment of such infections. We present high-resolution structures of the 70S ribosome from A. baumannii in complex with these antibiotics, as determined by cryoelectron microscopy. Comparison with the ribosomes of other bacteria reveals several unique structural features at functionally important sites, including around the exit of the polypeptide tunnel and the periphery of the subunit interface. The structures also reveal the mode and site of interaction of these drugs with the ribosome. This work paves the way for the design of new inhibitors of translation to address infections caused by MDR A. baumannii. Cryo-EM structures of the ribosome from the pathogenic bacteria A. baumannii Unique structural features compared with other bacterial ribosomes The site and mode of binding of amikacin and tigecycline to this ribosome A putative alternative tigecycline-binding site at the 50S central protuberance
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Affiliation(s)
- David Nicholson
- Astbury Centre for Structural Molecular Biology, School of Molecular & Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - Thomas A Edwards
- Astbury Centre for Structural Molecular Biology, School of Molecular & Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK.
| | - Alex J O'Neill
- Astbury Centre for Structural Molecular Biology, School of Molecular & Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK.
| | - Neil A Ranson
- Astbury Centre for Structural Molecular Biology, School of Molecular & Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK.
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32
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Shayan R, Rinaldi D, Larburu N, Plassart L, Balor S, Bouyssié D, Lebaron S, Marcoux J, Gleizes PE, Plisson-Chastang C. Good Vibrations: Structural Remodeling of Maturing Yeast Pre-40S Ribosomal Particles Followed by Cryo-Electron Microscopy. Molecules 2020; 25:molecules25051125. [PMID: 32138239 PMCID: PMC7179242 DOI: 10.3390/molecules25051125] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Revised: 02/24/2020] [Accepted: 02/27/2020] [Indexed: 12/03/2022] Open
Abstract
Assembly of eukaryotic ribosomal subunits is a very complex and sequential process that starts in the nucleolus and finishes in the cytoplasm with the formation of functional ribosomes. Over the past few years, characterization of the many molecular events underlying eukaryotic ribosome biogenesis has been drastically improved by the “resolution revolution” of cryo-electron microscopy (cryo-EM). However, if very early maturation events have been well characterized for both yeast ribosomal subunits, little is known regarding the final maturation steps occurring to the small (40S) ribosomal subunit. To try to bridge this gap, we have used proteomics together with cryo-EM and single particle analysis to characterize yeast pre-40S particles containing the ribosome biogenesis factor Tsr1. Our analyses lead us to refine the timing of the early pre-40S particle maturation steps. Furthermore, we suggest that after an early and structurally stable stage, the beak and platform domains of pre-40S particles enter a “vibrating” or “wriggling” stage, that might be involved in the final maturation of 18S rRNA as well as the fitting of late ribosomal proteins into their mature position.
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Affiliation(s)
- Ramtin Shayan
- Laboratoire de Biologie Moléculaire Eucaryote, Centre de Biologie Intégrative, Université de Toulouse, CNRS, UPS, 118 route de Narbonne, 31062 Toulouse CEDEX, France; (R.S.); (D.R.); (N.L.); (L.P.); (S.B.); (S.L.)
| | - Dana Rinaldi
- Laboratoire de Biologie Moléculaire Eucaryote, Centre de Biologie Intégrative, Université de Toulouse, CNRS, UPS, 118 route de Narbonne, 31062 Toulouse CEDEX, France; (R.S.); (D.R.); (N.L.); (L.P.); (S.B.); (S.L.)
| | - Natacha Larburu
- Laboratoire de Biologie Moléculaire Eucaryote, Centre de Biologie Intégrative, Université de Toulouse, CNRS, UPS, 118 route de Narbonne, 31062 Toulouse CEDEX, France; (R.S.); (D.R.); (N.L.); (L.P.); (S.B.); (S.L.)
| | - Laura Plassart
- Laboratoire de Biologie Moléculaire Eucaryote, Centre de Biologie Intégrative, Université de Toulouse, CNRS, UPS, 118 route de Narbonne, 31062 Toulouse CEDEX, France; (R.S.); (D.R.); (N.L.); (L.P.); (S.B.); (S.L.)
| | - Stéphanie Balor
- Laboratoire de Biologie Moléculaire Eucaryote, Centre de Biologie Intégrative, Université de Toulouse, CNRS, UPS, 118 route de Narbonne, 31062 Toulouse CEDEX, France; (R.S.); (D.R.); (N.L.); (L.P.); (S.B.); (S.L.)
| | - David Bouyssié
- Institut de Pharmacologie et Biologie Structurale, Université de Toulouse, CNRS, UPS, 205 route de Narbonne, 31062 Toulouse CEDEX, France;
| | - Simon Lebaron
- Laboratoire de Biologie Moléculaire Eucaryote, Centre de Biologie Intégrative, Université de Toulouse, CNRS, UPS, 118 route de Narbonne, 31062 Toulouse CEDEX, France; (R.S.); (D.R.); (N.L.); (L.P.); (S.B.); (S.L.)
| | - Julien Marcoux
- Laboratoire de Biologie Moléculaire Eucaryote, Centre de Biologie Intégrative, Université de Toulouse, CNRS, UPS, 118 route de Narbonne, 31062 Toulouse CEDEX, France; (R.S.); (D.R.); (N.L.); (L.P.); (S.B.); (S.L.)
- Correspondence: (J.M.); (P.-E.G.); (C.P.-C.)
| | - Pierre-Emmanuel Gleizes
- Laboratoire de Biologie Moléculaire Eucaryote, Centre de Biologie Intégrative, Université de Toulouse, CNRS, UPS, 118 route de Narbonne, 31062 Toulouse CEDEX, France; (R.S.); (D.R.); (N.L.); (L.P.); (S.B.); (S.L.)
