1
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Majumdar S, Emmerich A, Krakovka S, Mandava CS, Svärd SG, Sanyal S. Insights into translocation mechanism and ribosome evolution from cryo-EM structures of translocation intermediates of Giardia intestinalis. Nucleic Acids Res 2023; 51:3436-3451. [PMID: 36912103 PMCID: PMC10123126 DOI: 10.1093/nar/gkad176] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Revised: 02/06/2023] [Accepted: 02/24/2023] [Indexed: 03/14/2023] Open
Abstract
Giardia intestinalis is a protozoan parasite that causes diarrhea in humans. Using single-particle cryo-electron microscopy, we have determined high-resolution structures of six naturally populated translocation intermediates, from ribosomes isolated directly from actively growing Giardia cells. The highly compact and uniquely GC-rich Giardia ribosomes possess eukaryotic rRNAs and ribosomal proteins, but retain some bacterial features. The translocation intermediates, with naturally bound tRNAs and eukaryotic elongation factor 2 (eEF2), display characteristic ribosomal intersubunit rotation and small subunit's head swiveling-universal for translocation. In addition, we observe the eukaryote-specific 'subunit rolling' dynamics, albeit with limited features. Finally, the eEF2·GDP state features a uniquely positioned 'leaving phosphate (Pi)' that proposes hitherto unknown molecular events of Pi and eEF2 release from the ribosome at the final stage of translocation. In summary, our study elucidates the mechanism of translocation in the protists and illustrates evolution of the translation machinery from bacteria to eukaryotes from both the structural and mechanistic perspectives.
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Affiliation(s)
- Soneya Majumdar
- Department of Cell and Molecular Biology, Uppsala University, Box 596, 75124 Uppsala, Sweden
| | - Andrew Emmerich
- Department of Cell and Molecular Biology, Uppsala University, Box 596, 75124 Uppsala, Sweden
| | - Sascha Krakovka
- Department of Cell and Molecular Biology, Uppsala University, Box 596, 75124 Uppsala, Sweden
| | - Chandra Sekhar Mandava
- Department of Cell and Molecular Biology, Uppsala University, Box 596, 75124 Uppsala, Sweden
| | - Staffan G Svärd
- Department of Cell and Molecular Biology, Uppsala University, Box 596, 75124 Uppsala, Sweden
| | - Suparna Sanyal
- Department of Cell and Molecular Biology, Uppsala University, Box 596, 75124 Uppsala, Sweden
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2
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Singh S, Lahry K, Mandava CS, Singh J, Shah RA, Sanyal S, Varshney U. Lamotrigine compromises the fidelity of initiator tRNA recruitment to the ribosomal P-site by IF2 and the RbfA release from 30S ribosomes in Escherichia coli. RNA Biol 2023; 20:681-692. [PMID: 37676049 PMCID: PMC10486304 DOI: 10.1080/15476286.2023.2253395] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Revised: 08/09/2023] [Accepted: 08/24/2023] [Indexed: 09/08/2023] Open
Abstract
Lamotrigine (Ltg), an anticonvulsant drug, targets initiation factor 2 (IF2), compromises ribosome biogenesis and causes toxicity to Escherichia coli. However, our understanding of Ltg toxicity in E. coli remains unclear. While our in vitro assays reveal no effects of Ltg on the ribosome-dependent GTPase activity of IF2 or its role in initiation as measured by dipeptide formation in a fast kinetics assay, the in vivo experiments show that Ltg causes accumulation of the 17S precursor of 16S rRNA and leads to a decrease in polysome levels in E. coli. IF2 overexpression in E. coli increases Ltg toxicity. However, the overexpression of initiator tRNA (i-tRNA) protects it from the Ltg toxicity. The depletion of i-tRNA or overexpression of its 3GC mutant (lacking the characteristic 3GC base pairs in anticodon stem) enhances Ltg toxicity, and this enhancement in toxicity is synthetic with IF2 overexpression. The Ltg treatment itself causes a detectable increase in IF2 levels in E. coli and allows initiation with an elongator tRNA, suggesting compromise in the fidelity/specificity of IF2 function. Also, Ltg causes increased accumulation of ribosome-binding factor A (RbfA) on 30S ribosomal subunit. Based on our genetic and biochemical investigations, we show that Ltg compromises the function of i-tRNA/IF2 complex in ribosome maturation.
