1
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Ero R, Leppik M, Reier K, Liiv A, Remme J. Ribosomal RNA modification enzymes stimulate large ribosome subunit assembly in E. coli. Nucleic Acids Res 2024; 52:6614-6628. [PMID: 38554109 PMCID: PMC11194073 DOI: 10.1093/nar/gkae222] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Revised: 03/12/2024] [Accepted: 03/15/2024] [Indexed: 04/01/2024] Open
Abstract
Ribosomal RNA modifications are introduced by specific enzymes during ribosome assembly in bacteria. Deletion of individual modification enzymes has a minor effect on bacterial growth, ribosome biogenesis, and translation, which has complicated the definition of the function of the enzymes and their products. We have constructed an Escherichia coli strain lacking 10 genes encoding enzymes that modify 23S rRNA around the peptidyl-transferase center. This strain exhibits severely compromised growth and ribosome assembly, especially at lower temperatures. Re-introduction of the individual modification enzymes allows for the definition of their functions. The results demonstrate that in addition to previously known RlmE, also RlmB, RlmKL, RlmN and RluC facilitate large ribosome subunit assembly. RlmB and RlmKL have functions in ribosome assembly independent of their modification activities. While the assembly stage specificity of rRNA modification enzymes is well established, this study demonstrates that there is a mutual interdependence between the rRNA modification process and large ribosome subunit assembly.
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MESH Headings
- Escherichia coli/genetics
- Escherichia coli/metabolism
- Escherichia coli Proteins/metabolism
- Escherichia coli Proteins/genetics
- Methyltransferases/metabolism
- Methyltransferases/genetics
- Ribosome Subunits, Large/metabolism
- Ribosome Subunits, Large/genetics
- Ribosome Subunits, Large, Bacterial/metabolism
- Ribosome Subunits, Large, Bacterial/genetics
- Ribosomes/metabolism
- Ribosomes/genetics
- RNA, Ribosomal/metabolism
- RNA, Ribosomal/genetics
- RNA, Ribosomal, 23S/metabolism
- RNA, Ribosomal, 23S/genetics
- RNA, Ribosomal, 23S/chemistry
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Affiliation(s)
- Rya Ero
- IMCB University of Tartu, Riia 23, 51010 Tartu, Estonia
| | - Margus Leppik
- IMCB University of Tartu, Riia 23, 51010 Tartu, Estonia
| | - Kaspar Reier
- IMCB University of Tartu, Riia 23, 51010 Tartu, Estonia
| | - Aivar Liiv
- IMCB University of Tartu, Riia 23, 51010 Tartu, Estonia
| | - Jaanus Remme
- IMCB University of Tartu, Riia 23, 51010 Tartu, Estonia
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2
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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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3
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Morici M, Gabrielli S, Fujiwara K, Paternoga H, Beckert B, Bock LV, Chiba S, Wilson DN. RAPP-containing arrest peptides induce translational stalling by short circuiting the ribosomal peptidyltransferase activity. Nat Commun 2024; 15:2432. [PMID: 38503735 PMCID: PMC10951233 DOI: 10.1038/s41467-024-46761-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Accepted: 01/24/2024] [Indexed: 03/21/2024] Open
Abstract
Arrest peptides containing RAPP (ArgAlaProPro) motifs have been discovered in both Gram-positive and Gram-negative bacteria, where they are thought to regulate expression of important protein localization machinery components. Here we determine cryo-EM structures of ribosomes stalled on RAPP arrest motifs in both Bacillus subtilis and Escherichia coli. Together with molecular dynamics simulations, our structures reveal that the RAPP motifs allow full accommodation of the A-site tRNA, but prevent the subsequent peptide bond from forming. Our data support a model where the RAP in the P-site interacts and stabilizes a single hydrogen atom on the Pro-tRNA in the A-site, thereby preventing an optimal geometry for the nucleophilic attack required for peptide bond formation to occur. This mechanism to short circuit the ribosomal peptidyltransferase activity is likely to operate for the majority of other RAPP-like arrest peptides found across diverse bacterial phylogenies.
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Affiliation(s)
- Martino Morici
- Institute for Biochemistry and Molecular Biology, University of Hamburg, Martin-Luther-King-Platz 6, 20146, Hamburg, Germany
| | - Sara Gabrielli
- Theoretical and Computational Biophysics Department, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Keigo Fujiwara
- Faculty of Life Sciences and Institute for Protein Dynamics, Kyoto Sangyo University, Kamigamo, Motoyama, Kita-ku, Kyoto, 603-8555, Japan
| | - Helge Paternoga
- Institute for Biochemistry and Molecular Biology, University of Hamburg, Martin-Luther-King-Platz 6, 20146, Hamburg, Germany
| | - Bertrand Beckert
- Institute for Biochemistry and Molecular Biology, University of Hamburg, Martin-Luther-King-Platz 6, 20146, Hamburg, Germany
| | - Lars V Bock
- Theoretical and Computational Biophysics Department, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Shinobu Chiba
- Faculty of Life Sciences and Institute for Protein Dynamics, Kyoto Sangyo University, Kamigamo, Motoyama, Kita-ku, Kyoto, 603-8555, Japan.
| | - Daniel N Wilson
- Institute for Biochemistry and Molecular Biology, University of Hamburg, Martin-Luther-King-Platz 6, 20146, Hamburg, Germany.
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4
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Lasham J, Djurabekova A, Zickermann V, Vonck J, Sharma V. Role of Protonation States in the Stability of Molecular Dynamics Simulations of High-Resolution Membrane Protein Structures. J Phys Chem B 2024; 128:2304-2316. [PMID: 38430110 DOI: 10.1021/acs.jpcb.3c07421] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/03/2024]
Abstract
Classical molecular dynamics (MD) simulations provide unmatched spatial and time resolution of protein structure and function. However, the accuracy of MD simulations often depends on the quality of force field parameters and the time scale of sampling. Another limitation of conventional MD simulations is that the protonation states of titratable amino acid residues remain fixed during simulations, even though protonation state changes coupled to conformational dynamics are central to protein function. Due to the uncertainty in selecting protonation states, classical MD simulations are sometimes performed with all amino acids modeled in their standard charged states at pH 7. Here, we performed and analyzed classical MD simulations on high-resolution cryo-EM structures of two large membrane proteins that transfer protons by catalyzing protonation/deprotonation reactions. In simulations performed with titratable amino acids modeled in their standard protonation (charged) states, the structure diverges far from its starting conformation. In comparison, MD simulations performed with predetermined protonation states of amino acid residues reproduce the structural conformation, protein hydration, and protein-water and protein-protein interactions of the structure much better. The results support the notion that it is crucial to perform basic protonation state calculations, especially on structures where protonation changes play an important functional role, prior to the launch of any conventional MD simulations. Furthermore, the combined approach of fast protonation state prediction and MD simulations can provide valuable information about the charge states of amino acids in the cryo-EM sample. Even though accurate prediction of protonation states in proteinaceous environments currently remains a challenge, we introduce an approach of combining pKa prediction with cryo-EM density map analysis that helps in improving not only the protonation state predictions but also the atomic modeling of density data.
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Affiliation(s)
- Jonathan Lasham
- Department of Physics, University of Helsinki, 00014 Helsinki, Finland
| | - Amina Djurabekova
- Department of Physics, University of Helsinki, 00014 Helsinki, Finland
| | - Volker Zickermann
- Institute of Biochemistry II, University Hospital, Goethe University, 60590 Frankfurt am Main, Germany
- Centre for Biomolecular Magnetic Resonance, Institute for Biophysical Chemistry, Goethe University, 60438 Frankfurt am Main, Germany
| | - Janet Vonck
- Department of Structural Biology, Max Planck Institute of Biophysics, 60438 Frankfurt am Main, Germany
| | - Vivek Sharma
- Department of Physics, University of Helsinki, 00014 Helsinki, Finland
- HiLIFE Institute of Biotechnology, University of Helsinki, 00014 Helsinki, Finland
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5
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Byju S, Hassan A, Whitford PC. The energy landscape of the ribosome. Biopolymers 2024; 115:e23570. [PMID: 38051695 DOI: 10.1002/bip.23570] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2023] [Revised: 10/17/2023] [Accepted: 11/08/2023] [Indexed: 12/07/2023]
Abstract
The ribosome is a prototypical assembly that can be used to establish general principles and techniques for the study of biological molecular machines. Motivated by the fact that the dynamics of every biomolecule is governed by an underlying energy landscape, there has been great interest to understand and quantify ribosome energetics. In the present review, we will focus on theoretical and computational strategies for probing the interactions that shape the energy landscape of the ribosome, with an emphasis on more recent studies of the elongation cycle. These efforts include the application of quantum mechanical methods for describing chemical kinetics, as well as classical descriptions to characterize slower (microsecond to millisecond) large-scale (10-100 Å) rearrangements, where motion is described in terms of diffusion across an energy landscape. Together, these studies provide broad insights into the factors that control a diverse range of dynamical processes in this assembly.
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Affiliation(s)
- Sandra Byju
- Center for Theoretical Biological Physics, Northeastern University, Boston, Massachusetts, USA
- Department of Physics, Northeastern University, Boston, Massachusetts, USA
| | - Asem Hassan
- Department of Chemistry, The University of Texas at Austin, Austin, Texas, United States
| | - Paul C Whitford
- Center for Theoretical Biological Physics, Northeastern University, Boston, Massachusetts, USA
- Department of Physics, Northeastern University, Boston, Massachusetts, USA
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6
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Bhattacharya A, Renault TT, Innis CA. The ribosome as a small-molecule sensor. Curr Opin Microbiol 2024; 77:102418. [PMID: 38159358 DOI: 10.1016/j.mib.2023.102418] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Revised: 12/04/2023] [Accepted: 12/05/2023] [Indexed: 01/03/2024]
Abstract
Sensing small molecules is crucial for microorganisms to adapt their genetic programs to changes in their environment. Arrest peptides encoded by short regulatory open reading frames program the ribosomes that translate them to undergo translational arrest in response to specific metabolites. Ribosome stalling in turn controls the expression of downstream genes on the same messenger RNA by translational or transcriptional means. In this review, we present our current understanding of the mechanisms by which ribosomes translating arrest peptides sense different metabolites, such as antibiotics or amino acids, to control gene expression.
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Affiliation(s)
- Arunima Bhattacharya
- Univ. Bordeaux, Centre National de la Recherche Scientifique, Institut National de la Santé et de la Recherche Médicale, ARNA, UMR 5320, U1212, Institut Européen de Chimie et Biologie, F-33600 Pessac, France
| | - Thibaud T Renault
- Univ. Bordeaux, Centre National de la Recherche Scientifique, Institut National de la Santé et de la Recherche Médicale, ARNA, UMR 5320, U1212, Institut Européen de Chimie et Biologie, F-33600 Pessac, France
| | - C Axel Innis
- Univ. Bordeaux, Centre National de la Recherche Scientifique, Institut National de la Santé et de la Recherche Médicale, ARNA, UMR 5320, U1212, Institut Européen de Chimie et Biologie, F-33600 Pessac, France.
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7
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Shields KE, Ranava D, Tan Y, Zhang D, Yap MNF. Epitranscriptional m6A modification of rRNA negatively impacts translation and host colonization in Staphylococcus aureus. PLoS Pathog 2024; 20:e1011968. [PMID: 38252661 PMCID: PMC10833563 DOI: 10.1371/journal.ppat.1011968] [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: 08/24/2023] [Revised: 02/01/2024] [Accepted: 01/12/2024] [Indexed: 01/24/2024] Open
Abstract
Macrolides, lincosamides, and streptogramin B (MLS) are structurally distinct molecules that are among the safest antibiotics for prophylactic use and for the treatment of bacterial infections. The family of erythromycin resistance methyltransferases (Erm) invariantly install either one or two methyl groups onto the N6,6-adenosine of 2058 nucleotide (m6A2058) of the bacterial 23S rRNA, leading to bacterial cross-resistance to all MLS antibiotics. Despite extensive structural studies on the mechanism of Erm-mediated MLS resistance, how the m6A epitranscriptomic mark affects ribosome function and bacterial physiology is not well understood. Here, we show that Staphylococcus aureus cells harboring m6A2058 ribosomes are outcompeted by cells carrying unmodified ribosomes during infections and are severely impaired in colonization in the absence of an unmodified counterpart. The competitive advantage of m6A2058 ribosomes is manifested only upon antibiotic challenge. Using ribosome profiling (Ribo-Seq) and a dual-fluorescence reporter to measure ribosome occupancy and translational fidelity, we found that specific genes involved in host interactions, metabolism, and information processing are disproportionally deregulated in mRNA translation. This dysregulation is linked to a substantial reduction in translational capacity and fidelity in m6A2058 ribosomes. These findings point to a general "inefficient translation" mechanism of trade-offs associated with multidrug-resistant ribosomes.