- Correspondence: (J.M.); (P.-E.G.); (C.P.-C.)
| | - Célia Plisson-Chastang
- Laboratoire de Biologie Moléculaire Eucaryote, Centre de Biologie Intégrative, Université de Toulouse, CNRS, UPS, 118 route de Narbonne, 31062 Toulouse CEDEX, France; (R.S.); (D.R.); (N.L.); (L.P.); (S.B.); (S.L.)
- Correspondence: (J.M.); (P.-E.G.); (C.P.-C.)
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33
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Morgan CE, Huang W, Rudin SD, Taylor DJ, Kirby JE, Bonomo RA, Yu EW. Cryo-electron Microscopy Structure of the Acinetobacter baumannii 70S Ribosome and Implications for New Antibiotic Development. mBio 2020; 11:e03117-19. [PMID: 31964740 PMCID: PMC6974574 DOI: 10.1128/mbio.03117-19] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Accepted: 12/02/2019] [Indexed: 01/11/2023] Open
Abstract
Antimicrobial resistance is a major health threat as it limits treatment options for infection. At the forefront of this serious issue is Acinetobacter baumannii, a Gram-negative opportunistic pathogen that exhibits the remarkable ability to resist antibiotics through multiple mechanisms. As bacterial ribosomes represent a target for multiple distinct classes of existing antimicrobial agents, we here use single-particle cryo-electron microscopy (cryo-EM) to elucidate five different structural states of the A. baumannii ribosome, including the 70S, 50S, and 30S forms. We also determined interparticle motions of the 70S ribosome in different tRNA bound states using three-dimensional (3D) variability analysis. Together, our structural data further our understanding of the ribosome from A. baumannii and other Gram-negative pathogens and will enable structure-based drug discovery to combat antibiotic-resistant bacterial infections.IMPORTANCEAcinetobacter baumannii is a severe nosocomial threat largely due to its intrinsic antibiotic resistance and remarkable ability to acquire new resistance determinants. The bacterial ribosome serves as a major target for modern antibiotics and the design of new therapeutics. Here, we present cryo-EM structures of the A. baumannii 70S ribosome, revealing several unique species-specific structural features that may facilitate future drug development to combat this recalcitrant bacterial pathogen.
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Affiliation(s)
- Christopher E Morgan
- Department of Pharmacology, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
| | - Wei Huang
- Department of Pharmacology, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
| | - Susan D Rudin
- Louis Stokes Cleveland Veterans Affairs Medical Center, Cleveland, Ohio, USA
| | - Derek J Taylor
- Department of Pharmacology, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
| | - James E Kirby
- Department of Pathology, Beth Israel Deaconess Medical Center, Boston, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
| | - Robert A Bonomo
- Department of Medicine, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
- Louis Stokes Cleveland Veterans Affairs Medical Center, Cleveland, Ohio, USA
- Department of Pharmacology, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
- Department of Molecular Biology and Microbiology, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
- Department of Biochemistry, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
- Case Center for Proteomics and Bioinformatics, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
- CWRU-Cleveland VAMC Center for Antimicrobial Resistance and Epidemiology, Cleveland, Ohio, USA
| | - Edward W Yu
- Department of Pharmacology, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
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34
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Chang KC, Salawu EO, Chang YY, Wen JD, Yang LW. Resolution-exchanged structural modeling and simulations jointly unravel that subunit rolling underlies the mechanism of programmed ribosomal frameshifting. Bioinformatics 2019; 35:945-952. [PMID: 30169551 DOI: 10.1093/bioinformatics/bty762] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2018] [Revised: 07/26/2018] [Accepted: 08/28/2018] [Indexed: 12/20/2022] Open
Abstract
MOTIVATION Programmed ribosomal frameshifting (PRF) is widely used by viruses and bacteria to produce different proteins from a single mRNA template. How steric hindrance of a PRF-stimulatory mRNA structure transiently modifies the conformational dynamics of the ribosome, and thereby allows tRNA slippage, remains elusive. RESULTS Here, we leverage linear response theories and resolution-exchanged simulations to construct a structural/dynamics model that connects and rationalizes existing structural, single-molecule and mutagenesis data by resolution-exchanged structural modelling and simulations. Our combined theoretical techniques provide a temporal and spatial description of PRF with unprecedented mechanistic details. We discover that ribosomal unfolding of the PRF-stimulating pseudoknot exerts resistant forces on the mRNA entrance of the ribosome, and thereby drives 30S subunit rolling. Such motion distorts tRNAs, leads to tRNA slippage, and in turn serves as a delicate control of cis-element's unwinding forces over PRF. AVAILABILITY AND IMPLEMENTATION All the simulation scripts and computational implementations of our methods/analyses (including linear response theory) are included in the bioStructureM suite, provided through GitHub at https://github.com/Yuan-Yu/bioStructureM. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Kai-Chun Chang
- Institute of Molecular and Cellular Biology, National Taiwan University, Taipei, Taiwan
| | - Emmanuel Oluwatobi Salawu
- Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu, Taiwan.,TIGP Bioinformatics Program, Institute of Information Sciences, Academia Sinica, Taipei, Taiwan
| | - Yuan-Yu Chang
- Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu, Taiwan
| | - Jin-Der Wen
- Institute of Molecular and Cellular Biology, National Taiwan University, Taipei, Taiwan
| | - Lee-Wei Yang
- Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu, Taiwan.,TIGP Bioinformatics Program, Institute of Information Sciences, Academia Sinica, Taipei, Taiwan.,Physics Division, National Center for Theoretical Sciences, Hsinchu, Taiwan
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35
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Chan J, Takemura K, Lin HR, Chang KC, Chang YY, Joti Y, Kitao A, Yang LW. An Efficient Timer and Sizer of Biomacromolecular Motions. Structure 2019; 28:259-269.e8. [PMID: 31780433 DOI: 10.1016/j.str.2019.10.020] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2019] [Revised: 08/22/2019] [Accepted: 10/30/2019] [Indexed: 11/28/2022]
Abstract
Life ticks as fast as how proteins move. Computationally expensive molecular dynamics simulation has been the only theoretical tool to gauge the time and sizes of these motions, though barely to their slowest ends. Here, we convert a computationally cheap elastic network model (ENM) into a molecular timer and sizer to gauge the slowest functional motions of structured biomolecules. Quasi-harmonic analysis, fluctuation profile matching, and the Wiener-Khintchine theorem are used to define the "time periods," t, for anharmonic principal components (PCs), which are validated by nuclear magnetic resonance (NMR) order parameters. The PCs with their respective "time periods" are mapped to the eigenvalues (λENM) of the corresponding ENM modes. Thus, the power laws t(ns) = 56.1λENM-1.6 and σ2(Å2) = 32.7λENM-3.0 can be established allowing the characterization of the timescales of NMR-resolved conformers, crystallographic anisotropic displacement parameters, and important ribosomal motions, as well as motional sizes of the latter.