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Affiliation(s)
- Sudhir Singh
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, India
| | - Kuldeep Lahry
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, India
| | - Chandra Sekhar Mandava
- Department of Cell and Molecular Biology, Biomedical Centre, Uppsala University, Uppsala, Sweden
| | - Jitendra Singh
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, India
| | - Riyaz Ahmad Shah
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, India
| | - Suparna Sanyal
- Department of Cell and Molecular Biology, Biomedical Centre, Uppsala University, Uppsala, Sweden
| | - Umesh Varshney
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, India
- Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore, India
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3
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Parajuli NP, Mandava CS, Pavlov MY, Sanyal S. Mechanistic insights into translation inhibition by aminoglycoside antibiotic arbekacin. Nucleic Acids Res 2021; 49:6880-6892. [PMID: 34125898 PMCID: PMC8266624 DOI: 10.1093/nar/gkab495] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Revised: 05/17/2021] [Accepted: 05/26/2021] [Indexed: 11/13/2022] Open
Abstract
How aminoglycoside antibiotics limit bacterial growth and viability is not clearly understood. Here we employ fast kinetics to reveal the molecular mechanism of action of a clinically used, new-generation, semisynthetic aminoglycoside Arbekacin (ABK), which is designed to avoid enzyme-mediated deactivation common to other aminoglycosides. Our results portray complete picture of ABK inhibition of bacterial translation with precise quantitative characterizations. We find that ABK inhibits different steps of translation in nanomolar to micromolar concentrations by imparting pleotropic effects. ABK binding stalls elongating ribosomes to a state, which is unfavorable for EF-G binding. This prolongs individual translocation step from ∼50 ms to at least 2 s; the mean time of translocation increases inversely with EF-G concentration. ABK also inhibits translation termination by obstructing RF1/RF2 binding to the ribosome. Furthermore, ABK decreases accuracy of mRNA decoding (UUC vs. CUC) by ∼80 000 fold, causing aberrant protein production. Importantly, translocation and termination events cannot be completely stopped even with high ABK concentration. Extrapolating our kinetic model of ABK action, we postulate that aminoglycosides impose bacteriostatic effect mainly by inhibiting translocation, while they become bactericidal in combination with decoding errors.
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Affiliation(s)
- Narayan Prasad Parajuli
- Department of Cell and Molecular Biology, Biomedical Center, Uppsala University, SE-75124 Uppsala, Sweden
| | - Chandra Sekhar Mandava
- Department of Cell and Molecular Biology, Biomedical Center, Uppsala University, SE-75124 Uppsala, Sweden
| | - Michael Y Pavlov
- Department of Cell and Molecular Biology, Biomedical Center, Uppsala University, SE-75124 Uppsala, Sweden
| | - Suparna Sanyal
- Department of Cell and Molecular Biology, Biomedical Center, Uppsala University, SE-75124 Uppsala, Sweden
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4
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Albers S, Beckert B, Matthies MC, Mandava CS, Schuster R, Seuring C, Riedner M, Sanyal S, Torda AE, Wilson DN, Ignatova Z. Repurposing tRNAs for nonsense suppression. Nat Commun 2021; 12:3850. [PMID: 34158503 PMCID: PMC8219837 DOI: 10.1038/s41467-021-24076-x] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Accepted: 06/01/2021] [Indexed: 02/06/2023] Open
Abstract
Three stop codons (UAA, UAG and UGA) terminate protein synthesis and are almost exclusively recognized by release factors. Here, we design de novo transfer RNAs (tRNAs) that efficiently decode UGA stop codons in Escherichia coli. The tRNA designs harness various functionally conserved aspects of sense-codon decoding tRNAs. Optimization within the TΨC-stem to stabilize binding to the elongation factor, displays the most potent effect in enhancing suppression activity. We determine the structure of the ribosome in a complex with the designed tRNA bound to a UGA stop codon in the A site at 2.9 Å resolution. In the context of the suppressor tRNA, the conformation of the UGA codon resembles that of a sense-codon rather than when canonical translation termination release factors are bound, suggesting conformational flexibility of the stop codons dependent on the nature of the A-site ligand. The systematic analysis, combined with structural insights, provides a rationale for targeted repurposing of tRNAs to correct devastating nonsense mutations that introduce a premature stop codon.