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Affiliation(s)
- Kathryn E. Shields
- Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, Saint Louis, Missouri, United States of America
| | - David Ranava
- Department of Microbiology-Immunology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, United States of America
| | - Yongjun Tan
- Department of Biology, College of Arts and Sciences, Saint Louis University, St. Louis, Missouri, United States of America
| | - Dapeng Zhang
- Department of Biology, College of Arts and Sciences, Saint Louis University, St. Louis, Missouri, United States of America
- Program of Bioinformatics and Computational Biology, College of Arts and Sciences, St. Louis, Missouri, United States of America
| | - Mee-Ngan F. Yap
- Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, Saint Louis, Missouri, United States of America
- Department of Microbiology-Immunology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, United States of America
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8
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Kotev M, Diaz Gonzalez C. Molecular Dynamics and Other HPC Simulations for Drug Discovery. Methods Mol Biol 2024; 2716:265-291. [PMID: 37702944 DOI: 10.1007/978-1-0716-3449-3_12] [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] [Indexed: 09/14/2023]
Abstract
High performance computing (HPC) is taking an increasingly important place in drug discovery. It makes possible the simulation of complex biochemical systems with high precision in a short time, thanks to the use of sophisticated algorithms. It promotes the advancement of knowledge in fields that are inaccessible or difficult to access through experimentation and it contributes to accelerating the discovery of drugs for unmet medical needs while reducing costs. Herein, we report how computational performance has evolved over the past years, and then we detail three domains where HPC is essential. Molecular dynamics (MD) is commonly used to explore the flexibility of proteins, thus generating a better understanding of different possible approaches to modulate their activity. Modeling and simulation of biopolymer complexes enables the study of protein-protein interactions (PPI) in healthy and disease states, thus helping the identification of targets of pharmacological interest. Virtual screening (VS) also benefits from HPC to predict in a short time, among millions or billions of virtual chemical compounds, the best potential ligands that will be tested in relevant assays to start a rational drug design process.
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Affiliation(s)
- Martin Kotev
- Evotec SE, Integrated Drug Discovery, Molecular Architects, Campus Curie, Toulouse, France
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9
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Thaler J, Syroegin EA, Breuker K, Polikanov YS, Micura R. Practical Synthesis of N-Formylmethionylated Peptidyl-tRNA Mimics. ACS Chem Biol 2023; 18:2233-2239. [PMID: 37433044 PMCID: PMC10594587 DOI: 10.1021/acschembio.3c00237] [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: 04/24/2023] [Accepted: 06/22/2023] [Indexed: 07/13/2023]
Abstract
Hydrolysis-resistant RNA-peptide conjugates that mimic peptidyl-tRNAs are frequently needed for structural and functional studies of protein synthesis in the ribosome. Such conjugates are accessible by chemical solid-phase synthesis, allowing for the utmost flexibility of both the peptide and the RNA sequence. Commonly used protection group strategies, however, have severe limitations with respect to generating the characteristic Nα-formylmethionyl terminus because the formyl group of the conjugate synthesized at the solid support is easily cleaved during the final basic deprotection/release step. In this study, we demonstrate a simple solution to the problem by coupling appropriately activated Nα-formyl methionine to the fully deprotected conjugate. The structural integrity of the obtained Nα-formylmethionyl conjugate─and hence the chemoselectivity of the reaction─were verified by Fourier transform ion cyclotron resonance (FT-ICR) mass spectrometry sequence analysis. Additionally, we confirmed the applicability of our procedure for structural studies by obtaining two structures of the ribosome in complex with either fMAI-nh-ACCA or fMFI-nh-ACCA in the P site and ACC-PMN in the A site of the bacterial ribosome at 2.65 and 2.60 Å resolution, respectively. In summary, our approach for hydrolysis-resistant Nα-formylated RNA-peptide conjugates is synthetically straightforward and opens up new avenues to explore ribosomal translation with high-precision substrate mimics.
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Affiliation(s)
- Julia Thaler
- Institute
of Organic Chemistry and Center for Molecular Biosciences, University of Innsbruck, Innrain 80-82, 6020 Innsbruck, Austria
| | - Egor A. Syroegin
- Department
of Biological Sciences, University of Illinois
at Chicago, Chicago, Illinois 60607, United States
| | - Kathrin Breuker
- Institute
of Organic Chemistry and Center for Molecular Biosciences, University of Innsbruck, Innrain 80-82, 6020 Innsbruck, Austria
| | - Yury S. Polikanov
- Department
of Biological Sciences, University of Illinois
at Chicago, Chicago, Illinois 60607, United States
- Department
of Pharmaceutical Sciences, University of
Illinois at Chicago, Chicago, Illinois 60607, United States
- Center
for Biomolecular Sciences, University of
Illinois at Chicago, Chicago, Illinois 60607, United States
| | - Ronald Micura
- Institute
of Organic Chemistry and Center for Molecular Biosciences, University of Innsbruck, Innrain 80-82, 6020 Innsbruck, Austria
- Center
for Biomolecular Sciences, University of
Illinois at Chicago, Chicago, Illinois 60607, United States
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10
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Polikanov YS, Etheve-Quelquejeu M, Micura R. Synthesis of Peptidyl-tRNA Mimics for Structural Biology Applications. Acc Chem Res 2023; 56:2713-2725. [PMID: 37728742 PMCID: PMC10552525 DOI: 10.1021/acs.accounts.3c00412] [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: 07/19/2023] [Indexed: 09/21/2023]
Abstract
Protein biosynthesis is a central process in all living cells that is catalyzed by a complex molecular machine─the ribosome. This process is termed translation because the language of nucleotides in mRNAs is translated into the language of amino acids in proteins. Transfer RNA (tRNA) molecules charged with amino acids serve as adaptors and recognize codons of mRNA in the decoding center while simultaneously the individual amino acids are assembled into a peptide chain in the peptidyl transferase center (PTC). As the nascent peptide emerges from the ribosome, it is threaded through a long tunnel referred to as a nascent peptide exit tunnel (NPET). The PTC and NPET are the sites targeted by many antibiotics and are thus of tremendous importance from a biomedical perspective and for drug development in the pharmaceutical industry.Researchers have achieved much progress in characterizing ribosomal translation at the molecular level; an impressive number of high-resolution structures of different functional and inhibited states of the ribosome are now available. These structures have significantly contributed to our understanding of how the ribosome interacts with its key substrates, namely, mRNA, tRNAs, and translation factors. In contrast, much less is known about the mechanisms of how small molecules, especially antibiotics, affect ribosomal protein synthesis. This mainly concerns the structural basis of small molecule-NPET interference with cotranslational protein folding and the regulation of protein synthesis. Growing biochemical evidence suggests that NPET plays an active role in the regulation of protein synthesis.Much-needed progress in this field is hampered by the fact that during the preparation of ribosome complexes for structural studies (i.e., X-ray crystallography, cryoelectron microscopy, and NMR spectroscopy) the aminoacyl- or peptidyl-tRNAs are unstable and become hydrolyzed. A solution to this problem is the application of hydrolysis-resistant mimics of aminoacyl- or peptidyl-tRNAs.In this Account, we present an overview of synthetic methods for the generation of peptidyl-tRNA analogs. Modular approaches have been developed that combine (i) RNA and peptide solid-phase synthesis on 3'-aminoacylamino-adenosine resins, (ii) native chemical ligations and Staudinger ligations, (iii) tailoring of tRNAs by the selective cleavage of natural native tRNAs with DNAzymes followed by reassembly with enzymatic ligation to synthetic peptidyl-RNA fragments, and (iv) enzymatic tailing and cysteine charging of the tRNA to obtain modified CCA termini of a tRNA that are chemically ligated to the peptide moiety of interest. With this arsenal of tools, in principle, any desired sequence of a stably linked peptidyl-tRNA mimic is accessible. To underline the significance of the synthetic conjugates, we briefly point to the most critical applications that have shed new light on the molecular mechanisms underlying the context-specific activity of ribosome-targeting antibiotics, ribosome-dependent incorporation of multiple consecutive proline residues, the incorporation of d-amino acids, and tRNA mischarging.Furthermore, we discuss new types of stably charged tRNA analogs, relying on triazole- and squarate (instead of amide)-linked conjugates. Those have pushed forward our mechanistic understanding of nonribosomal peptide synthesis, where aminoacyl-tRNA-dependent enzymes are critically involved in various cellular processes in primary and secondary metabolism and in bacterial cell wall synthesis.
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Affiliation(s)
- Yury S. Polikanov
- Department
of Biological Sciences, University of Illinois
at Chicago, Chicago, Illinois 60607, United States
- Department
of Pharmaceutical Sciences, University of
Illinois at Chicago, Chicago, Illinois 60607, United States
- Center for
Biomolecular Sciences, University of Illinois
at Chicago, Chicago, Illinois 60607, United States
| | - Mélanie Etheve-Quelquejeu
- Université
Paris Cité, CNRS, Laboratoire de Chimie et Biochimie Pharmacologiques
et Toxicologiques, Paris F-75006, France
| | - Ronald Micura
- Institute
of Organic Chemistry and Center for Molecular Biosciences, University of Innsbruck, Innrain 80-82, 6020 Innsbruck, Austria
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11
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Jain S, Koziej L, Poulis P, Kaczmarczyk I, Gaik M, Rawski M, Ranjan N, Glatt S, Rodnina MV. Modulation of translational decoding by m 6A modification of mRNA. Nat Commun 2023; 14:4784. [PMID: 37553384 PMCID: PMC10409866 DOI: 10.1038/s41467-023-40422-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Accepted: 07/27/2023] [Indexed: 08/10/2023] Open
Abstract
N6-methyladenosine (m6A) is an abundant, dynamic mRNA modification that regulates key steps of cellular mRNA metabolism. m6A in the mRNA coding regions inhibits translation elongation. Here, we show how m6A modulates decoding in the bacterial translation system using a combination of rapid kinetics, smFRET and single-particle cryo-EM. We show that, while the modification does not impair the initial binding of aminoacyl-tRNA to the ribosome, in the presence of m6A fewer ribosomes complete the decoding process due to the lower stability of the complexes and enhanced tRNA drop-off. The mRNA codon adopts a π-stacked codon conformation that is remodeled upon aminoacyl-tRNA binding. m6A does not exclude canonical codon-anticodon geometry, but favors alternative more dynamic conformations that are rejected by the ribosome. These results highlight how modifications outside the Watson-Crick edge can still interfere with codon-anticodon base pairing and complex recognition by the ribosome, thereby modulating the translational efficiency of modified mRNAs.
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Affiliation(s)
- Sakshi Jain
- Max Planck Institute for Multidisciplinary Sciences, Göttingen, 37077, Germany
| | - Lukasz Koziej
- Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, 30-387, Poland
| | - Panagiotis Poulis
- Max Planck Institute for Multidisciplinary Sciences, Göttingen, 37077, Germany
| | - Igor Kaczmarczyk
- Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, 30-387, Poland
- Doctoral School of Exact and Natural Sciences, Jagiellonian University, Krakow, 30-387, Poland
| | - Monika Gaik
- Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, 30-387, Poland
| | - Michal Rawski
- Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, 30-387, Poland
- National Synchrotron Radiation Centre SOLARIS, Jagiellonian University, Krakow, 30-387, Poland
| | - Namit Ranjan
- Max Planck Institute for Multidisciplinary Sciences, Göttingen, 37077, Germany
| | - Sebastian Glatt
- Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, 30-387, Poland.
| | - Marina V Rodnina
- Max Planck Institute for Multidisciplinary Sciences, Göttingen, 37077, Germany.
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12
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Fostier CR, Ousalem F, Leroy EC, Ngo S, Soufari H, Innis CA, Hashem Y, Boël G. Regulation of the macrolide resistance ABC-F translation factor MsrD. Nat Commun 2023; 14:3891. [PMID: 37393329 PMCID: PMC10314930 DOI: 10.1038/s41467-023-39553-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Accepted: 06/19/2023] [Indexed: 07/03/2023] Open
Abstract
Antibiotic resistance ABC-Fs (ARE ABC-Fs) are translation factors that provide resistance against clinically important ribosome-targeting antibiotics which are proliferating among pathogens. Here, we combine genetic and structural approaches to determine the regulation of streptococcal ARE ABC-F gene msrD in response to macrolide exposure. We show that binding of cladinose-containing macrolides to the ribosome prompts insertion of the leader peptide MsrDL into a crevice of the ribosomal exit tunnel, which is conserved throughout bacteria and eukaryotes. This leads to a local rearrangement of the 23 S rRNA that prevents peptide bond formation and accommodation of release factors. The stalled ribosome obstructs the formation of a Rho-independent terminator structure that prevents msrD transcriptional attenuation. Erythromycin induction of msrD expression via MsrDL, is suppressed by ectopic expression of mrsD, but not by mutants which do not provide antibiotic resistance, showing correlation between MsrD function in antibiotic resistance and its action on this stalled complex.
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Affiliation(s)
- Corentin R Fostier
- Expression Génétique Microbienne, CNRS, Université Paris Cité, Institut de Biologie Physico-Chimique, 75005, Paris, France
| | - Farès Ousalem
- Expression Génétique Microbienne, CNRS, Université Paris Cité, Institut de Biologie Physico-Chimique, 75005, Paris, France
| | - Elodie C Leroy
- ARNA Laboratory, UMR 5320, U1212, Institut Européen de Chimie et Biologie, Univ. Bordeaux, Centre National de la Recherche Scientifique, Institut National de la Santé et de la Recherche Médicale, 33607, Pessac, France
| | - Saravuth Ngo
- Expression Génétique Microbienne, CNRS, Université Paris Cité, Institut de Biologie Physico-Chimique, 75005, Paris, France
| | - Heddy Soufari
- ARNA Laboratory, UMR 5320, U1212, Institut Européen de Chimie et Biologie, Univ. Bordeaux, Centre National de la Recherche Scientifique, Institut National de la Santé et de la Recherche Médicale, 33607, Pessac, France
- SPT Labtech Ltd., SG8 6HB, Melbourn, United Kingdom
| | - C Axel Innis
- ARNA Laboratory, UMR 5320, U1212, Institut Européen de Chimie et Biologie, Univ. Bordeaux, Centre National de la Recherche Scientifique, Institut National de la Santé et de la Recherche Médicale, 33607, Pessac, France
| | - Yaser Hashem
- ARNA Laboratory, UMR 5320, U1212, Institut Européen de Chimie et Biologie, Univ. Bordeaux, Centre National de la Recherche Scientifique, Institut National de la Santé et de la Recherche Médicale, 33607, Pessac, France.
| | - Grégory Boël
- Expression Génétique Microbienne, CNRS, Université Paris Cité, Institut de Biologie Physico-Chimique, 75005, Paris, France.