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Affiliation(s)
- Justin Chan
- Institute of Bioinformatics and Structural Biology, National Tsing Hua Univ., No. 101, Section 2, Kuang-Fu Road, Hsinchu 30013, Taiwan; Bioinformatics Program, Taiwan International Graduate Program, Institute of Information Science, Academia Sinica, Taipei, Taiwan
| | - Kazuhiro Takemura
- School of Life Science and Technology, Tokyo Institute of Technology, M6-13, 2-12-1 Ookayama, Meguro, Tokyo 152-8550, Japan
| | - Hong-Rui Lin
- Institute of Bioinformatics and Structural Biology, National Tsing Hua Univ., No. 101, Section 2, Kuang-Fu Road, Hsinchu 30013, Taiwan
| | - Kai-Chun Chang
- Institute of Molecular and Cellular Biology, National Taiwan University, Taipei, Taiwan
| | - Yuan-Yu Chang
- Institute of Bioinformatics and Structural Biology, National Tsing Hua Univ., No. 101, Section 2, Kuang-Fu Road, Hsinchu 30013, Taiwan
| | - Yasumasa Joti
- XFEL Utilization Division, Japan Synchrotron Radiation Research Institute, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5198, Japan
| | - Akio Kitao
- School of Life Science and Technology, Tokyo Institute of Technology, M6-13, 2-12-1 Ookayama, Meguro, Tokyo 152-8550, Japan.
| | - Lee-Wei Yang
- Institute of Bioinformatics and Structural Biology, National Tsing Hua Univ., No. 101, Section 2, Kuang-Fu Road, Hsinchu 30013, Taiwan; Bioinformatics Program, Taiwan International Graduate Program, Institute of Information Science, Academia Sinica, Taipei, Taiwan; Physics Division, National Center for Theoretical Sciences, Hsinchu, Taiwan.
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36
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Sengupta A, Rice GM, Weeks KM. Single-molecule correlated chemical probing reveals large-scale structural communication in the ribosome and the mechanism of the antibiotic spectinomycin in living cells. PLoS Biol 2019; 17:e3000393. [PMID: 31487286 PMCID: PMC6748448 DOI: 10.1371/journal.pbio.3000393] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2018] [Revised: 09/17/2019] [Accepted: 08/14/2019] [Indexed: 11/18/2022] Open
Abstract
The ribosome moves between distinct structural states and is organized into multiple functional domains. Here, we examined hundreds of occurrences of pairwise through-space communication between nucleotides in the ribosome small subunit RNA using RNA interaction groups analyzed by mutational profiling (RING-MaP) single-molecule correlated chemical probing in bacterial cells. RING-MaP revealed four structural communities in the small subunit RNA, each distinct from the organization defined by the RNA secondary structure. The head domain contains 2 structural communities: the outer-head contains the pivot for head swiveling, and an inner-head community is structurally integrated with helix 44 and spans the entire ribosome intersubunit interface. In-cell binding by the antibiotic spectinomycin (Spc) barely perturbs its local binding pocket as revealed by the per-nucleotide chemical probing signal. In contrast, Spc binding overstabilizes long-range RNA–RNA contacts that extend 95 Å across the ribosome that connect the pivot for head swiveling with the axis of intersubunit rotation. The two major motions of the small subunit—head swiveling and intersubunit rotation—are thus coordinated via long-range RNA structural communication, which is specifically modulated by Spc. Single-molecule correlated chemical probing reveals trans-domain structural communication and rationalizes the profound functional effects of binding by a low–molecular-mass antibiotic to the megadalton ribosome. Single molecule chemical probing of pair-wise interactions across the ribosome in living cells redefines the domains of the small subunit of the ribosome and reveals that the antibiotic spectinomycin disrupts ribosome function by over-stabilizing interactions that span nearly 100 Å.