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Affiliation(s)
- Suki Albers
- grid.9026.d0000 0001 2287 2617Institute of Biochemistry and Molecular Biology, University of Hamburg, Hamburg, Germany
| | - Bertrand Beckert
- grid.9026.d0000 0001 2287 2617Institute of Biochemistry and Molecular Biology, University of Hamburg, Hamburg, Germany
| | - Marco C. Matthies
- grid.9026.d0000 0001 2287 2617Center for Bioinformatics, University of Hamburg, Hamburg, Germany
| | - Chandra Sekhar Mandava
- grid.8993.b0000 0004 1936 9457Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
| | - Raphael Schuster
- grid.9026.d0000 0001 2287 2617Institute of Organic Chemistry, University of Hamburg, Hamburg, Germany
| | | | - Maria Riedner
- grid.9026.d0000 0001 2287 2617Institute of Organic Chemistry, University of Hamburg, Hamburg, Germany
| | - Suparna Sanyal
- grid.8993.b0000 0004 1936 9457Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
| | - Andrew E. Torda
- grid.9026.d0000 0001 2287 2617Center for Bioinformatics, University of Hamburg, Hamburg, Germany
| | - Daniel N. Wilson
- grid.9026.d0000 0001 2287 2617Institute of Biochemistry and Molecular Biology, University of Hamburg, Hamburg, Germany
| | - Zoya Ignatova
- grid.9026.d0000 0001 2287 2617Institute of Biochemistry and Molecular Biology, University of Hamburg, Hamburg, Germany
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5
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Kim C, Holm M, Mandava CS, Sanyal S. Optimization of a fluorescent-mRNA based real-time assay for precise kinetic measurements of ribosomal translocation. RNA Biol 2021; 18:2363-2375. [PMID: 33938388 PMCID: PMC8632105 DOI: 10.1080/15476286.2021.1913312] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
Abstract
Kinetic characterization of ribosomal translocation is important for understanding the mechanism of elongation in protein synthesis. Here we have optimized a popular fluorescent-mRNA based translocation assay conducted in stopped-flow, by calibrating it with the functional tripeptide formation assay in quench-flow. We found that a fluorescently labelled mRNA, ten bases long from position +1 (mRNA+10), is best suited for both assays as it forms tripeptide at a fast rate equivalent to the longer mRNAs, and yet produces a large fluorescence change upon mRNA movement. Next, we compared the commonly used peptidyl tRNA analog, N-acetyl-Phe-tRNAPhe, with the natural dipeptidyl fMet-Phe-tRNAPhe in the stopped-flow assay. This analog translocates about two times slower than the natural dipeptidyl tRNA and produces biphasic kinetics. The rates reduce further at lower temperatures and with higher Mg2+ concentration, but improve with higher elongation factor G (EF-G) concentration, which increase both rate and amplitude of the fast phase significantly. In summary, we present here an improved real time assay for monitoring mRNA-translocation with the natural- and an N-Ac-analog of dipeptidyl tRNA.
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Affiliation(s)
- Changil Kim
- Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
| | - Mikael Holm
- Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
| | | | - Suparna Sanyal
- Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
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6
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Fislage M, Zhang J, Brown ZP, Mandava CS, Sanyal S, Ehrenberg M, Frank J. Cryo-EM shows stages of initial codon selection on the ribosome by aa-tRNA in ternary complex with GTP and the GTPase-deficient EF-TuH84A. Nucleic Acids Res 2019; 46:5861-5874. [PMID: 29733411 PMCID: PMC6009598 DOI: 10.1093/nar/gky346] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Accepted: 04/30/2018] [Indexed: 11/25/2022] Open
Abstract
The GTPase EF-Tu in ternary complex with GTP and aminoacyl-tRNA (aa-tRNA) promotes rapid and accurate delivery of cognate aa-tRNAs to the ribosomal A site. Here we used cryo-EM to study the molecular origins of the accuracy of ribosome-aided recognition of a cognate ternary complex and the accuracy-amplifying role of the monitoring bases A1492, A1493 and G530 of the 16S rRNA. We used the GTPase-deficient EF-Tu variant H84A with native GTP, rather than non-cleavable GTP analogues, to trap a near-cognate ternary complex in high-resolution ribosomal complexes of varying codon-recognition accuracy. We found that ribosome complexes trapped by GTPase-deficicent ternary complex due to the presence of EF-TuH84A or non-cleavable GTP analogues have very similar structures. We further discuss speed and accuracy of initial aa-tRNA selection in terms of conformational changes of aa-tRNA and stepwise activation of the monitoring bases at the decoding center of the ribosome.