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13
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Assmann SM, Chou HL, Bevilacqua PC. Rock, scissors, paper: How RNA structure informs function. THE PLANT CELL 2023; 35:1671-1707. [PMID: 36747354 DOI: 10.1093/plcell/koad026] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Revised: 01/05/2023] [Accepted: 01/30/2023] [Indexed: 05/30/2023]
Abstract
RNA can fold back on itself to adopt a wide range of structures. These range from relatively simple hairpins to intricate 3D folds and can be accompanied by regulatory interactions with both metabolites and macromolecules. The last 50 yr have witnessed elucidation of an astonishing array of RNA structures including transfer RNAs, ribozymes, riboswitches, the ribosome, the spliceosome, and most recently entire RNA structuromes. These advances in RNA structural biology have deepened insight into fundamental biological processes including gene editing, transcription, translation, and structure-based detection and response to temperature and other environmental signals. These discoveries reveal that RNA can be relatively static, like a rock; that it can have catalytic functions of cutting bonds, like scissors; and that it can adopt myriad functional shapes, like paper. We relate these extraordinary discoveries in the biology of RNA structure to the plant way of life. We trace plant-specific discovery of ribozymes and riboswitches, alternative splicing, organellar ribosomes, thermometers, whole-transcriptome structuromes and pan-structuromes, and conclude that plants have a special set of RNA structures that confer unique types of gene regulation. We finish with a consideration of future directions for the RNA structure-function field.
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Affiliation(s)
- Sarah M Assmann
- Department of Biology, Pennsylvania State University, University Park, PA 16802, USA
- Center for RNA Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA
| | - Hong-Li Chou
- Department of Biology, Pennsylvania State University, University Park, PA 16802, USA
| | - Philip C Bevilacqua
- Center for RNA Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA
- Department of Chemistry, Pennsylvania State University, University Park, PA 16802, USA
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA
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14
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Jiang Y, Neti SS, Sitarik I, Pradhan P, To P, Xia Y, Fried SD, Booker SJ, O'Brien EP. How synonymous mutations alter enzyme structure and function over long timescales. Nat Chem 2023; 15:308-318. [PMID: 36471044 PMCID: PMC11267483 DOI: 10.1038/s41557-022-01091-z] [Citation(s) in RCA: 27] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Accepted: 10/17/2022] [Indexed: 12/12/2022]
Abstract
The specific activity of enzymes can be altered over long timescales in cells by synonymous mutations that alter a messenger RNA molecule's sequence but not the encoded protein's primary structure. How this happens at the molecular level is unknown. Here, we use multiscale modelling of three Escherichia coli enzymes (type III chloramphenicol acetyltransferase, D-alanine-D-alanine ligase B and dihydrofolate reductase) to understand experimentally measured changes in specific activity due to synonymous mutations. The modelling involves coarse-grained simulations of protein synthesis and post-translational behaviour, all-atom simulations to test robustness and quantum mechanics/molecular mechanics calculations to characterize enzymatic function. We show that changes in codon translation rates induced by synonymous mutations cause shifts in co-translational and post-translational folding pathways that kinetically partition molecules into subpopulations that very slowly interconvert to the native, functional state. Structurally, these states resemble the native state, with localized misfolding near the active sites of the enzymes. These long-lived states exhibit reduced catalytic activity, as shown by their increased activation energies for the reactions they catalyse.
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Affiliation(s)
- Yang Jiang
- Department of Chemistry, Pennsylvania State University, University Park, PA, USA
| | - Syam Sundar Neti
- Department of Chemistry, Pennsylvania State University, University Park, PA, USA
| | - Ian Sitarik
- Department of Chemistry, Pennsylvania State University, University Park, PA, USA
| | - Priya Pradhan
- Department of Chemistry, Pennsylvania State University, University Park, PA, USA
| | - Philip To
- Department of Chemistry, Johns Hopkins University, Baltimore, MD, USA
| | - Yingzi Xia
- Department of Chemistry, Johns Hopkins University, Baltimore, MD, USA
| | - Stephen D Fried
- Department of Chemistry, Johns Hopkins University, Baltimore, MD, USA
- Thomas C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, MD, USA
| | - Squire J Booker
- Department of Chemistry, Pennsylvania State University, University Park, PA, USA
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA, USA
- Howard Hughes Medical Institute, Pennsylvania State University, University Park, PA, USA
| | - Edward P O'Brien
- Department of Chemistry, Pennsylvania State University, University Park, PA, USA.
- Bioinformatics and Genomics Graduate Program, The Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA, USA.
- Institute for Computational and Data Sciences, Pennsylvania State University, University Park, PA, USA.
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15
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Koller TO, Scheid U, Kösel T, Herrmann J, Krug D, Boshoff HIM, Beckert B, Evans JC, Schlemmer J, Sloan B, Weiner DM, Via LE, Moosa A, Ioerger TR, Graf M, Zinshteyn B, Abdelshahid M, Nguyen F, Arenz S, Gille F, Siebke M, Seedorf T, Plettenburg O, Green R, Warnke AL, Ullrich J, Warrass R, Barry CE, Warner DF, Mizrahi V, Kirschning A, Wilson DN, Müller R. The Myxobacterial Antibiotic Myxovalargin: Biosynthesis, Structural Revision, Total Synthesis, and Molecular Characterization of Ribosomal Inhibition. J Am Chem Soc 2023; 145:851-863. [PMID: 36603206 PMCID: PMC9853869 DOI: 10.1021/jacs.2c08816] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Resistance of bacterial pathogens against antibiotics is declared by WHO as a major global health threat. As novel antibacterial agents are urgently needed, we re-assessed the broad-spectrum myxobacterial antibiotic myxovalargin and found it to be extremely potent against Mycobacterium tuberculosis. To ensure compound supply for further development, we studied myxovalargin biosynthesis in detail enabling production via fermentation of a native producer. Feeding experiments as well as functional genomics analysis suggested a structural revision, which was eventually corroborated by the development of a concise total synthesis. The ribosome was identified as the molecular target based on resistant mutant sequencing, and a cryo-EM structure revealed that myxovalargin binds within and completely occludes the exit tunnel, consistent with a mode of action to arrest translation during a late stage of translation initiation. These studies open avenues for structure-based scaffold improvement toward development as an antibacterial agent.
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Affiliation(s)
- Timm O. Koller
- Institute
for Biochemistry and Molecular Biology, University of Hamburg, Martin-Luther-King-Platz 6, 20146 Hamburg, Germany
| | - Ullrich Scheid
- Helmholtz
Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Center
for Infection Research (HZI), Saarland University Campus, 66123 Saarbrücken, Germany
| | - Teresa Kösel
- Leibniz
Universität Hannover, Institute of
Organic Chemistry and Center for Biomolecular Drug Research (BMWZ), Schneiderberg 1B, 30167 Hannover, Germany
| | - Jennifer Herrmann
- Helmholtz
Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Center
for Infection Research (HZI), Saarland University Campus, 66123 Saarbrücken, Germany,German
Center for Infection Research (DZIF), partner site Hannover-Braunschweig, 38124 Braunschweig, Germany
| | - Daniel Krug
- Helmholtz
Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Center
for Infection Research (HZI), Saarland University Campus, 66123 Saarbrücken, Germany,Department
of Pharmacy, Saarland University, 66123 Saarbrücken, Germany,German
Center for Infection Research (DZIF), partner site Hannover-Braunschweig, 38124 Braunschweig, Germany
| | - Helena I. M. Boshoff
- Tuberculosis
Research Section, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Disease,
National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Bertrand Beckert
- Institute
for Biochemistry and Molecular Biology, University of Hamburg, Martin-Luther-King-Platz 6, 20146 Hamburg, Germany
| | - Joanna C. Evans
- SAMRC/NHLS/UCT
Molecular Mycobacteriology Research Unit & DST/NRF Centre of Excellence
for Biomedical TB Research, Institute of Infectious Disease and Molecular
Medicine and Department of Pathology, University
of Cape Town, Rondebosch 7700, South Africa
| | - Jan Schlemmer
- Helmholtz
Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Center
for Infection Research (HZI), Saarland University Campus, 66123 Saarbrücken, Germany,German
Center for Infection Research (DZIF), partner site Hannover-Braunschweig, 38124 Braunschweig, Germany
| | - Becky Sloan
- Tuberculosis
Research Section, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Disease,
National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Danielle M. Weiner
- Tuberculosis
Research Section, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Disease,
National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Laura E. Via
- Tuberculosis
Research Section, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Disease,
National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Atica Moosa
- SAMRC/NHLS/UCT
Molecular Mycobacteriology Research Unit & DST/NRF Centre of Excellence
for Biomedical TB Research, Institute of Infectious Disease and Molecular
Medicine and Department of Pathology, University
of Cape Town, Rondebosch 7700, South Africa
| | - Thomas R. Ioerger
- Department
of Computer Science and Engineering, Texas
A&M University, College
Station, Texas 77843, United States
| | - Michael Graf
- Institute
for Biochemistry and Molecular Biology, University of Hamburg, Martin-Luther-King-Platz 6, 20146 Hamburg, Germany
| | - Boris Zinshteyn
- Department
of Molecular Biology and Genetics, Johns Hopkins University, Baltimore,
Maryland 21205, United States; Howard Hughes Medical Institute, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, United States
| | - Maha Abdelshahid
- Institute
for Biochemistry and Molecular Biology, University of Hamburg, Martin-Luther-King-Platz 6, 20146 Hamburg, Germany
| | - Fabian Nguyen
- Institute
for Biochemistry and Molecular Biology, University of Hamburg, Martin-Luther-King-Platz 6, 20146 Hamburg, Germany
| | - Stefan Arenz
- Institute
for Biochemistry and Molecular Biology, University of Hamburg, Martin-Luther-King-Platz 6, 20146 Hamburg, Germany
| | - Franziska Gille
- Leibniz
Universität Hannover, Institute of
Organic Chemistry and Center for Biomolecular Drug Research (BMWZ), Schneiderberg 1B, 30167 Hannover, Germany
| | - Maik Siebke
- Leibniz
Universität Hannover, Institute of
Organic Chemistry and Center for Biomolecular Drug Research (BMWZ), Schneiderberg 1B, 30167 Hannover, Germany,Institute
of Medicinal Chemistry, Helmholtz Zentrum
München, German Research Center for Environmental Health (GmbH), Ingolstaedter Landstr. 1, 85764 Neuherberg, Germany
| | - Tim Seedorf
- Leibniz
Universität Hannover, Institute of
Organic Chemistry and Center for Biomolecular Drug Research (BMWZ), Schneiderberg 1B, 30167 Hannover, Germany
| | - Oliver Plettenburg
- Leibniz
Universität Hannover, Institute of
Organic Chemistry and Center for Biomolecular Drug Research (BMWZ), Schneiderberg 1B, 30167 Hannover, Germany,Institute
of Medicinal Chemistry, Helmholtz Zentrum
München, German Research Center for Environmental Health (GmbH), Ingolstaedter Landstr. 1, 85764 Neuherberg, Germany
| | - Rachel Green
- Department
of Molecular Biology and Genetics, Johns Hopkins University, Baltimore,
Maryland 21205, United States; Howard Hughes Medical Institute, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, United States
| | - Anna-Luisa Warnke
- Leibniz
Universität Hannover, Institute of
Organic Chemistry and Center for Biomolecular Drug Research (BMWZ), Schneiderberg 1B, 30167 Hannover, Germany,Institute
of Medicinal Chemistry, Helmholtz Zentrum
München, German Research Center for Environmental Health (GmbH), Ingolstaedter Landstr. 1, 85764 Neuherberg, Germany
| | - Joachim Ullrich
- MSD
Animal Health Innovation GmbH, Zur Propstei, 55270 Schwabenheim, Germany
| | - Ralf Warrass
- MSD
Animal Health Innovation GmbH, Zur Propstei, 55270 Schwabenheim, Germany
| | - Clifton E. Barry
- Tuberculosis
Research Section, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Disease,
National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Digby F. Warner
- SAMRC/NHLS/UCT
Molecular Mycobacteriology Research Unit & DST/NRF Centre of Excellence
for Biomedical TB Research, Institute of Infectious Disease and Molecular
Medicine and Department of Pathology, University
of Cape Town, Rondebosch 7700, South Africa
| | - Valerie Mizrahi
- SAMRC/NHLS/UCT
Molecular Mycobacteriology Research Unit & DST/NRF Centre of Excellence
for Biomedical TB Research, Institute of Infectious Disease and Molecular
Medicine and Department of Pathology, University
of Cape Town, Rondebosch 7700, South Africa
| | - Andreas Kirschning
- Leibniz
Universität Hannover, Institute of
Organic Chemistry and Center for Biomolecular Drug Research (BMWZ), Schneiderberg 1B, 30167 Hannover, Germany,
| | - Daniel N. Wilson
- Institute
for Biochemistry and Molecular Biology, University of Hamburg, Martin-Luther-King-Platz 6, 20146 Hamburg, Germany,
| | - Rolf Müller
- Helmholtz
Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Center
for Infection Research (HZI), Saarland University Campus, 66123 Saarbrücken, Germany,Department
of Pharmacy, Saarland University, 66123 Saarbrücken, Germany,German
Center for Infection Research (DZIF), partner site Hannover-Braunschweig, 38124 Braunschweig, Germany,
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16
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Insights into the ribosome function from the structures of non-arrested ribosome-nascent chain complexes. Nat Chem 2023; 15:143-153. [PMID: 36316410 PMCID: PMC9840698 DOI: 10.1038/s41557-022-01073-1] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Accepted: 09/23/2022] [Indexed: 12/24/2022]
Abstract
During protein synthesis, the growing polypeptide threads through the ribosomal exit tunnel and modulates ribosomal activity by itself or by sensing various small molecules, such as metabolites or antibiotics, appearing in the tunnel. While arrested ribosome-nascent chain complexes (RNCCs) have been extensively studied structurally, the lack of a simple procedure for the large-scale preparation of peptidyl-tRNAs, intermediates in polypeptide synthesis that carry the growing chain, means that little attention has been given to RNCCs representing functionally active states of the ribosome. Here we report the facile synthesis of stably linked peptidyl-tRNAs through a chemoenzymatic approach based on native chemical ligation and use them to determine several structures of RNCCs in the functional pre-attack state of the peptidyl transferase centre. These structures reveal that C-terminal parts of the growing peptides adopt the same uniform β-strand conformation stabilized by an intricate network of hydrogen bonds with the universally conserved 23S rRNA nucleotides, and explain how the ribosome synthesizes growing peptides containing various sequences with comparable efficiencies.