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Affiliation(s)
- Arnab Sengupta
- Department of Chemistry, University of North Carolina Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Greggory M. Rice
- Department of Chemistry, University of North Carolina Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Kevin M. Weeks
- Department of Chemistry, University of North Carolina Chapel Hill, Chapel Hill, North Carolina, United States of America
- * E-mail:
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37
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Desai VP, Frank F, Lee A, Righini M, Lancaster L, Noller HF, Tinoco I, Bustamante C. Co-temporal Force and Fluorescence Measurements Reveal a Ribosomal Gear Shift Mechanism of Translation Regulation by Structured mRNAs. Mol Cell 2019; 75:1007-1019.e5. [PMID: 31471187 DOI: 10.1016/j.molcel.2019.07.024] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Revised: 06/12/2019] [Accepted: 07/15/2019] [Indexed: 11/18/2022]
Abstract
The movement of ribosomes on mRNA is often interrupted by secondary structures that present mechanical barriers and play a central role in translation regulation. We investigate how ribosomes couple their internal conformational changes with the activity of translocation factor EF-G to unwind mRNA secondary structures using high-resolution optical tweezers with single-molecule fluorescence capability. We find that hairpin opening occurs during EF-G-catalyzed translocation and is driven by the forward rotation of the small subunit head. Modulating the magnitude of the hairpin barrier by force shows that ribosomes respond to strong barriers by shifting their operation to an alternative 7-fold-slower kinetic pathway prior to translocation. Shifting into a slow gear results from an allosteric switch in the ribosome that may allow it to exploit thermal fluctuations to overcome mechanical barriers. Finally, we observe that ribosomes occasionally open the hairpin in two successive sub-codon steps, revealing a previously unobserved translocation intermediate.
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Affiliation(s)
- Varsha P Desai
- Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720, USA; Jason L. Choy Laboratory of Single-Molecule Biophysics, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Filipp Frank
- Jason L. Choy Laboratory of Single-Molecule Biophysics, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Antony Lee
- Jason L. Choy Laboratory of Single-Molecule Biophysics, University of California, Berkeley, Berkeley, CA 94720, USA; Department of Physics, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Maurizio Righini
- Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720, USA; Jason L. Choy Laboratory of Single-Molecule Biophysics, University of California, Berkeley, Berkeley, CA 94720, USA; California Institute for Quantitative Biosciences, QB3, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Laura Lancaster
- Department of Molecular, Cell, and Developmental Biology and Center for Molecular Biology of RNA, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | - Harry F Noller
- Department of Molecular, Cell, and Developmental Biology and Center for Molecular Biology of RNA, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | - Ignacio Tinoco
- Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Carlos Bustamante
- Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720, USA; Jason L. Choy Laboratory of Single-Molecule Biophysics, University of California, Berkeley, Berkeley, CA 94720, USA; Department of Physics, University of California, Berkeley, Berkeley, CA 94720, USA; California Institute for Quantitative Biosciences, QB3, University of California, Berkeley, Berkeley, CA 94720, USA; Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA 94720, USA; Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA; Kavli Energy Nanoscience Institute, University of California, Berkeley, Berkeley, CA 94720, USA.
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38
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Maslov DA. Separating the Wheat from the Chaff: RNA Editing and Selection of Translatable mRNA in Trypanosome Mitochondria. Pathogens 2019; 8:E105. [PMID: 31323762 PMCID: PMC6789859 DOI: 10.3390/pathogens8030105] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Revised: 07/14/2019] [Accepted: 07/16/2019] [Indexed: 11/16/2022] Open
Abstract
In the mitochondria of trypanosomes and related kinetoplastid protists, most mRNAs undergo a long and sophisticated maturation pathway before they can be productively translated by mitochondrial ribosomes. Some of the aspects of this pathway (identity of the promotors, transcription initiation, and termination signals) remain obscure, and some (post-transcriptional modification by U-insertion/deletion, RNA editing, 3'-end maturation) have been illuminated by research during the last decades. The RNA editing creates an open reading frame for a productive translation, but the fully edited mRNA often represents a minor fraction in the pool of pre-edited and partially edited precursors. Therefore, it has been expected that the final stages of the mRNA processing generate molecular hallmarks, which allow for the efficient and selective recognition of translation-competent templates. The general contours and several important details of this process have become known only recently and represent the subject of this review.
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Affiliation(s)
- Dmitri A Maslov
- Department of Molecular, Cell and Systems Biology, University of California, Riverside, CA 92521, USA.
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39
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Studying ribosome dynamics with simplified models. Methods 2019; 162-163:128-140. [DOI: 10.1016/j.ymeth.2019.03.023] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Revised: 03/22/2019] [Accepted: 03/23/2019] [Indexed: 12/24/2022] Open
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40
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Sanbonmatsu KY. Large-scale simulations of nucleoprotein complexes: ribosomes, nucleosomes, chromatin, chromosomes and CRISPR. Curr Opin Struct Biol 2019; 55:104-113. [PMID: 31125796 DOI: 10.1016/j.sbi.2019.03.004] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Accepted: 03/01/2019] [Indexed: 12/11/2022]
Abstract
Recent advances in biotechnology such as Hi-C, CRISPR/Cas9 and ribosome display have placed nucleoprotein complexes at center stage. Understanding the structural dynamics of these complexes aids in optimizing protocols and interpreting data for these new technologies. The integration of simulation and experiment has helped advance mechanistic understanding of these systems. Coarse-grained simulations, reduced-description models, and explicit solvent molecular dynamics simulations yield useful complementary perspectives on nucleoprotein complex structural dynamics. When combined with Hi-C, cryo-EM, and single molecule measurements, these simulations integrate disparate forms of experimental data into a coherent mechanism.