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Affiliation(s)
- Marcus Fislage
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
| | - Jingji Zhang
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA.,Department of Cell and Molecular Biology, Uppsala University, Uppsala 75124, Sweden
| | - Zuben Patrick Brown
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
| | | | - Suparna Sanyal
- Department of Cell and Molecular Biology, Uppsala University, Uppsala 75124, Sweden
| | - Måns Ehrenberg
- Department of Cell and Molecular Biology, Uppsala University, Uppsala 75124, Sweden
| | - Joachim Frank
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA.,Department of Biological Sciences, Columbia University, New York, NY, USA
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7
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Holm M, Mandava CS, Ehrenberg M, Sanyal S. The mechanism of error induction by the antibiotic viomycin provides insight into the fidelity mechanism of translation. eLife 2019; 8:46124. [PMID: 31172942 PMCID: PMC6594751 DOI: 10.7554/elife.46124] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Accepted: 06/04/2019] [Indexed: 01/04/2023] Open
Abstract
Applying pre-steady state kinetics to an Escherichia-coli-based reconstituted translation system, we have studied how the antibiotic viomycin affects the accuracy of genetic code reading. We find that viomycin binds to translating ribosomes associated with a ternary complex (TC) consisting of elongation factor Tu (EF-Tu), aminoacyl tRNA and GTP, and locks the otherwise dynamically flipping monitoring bases A1492 and A1493 into their active conformation. This effectively prevents dissociation of near- and non-cognate TCs from the ribosome, thereby enhancing errors in initial selection. Moreover, viomycin shuts down proofreading-based error correction. Our results imply a mechanism in which the accuracy of initial selection is achieved by larger backward rate constants toward TC dissociation rather than by a smaller rate constant for GTP hydrolysis for near- and non-cognate TCs. Additionally, our results demonstrate that translocation inhibition, rather than error induction, is the major cause of cell growth inhibition by viomycin.
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Affiliation(s)
- Mikael Holm
- Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
| | | | - Måns Ehrenberg
- Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
| | - Suparna Sanyal
- Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
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8
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Chan S, Frasch A, Mandava CS, Ch'ng JH, Quintana MDP, Vesterlund M, Ghorbal M, Joannin N, Franzén O, Lopez-Rubio JJ, Barbieri S, Lanzavecchia A, Sanyal S, Wahlgren M. Regulation of PfEMP1-VAR2CSA translation by a Plasmodium translation-enhancing factor. Nat Microbiol 2017; 2:17068. [PMID: 28481333 DOI: 10.1038/nmicrobiol.2017.68] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2017] [Accepted: 03/29/2017] [Indexed: 12/22/2022]
Abstract
Pregnancy-associated malaria commonly involves the binding of Plasmodium falciparum-infected erythrocytes to placental chondroitin sulfate A (CSA) through the PfEMP1-VAR2CSA protein. VAR2CSA is translationally repressed by an upstream open reading frame. In this study, we report that the P. falciparum translation enhancing factor (PTEF) relieves upstream open reading frame repression and thereby facilitates VAR2CSA translation. VAR2CSA protein levels in var2csa-transcribing parasites are dependent on the expression level of PTEF, and the alleviation of upstream open reading frame repression requires the proteolytic processing of PTEF by PfCalpain. Cleavage generates a C-terminal domain that contains a sterile-alpha-motif-like domain. The C-terminal domain is permissive to cytoplasmic shuttling and interacts with ribosomes to facilitate translational derepression of the var2csa coding sequence. It also enhances translation in a heterologous translation system and thus represents the first non-canonical translation enhancing factor to be found in a protozoan. Our results implicate PTEF in regulating placental CSA binding of infected erythrocytes.