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17
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McGrath H, Černeková M, Kolář MH. Binding of the peptide deformylase on the ribosome surface modulates the exit tunnel interior. Biophys J 2022; 121:4443-4451. [PMID: 36335428 PMCID: PMC9748369 DOI: 10.1016/j.bpj.2022.11.004] [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: 06/09/2022] [Revised: 08/26/2022] [Accepted: 11/01/2022] [Indexed: 11/06/2022] Open
Abstract
Proteosynthesis on ribosomes is regulated at many levels. Conformational changes of the ribosome, possibly induced by external factors, may transfer over large distances and contribute to the regulation. The molecular principles of this long-distance allostery within the ribosome remain poorly understood. Here, we use structural analysis and atomistic molecular dynamics simulations to investigate peptide deformylase (PDF), an enzyme that binds to the ribosome surface near the ribosomal protein uL22 during translation and chemically modifies the emerging nascent peptide. Our simulations of the entire ribosome-PDF complex reveal that the PDF undergoes a swaying motion on the ribosome surface at the submicrosecond timescale. We show that the PDF affects the conformational dynamics of parts of the ribosome over distances of more than 5 nm. Using a supervised-learning algorithm, we demonstrate that the exit tunnel is influenced by the presence or absence of PDF. Our findings suggest a possible effect of the PDF on the nascent peptide translocation through the ribosome exit tunnel.
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Affiliation(s)
- Hugo McGrath
- Department of Physical Chemistry, University of Chemistry and Technology, Prague, Czech Republic
| | - Michaela Černeková
- Department of Physical Chemistry, University of Chemistry and Technology, Prague, Czech Republic
| | - Michal H Kolář
- Department of Physical Chemistry, University of Chemistry and Technology, Prague, Czech Republic.
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18
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Compounds for selective translational inhibition. Curr Opin Chem Biol 2022; 69:102158. [DOI: 10.1016/j.cbpa.2022.102158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 03/04/2022] [Accepted: 04/17/2022] [Indexed: 11/23/2022]
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19
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He W, Jiang K, Qiu H, Liao L, Wang S. 16-membered ring macrolides and erythromycin induce ermB expression by different mechanisms. BMC Microbiol 2022; 22:152. [PMID: 35681117 PMCID: PMC9178857 DOI: 10.1186/s12866-022-02565-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2022] [Accepted: 06/01/2022] [Indexed: 11/24/2022] Open
Abstract
Background Ribosome stalling on ermBL at the tenth codon (Asp) and mRNA stabilization are believed to be mechanisms by which erythromycin (Ery) induces ermB expression. Expression of ermB is also induced by 16-membered ring macrolides (tylosin, josamycin and spiramycin), but the mechanism underlying this induction is unknown. Methods We introduced premature termination codons, alanine-scanning mutagenesis and amino acid mutations in ermBL and ermBL2. Results In this paper, we demonstrated that 16-membered ring macrolides can induce ermB expression but not ermC expression. The truncated mutants of the ermB-coding sequence indicate that the regulatory regions of ermB whose expression is induced by Ery and 16-membered ring macrolides are different. We proved that translation of the N-terminal region of ermBL is key for the induction of ermB expression by Ery, spiramycin (Spi) and tylosin (Tyl). We also demonstrated that ermBL2 is critical for the induction of ermB expression by erythromycin but not by 16-membered ring macrolides. Conclusions The translation of ermBL and the RNA sequence of the C-terminus of ermBL are critical for the induction of ermB expression by Spi and Tyl. Supplementary Information The online version contains supplementary material available at 10.1186/s12866-022-02565-3.
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Affiliation(s)
- Weizhi He
- Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism (Ministry of Science and Technology), Shanghai Medical College of Fudan University, Shanghai, 200032, China.
| | - Kai Jiang
- Department of Biobank, Renji Hospital, School of Medicine, Shanghai JiaoTong University, Shanghai, China
| | - Hua Qiu
- Department of General Surgery, The First Affiliated Hospital of Nanchang University, No.17 Yongwai Zheng Street, Nanchang, 330006, Jiangxi Province, China
| | - Lijun Liao
- Department of Anesthesiology and Pain Management, Shanghai East Hospital, School of Medicine, Tongji University, Shanghai, 200120, China.
| | - Shasha Wang
- Department of Anesthesiology and Pain Management, Shanghai East Hospital, School of Medicine, Tongji University, Shanghai, 200120, China.
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20
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Wang A, Levi M, Mohanty U, Whitford PC. Diffuse Ions Coordinate Dynamics in a Ribonucleoprotein Assembly. J Am Chem Soc 2022; 144:9510-9522. [PMID: 35593477 DOI: 10.1021/jacs.2c04082] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Proper ionic concentrations are required for the functional dynamics of RNA and ribonucleoprotein (RNP) assemblies. While experimental and computational techniques have provided many insights into the properties of chelated ions, less is known about the energetic contributions of diffuse ions to large-scale conformational rearrangements. To address this, we present a model that is designed to quantify the influence of diffuse monovalent and divalent ions on the dynamics of biomolecular assemblies. This model employs all-atom (non-H) resolution and explicit ions, where effective potentials account for hydration effects. We first show that the model accurately predicts the number of excess Mg2+ ions for prototypical RNA systems, at a level comparable to modern coarse-grained models. We then apply the model to a complete ribosome and show how the balance between diffuse Mg2+ and K+ ions can control the dynamics of tRNA molecules during translation. The model predicts differential effects of diffuse ions on the free-energy barrier associated with tRNA entry and the energy of tRNA binding to the ribosome. Together, this analysis reveals the direct impact of diffuse ions on the dynamics of an RNP assembly.
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Affiliation(s)
- Ailun Wang
- Department of Chemistry, Boston College, Chestnut Hill, Massachusetts 02467, United States.,Center for Theoretical Biological Physics, Northeastern University, 360 Huntington Avenue, Boston, Massachusetts 02115, United States
| | - Mariana Levi
- Department of Physics, Northeastern University, Dana Research Center 111, 360 Huntington Avenue, Boston, Massachusetts 02115, United States
| | - Udayan Mohanty
- Department of Chemistry, Boston College, Chestnut Hill, Massachusetts 02467, United States
| | - Paul C Whitford
- Center for Theoretical Biological Physics, Northeastern University, 360 Huntington Avenue, Boston, Massachusetts 02115, United States.,Department of Physics, Northeastern University, Dana Research Center 111, 360 Huntington Avenue, Boston, Massachusetts 02115, United States
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21
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Kolář MH, Nagy G, Kunkel J, Vaiana SM, Bock LV, Grubmüller H. Folding of VemP into translation-arresting secondary structure is driven by the ribosome exit tunnel. Nucleic Acids Res 2022; 50:2258-2269. [PMID: 35150281 PMCID: PMC8887479 DOI: 10.1093/nar/gkac038] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Revised: 11/30/2021] [Accepted: 01/25/2022] [Indexed: 01/09/2023] Open
Abstract
The ribosome is a fundamental biomolecular complex that synthesizes proteins in cells. Nascent proteins emerge from the ribosome through a tunnel, where they may interact with the tunnel walls or small molecules such as antibiotics. These interactions can cause translational arrest with notable physiological consequences. Here, we studied the arrest caused by the regulatory peptide VemP, which is known to form α-helices inside the ribosome tunnel near the peptidyl transferase center under specific conditions. We used all-atom molecular dynamics simulations of the entire ribosome and circular dichroism spectroscopy to study the driving forces of helix formation and how VemP causes the translational arrest. To that aim, we compared VemP dynamics in the ribosome tunnel with its dynamics in solution. We show that the VemP peptide has a low helical propensity in water and that the propensity is higher in mixtures of water and trifluorethanol. We propose that helix formation within the ribosome is driven by the interactions of VemP with the tunnel and that a part of VemP acts as an anchor. This anchor might slow down VemP progression through the tunnel enabling α-helix formation, which causes the elongation arrest.
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Affiliation(s)
- Michal H Kolář
- Department of Theoretical and Computational Biophysics, Max Planck Institute for Multidisciplinary Sciences, Am Fassberg 11, 370 77 Göttingen, Germany
- Department of Physical Chemistry, University of Chemistry and Technology in Prague, Technická 5, 166 28 Prague, Czech Republic
| | - Gabor Nagy
- Department of Theoretical and Computational Biophysics, Max Planck Institute for Multidisciplinary Sciences, Am Fassberg 11, 370 77 Göttingen, Germany
| | - John Kunkel
- Department of Physics and Center for Biological Physics, Arizona State University, Tempe, AZ 85287, USA
| | - Sara M Vaiana
- Department of Physics and Center for Biological Physics, Arizona State University, Tempe, AZ 85287, USA
| | - Lars V Bock
- Department of Theoretical and Computational Biophysics, Max Planck Institute for Multidisciplinary Sciences, Am Fassberg 11, 370 77 Göttingen, Germany
| | - Helmut Grubmüller
- Department of Theoretical and Computational Biophysics, Max Planck Institute for Multidisciplinary Sciences, Am Fassberg 11, 370 77 Göttingen, Germany
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22
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Exploring cryo-electron microscopy with molecular dynamics. Biochem Soc Trans 2022; 50:569-581. [PMID: 35212361 DOI: 10.1042/bst20210485] [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: 12/10/2021] [Revised: 01/31/2022] [Accepted: 02/02/2022] [Indexed: 11/17/2022]
Abstract
Single particle analysis cryo-electron microscopy (EM) and molecular dynamics (MD) have been complimentary methods since cryo-EM was first applied to the field of structural biology. The relationship started by biasing structural models to fit low-resolution cryo-EM maps of large macromolecular complexes not amenable to crystallization. The connection between cryo-EM and MD evolved as cryo-EM maps improved in resolution, allowing advanced sampling algorithms to simultaneously refine backbone and sidechains. Moving beyond a single static snapshot, modern inferencing approaches integrate cryo-EM and MD to generate structural ensembles from cryo-EM map data or directly from the particle images themselves. We summarize the recent history of MD innovations in the area of cryo-EM modeling. The merits for the myriad of MD based cryo-EM modeling methods are discussed, as well as, the discoveries that were made possible by the integration of molecular modeling with cryo-EM. Lastly, current challenges and potential opportunities are reviewed.
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23
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Crowe-McAuliffe C, Wilson DN. Putting the antibiotics chloramphenicol and linezolid into context. Nat Struct Mol Biol 2022; 29:79-81. [DOI: 10.1038/s41594-022-00725-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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24
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Syroegin EA, Flemmich L, Klepacki D, Vazquez-Laslop N, Micura R, Polikanov YS. Structural basis for the context-specific action of the classic peptidyl transferase inhibitor chloramphenicol. Nat Struct Mol Biol 2022; 29:152-161. [DOI: 10.1038/s41594-022-00720-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Accepted: 12/23/2021] [Indexed: 02/06/2023]
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25
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Tsai K, Stojković V, Lee DJ, Young ID, Szal T, Klepacki D, Vázquez-Laslop N, Mankin AS, Fraser JS, Fujimori DG. Structural basis for context-specific inhibition of translation by oxazolidinone antibiotics. Nat Struct Mol Biol 2022; 29:162-171. [DOI: 10.1038/s41594-022-00723-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Accepted: 01/05/2022] [Indexed: 01/02/2023]
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26
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The context of the ribosome binding site in mRNAs defines specificity of action of kasugamycin, an inhibitor of translation initiation. Proc Natl Acad Sci U S A 2022; 119:2118553119. [PMID: 35064089 PMCID: PMC8794815 DOI: 10.1073/pnas.2118553119] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/21/2021] [Indexed: 11/18/2022] Open
Abstract
Several antibiotics targeting the large ribosomal subunit interfere with translation in a context-specific manner, preventing ribosomes from polymerizing specific amino acid sequences. Here, we reveal kasugamycin as a small ribosomal subunit-targeting antibiotic whose action depends on the sequence context of the untranslated messenger RNA (mRNA) segments. We show that kasugamycin-induced ribosomal arrest at the start codons of the genes and the resulting inhibition of gene expression depend on the nature of the mRNA nucleotide immediately preceding the start codon and on the proximity of the stop codon of the upstream cistron. Our findings underlie the importance of mRNA context for the action of protein synthesis inhibitors and might help to guide the development of better antibiotics. Kasugamycin (KSG) is an aminoglycoside antibiotic widely used in agriculture and exhibits considerable medical potential. Previous studies suggested that KSG interferes with translation by blocking binding of canonical messenger RNA (mRNA) and initiator transfer tRNA (tRNA) to the small ribosomal subunit, thereby preventing initiation of protein synthesis. Here, by using genome-wide approaches, we show that KSG can interfere with translation even after the formation of the 70S initiation complex on mRNA, as the extent of KSG-mediated translation inhibition correlates with increased occupancy of start codons by 70S ribosomes. Even at saturating concentrations, KSG does not completely abolish translation, allowing for continuing expression of some Escherichia coli proteins. Differential action of KSG significantly depends on the nature of the mRNA residue immediately preceding the start codon, with guanine in this position being the most conducive to inhibition by the drug. In addition, the activity of KSG is attenuated by translational coupling as genes whose start codons overlap with the coding regions or the stop codons of the upstream cistrons tend to be less susceptible to drug-mediated inhibition. Altogether, our findings reveal KSG as an example of a small ribosomal subunit-targeting antibiotic with a well-pronounced context specificity of action.