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41
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Spontaneous ribosomal translocation of mRNA and tRNAs into a chimeric hybrid state. Proc Natl Acad Sci U S A 2019; 116:7813-7818. [PMID: 30936299 DOI: 10.1073/pnas.1901310116] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
The elongation factor G (EF-G)-catalyzed translocation of mRNA and tRNA through the ribosome is essential for vacating the ribosomal A site for the next incoming aminoacyl-tRNA, while precisely maintaining the translational reading frame. Here, the 3.2-Å crystal structure of a ribosome translocation intermediate complex containing mRNA and two tRNAs, formed in the absence of EF-G or GTP, provides insight into the respective roles of EF-G and the ribosome in translocation. Unexpectedly, the head domain of the 30S subunit is rotated by 21°, creating a ribosomal conformation closely resembling the two-tRNA chimeric hybrid state that was previously observed only in the presence of bound EF-G. The two tRNAs have moved spontaneously from their A/A and P/P binding states into ap/P and pe/E states, in which their anticodon loops are bound between the 30S body domain and its rotated head domain, while their acceptor ends have moved fully into the 50S P and E sites, respectively. Remarkably, the A-site tRNA translocates fully into the classical P-site position. Although the mRNA also undergoes movement, codon-anticodon interaction is disrupted in the absence of EF-G, resulting in slippage of the translational reading frame. We conclude that, although movement of both tRNAs and mRNA (along with rotation of the 30S head domain) can occur in the absence of EF-G and GTP, EF-G is essential for enforcing coupled movement of the tRNAs and their mRNA codons to maintain the reading frame.
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42
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Levi M, Whitford PC. Dissecting the Energetics of Subunit Rotation in the Ribosome. J Phys Chem B 2019; 123:2812-2823. [PMID: 30844276 DOI: 10.1021/acs.jpcb.9b00178] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The accurate expression of proteins requires the ribosome to efficiently undergo elaborate conformational rearrangements. The most dramatic of these motions is subunit rotation, which is necessary for tRNA molecules to transition between ribosomal binding sites. While rigid-body descriptions provide a qualitative picture of the process, obtaining quantitative mechanistic insights requires one to account for the relationship between molecular flexibility and collective dynamics. Using simulated rotation events, we assess the quality of experimentally accessible measures for describing the collective displacement of the ∼4000-residue small subunit. For this, we ask whether each coordinate is able to identify the underlying free-energy barrier and transition state ensemble (TSE). We find that intuitive structurally motivated coordinates (e.g., rotation angle, interprotein distances) can distinguish between the endpoints, though they are poor indicators of barrier-crossing events, and they underestimate the free-energy barrier. In contrast, coordinates based on intersubunit bridges can identify the TSE. We additionally verify that the committor probability for the putative TSE configurations is 0.5, a hallmark feature of any transition state. In terms of structural properties, these calculations implicate a transition state in which flexibility allows for asynchronous rearrangements of the bridges, as the ribosome adopts a partially rotated orientation. This provides a theoretical foundation, upon which experimental techniques may precisely quantify the energy landscape of the ribosome.
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Affiliation(s)
- Mariana Levi
- Department of Physics , Northeastern University , Dana Research Center 111, 360 Huntington Avenue , Boston , Massachusetts 02115 , United States
| | - Paul C Whitford
- Department of Physics , Northeastern University , Dana Research Center 111, 360 Huntington Avenue , Boston , Massachusetts 02115 , United States
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43
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Dao EH, Poitevin F, Sierra RG, Gati C, Rao Y, Ciftci HI, Akşit F, McGurk A, Obrinski T, Mgbam P, Hayes B, De Lichtenberg C, Pardo-Avila F, Corsepius N, Zhang L, Seaberg MH, Hunter MS, Liang M, Koglin JE, Wakatsuki S, Demirci H. Structure of the 30S ribosomal decoding complex at ambient temperature. RNA (NEW YORK, N.Y.) 2018; 24:1667-1676. [PMID: 30139800 PMCID: PMC6239188 DOI: 10.1261/rna.067660.118] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Accepted: 08/14/2018] [Indexed: 05/29/2023]
Abstract
The ribosome translates nucleotide sequences of messenger RNA to proteins through selection of cognate transfer RNA according to the genetic code. To date, structural studies of ribosomal decoding complexes yielding high-resolution data have predominantly relied on experiments performed at cryogenic temperatures. New light sources like the X-ray free electron laser (XFEL) have enabled data collection from macromolecular crystals at ambient temperature. Here, we report an X-ray crystal structure of the Thermus thermophilus 30S ribosomal subunit decoding complex to 3.45 Å resolution using data obtained at ambient temperature at the Linac Coherent Light Source (LCLS). We find that this ambient-temperature structure is largely consistent with existing cryogenic-temperature crystal structures, with key residues of the decoding complex exhibiting similar conformations, including adenosine residues 1492 and 1493. Minor variations were observed, namely an alternate conformation of cytosine 1397 near the mRNA channel and the A-site. Our serial crystallography experiment illustrates the amenability of ribosomal microcrystals to routine structural studies at ambient temperature, thus overcoming a long-standing experimental limitation to structural studies of RNA and RNA-protein complexes at near-physiological temperatures.