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Affiliation(s)
- Sherwin Chan
- Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, Box 280, Nobels väg 16, 171 77 Stockholm, Sweden
| | - Alejandra Frasch
- Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, Box 280, Nobels väg 16, 171 77 Stockholm, Sweden
| | - Chandra Sekhar Mandava
- Department of Cell and Molecular Biology, Uppsala University, Box-596, 751 24 Uppsala, Sweden
| | - Jun-Hong Ch'ng
- Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, Box 280, Nobels väg 16, 171 77 Stockholm, Sweden.,Department of Microbiology, National University of Singapore 117545, Singapore
| | - Maria Del Pilar Quintana
- Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, Box 280, Nobels väg 16, 171 77 Stockholm, Sweden.,Escuela de Medicina y Ciencias de la Salud, Facultad de Ciencias Naturales y Matemáticas, Universidad del Rosario, Calle 12C No. 6-25, Bogotá, Colombia
| | - Mattias Vesterlund
- Cancer Proteomics, Department of Oncology-Pathology, Karolinska Institutet, 17176 Stockholm, Sweden
| | - Mehdi Ghorbal
- University of Montpellier, Faculty of Medicine, Laboratory of Parasitology-Mycology, Montpellier F34090, France.,CNRS - 5290, IRD 224 - University of Montpellier (UMR 'MiVEGEC'), Montpellier, France
| | - Nicolas Joannin
- Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, Box 280, Nobels väg 16, 171 77 Stockholm, Sweden
| | - Oscar Franzén
- Department of Genetics and Genomic Sciences, Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
| | - Jose-Juan Lopez-Rubio
- University of Montpellier, Faculty of Medicine, Laboratory of Parasitology-Mycology, Montpellier F34090, France.,CNRS - 5290, IRD 224 - University of Montpellier (UMR 'MiVEGEC'), Montpellier, France
| | - Sonia Barbieri
- Institute for Research in Biomedicine, Università della Svizzera italiana, Bellinzona 6500, Switzerland
| | - Antonio Lanzavecchia
- Institute for Research in Biomedicine, Università della Svizzera italiana, Bellinzona 6500, Switzerland.,Institute of Microbiology, ETH Zurich, Zurich 8093, Switzerland
| | - Suparna Sanyal
- Department of Cell and Molecular Biology, Uppsala University, Box-596, 751 24 Uppsala, Sweden
| | - Mats Wahlgren
- Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, Box 280, Nobels väg 16, 171 77 Stockholm, Sweden
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9
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Degiacomi G, Personne Y, Mondésert G, Ge X, Mandava CS, Hartkoorn RC, Boldrin F, Goel P, Peisker K, Benjak A, Barrio MB, Ventura M, Brown AC, Leblanc V, Bauer A, Sanyal S, Cole ST, Lagrange S, Parish T, Manganelli R. Micrococcin P1 - A bactericidal thiopeptide active against Mycobacterium tuberculosis. Tuberculosis (Edinb) 2016; 100:95-101. [PMID: 27553416 DOI: 10.1016/j.tube.2016.07.011] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2016] [Revised: 07/13/2016] [Accepted: 07/20/2016] [Indexed: 10/21/2022]
Abstract
The lack of proper treatment for serious infectious diseases due to the emergence of multidrug resistance reinforces the need for the discovery of novel antibiotics. This is particularly true for tuberculosis (TB) for which 3.7% of new cases and 20% of previously treated cases are estimated to be caused by multi-drug resistant strains. In addition, in the case of TB, which claimed 1.5 million lives in 2014, the treatment of the least complicated, drug sensitive cases is lengthy and disagreeable. Therefore, new drugs with novel targets are urgently needed to control resistant Mycobacterium tuberculosis strains. In this manuscript we report the characterization of the thiopeptide micrococcin P1 as an anti-tubercular agent. Our biochemical experiments show that this antibiotic inhibits the elongation step of protein synthesis in mycobacteria. We have further identified micrococcin resistant mutations in the ribosomal protein L11 (RplK); the mutations were located in the proline loop at the N-terminus. Reintroduction of the mutations into a clean genetic background, confirmed that they conferred resistance, while introduction of the wild type RplK allele into resistant strains re-established sensitivity. We also identified a mutation in the 23S rRNA gene. These data, in good agreement with previous structural studies suggest that also in M. tuberculosis micrococcin P1 functions by binding to the cleft between the 23S rRNA and the L11 protein loop, thus interfering with the binding of elongation factors Tu and G (EF-Tu and EF-G) and inhibiting protein translocation.