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27
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Jia B, Wang T, Lehmann J. Peptidyl transferase center decompaction and structural constraints during early protein elongation on the ribosome. Sci Rep 2021; 11:24061. [PMID: 34911999 PMCID: PMC8674327 DOI: 10.1038/s41598-021-02985-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2021] [Accepted: 11/15/2021] [Indexed: 11/09/2022] Open
Abstract
Peptide bond formation on the ribosome requires that aminoacyl-tRNAs and peptidyl-tRNAs are properly positioned on the A site and the P site of the peptidyl transferase center (PTC) so that nucleophilic attack can occur. Here we analyse some constraints associated with the induced-fit mechanism of the PTC, that promotes this positioning through a compaction around the aminoacyl ester orchestrated by U2506. The physical basis of PTC decompaction, that allows the elongated peptidyl-tRNA to free itself from that state and move to the P site of the PTC, is still unclear. From thermodynamics considerations and an analysis of published ribosome structures, the present work highlights the rational of this mechanism, in which the free-energy released by the new peptide bond is used to kick U2506 away from the reaction center. Furthermore, we show the evidence that decompaction is impaired when the nascent peptide is not yet anchored inside the exit tunnel, which may contribute to explain why the first rounds of elongation are inefficient, an issue that has attracted much interest for about two decades. Results in this field are examined in the light of the present analysis and a physico-chemical correlation in the genetic code, which suggest that elementary constraints associated with the size of the side-chain of the amino acids penalize early elongation events.
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Affiliation(s)
- Bin Jia
- Department of Anesthesiology, Xuanwu Hospital, Capital Medical University, Beijing, China
| | - Tianlong Wang
- Department of Anesthesiology, Xuanwu Hospital, Capital Medical University, Beijing, China.
| | - Jean Lehmann
- CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), University of Paris-Saclay, 91198, Gif-sur-Yvette, France.
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28
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Di Palma F, Decherchi S, Pardo-Avila F, Succi S, Levitt M, von Heijne G, Cavalli A. Probing Interplays between Human XBP1u Translational Arrest Peptide and 80S Ribosome. J Chem Theory Comput 2021; 18:1905-1914. [PMID: 34881571 PMCID: PMC8908735 DOI: 10.1021/acs.jctc.1c00796] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
![]()
The ribosome stalling
mechanism is a crucial biological process,
yet its atomistic underpinning is still elusive. In this framework,
the human XBP1u translational arrest peptide (AP) plays a central
role in regulating the unfolded protein response (UPR) in eukaryotic
cells. Here, we report multimicrosecond all-atom molecular dynamics
simulations designed to probe the interactions between the XBP1u AP
and the mammalian ribosome exit tunnel, both for the wild type AP
and for four mutant variants of different arrest potencies. Enhanced
sampling simulations allow investigating the AP release process of
the different variants, shedding light on this complex mechanism.
The present outcomes are in qualitative/quantitative agreement with
available experimental data. In conclusion, we provide an unprecedented
atomistic picture of this biological process and clear-cut insights
into the key AP–ribosome interactions.
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Affiliation(s)
- Francesco Di Palma
- Computational & Chemical Biology, Fondazione Istituto Italiano di Tecnologia, Via Morego 30, I-16163 Genova, Italy
| | - Sergio Decherchi
- Computational & Chemical Biology, Fondazione Istituto Italiano di Tecnologia, Via Morego 30, I-16163 Genova, Italy
| | - Fátima Pardo-Avila
- Department of Structural Biology, Stanford University, Palo Alto, California 94305, United States
| | - Sauro Succi
- Computational & Chemical Biology, Fondazione Istituto Italiano di Tecnologia, Via Morego 30, I-16163 Genova, Italy.,Center for Life Nano & Neurosciences at La Sapienza, Fondazione Istituto Italiano di Tecnologia, via Regina Elena, 295, I-00161 Roma, Italy.,Physics Department, Harvard University, 17 Oxford Street, Cambridge, Massachusetts 02138, United States
| | - Michael Levitt
- Department of Structural Biology, Stanford University, Palo Alto, California 94305, United States
| | - Gunnar von Heijne
- Department of Biochemistry and Biophysics, Stockholm University, SE-106 91 Stockholm, Sweden.,Science for Life Laboratory, Stockholm University, 17165 Solna, Sweden
| | - Andrea Cavalli
- Computational & Chemical Biology, Fondazione Istituto Italiano di Tecnologia, Via Morego 30, I-16163 Genova, Italy.,Department of Pharmacy and Biotechnology, University of Bologna, Via Belmeloro 6, I-40126 Bologna, Italy
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29
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Hassan A, Byju S, Whitford PC. The energetics of subunit rotation in the ribosome. Biophys Rev 2021; 13:1029-1037. [PMID: 35059025 PMCID: PMC8724491 DOI: 10.1007/s12551-021-00877-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Accepted: 10/26/2021] [Indexed: 12/12/2022] Open
Abstract
Protein synthesis in the cell is controlled by an elaborate sequence of conformational rearrangements in the ribosome. The composition of a ribosome varies by species, though they typically contain ∼ 50-100 RNA and protein molecules. While advances in structural techniques have revolutionized our understanding of long-lived conformational states, a vast range of transiently visited configurations can not be directly observed. In these cases, computational/simulation methods can be used to understand the mechanical properties of the ribosome. Insights from these approaches can then help guide next-generation experimental measurements. In this short review, we discuss theoretical strategies that have been deployed to quantitatively describe the energetics of collective rearrangements in the ribosome. We focus on efforts to probe large-scale subunit rotation events, which involve the coordinated displacement of large numbers of atoms (tens of thousands). These investigations are revealing how the molecular structure of the ribosome encodes the mechanical properties that control large-scale dynamics.
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Affiliation(s)
- Asem Hassan
- Center for Theoretical Biological Physics, 360 Huntington Ave, Boston, 02115 MA USA
- Physics Department, Northeastern University, 360 Huntington Ave, Boston, 02115 MA USA
| | - Sandra Byju
- Center for Theoretical Biological Physics, 360 Huntington Ave, Boston, 02115 MA USA
- Physics Department, Northeastern University, 360 Huntington Ave, Boston, 02115 MA USA
| | - Paul C. Whitford
- Center for Theoretical Biological Physics, 360 Huntington Ave, Boston, 02115 MA USA
- Physics Department, Northeastern University, 360 Huntington Ave, Boston, 02115 MA USA
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30
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Structural basis for the tryptophan sensitivity of TnaC-mediated ribosome stalling. Nat Commun 2021; 12:5340. [PMID: 34504068 PMCID: PMC8429421 DOI: 10.1038/s41467-021-25663-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Accepted: 08/24/2021] [Indexed: 02/07/2023] Open
Abstract
Free L-tryptophan (L-Trp) stalls ribosomes engaged in the synthesis of TnaC, a leader peptide controlling the expression of the Escherichia coli tryptophanase operon. Despite extensive characterization, the molecular mechanism underlying the recognition and response to L-Trp by the TnaC-ribosome complex remains unknown. Here, we use a combined biochemical and structural approach to characterize a TnaC variant (R23F) with greatly enhanced sensitivity for L-Trp. We show that the TnaC-ribosome complex captures a single L-Trp molecule to undergo termination arrest and that nascent TnaC prevents the catalytic GGQ loop of release factor 2 from adopting an active conformation at the peptidyl transferase center. Importantly, the L-Trp binding site is not altered by the R23F mutation, suggesting that the relative rates of L-Trp binding and peptidyl-tRNA cleavage determine the tryptophan sensitivity of each variant. Thus, our study reveals a strategy whereby a nascent peptide assists the ribosome in detecting a small metabolite.
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31
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Beckert B, Leroy EC, Sothiselvam S, Bock LV, Svetlov MS, Graf M, Arenz S, Abdelshahid M, Seip B, Grubmüller H, Mankin AS, Innis CA, Vázquez-Laslop N, Wilson DN. Structural and mechanistic basis for translation inhibition by macrolide and ketolide antibiotics. Nat Commun 2021; 12:4466. [PMID: 34294725 PMCID: PMC8298421 DOI: 10.1038/s41467-021-24674-9] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Accepted: 06/30/2021] [Indexed: 12/23/2022] Open
Abstract
Macrolides and ketolides comprise a family of clinically important antibiotics that inhibit protein synthesis by binding within the exit tunnel of the bacterial ribosome. While these antibiotics are known to interrupt translation at specific sequence motifs, with ketolides predominantly stalling at Arg/Lys-X-Arg/Lys motifs and macrolides displaying a broader specificity, a structural basis for their context-specific action has been lacking. Here, we present structures of ribosomes arrested during the synthesis of an Arg-Leu-Arg sequence by the macrolide erythromycin (ERY) and the ketolide telithromycin (TEL). Together with deep mutagenesis and molecular dynamics simulations, the structures reveal how ERY and TEL interplay with the Arg-Leu-Arg motif to induce translational arrest and illuminate the basis for the less stringent sequence-specific action of ERY over TEL. Because programmed stalling at the Arg/Lys-X-Arg/Lys motifs is used to activate expression of antibiotic resistance genes, our study also provides important insights for future development of improved macrolide antibiotics.
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Affiliation(s)
- Bertrand Beckert
- Institute for Biochemistry and Molecular Biology, University of Hamburg, Hamburg, Germany
| | - Elodie C Leroy
- Univ. Bordeaux, Centre National de la Recherche Scientifique, Institut National de la Santé et de la Recherche Médicale, ARNA, UMR 5320, U1212, Institut Européen de Chimie et Biologie, Pessac, France
| | | | - Lars V Bock
- Theoretical and Computational Biophysics Department, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany.
| | - Maxim S Svetlov
- Center for Biomolecular Sciences, University of Illinois at Chicago, Chicago, IL, USA
| | - Michael Graf
- Institute for Biochemistry and Molecular Biology, University of Hamburg, Hamburg, Germany
| | - Stefan Arenz
- Institute for Biochemistry and Molecular Biology, University of Hamburg, Hamburg, Germany
| | - Maha Abdelshahid
- Institute for Biochemistry and Molecular Biology, University of Hamburg, Hamburg, Germany
| | - Britta Seip
- Univ. Bordeaux, Centre National de la Recherche Scientifique, Institut National de la Santé et de la Recherche Médicale, ARNA, UMR 5320, U1212, Institut Européen de Chimie et Biologie, Pessac, France
| | - Helmut Grubmüller
- Theoretical and Computational Biophysics Department, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Alexander S Mankin
- Center for Biomolecular Sciences, University of Illinois at Chicago, Chicago, IL, USA
| | - C Axel Innis
- Univ. Bordeaux, Centre National de la Recherche Scientifique, Institut National de la Santé et de la Recherche Médicale, ARNA, UMR 5320, U1212, Institut Européen de Chimie et Biologie, Pessac, France.
| | - Nora Vázquez-Laslop
- Center for Biomolecular Sciences, University of Illinois at Chicago, Chicago, IL, USA.
| | - Daniel N Wilson
- Institute for Biochemistry and Molecular Biology, University of Hamburg, Hamburg, Germany.
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32
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Jiang Y, O'Brien EP. Mechanical Forces Have a Range of Effects on the Rate of Ribosome Catalyzed Peptidyl Transfer Depending on Direction. J Phys Chem B 2021; 125:7128-7136. [PMID: 34166592 PMCID: PMC8291131 DOI: 10.1021/acs.jpcb.1c02263] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Mechanical forces acting on the nascent chain residue located at the P-site of the ribosome can influence codon translation rates. Most observations to date involve force vectors aligned collinear with the long axis of the ribosome exit tunnel. What is poorly understood is how force applied in other directions will impact the rate of peptide bond formation catalyzed by the ribosome. Here, we utilize quantum mechanical/molecular mechanics simulations to estimate the changes in the activation free energy as a consequence of applying a constant force in various directions on the C-terminal residue at the P-site. Qualitatively consistent with the Bell model, we find this force can either accelerate, decelerate, or not alter the reaction rate depending on the force direction. A force in the average direction between the P-site 3' O-C ester bond that breaks and the peptide bond that forms accelerates the reaction. A force in the opposite direction slows down the reaction as it opposes these bonds breaking and forming, but surprisingly it does not do so to the maximum extent possible. In this case, there is a counterbalancing trend; the force in this direction brings the A-site amino nitrogen and the P-site tRNA A76 3' oxygen groups closer together, which promotes one of the proton shuttling steps of the reaction. We find the maximum force-induced slowdown occurs 37° off this axis. If force is applied in orthogonal directions to the reaction coordinates, there is no significant change in the reaction speed. These results indicate that there is a richer set of scenarios of force effects on translation speed that have yet to be experimentally explored and raise the possibility that cells could use these mechanochemical effects to modulate and regulate protein synthesis.