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Affiliation(s)
- E Han Dao
- Stanford PULSE Institute, SLAC National Laboratory, Menlo Park, California 94025, USA
| | - Frédéric Poitevin
- Stanford PULSE Institute, SLAC National Laboratory, Menlo Park, California 94025, USA
- Department of Structural Biology, Stanford University, Palo Alto, California 94305, USA
| | - Raymond G Sierra
- Stanford PULSE Institute, SLAC National Laboratory, Menlo Park, California 94025, USA
- Linac Coherent Light Source, SLAC National Laboratory, Menlo Park, California 94025, USA
| | - Cornelius Gati
- Department of Structural Biology, Stanford University, Palo Alto, California 94305, USA
- Biosciences Division, SLAC National Laboratory, Menlo Park, California 94025, USA
| | - Yashas Rao
- Stanford PULSE Institute, SLAC National Laboratory, Menlo Park, California 94025, USA
- Linac Coherent Light Source, SLAC National Laboratory, Menlo Park, California 94025, USA
| | - Halil Ibrahim Ciftci
- Stanford PULSE Institute, SLAC National Laboratory, Menlo Park, California 94025, USA
| | - Fulya Akşit
- Stanford PULSE Institute, SLAC National Laboratory, Menlo Park, California 94025, USA
| | - Alex McGurk
- Linac Coherent Light Source, SLAC National Laboratory, Menlo Park, California 94025, USA
| | - Trevor Obrinski
- Linac Coherent Light Source, SLAC National Laboratory, Menlo Park, California 94025, USA
| | - Paul Mgbam
- Linac Coherent Light Source, SLAC National Laboratory, Menlo Park, California 94025, USA
| | - Brandon Hayes
- Linac Coherent Light Source, SLAC National Laboratory, Menlo Park, California 94025, USA
| | - Casper De Lichtenberg
- Institutionen för Kemi, Kemiskt Biologiskt Centrum, Umeå Universitet, SE-901 87 Umeå, Sweden
| | - Fatima Pardo-Avila
- Department of Structural Biology, Stanford University, Palo Alto, California 94305, USA
| | - Nicholas Corsepius
- Department of Structural Biology, Stanford University, Palo Alto, California 94305, USA
| | - Lindsey Zhang
- Linac Coherent Light Source, SLAC National Laboratory, Menlo Park, California 94025, USA
| | - Matthew H Seaberg
- Linac Coherent Light Source, SLAC National Laboratory, Menlo Park, California 94025, USA
| | - Mark S Hunter
- Linac Coherent Light Source, SLAC National Laboratory, Menlo Park, California 94025, USA
| | - Mengling Liang
- Linac Coherent Light Source, SLAC National Laboratory, Menlo Park, California 94025, USA
| | - Jason E Koglin
- Linac Coherent Light Source, SLAC National Laboratory, Menlo Park, California 94025, USA
| | - Soichi Wakatsuki
- Department of Structural Biology, Stanford University, Palo Alto, California 94305, USA
- Biosciences Division, SLAC National Laboratory, Menlo Park, California 94025, USA
| | - Hasan Demirci
- Stanford PULSE Institute, SLAC National Laboratory, Menlo Park, California 94025, USA
- Department of Structural Biology, Stanford University, Palo Alto, California 94305, USA
- Biosciences Division, SLAC National Laboratory, Menlo Park, California 94025, USA
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44
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Mori T, Kulik M, Miyashita O, Jung J, Tama F, Sugita Y. Acceleration of cryo-EM Flexible Fitting for Large Biomolecular Systems by Efficient Space Partitioning. Structure 2018; 27:161-174.e3. [PMID: 30344106 DOI: 10.1016/j.str.2018.09.004] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Revised: 06/22/2018] [Accepted: 09/18/2018] [Indexed: 01/21/2023]
Abstract
Flexible fitting is a powerful technique to build the 3D structures of biomolecules from cryoelectron microscopy (cryo-EM) density maps. One popular method is a cross-correlation coefficient-based approach, where the molecular dynamics (MD) simulation is carried out with the biasing potential that includes the cross-correlation coefficient between the experimental and simulated density maps. Here, we propose efficient parallelization schemes for the calculation of the cross-correlation coefficient to accelerate flexible fitting. Our schemes are tested for small, medium, and large biomolecules using CPU and hybrid CPU + GPU architectures. The scheme for the atomic decomposition MD is suitable for small proteins such as Ca2+-ATPase with the all-atom Go model, while that for the domain decomposition MD is better for larger systems such as ribosome with the all-atom Go or the all-atom explicit solvent models. Our methods allow flexible fitting for various biomolecules with reasonable computational cost. This approach also connects high-resolution structure refinements with investigation of protein structure-function relationship.
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Affiliation(s)
- Takaharu Mori
- Theoretical Molecular Science Laboratory, RIKEN Cluster for Pioneering Research, 2-1 Hirosawa, Wako-shi, Saitama 351-0198, Japan
| | - Marta Kulik
- Theoretical Molecular Science Laboratory, RIKEN Cluster for Pioneering Research, 2-1 Hirosawa, Wako-shi, Saitama 351-0198, Japan
| | - Osamu Miyashita
- RIKEN Center for Computational Science, 7-1-26 Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan
| | - Jaewoon Jung
- Theoretical Molecular Science Laboratory, RIKEN Cluster for Pioneering Research, 2-1 Hirosawa, Wako-shi, Saitama 351-0198, Japan; RIKEN Center for Computational Science, 7-1-26 Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan
| | - Florence Tama
- RIKEN Center for Computational Science, 7-1-26 Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan; Department of Physics, Graduate School of Science, and Institute of Transformative Bio-Molecules, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8602, Japan
| | - Yuji Sugita
- Theoretical Molecular Science Laboratory, RIKEN Cluster for Pioneering Research, 2-1 Hirosawa, Wako-shi, Saitama 351-0198, Japan; RIKEN Center for Computational Science, 7-1-26 Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan; RIKEN Center for Biosystems Dynamics Research, 7-1-26 Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan.