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Affiliation(s)
- Giulia Degiacomi
- Department of Molecular Medicine, University of Padova, Padova, Italy
| | - Yoann Personne
- Queen Mary University of London, London E1 2AD, United Kingdom
| | | | - Xueliang Ge
- Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
| | | | - Ruben C Hartkoorn
- Ecole Polytechnique Fédérale de Lausanne, Global Health Institute, Lausanne, Switzerland
| | - Francesca Boldrin
- Department of Molecular Medicine, University of Padova, Padova, Italy
| | - Pavitra Goel
- Queen Mary University of London, London E1 2AD, United Kingdom
| | - Kristin Peisker
- Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
| | - Andrej Benjak
- Ecole Polytechnique Fédérale de Lausanne, Global Health Institute, Lausanne, Switzerland
| | | | - Marcello Ventura
- Department of Molecular Medicine, University of Padova, Padova, Italy
| | - Amanda C Brown
- Queen Mary University of London, London E1 2AD, United Kingdom
| | | | - Armin Bauer
- Sanofi-Aventis R&D, Drug Disposition, 69367 Lyon, France
| | - Suparna Sanyal
- Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
| | - Stewart T Cole
- Ecole Polytechnique Fédérale de Lausanne, Global Health Institute, Lausanne, Switzerland
| | | | - Tanya Parish
- Queen Mary University of London, London E1 2AD, United Kingdom
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10
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Zhang Y, Mandava CS, Cao W, Li X, Zhang D, Li N, Zhang Y, Zhang X, Qin Y, Mi K, Lei J, Sanyal S, Gao N. HflX is a ribosome-splitting factor rescuing stalled ribosomes under stress conditions. Nat Struct Mol Biol 2015; 22:906-13. [PMID: 26458047 DOI: 10.1038/nsmb.3103] [Citation(s) in RCA: 66] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2015] [Accepted: 09/04/2015] [Indexed: 12/16/2022]
Abstract
Adverse cellular conditions often lead to nonproductive translational stalling and arrest of ribosomes on mRNAs. Here, we used fast kinetics and cryo-EM to characterize Escherichia coli HflX, a GTPase with unknown function. Our data reveal that HflX is a heat shock-induced ribosome-splitting factor capable of dissociating vacant as well as mRNA-associated ribosomes with deacylated tRNA in the peptidyl site. Structural data demonstrate that the N-terminal effector domain of HflX binds to the peptidyl transferase center in a strikingly similar manner as that of the class I release factors and induces dramatic conformational changes in central intersubunit bridges, thus promoting subunit dissociation. Accordingly, loss of HflX results in an increase in stalled ribosomes upon heat shock. These results suggest a primary role of HflX in rescuing translationally arrested ribosomes under stress conditions.
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Affiliation(s)
- Yanqing Zhang
- Ministry of Education Key Laboratory of Protein Sciences, Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing, China
| | | | - Wei Cao
- Ministry of Education Key Laboratory of Protein Sciences, Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing, China
| | - Xiaojing Li
- Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Dejiu Zhang
- Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Ningning Li
- Ministry of Education Key Laboratory of Protein Sciences, Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing, China
| | - Yixiao Zhang
- Ministry of Education Key Laboratory of Protein Sciences, Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing, China
| | - Xiaoxiao Zhang
- Ministry of Education Key Laboratory of Protein Sciences, Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing, China
| | - Yan Qin
- Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Kaixia Mi
- Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Jianlin Lei
- Ministry of Education Key Laboratory of Protein Sciences, Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing, China
| | - Suparna Sanyal
- Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
| | - Ning Gao
- Ministry of Education Key Laboratory of Protein Sciences, Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing, China
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11
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Koripella RK, Holm M, Dourado D, Mandava CS, Flores S, Sanyal S. A conserved histidine in switch-II of EF-G moderates release of inorganic phosphate. Sci Rep 2015; 5:12970. [PMID: 26264741 PMCID: PMC4532990 DOI: 10.1038/srep12970] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2015] [Accepted: 07/13/2015] [Indexed: 01/13/2023] Open
Abstract
Elongation factor G (EF-G), a translational GTPase responsible for tRNA-mRNA translocation possesses a conserved histidine (H91 in Escherichia coli) at the apex of switch-II, which has been implicated in GTPase activation and GTP hydrolysis. While H91A, H91R and H91E mutants showed different degrees of defect in ribosome associated GTP hydrolysis, H91Q behaved like the WT. However, all these mutants, including H91Q, are much more defective in inorganic phosphate (Pi) release, thereby suggesting that H91 facilitates Pi release. In crystal structures of the ribosome bound EF-G•GTP a tight coupling between H91 and the γ-phosphate of GTP can be seen. Following GTP hydrolysis, H91 flips ~140° in the opposite direction, probably with Pi still coupled to it. This, we suggest, promotes Pi to detach from GDP and reach the inter-domain space of EF-G, which constitutes an exit path for the Pi. Molecular dynamics simulations are consistent with this hypothesis and demonstrate a vital role of an Mg2+ ion in the process.