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Affiliation(s)
- Yang Jiang
- Department of Chemistry, Penn State University, University Park, Pennsylvania 16802, United States
| | - Edward P O'Brien
- Department of Chemistry, Penn State University, University Park, Pennsylvania 16802, United States
- Bioinformatics and Genomics Graduate Program, The Huck Institutes of the Life Sciences, Penn State University, University Park, Pennsylvania 16802, United States
- Institute for Computational and Data Sciences, Penn State University, University Park, Pennsylvania 16802, United States
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33
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Wang S, Jiang K, Du X, Lu Y, Liao L, He Z, He W. Translational Attenuation Mechanism of ErmB Induction by Erythromycin Is Dependent on Two Leader Peptides. Front Microbiol 2021; 12:690744. [PMID: 34262551 PMCID: PMC8274638 DOI: 10.3389/fmicb.2021.690744] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2021] [Accepted: 06/03/2021] [Indexed: 11/13/2022] Open
Abstract
Ribosome stalling on ermBL at the tenth codon (Asp) is believed to be a major mechanism of ermB induction by erythromycin (Ery). In this study, we demonstrated that the mechanism of ermB induction by Ery depends not only on ermBL expression but also on previously unreported ermBL2 expression. Introducing premature termination codons in ermBL, we proved that translation of the N-terminal region of ermBL is the key component for ermB induced by Ery, whereas translation of the C-terminal region of ermBL did not affect Ery-induced ermB. Mutation of the tenth codon (Asp10) of ermBL with other amino acids showed that the degree of induction in vivo was not completely consistent with the data from the in vitro toe printing assay. Alanine-scanning mutagenesis of ermBL demonstrated that both N-terminal residues (R7-K11) and the latter part of ermBL (K20-K27) are critical for Ery induction of ermB. The frameshifting reporter plasmid showed that a new leader peptide, ermBL2, exists in the ermB regulatory region. Further, introducing premature termination mutation and alanine-scanning mutagenesis of ermBL2 demonstrated that the N-terminus of ermBL2 is essential for induction by Ery. Therefore, the detailed function of ermBL2 requires further study.
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Affiliation(s)
- Shasha Wang
- Institute for Regenerative Medicine, Shanghai East Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, China.,Department of Anesthesiology and Pain Management, Shanghai East Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Kai Jiang
- Department of Biobank, Renji Hospital, School of Medicine, Shanghai JiaoTong University, Shanghai, China
| | - Xinyue Du
- Institute for Regenerative Medicine, Shanghai East Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Yanli Lu
- Institute for Regenerative Medicine, Shanghai East Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Lijun Liao
- Department of Anesthesiology and Pain Management, Shanghai East Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Zhiying He
- Institute for Regenerative Medicine, Shanghai East Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, China.,Shanghai Engineering Research Center of Stem Cells Translational Medicine, Shanghai, China
| | - Weizhi He
- Institute for Regenerative Medicine, Shanghai East Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, China
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34
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Context-specific action of macrolide antibiotics on the eukaryotic ribosome. Nat Commun 2021; 12:2803. [PMID: 33990576 PMCID: PMC8121947 DOI: 10.1038/s41467-021-23068-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Accepted: 04/14/2021] [Indexed: 01/09/2023] Open
Abstract
Macrolide antibiotics bind in the nascent peptide exit tunnel of the bacterial ribosome and prevent polymerization of specific amino acid sequences, selectively inhibiting translation of a subset of proteins. Because preventing translation of individual proteins could be beneficial for the treatment of human diseases, we asked whether macrolides, if bound to the eukaryotic ribosome, would retain their context- and protein-specific action. By introducing a single mutation in rRNA, we rendered yeast Saccharomyces cerevisiae cells sensitive to macrolides. Cryo-EM structural analysis showed that the macrolide telithromycin binds in the tunnel of the engineered eukaryotic ribosome. Genome-wide analysis of cellular translation and biochemical studies demonstrated that the drug inhibits eukaryotic translation by preferentially stalling ribosomes at distinct sequence motifs. Context-specific action markedly depends on the macrolide structure. Eliminating macrolide-arrest motifs from a protein renders its translation macrolide-tolerant. Our data illuminate the prospects of adapting macrolides for protein-selective translation inhibition in eukaryotic cells.
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35
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Zimmer MH, Niesen MJM, Miller TF. Force transduction creates long-ranged coupling in ribosomes stalled by arrest peptides. Biophys J 2021; 120:2425-2435. [PMID: 33932440 DOI: 10.1016/j.bpj.2021.03.041] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Revised: 03/09/2021] [Accepted: 03/19/2021] [Indexed: 11/16/2022] Open
Abstract
Force-sensitive arrest peptides regulate protein biosynthesis by stalling the ribosome as they are translated. Synthesis can be resumed when the nascent arrest peptide experiences a pulling force of sufficient magnitude to break the stall. Efficient stalling is dependent on the specific identity of a large number of amino acids, including amino acids that are tens of angstroms away from the peptidyl transferase center (PTC). The mechanism of force-induced restart and the role of these essential amino acids far from the PTC is currently unknown. We use hundreds of independent molecular dynamics trajectories spanning over 120 μs in combination with kinetic analysis to characterize multiple barriers along the force-induced restart pathway for the arrest peptide SecM. We find that the essential amino acids far from the PTC play a major role in controlling the transduction of applied force. In successive states along the stall-breaking pathway, the applied force propagates up the nascent chain until it reaches the C-terminus of SecM and the PTC, inducing conformational changes that allow for restart of translation. A similar mechanism of force propagation through multiple states is observed in the VemP stall-breaking pathway, but secondary structure in VemP allows for heterogeneity in the order of transitions through intermediate states. Results from both arrest peptides explain how residues that are tens of angstroms away from the catalytic center of the ribosome impact stalling efficiency by mediating the response to an applied force and shielding the amino acids responsible for maintaining the stalled state of the PTC.
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Affiliation(s)
- Matthew H Zimmer
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California
| | - Michiel J M Niesen
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California
| | - Thomas F Miller
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California.
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36
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Seefeldt AC, Aguirre Rivera J, Johansson M. Direct Measurements of Erythromycin's Effect on Protein Synthesis Kinetics in Living Bacterial Cells. J Mol Biol 2021; 433:166942. [PMID: 33744313 DOI: 10.1016/j.jmb.2021.166942] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Revised: 03/09/2021] [Accepted: 03/09/2021] [Indexed: 10/21/2022]
Abstract
Macrolide antibiotics, such as erythromycin, bind to the nascent peptide exit tunnel (NPET) of the bacterial ribosome and modulate protein synthesis depending on the nascent peptide sequence. Whereas in vitro biochemical and structural methods have been instrumental in dissecting and explaining the molecular details of macrolide-induced peptidyl-tRNA drop-off and ribosome stalling, the dynamic effects of the drugs on ongoing protein synthesis inside live bacterial cells are far less explored. In the present study, we used single-particle tracking of dye-labeled tRNAs to study the kinetics of mRNA translation in the presence of erythromycin, directly inside live Escherichia coli cells. In erythromycin-treated cells, we find that the dwells of elongator tRNAPhe on ribosomes extend significantly, but they occur much more seldom. In contrast, the drug barely affects the ribosome binding events of the initiator tRNAfMet. By overexpressing specific short peptides, we further find context-specific ribosome binding dynamics of tRNAPhe, underscoring the complexity of erythromycin's effect on protein synthesis in bacterial cells.
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Affiliation(s)
| | | | - Magnus Johansson
- Department of Cell and Molecular Biology, Uppsala University, Sweden.
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37
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Müller C, Crowe-McAuliffe C, Wilson DN. Ribosome Rescue Pathways in Bacteria. Front Microbiol 2021; 12:652980. [PMID: 33815344 PMCID: PMC8012679 DOI: 10.3389/fmicb.2021.652980] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Accepted: 02/23/2021] [Indexed: 12/18/2022] Open
Abstract
Ribosomes that become stalled on truncated or damaged mRNAs during protein synthesis must be rescued for the cell to survive. Bacteria have evolved a diverse array of rescue pathways to remove the stalled ribosomes from the aberrant mRNA and return them to the free pool of actively translating ribosomes. In addition, some of these pathways target the damaged mRNA and the incomplete nascent polypeptide chain for degradation. This review highlights the recent developments in our mechanistic understanding of bacterial ribosomal rescue systems, including drop-off, trans-translation mediated by transfer-messenger RNA and small protein B, ribosome rescue by the alternative rescue factors ArfA and ArfB, as well as Bacillus ribosome rescue factor A, an additional rescue system found in some Gram-positive bacteria, such as Bacillus subtilis. Finally, we discuss the recent findings of ribosome-associated quality control in particular bacterial lineages mediated by RqcH and RqcP. The importance of rescue pathways for bacterial survival suggests they may represent novel targets for the development of new antimicrobial agents against multi-drug resistant pathogenic bacteria.
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Affiliation(s)
| | | | - Daniel N. Wilson
- Institute for Biochemistry and Molecular Biology, University of Hamburg, Hamburg, Germany
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38
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Sakiyama K, Shimokawa-Chiba N, Fujiwara K, Chiba S. Search for translation arrest peptides encoded upstream of genes for components of protein localization pathways. Nucleic Acids Res 2021; 49:1550-1566. [PMID: 33503266 PMCID: PMC7897499 DOI: 10.1093/nar/gkab024] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2020] [Revised: 01/05/2021] [Accepted: 01/08/2021] [Indexed: 02/06/2023] Open
Abstract
Regulatory nascent peptides participate in the regulation of cellular functions by the mechanisms involving regulated translation arrest. A class of them in bacteria, called monitoring substrates, feedback-regulates the expression of a specific component of protein localization machinery. Three monitoring substrates, SecM, MifM and VemP have previously been identified. Here, we attempt at identifying additional arrest peptides in bacteria. Our bioinformatic searches over more than 400 bacterial genomic sequences for proteins that have the common characteristic features shared by the known monitoring substrates and subsequent in vitro and in vivo characterization of the highlighted sequences allowed the identification of three arrest peptides termed ApcA, ApdA and ApdP. ApcA and ApdA homologs are conserved among a subset of actinobacteria, whereas ApdP has homologs in a subset of α-proteobacteria. We demonstrate that these arrest peptides, in their ribosome-tethered nascent states, inhibit peptidyl transfer. The elongation arrest occurs at a specific codon near the 3′ end of the coding region, in a manner depending on the amino acid sequence of the nascent chain. Interestingly, the arrest sequences of ApcA, ApdA and ApdP share a sequence R-A-P-G/P that is essential for the elongation arrest.
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Affiliation(s)
- Karen Sakiyama
- Faculty of Life Sciences, Kyoto Sangyo University, Motoyama, Kamigamo, Kita-Ku, Kyoto 603-8555, Japan
| | - Naomi Shimokawa-Chiba
- Faculty of Life Sciences, Kyoto Sangyo University, Motoyama, Kamigamo, Kita-Ku, Kyoto 603-8555, Japan.,Institute for Protein Dynamics, Kyoto Sangyo University, Japan
| | - Keigo Fujiwara
- Faculty of Life Sciences, Kyoto Sangyo University, Motoyama, Kamigamo, Kita-Ku, Kyoto 603-8555, Japan.,Institute for Protein Dynamics, Kyoto Sangyo University, Japan
| | - Shinobu Chiba
- Faculty of Life Sciences, Kyoto Sangyo University, Motoyama, Kamigamo, Kita-Ku, Kyoto 603-8555, Japan.,Institute for Protein Dynamics, Kyoto Sangyo University, Japan
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39
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Jednačak T, Mikulandra I, Novak P. Advanced Methods for Studying Structure and Interactions of Macrolide Antibiotics. Int J Mol Sci 2020; 21:E7799. [PMID: 33096889 PMCID: PMC7589898 DOI: 10.3390/ijms21207799] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2020] [Revised: 10/09/2020] [Accepted: 10/19/2020] [Indexed: 11/17/2022] Open
Abstract
Macrolide antibiotics are macrocyclic compounds that are clinically used and prescribed for the treatment of upper and lower respiratory tract infections. They inhibit the synthesis of bacterial proteins by reversible binding to the 23S rRNA at or near the peptidyl transferase center. However, their excellent antibacterial profile was largely compromised by the emergence of bacterial resistance. Today, fighting resistance to antibiotics is one of the greatest challenges in medicinal chemistry. Considering various physicochemical properties of macrolides, understanding their structure and interactions with macromolecular targets is crucial for the design of new antibiotics efficient against resistant pathogens. The solid-state structures of some macrolide-ribosome complexes have recently been solved, throwing new light on the macrolide binding mechanisms. On the other hand, a combination of NMR spectroscopy and molecular modeling calculations can be applied to study free and bound conformations in solution. In this article, a description of advanced physicochemical methods for elucidating the structure and interactions of macrolide antibiotics in solid state and solution will be provided, and their principal advantages and drawbacks will be discussed.