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45
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Abstract
Accurate translation of the genetic code is critical to ensure expression of proteins with correct amino acid sequences. Certain tRNAs can cause a shift out of frame (i.e., frameshifting) due to imbalances in tRNA concentrations, lack of tRNA modifications or insertions or deletions in tRNAs (called frameshift suppressors). Here, we determined the structural basis for how frameshift-suppressor tRNASufA6 (a derivative of tRNAPro) reprograms the mRNA frame to translate a 4-nt codon when bound to the bacterial ribosome. After decoding at the aminoacyl (A) site, the crystal structure of the anticodon stem-loop of tRNASufA6 bound in the peptidyl (P) site reveals ASL conformational changes that allow for recoding into the +1 mRNA frame. Furthermore, a crystal structure of full-length tRNASufA6 programmed in the P site shows extensive conformational rearrangements of the 30S head and body domains similar to what is observed in a translocation intermediate state containing elongation factor G (EF-G). The 30S movement positions tRNASufA6 toward the 30S exit (E) site disrupting key 16S rRNA-mRNA interactions that typically define the mRNA frame. In summary, this tRNA-induced 30S domain change in the absence of EF-G causes the ribosome to lose its grip on the mRNA and uncouples the canonical forward movement of the tRNAs during elongation.
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46
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Ramrath DJF, Niemann M, Leibundgut M, Bieri P, Prange C, Horn EK, Leitner A, Boehringer D, Schneider A, Ban N. Evolutionary shift toward protein-based architecture in trypanosomal mitochondrial ribosomes. Science 2018; 362:science.aau7735. [PMID: 30213880 DOI: 10.1126/science.aau7735] [Citation(s) in RCA: 88] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2018] [Accepted: 09/03/2018] [Indexed: 01/19/2023]
Abstract
Ribosomal RNA (rRNA) plays key functional and architectural roles in ribosomes. Using electron microscopy, we determined the atomic structure of a highly divergent ribosome found in mitochondria of Trypanosoma brucei, a unicellular parasite that causes sleeping sickness in humans. The trypanosomal mitoribosome features the smallest rRNAs and contains more proteins than all known ribosomes. The structure shows how the proteins have taken over the role of architectural scaffold from the rRNA: They form an autonomous outer shell that surrounds the entire particle and stabilizes and positions the functionally important regions of the rRNA. Our results also reveal the "minimal" set of conserved rRNA and protein components shared by all ribosomes that help us define the most essential functional elements.
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Affiliation(s)
- David J F Ramrath
- Department of Biology, Institute of Molecular Biology and Biophysics, Otto-Stern-Weg 5, ETH Zurich, CH-8093 Zurich, Switzerland
| | - Moritz Niemann
- Department of Chemistry and Biochemistry, University of Bern, CH-3012 Bern, Switzerland
| | - Marc Leibundgut
- Department of Biology, Institute of Molecular Biology and Biophysics, Otto-Stern-Weg 5, ETH Zurich, CH-8093 Zurich, Switzerland
| | - Philipp Bieri
- Department of Biology, Institute of Molecular Biology and Biophysics, Otto-Stern-Weg 5, ETH Zurich, CH-8093 Zurich, Switzerland
| | - Céline Prange
- Department of Biology, Institute of Molecular Biology and Biophysics, Otto-Stern-Weg 5, ETH Zurich, CH-8093 Zurich, Switzerland
| | - Elke K Horn
- Department of Chemistry and Biochemistry, University of Bern, CH-3012 Bern, Switzerland
| | - Alexander Leitner
- Department of Biology, Institute of Molecular Systems Biology, Auguste-Piccard-Hof 1, ETH Zurich, CH-8093 Zurich, Switzerland
| | - Daniel Boehringer
- Department of Biology, Institute of Molecular Biology and Biophysics, Otto-Stern-Weg 5, ETH Zurich, CH-8093 Zurich, Switzerland
| | - André Schneider
- Department of Chemistry and Biochemistry, University of Bern, CH-3012 Bern, Switzerland
| | - Nenad Ban
- Department of Biology, Institute of Molecular Biology and Biophysics, Otto-Stern-Weg 5, ETH Zurich, CH-8093 Zurich, Switzerland.
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47
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Jia H, Wang Y, Xu S. Super-resolution force spectroscopy reveals ribosomal motion at sub-nucleotide steps. Chem Commun (Camb) 2018; 54:5883-5886. [PMID: 29785422 DOI: 10.1039/c8cc02658k] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Probing biomolecular motion beyond a single nucleotide is technically challenging but fundamentally significant. We have developed super-resolution force spectroscopy (SURFS) with 0.5 pN force resolution and revealed that the ribosome moves by half a nucleotide upon the formation of the pre-translocation complex, which is beyond the resolution of other techniques.
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Affiliation(s)
- Haina Jia
- Department of Chemistry, University of Houston, Houston, TX 77204, USA.
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48
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Pellegrino S, Demeshkina N, Mancera-Martinez E, Melnikov S, Simonetti A, Myasnikov A, Yusupov M, Yusupova G, Hashem Y. Structural Insights into the Role of Diphthamide on Elongation Factor 2 in mRNA Reading-Frame Maintenance. J Mol Biol 2018; 430:2677-2687. [PMID: 29886014 DOI: 10.1016/j.jmb.2018.06.006] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Revised: 05/11/2018] [Accepted: 06/04/2018] [Indexed: 01/27/2023]
Abstract
One of the most critical steps of protein biosynthesis is the coupled movement of mRNA, which encodes genetic information, with tRNAs on the ribosome. In eukaryotes, this process is catalyzed by a conserved G-protein, the elongation factor 2 (eEF2), which carries a unique post-translational modification, called diphthamide, found in all eukaryotic species. Here we present near-atomic resolution cryo-electron microscopy structures of yeast 80S ribosome complexes containing mRNA, tRNA and eEF2 trapped in different GTP-hydrolysis states which provide further structural insights into the role of diphthamide in the mechanism of translation fidelity in eukaryotes.