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Affiliation(s)
- Ravi Kiran Koripella
- Department of Cell and Molecular Biology, Uppsala University, Box-596, BMC, 75124, Uppsala, Sweden
| | - Mikael Holm
- Department of Cell and Molecular Biology, Uppsala University, Box-596, BMC, 75124, Uppsala, Sweden
| | - Daniel Dourado
- Department of Cell and Molecular Biology, Uppsala University, Box-596, BMC, 75124, Uppsala, Sweden
| | - Chandra Sekhar Mandava
- Department of Cell and Molecular Biology, Uppsala University, Box-596, BMC, 75124, Uppsala, Sweden
| | - Samuel Flores
- Department of Cell and Molecular Biology, Uppsala University, Box-596, BMC, 75124, Uppsala, Sweden
| | - Suparna Sanyal
- Department of Cell and Molecular Biology, Uppsala University, Box-596, BMC, 75124, Uppsala, Sweden
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Feng B, Mandava CS, Guo Q, Wang J, Cao W, Li N, Zhang Y, Zhang Y, Wang Z, Wu J, Sanyal S, Lei J, Gao N. Structural and functional insights into the mode of action of a universally conserved Obg GTPase. PLoS Biol 2014; 12:e1001866. [PMID: 24844575 PMCID: PMC4028186 DOI: 10.1371/journal.pbio.1001866] [Citation(s) in RCA: 90] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2013] [Accepted: 04/10/2014] [Indexed: 01/13/2023] Open
Abstract
Kinetics and cryo-electronmicroscopy data provide insights into GTPase ObgE’s role as a ribosome anti-association factor that is modulated by nutrient availability, coupling growth control to ribosome biosynthesis and protein translation. Obg proteins are a family of P-loop GTPases, conserved from bacteria to human. The Obg protein in Escherichia coli (ObgE) has been implicated in many diverse cellular functions, with proposed molecular roles in two global processes, ribosome assembly and stringent response. Here, using pre-steady state fast kinetics we demonstrate that ObgE is an anti-association factor, which prevents ribosomal subunit association and downstream steps in translation by binding to the 50S subunit. ObgE is a ribosome dependent GTPase; however, upon binding to guanosine tetraphosphate (ppGpp), the global regulator of stringent response, ObgE exhibits an enhanced interaction with the 50S subunit, resulting in increased equilibrium dissociation of the 70S ribosome into subunits. Furthermore, our cryo-electron microscopy (cryo-EM) structure of the 50S·ObgE·GMPPNP complex indicates that the evolutionarily conserved N-terminal domain (NTD) of ObgE is a tRNA structural mimic, with specific interactions with peptidyl-transferase center, displaying a marked resemblance to Class I release factors. These structural data might define ObgE as a specialized translation factor related to stress responses, and provide a framework towards future elucidation of functional interplay between ObgE and ribosome-associated (p)ppGpp regulators. Together with published data, our results suggest that ObgE might act as a checkpoint in final stages of the 50S subunit assembly under normal growth conditions. And more importantly, ObgE, as a (p)ppGpp effector, might also have a regulatory role in the production of the 50S subunit and its participation in translation under certain stressed conditions. Thus, our findings might have uncovered an under-recognized mechanism of translation control by environmental cues. GTPases commonly act as molecular switches in biological systems. By oscillating between two conformational states, depending on the type of guanine nucleotide bound (GTP or GDP), GTPases are essential regulators of many aspects of cell biology. Additional levels of regulation can be acquired through the synthesis of other guanine nucleotide derivatives that target GTPases; for instance, when nutrients are limited, bacterial cells produce guanine tetraphosphate/pentaphosphate—(p)ppGpp—as part of the “stringent response” to adjust the balance between growth and survival. ObgE is a GTPase with many reported cellular functions that include ribosome biogenesis, but none of its functions is understood at the molecular level. Here we characterize, both biochemically and structurally, the binding of ObgE to its cellular partner, the 50S ribosomal subunit. Our results show that ObgE is an anti-association factor, which binds to the 50S subunit to block the formation of the 70S ribosome, thereby inhibiting the initiation of translation. Furthermore, the binding and anti-association activities of ObgE are regulated by guanine nucleotides, as well as by (p)ppGpp. We thus propose that ObgE is a checkpoint protein in the assembly of the 50S subunit, which senses the cellular energy stress via levels of (p)ppGpp and links ribosome assembly to other global growth control pathways.