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Affiliation(s)
- Tomislav Jednačak
- Department of Chemistry, Faculty of Science, University of Zagreb, Horvatovac 102a, HR-10000 Zagreb, Croatia;
| | | | - Predrag Novak
- Department of Chemistry, Faculty of Science, University of Zagreb, Horvatovac 102a, HR-10000 Zagreb, Croatia;
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40
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Ji ZS, Liu QL, Zhang JF, Yang YH, Li J, Zhang GW, Tan MH, Lin HS, Guo GQ. SUMOylation of spastin promotes the internalization of GluA1 and regulates dendritic spine morphology by targeting microtubule dynamics. Neurobiol Dis 2020; 146:105133. [PMID: 33049318 DOI: 10.1016/j.nbd.2020.105133] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Revised: 09/24/2020] [Accepted: 10/06/2020] [Indexed: 10/23/2022] Open
Abstract
Dendritic spines are specialized structures involved in neuronal processes on which excitatory synaptic contact occurs. The microtubule cytoskeleton is vital for maintaining spine morphology and mature synapses. Spastin is related to microtubule-severing proteases and is involved in synaptic bouton formation. However, it is not yet known if spastin can be modified by Small Ubiquitin-like Modifier (SUMO) or how this modification regulates dendritic spines. Spastin was shown to be SUMOylated at K427, and its deSUMOylation promoted microtubule stability. In addition, SUMOylation of spastin was shown to affect signalling pathways associated with long term synaptic depression. SUMOylated spastin promoted the development of dendrites and dendritic spines. Moreover, SUMOylated spastin regulated endocytosis and affected the transport of the AMPA receptor, GluA1. Our findings suggest that SUMOylation of spastin promotes GluA1 internalization and regulates dendritic spine morphology through targeting of microtubule dynamics.
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Affiliation(s)
- Zhi-Sheng Ji
- Department of Orthopedics, The First Affiliated Hospital of Jinan University, No.601 West Huangpu Avenue, Tianhe, Guangzhou 510630, China
| | - Qiu-Ling Liu
- Department of Orthopedics, The First Affiliated Hospital of Jinan University, No.601 West Huangpu Avenue, Tianhe, Guangzhou 510630, China
| | - Ji-Feng Zhang
- Department of Anatomy, Neuroscience Laboratory for Cognitive and Developmental Disorders, Medical College of Jinan University, No.601 West Huangpu Avenue, Tianhe, Guangzhou 510630, China
| | - Yu-Hao Yang
- Department of Orthopedics, The First Affiliated Hospital of Jinan University, No.601 West Huangpu Avenue, Tianhe, Guangzhou 510630, China
| | - Jiong Li
- Department of Anatomy, Neuroscience Laboratory for Cognitive and Developmental Disorders, Medical College of Jinan University, No.601 West Huangpu Avenue, Tianhe, Guangzhou 510630, China
| | - Guo-Wei Zhang
- Department of Orthopedics, The First Affiliated Hospital of Jinan University, No.601 West Huangpu Avenue, Tianhe, Guangzhou 510630, China
| | - Ming-Hui Tan
- Department of Orthopedics, The First Affiliated Hospital of Jinan University, No.601 West Huangpu Avenue, Tianhe, Guangzhou 510630, China.
| | - Hong-Sheng Lin
- Department of Orthopedics, The First Affiliated Hospital of Jinan University, No.601 West Huangpu Avenue, Tianhe, Guangzhou 510630, China.
| | - Guo-Qing Guo
- Department of Anatomy, Neuroscience Laboratory for Cognitive and Developmental Disorders, Medical College of Jinan University, No.601 West Huangpu Avenue, Tianhe, Guangzhou 510630, China.
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41
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Dever TE, Ivanov IP, Sachs MS. Conserved Upstream Open Reading Frame Nascent Peptides That Control Translation. Annu Rev Genet 2020; 54:237-264. [PMID: 32870728 DOI: 10.1146/annurev-genet-112618-043822] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Cells utilize transcriptional and posttranscriptional mechanisms to alter gene expression in response to environmental cues. Gene-specific controls, including changing the translation of specific messenger RNAs (mRNAs), provide a rapid means to respond precisely to different conditions. Upstream open reading frames (uORFs) are known to control the translation of mRNAs. Recent studies in bacteria and eukaryotes have revealed the functions of evolutionarily conserved uORF-encoded peptides. Some of these uORF-encoded nascent peptides enable responses to specific metabolites to modulate the translation of their mRNAs by stalling ribosomes and through ribosome stalling may also modulate the level of their mRNAs. In this review, we highlight several examples of conserved uORF nascent peptides that stall ribosomes to regulate gene expression in response to specific metabolites in bacteria, fungi, mammals, and plants.
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Affiliation(s)
- Thomas E Dever
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892, USA; ,
| | - Ivaylo P Ivanov
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892, USA; ,
| | - Matthew S Sachs
- Department of Biology, Texas A&M University, College Station, Texas 77843, USA;
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42
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Herrero del Valle A, Innis CA. Prospects for antimicrobial development in the cryo-EM era – a focus on the ribosome. FEMS Microbiol Rev 2020; 44:793-803. [DOI: 10.1093/femsre/fuaa032] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Accepted: 07/25/2020] [Indexed: 12/12/2022] Open
Abstract
ABSTRACT
Resistance to antimicrobial drugs used to treat bacterial, viral, fungal and parasitic infections is a major health concern requiring a coordinated response across the globe. An important aspect in the fight against antimicrobial resistance is the development of novel drugs that are effective against resistant pathogens. Drug development is a complex trans-disciplinary endeavor, in which structural biology plays a major role by providing detailed functional and mechanistic information on an antimicrobial target and its interactions with small molecule inhibitors. Although X-ray crystallography and nuclear magnetic resonance have until now been the methods of choice to characterize microbial targets and drive structure-based drug development, cryo-electron microscopy is rapidly gaining ground in these areas. In this perspective, we will discuss how cryo-electron microscopy is changing our understanding of an established antimicrobial target, the ribosome, and how methodological developments could help this technique become an integral part of the antimicrobial drug discovery pipeline.
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Affiliation(s)
- Alba Herrero del Valle
- Institut Européen de Chimie et Biologie, Univ. Bordeaux, Institut National de la Santé et de la Recherche Médicale (U1212) and Centre National de la Recherche Scientifique (UMR 5320), 2 rue Robert Escarpit, 33607 Pessac, France
| | - C Axel Innis
- Institut Européen de Chimie et Biologie, Univ. Bordeaux, Institut National de la Santé et de la Recherche Médicale (U1212) and Centre National de la Recherche Scientifique (UMR 5320), 2 rue Robert Escarpit, 33607 Pessac, France
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43
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Osterman IA, Wieland M, Maviza TP, Lashkevich KA, Lukianov DA, Komarova ES, Zakalyukina YV, Buschauer R, Shiriaev DI, Leyn SA, Zlamal JE, Biryukov MV, Skvortsov DA, Tashlitsky VN, Polshakov VI, Cheng J, Polikanov YS, Bogdanov AA, Osterman AL, Dmitriev SE, Beckmann R, Dontsova OA, Wilson DN, Sergiev PV. Tetracenomycin X inhibits translation by binding within the ribosomal exit tunnel. Nat Chem Biol 2020; 16:1071-1077. [PMID: 32601485 DOI: 10.1038/s41589-020-0578-x] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Accepted: 05/28/2020] [Indexed: 11/09/2022]
Abstract
The increase in multi-drug resistant pathogenic bacteria is making our current arsenal of clinically used antibiotics obsolete, highlighting the urgent need for new lead compounds with distinct target binding sites to avoid cross-resistance. Here we report that the aromatic polyketide antibiotic tetracenomycin (TcmX) is a potent inhibitor of protein synthesis, and does not induce DNA damage as previously thought. Despite the structural similarity to the well-known translation inhibitor tetracycline, we show that TcmX does not interact with the small ribosomal subunit, but rather binds to the large subunit, within the polypeptide exit tunnel. This previously unappreciated binding site is located adjacent to the macrolide-binding site, where TcmX stacks on the noncanonical basepair formed by U1782 and U2586 of the 23S ribosomal RNA. Although the binding site is distinct from the macrolide antibiotics, our results indicate that like macrolides, TcmX allows translation of short oligopeptides before further translation is blocked.
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Affiliation(s)
- Ilya A Osterman
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Skolkovo, Russia. .,Department of Chemistry, Faculty of Bioengineering and Bioinformatics and Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia.
| | - Maximiliane Wieland
- Institute for Biochemistry and Molecular Biology, University of Hamburg, Hamburg, Germany
| | - Tinashe P Maviza
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Skolkovo, Russia
| | - Kseniya A Lashkevich
- Department of Chemistry, Faculty of Bioengineering and Bioinformatics and Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Dmitrii A Lukianov
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Skolkovo, Russia
| | - Ekaterina S Komarova
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Skolkovo, Russia.,Department of Chemistry, Faculty of Bioengineering and Bioinformatics and Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Yuliya V Zakalyukina
- Department of Soil Science and Department of Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Robert Buschauer
- Gene Center, Department of Biochemistry, University of Munich, Munich, Germany
| | - Dmitrii I Shiriaev
- Department of Chemistry, Faculty of Bioengineering and Bioinformatics and Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Semen A Leyn
- Infectious and Inflammatory Disease Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA.,A.A. Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow, Russia
| | - Jaime E Zlamal
- Infectious and Inflammatory Disease Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - Mikhail V Biryukov
- Department of Soil Science and Department of Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Dmitry A Skvortsov
- Department of Chemistry, Faculty of Bioengineering and Bioinformatics and Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Vadim N Tashlitsky
- Department of Chemistry, Faculty of Bioengineering and Bioinformatics and Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Vladimir I Polshakov
- Center for Magnetic Tomography and Spectroscopy, Faculty of Fundamental Medicine, Lomonosov Moscow State University, Moscow, Russia
| | - Jingdong Cheng
- Gene Center, Department of Biochemistry, University of Munich, Munich, Germany
| | - Yury S Polikanov
- Department of Biological Sciences, University of Illinois at Chicago, Chicago, IL, USA
| | - Alexey A Bogdanov
- Department of Chemistry, Faculty of Bioengineering and Bioinformatics and Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Andrei L Osterman
- Infectious and Inflammatory Disease Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - Sergey E Dmitriev
- Department of Chemistry, Faculty of Bioengineering and Bioinformatics and Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Roland Beckmann
- Gene Center, Department of Biochemistry, University of Munich, Munich, Germany
| | - Olga A Dontsova
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Skolkovo, Russia.,Department of Chemistry, Faculty of Bioengineering and Bioinformatics and Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia.,Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Daniel N Wilson
- Institute for Biochemistry and Molecular Biology, University of Hamburg, Hamburg, Germany.
| | - Petr V Sergiev
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Skolkovo, Russia. .,Department of Chemistry, Faculty of Bioengineering and Bioinformatics and Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia.
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44
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Loss of a single methylation in 23S rRNA delays 50S assembly at multiple late stages and impairs translation initiation and elongation. Proc Natl Acad Sci U S A 2020; 117:15609-15619. [PMID: 32571953 DOI: 10.1073/pnas.1914323117] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Ribosome biogenesis is a complex process, and dozens of factors are required to facilitate and regulate the subunit assembly in bacteria. The 2'-O-methylation of U2552 in 23S rRNA by methyltransferase RrmJ is a crucial step in late-stage assembly of the 50S subunit. Its absence results in severe growth defect and marked accumulation of pre50S assembly intermediates. In the present work, we employed cryoelectron microscopy to characterize a set of late-stage pre50S particles isolated from an Escherichia coli ΔrrmJ strain. These assembly intermediates (solved at 3.2 to 3.8 Å resolution) define a collection of late-stage particles on a progressive assembly pathway. Apart from the absence of L16, L35, and L36, major structural differences between these intermediates and the mature 50S subunit are clustered near the peptidyl transferase center, such as H38, H68-71, and H89-93. In addition, the ribosomal A-loop of the mature 50S subunit from ΔrrmJ strain displays large local flexibility on nucleotides next to unmethylated U2552. Fast kinetics-based biochemical assays demonstrate that the ΔrrmJ 50S subunit is only 50% active and two times slower than the WT 50S subunit in rapid subunit association. While the ΔrrmJ 70S ribosomes show no defect in peptide bond formation, peptide release, and ribosome recycling, they translocate with 20% slower rate than the WT ribosomes in each round of elongation. These defects amplify during synthesis of the full-length proteins and cause overall defect in protein synthesis. In conclusion, our data reveal the molecular roles of U2552 methylation in both ribosome biogenesis and protein translation.
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45
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Pichkur EB, Paleskava A, Tereshchenkov AG, Kasatsky P, Komarova ES, Shiriaev DI, Bogdanov AA, Dontsova OA, Osterman IA, Sergiev PV, Polikanov YS, Myasnikov AG, Konevega AL. Insights into the improved macrolide inhibitory activity from the high-resolution cryo-EM structure of dirithromycin bound to the E. coli 70S ribosome. RNA (NEW YORK, N.Y.) 2020; 26:715-723. [PMID: 32144191 PMCID: PMC7266154 DOI: 10.1261/rna.073817.119] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Accepted: 12/27/2019] [Indexed: 05/05/2023]
Abstract
Macrolides are one of the most successful and widely used classes of antibacterials, which kill or stop the growth of pathogenic bacteria by binding near the active site of the ribosome and interfering with protein synthesis. Dirithromycin is a derivative of the prototype macrolide erythromycin with additional hydrophobic side chain. In our recent study, we have discovered that the side chain of dirithromycin forms lone pair-π stacking interaction with the aromatic imidazole ring of the His69 residue in ribosomal protein uL4 of the Thermus thermophilus 70S ribosome. In the current work, we found that neither the presence of the side chain, nor the additional contact with the ribosome, improve the binding affinity of dirithromycin to the ribosome. Nevertheless, we found that dirithromycin is a more potent inhibitor of in vitro protein synthesis in comparison with its parent compound, erythromycin. Using high-resolution cryo-electron microscopy, we determined the structure of the dirithromycin bound to the translating Escherichia coli 70S ribosome, which suggests that the better inhibitory properties of the drug could be rationalized by the side chain of dirithromycin pointing into the lumen of the nascent peptide exit tunnel, where it can interfere with the normal passage of the growing polypeptide chain.