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Affiliation(s)
- Simone Pellegrino
- Department of Integrated Structural Biology, Institute of Genetics and Molecular and Cellular Biology, CNRS UMR710, INSERM U964, University of Strasbourg, Strasbourg 67000, France
| | - Natalia Demeshkina
- Department of Integrated Structural Biology, Institute of Genetics and Molecular and Cellular Biology, CNRS UMR710, INSERM U964, University of Strasbourg, Strasbourg 67000, France
| | - Eder Mancera-Martinez
- Architecture and Reactivity of RNA, University of Strasbourg, Institute of Molecular and Cellular Biology of the CNRS UPR9002, Strasbourg 67084, France
| | - Sergey Melnikov
- Department of Integrated Structural Biology, Institute of Genetics and Molecular and Cellular Biology, CNRS UMR710, INSERM U964, University of Strasbourg, Strasbourg 67000, France
| | - Angelita Simonetti
- Architecture and Reactivity of RNA, University of Strasbourg, Institute of Molecular and Cellular Biology of the CNRS UPR9002, Strasbourg 67084, France
| | - Alexander Myasnikov
- Department of Integrated Structural Biology, Institute of Genetics and Molecular and Cellular Biology, CNRS UMR710, INSERM U964, University of Strasbourg, Strasbourg 67000, France
| | - Marat Yusupov
- Department of Integrated Structural Biology, Institute of Genetics and Molecular and Cellular Biology, CNRS UMR710, INSERM U964, University of Strasbourg, Strasbourg 67000, France; Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan 420008, Russia.
| | - Gulnara Yusupova
- Department of Integrated Structural Biology, Institute of Genetics and Molecular and Cellular Biology, CNRS UMR710, INSERM U964, University of Strasbourg, Strasbourg 67000, France.
| | - Yaser Hashem
- ARNA, U1212 Université de Bordeaux, Institut Européen de Chimie et de Biologie (IECB) Inserm, Pessac 33600, France.
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49
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Lin J, Zhou D, Steitz TA, Polikanov YS, Gagnon MG. Ribosome-Targeting Antibiotics: Modes of Action, Mechanisms of Resistance, and Implications for Drug Design. Annu Rev Biochem 2018; 87:451-478. [PMID: 29570352 DOI: 10.1146/annurev-biochem-062917-011942] [Citation(s) in RCA: 170] [Impact Index Per Article: 28.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Genetic information is translated into proteins by the ribosome. Structural studies of the ribosome and of its complexes with factors and inhibitors have provided invaluable information on the mechanism of protein synthesis. Ribosome inhibitors are among the most successful antimicrobial drugs and constitute more than half of all medicines used to treat infections. However, bacterial infections are becoming increasingly difficult to treat because the microbes have developed resistance to the most effective antibiotics, creating a major public health care threat. This has spurred a renewed interest in structure-function studies of protein synthesis inhibitors, and in few cases, compounds have been developed into potent therapeutic agents against drug-resistant pathogens. In this review, we describe the modes of action of many ribosome-targeting antibiotics, highlight the major resistance mechanisms developed by pathogenic bacteria, and discuss recent advances in structure-assisted design of new molecules.
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Affiliation(s)
- Jinzhong Lin
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai 200438, China;
| | - Dejian Zhou
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai 200438, China;
| | - Thomas A Steitz
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520, USA; .,Department of Chemistry, Yale University, New Haven, Connecticut 06520, USA.,Howard Hughes Medical Institute, Yale University, New Haven, Connecticut 06520, USA
| | - Yury S Polikanov
- Department of Biological Sciences, and Department of Medicinal Chemistry and Pharmacognosy, University of Illinois at Chicago, Chicago, Illinois 60607, USA;
| | - Matthieu G Gagnon
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520, USA; .,Howard Hughes Medical Institute, Yale University, New Haven, Connecticut 06520, USA.,Current affiliation: Department of Microbiology and Immunology, and Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, Texas 77555, USA;
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50
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Levi M, Nguyen K, Dukaye L, Whitford PC. Quantifying the Relationship between Single-Molecule Probes and Subunit Rotation in the Ribosome. Biophys J 2018; 113:2777-2786. [PMID: 29262370 DOI: 10.1016/j.bpj.2017.10.021] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2017] [Revised: 10/12/2017] [Accepted: 10/16/2017] [Indexed: 11/18/2022] Open
Abstract
A major challenge in the study of biomolecular assemblies is to identify reaction coordinates that precisely monitor conformational rearrangements. This is central to the interpretation of single-molecule fluorescence resonance energy transfer measurements, where the observed dynamics depends on the labeling strategy. As an example, different probes of subunit rotation in the ribosome have provided qualitatively distinct descriptions. In one study, changes in fluorescence suggested that the 30S body undergoes a single rotation/back-rotation cycle during the process of mRNA-tRNA translocation. In contrast, an alternate assay implicated the presence of reversible rotation events before completing translocation. For future single-molecule experiments to unambiguously measure the relationship between subunit rotation and translocation, it is necessary to rationalize these conflicting descriptions. To this end, we have simulated hundreds of spontaneous subunit rotation events (≈8°) using a residue-level coarse-grained model of the ribosome. We analyzed nine different reaction coordinates and found that the apparently inconsistent measurements are likely a consequence of ribosomal flexibility. Further, we propose a metric for quantifying the degree of energetic coupling between experimentally measured degrees of freedom and subunit rotation. This analysis provides a physically grounded framework that can guide the development of more precise single-molecule techniques.
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Affiliation(s)
- Mariana Levi
- Department of Physics, Northeastern University, Boston, Massachusetts
| | - Kien Nguyen
- Department of Physics, Northeastern University, Boston, Massachusetts
| | - Liah Dukaye
- Department of Physics, Northeastern University, Boston, Massachusetts
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