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Affiliation(s)
- Evgeny B Pichkur
- Petersburg Nuclear Physics Institute named by B.P. Konstantinov of NRC "Kurchatov Institute," Gatchina, 188300, Russia
- National Research Center "Kurchatov Institute," Moscow, 123182, Russia
| | - Alena Paleskava
- Petersburg Nuclear Physics Institute named by B.P. Konstantinov of NRC "Kurchatov Institute," Gatchina, 188300, Russia
- Peter the Great St. Petersburg Polytechnic University, Saint Petersburg, 195251, Russia
| | - Andrey G Tereshchenkov
- Department of Chemistry and A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119992, Russia
| | - Pavel Kasatsky
- Petersburg Nuclear Physics Institute named by B.P. Konstantinov of NRC "Kurchatov Institute," Gatchina, 188300, Russia
| | - Ekaterina S Komarova
- Department of Bioengineering and Bioinformatics and A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119992, Russia
- Skolkovo Institute of Science and Technology, Skolkovo, Moscow region, 143025, Russia
| | - Dmitrii I Shiriaev
- Department of Chemistry and A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119992, Russia
| | - Alexey A Bogdanov
- Department of Chemistry and A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119992, Russia
| | - Olga A Dontsova
- Department of Chemistry and A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119992, Russia
- Skolkovo Institute of Science and Technology, Skolkovo, Moscow region, 143025, Russia
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia
| | - Ilya A Osterman
- Department of Chemistry and A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119992, Russia
- Skolkovo Institute of Science and Technology, Skolkovo, Moscow region, 143025, Russia
| | - Petr V Sergiev
- Department of Chemistry and A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119992, Russia
- Skolkovo Institute of Science and Technology, Skolkovo, Moscow region, 143025, Russia
| | - Yury S Polikanov
- Departments of Biological Sciences and Pharmaceutical Sciences, University of Illinois at Chicago, Chicago, Illinois 60607, USA
- Center for Biomolecular Sciences, University of Illinois at Chicago, Chicago, Illinois 60607, USA
| | - Alexander G Myasnikov
- Petersburg Nuclear Physics Institute named by B.P. Konstantinov of NRC "Kurchatov Institute," Gatchina, 188300, Russia
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, USA
- Centre for Integrative Biology, IGBMC, CNRS, Inserm, Université de Strasbourg, Illkirch, 67404, France
| | - Andrey L Konevega
- Petersburg Nuclear Physics Institute named by B.P. Konstantinov of NRC "Kurchatov Institute," Gatchina, 188300, Russia
- National Research Center "Kurchatov Institute," Moscow, 123182, Russia
- Peter the Great St. Petersburg Polytechnic University, Saint Petersburg, 195251, Russia
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46
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Herrero Del Valle A, Seip B, Cervera-Marzal I, Sacheau G, Seefeldt AC, Innis CA. Ornithine capture by a translating ribosome controls bacterial polyamine synthesis. Nat Microbiol 2020; 5:554-561. [PMID: 32094585 PMCID: PMC7250644 DOI: 10.1038/s41564-020-0669-1] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Accepted: 01/10/2020] [Indexed: 02/06/2023]
Abstract
Polyamines are essential metabolites that play an important role in cell growth, stress adaptation, and microbial virulence1–3. In order to survive and multiply within a human host, pathogenic bacteria adjust the expression and activity of polyamine biosynthetic enzymes in response to different environmental stresses and metabolic cues2. Here, we show that ornithine capture by the ribosome and the nascent peptide SpeFL controls polyamine synthesis in γ-proteobacteria by inducing the expression of the ornithine decarboxylase SpeF4, via a mechanism involving ribosome stalling and transcription antitermination. In addition, we present the cryo-EM structure of an Escherichia coli (E. coli) ribosome stalled during translation of speFL in the presence of ornithine. The structure shows how the ribosome and the SpeFL sensor domain form a highly selective binding pocket that accommodates a single ornithine molecule but excludes near-cognate ligands. Ornithine pre-associates with the ribosome and is then held in place by the sensor domain, leading to the compaction of the SpeFL effector domain and blocking the action of release factor RF1. Thus, our study not only reveals basic strategies by which nascent peptides assist the ribosome in detecting a specific metabolite, but also provides a framework for assessing how ornithine promotes virulence in several human pathogens.
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Affiliation(s)
- Alba Herrero Del Valle
- Institut Européen de Chimie et Biologie, Université de Bordeaux, Pessac, France.,Institut National de la Santé et de la Recherche Médicale (U1212), Bordeaux, France.,Centre National de la Recherche Scientifique (UMR 5320), Bordeaux, France
| | - Britta Seip
- Institut Européen de Chimie et Biologie, Université de Bordeaux, Pessac, France.,Institut National de la Santé et de la Recherche Médicale (U1212), Bordeaux, France.,Centre National de la Recherche Scientifique (UMR 5320), Bordeaux, France.,Evotec International GmbH, Göttingen, Germany
| | - Iñaki Cervera-Marzal
- Institut Européen de Chimie et Biologie, Université de Bordeaux, Pessac, France.,Institut National de la Santé et de la Recherche Médicale (U1212), Bordeaux, France.,Centre National de la Recherche Scientifique (UMR 5320), Bordeaux, France.,Aix Marseille Université, CNRS, INSERM, CIML, Centre d'Immunologie de Marseille-Luminy, Marseille, France
| | - Guénaël Sacheau
- Institut Européen de Chimie et Biologie, Université de Bordeaux, Pessac, France.,Institut National de la Santé et de la Recherche Médicale (U1212), Bordeaux, France.,Centre National de la Recherche Scientifique (UMR 5320), Bordeaux, France.,Sopra Steria, Saint-Herblain, France
| | - A Carolin Seefeldt
- Institut Européen de Chimie et Biologie, Université de Bordeaux, Pessac, France.,Institut National de la Santé et de la Recherche Médicale (U1212), Bordeaux, France.,Centre National de la Recherche Scientifique (UMR 5320), Bordeaux, France.,Department of Cell and Molecular Biology, Biomedical Center, Uppsala University, Uppsala, Sweden
| | - C Axel Innis
- Institut Européen de Chimie et Biologie, Université de Bordeaux, Pessac, France. .,Institut National de la Santé et de la Recherche Médicale (U1212), Bordeaux, France. .,Centre National de la Recherche Scientifique (UMR 5320), Bordeaux, France.
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47
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Warias M, Grubmüller H, Bock LV. tRNA Dissociation from EF-Tu after GTP Hydrolysis: Primary Steps and Antibiotic Inhibition. Biophys J 2020; 118:151-161. [PMID: 31711607 PMCID: PMC6950810 DOI: 10.1016/j.bpj.2019.10.028] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Revised: 09/25/2019] [Accepted: 10/22/2019] [Indexed: 11/25/2022] Open
Abstract
In each round of ribosomal translation, the translational GTPase elongation factor Tu (EF-Tu) delivers a transfer RNA (tRNA) to the ribosome. After successful decoding, EF-Tu hydrolyzes GTP, which triggers a conformational change that ultimately results in the release of the tRNA from EF-Tu. To identify the primary steps of these conformational changes and how they are prevented by the antibiotic kirromycin, we employed all-atom explicit-solvent molecular dynamics simulations of the full ribosome-EF-Tu complex. Our results suggest that after GTP hydrolysis and Pi release, the loss of interactions between the nucleotide and the switch 1 loop of EF-Tu allows domain D1 of EF-Tu to rotate relative to domains D2 and D3 and leads to an increased flexibility of the switch 1 loop. This rotation induces a closing of the D1-D3 interface and an opening of the D1-D2 interface. We propose that the opening of the D1-D2 interface, which binds the CCA tail of the tRNA, weakens the crucial EF-Tu-tRNA interactions, which lowers tRNA binding affinity, representing the first step of tRNA release. Kirromycin binds within the D1-D3 interface, sterically blocking its closure, but does not prevent hydrolysis. The resulting increased flexibility of switch 1 explains why it is not resolved in kirromycin-bound structures.
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Affiliation(s)
- Malte Warias
- Theoretical and Computational Biophysics, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Helmut Grubmüller
- Theoretical and Computational Biophysics, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Lars V Bock
- Theoretical and Computational Biophysics, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany.
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48
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van der Horst S, Filipovska T, Hanson J, Smeekens S. Metabolite Control of Translation by Conserved Peptide uORFs: The Ribosome as a Metabolite Multisensor. PLANT PHYSIOLOGY 2020; 182:110-122. [PMID: 31451550 PMCID: PMC6945846 DOI: 10.1104/pp.19.00940] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Accepted: 08/16/2019] [Indexed: 05/19/2023]
Abstract
Ribosomes translate the mRNA code into protein, and this process can be controlled by metabolites that bind to the translating ribosome in interaction with the nascent protein.
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Affiliation(s)
- Sjors van der Horst
- Molecular Plant Physiology, Institute of Environmental Biology, Utrecht University, 3584CH Utrecht, The Netherlands
| | - Teodora Filipovska
- Molecular Plant Physiology, Institute of Environmental Biology, Utrecht University, 3584CH Utrecht, The Netherlands
| | - Johannes Hanson
- Molecular Plant Physiology, Institute of Environmental Biology, Utrecht University, 3584CH Utrecht, The Netherlands
- Umeå Plant Science Center, Department of Plant Physiology, Umeå University, SE-901 87 Umea, Sweden
| | - Sjef Smeekens
- Molecular Plant Physiology, Institute of Environmental Biology, Utrecht University, 3584CH Utrecht, The Netherlands
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Takakura M, Ishiguro K, Akichika S, Miyauchi K, Suzuki T. Biogenesis and functions of aminocarboxypropyluridine in tRNA. Nat Commun 2019; 10:5542. [PMID: 31804502 PMCID: PMC6895100 DOI: 10.1038/s41467-019-13525-3] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Accepted: 11/11/2019] [Indexed: 12/17/2022] Open
Abstract
Transfer (t)RNAs contain a wide variety of post-transcriptional modifications, which play critical roles in tRNA stability and functions. 3-(3-amino-3-carboxypropyl)uridine (acp3U) is a highly conserved modification found in variable- and D-loops of tRNAs. Biogenesis and functions of acp3U have not been extensively investigated. Using a reverse-genetic approach supported by comparative genomics, we find here that the Escherichia coli yfiP gene, which we rename tapT (tRNA aminocarboxypropyltransferase), is responsible for acp3U formation in tRNA. Recombinant TapT synthesizes acp3U at position 47 of tRNAs in the presence of S-adenosylmethionine. Biochemical experiments reveal that acp3U47 confers thermal stability on tRNA. Curiously, the ΔtapT strain exhibits genome instability under continuous heat stress. We also find that the human homologs of tapT, DTWD1 and DTWD2, are responsible for acp3U formation at positions 20 and 20a of tRNAs, respectively. Double knockout cells of DTWD1 and DTWD2 exhibit growth retardation, indicating that acp3U is physiologically important in mammals.
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Affiliation(s)
- Mayuko Takakura
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan
| | - Kensuke Ishiguro
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan
| | - Shinichiro Akichika
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan
| | - Kenjyo Miyauchi
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan
| | - Tsutomu Suzuki
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan.
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Structure of ribosome-bound azole-modified peptide phazolicin rationalizes its species-specific mode of bacterial translation inhibition. Nat Commun 2019; 10:4563. [PMID: 31594941 PMCID: PMC6783444 DOI: 10.1038/s41467-019-12589-5] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2019] [Accepted: 09/09/2019] [Indexed: 02/04/2023] Open
Abstract
Ribosome-synthesized post-translationally modified peptides (RiPPs) represent a rapidly expanding class of natural products with various biological activities. Linear azol(in)e-containing peptides (LAPs) comprise a subclass of RiPPs that display outstanding diversity of mechanisms of action while sharing common structural features. Here, we report the discovery of a new LAP biosynthetic gene cluster in the genome of Rhizobium Pop5, which encodes the precursor peptide and modification machinery of phazolicin (PHZ) – an extensively modified peptide exhibiting narrow-spectrum antibacterial activity against some symbiotic bacteria of leguminous plants. The cryo-EM structure of the Escherichia coli 70S-PHZ complex reveals that the drug interacts with the 23S rRNA and uL4/uL22 proteins and obstructs ribosomal exit tunnel in a way that is distinct from other compounds. We show that the uL4 loop sequence determines the species-specificity of antibiotic action. PHZ expands the known diversity of LAPs and may be used in the future as biocontrol agent for agricultural needs. The authors report the identification of phazolicin (PHZ) - a prokaryotic translation inhibitory peptide - and its structure in complex with the E. coli ribosome, delineating PHZ’s mode of action and suggesting a basis for its bacterial species-specific activity.
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