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Affiliation(s)
- Boya Feng
- Ministry of Education Key Laboratory of Protein Sciences, Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing, China
| | | | - Qiang Guo
- Ministry of Education Key Laboratory of Protein Sciences, Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing, China
| | - Jie Wang
- Ministry of Education Key Laboratory of Protein Sciences, Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing, China
- Tsinghua-Peking Joint Center for Life Sciences, Tsinghua University, Beijing, China
| | - Wei Cao
- Ministry of Education Key Laboratory of Protein Sciences, Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing, China
| | - Ningning Li
- Ministry of Education Key Laboratory of Protein Sciences, Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing, China
| | - Yixiao Zhang
- Ministry of Education Key Laboratory of Protein Sciences, Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing, China
| | - Yanqing Zhang
- Ministry of Education Key Laboratory of Protein Sciences, Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing, China
| | - Zhixin Wang
- Ministry of Education Key Laboratory of Protein Sciences, Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing, China
| | - Jiawei Wu
- Ministry of Education Key Laboratory of Protein Sciences, Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing, China
- Tsinghua-Peking Joint Center for Life Sciences, Tsinghua University, Beijing, China
| | - Suparna Sanyal
- Department of Cell and Molecular Biology, Uppsala University, BMC, Uppsala, Sweden
- * E-mail: (NG); (JL); (SS)
| | - Jianlin Lei
- Ministry of Education Key Laboratory of Protein Sciences, Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing, China
- * E-mail: (NG); (JL); (SS)
| | - Ning Gao
- Ministry of Education Key Laboratory of Protein Sciences, Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing, China
- * E-mail: (NG); (JL); (SS)
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Guo X, Peisker K, Bäckbro K, Chen Y, Koripella RK, Mandava CS, Sanyal S, Selmer M. Structure and function of FusB: an elongation factor G-binding fusidic acid resistance protein active in ribosomal translocation and recycling. Open Biol 2013; 2:120016. [PMID: 22645663 PMCID: PMC3352095 DOI: 10.1098/rsob.120016] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2012] [Accepted: 02/23/2012] [Indexed: 11/12/2022] Open
Abstract
Fusidic acid (FA) is a bacteriostatic antibiotic that locks elongation factor G (EF-G) to the ribosome after GTP hydrolysis during elongation and ribosome recycling. The plasmid pUB101-encoded protein FusB causes FA resistance in clinical isolates of Staphylococcus aureus through an interaction with EF-G. Here, we report 1.6 and 2.3 Å crystal structures of FusB. We show that FusB is a two-domain protein lacking homology to known structures, where the N-terminal domain is a four-helix bundle and the C-terminal domain has an alpha/beta fold containing a C4 treble clef zinc finger motif and two loop regions with conserved basic residues. Using hybrid constructs between S. aureus EF-G that binds to FusB and Escherichia coli EF-G that does not, we show that the sequence determinants for FusB recognition reside in domain IV and involve the C-terminal helix of S. aureus EF-G. Further, using kinetic assays in a reconstituted translation system, we demonstrate that FusB can rescue FA inhibition of tRNA translocation as well as ribosome recycling. We propose that FusB rescues S. aureus from FA inhibition by preventing formation or facilitating dissociation of the FA-locked EF-G–ribosome complex.
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Affiliation(s)
- Xiaohu Guo
- Department of Cell and Molecular Biology, BMC, P.O. Box 596, SE 751 24, Uppsala, Sweden
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Mandava CS, Peisker K, Ederth J, Kumar R, Ge X, Szaflarski W, Sanyal S. Bacterial ribosome requires multiple L12 dimers for efficient initiation and elongation of protein synthesis involving IF2 and EF-G. Nucleic Acids Res 2011; 40:2054-64. [PMID: 22102582 PMCID: PMC3299993 DOI: 10.1093/nar/gkr1031] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The ribosomal stalk in bacteria is composed of four or six copies of L12 proteins arranged in dimers that bind to the adjacent sites on protein L10, spanning 10 amino acids each from the L10 C-terminus. To study why multiple L12 dimers are required on the ribosome, we created a chromosomally engineered Escherichia coli strain, JE105, in which the peripheral L12 dimer binding site was deleted. Thus JE105 harbors ribosomes with only a single L12 dimer. Compared to MG1655, the parental strain with two L12 dimers, JE105 showed significant growth defect suggesting suboptimal function of the ribosomes with one L12 dimer. When tested in a cell-free reconstituted transcription–translation assay the synthesis of a full-length protein, firefly luciferase, was notably slower with JE105 70S ribosomes and 50S subunits. Further, in vitro analysis by fast kinetics revealed that single L12 dimer ribosomes from JE105 are defective in two major steps of translation, namely initiation and elongation involving translational GTPases IF2 and EF-G. Varying number of L12 dimers on the ribosome can be a mechanism in bacteria for modulating the rate of translation in response to growth condition.
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Affiliation(s)
- Chandra Sekhar Mandava
- Department of Cell and Molecular Biology, Uppsala University, BMC, Box-596, SE-751 24 Uppsala, Sweden
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15
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Tobin C, Mandava CS, Ehrenberg M, Andersson DI, Sanyal S. Ribosomes lacking protein S20 are defective in mRNA binding and subunit association. J Mol Biol 2010; 397:767-76. [PMID: 20149799 DOI: 10.1016/j.jmb.2010.02.004] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2009] [Revised: 01/29/2010] [Accepted: 02/02/2010] [Indexed: 10/19/2022]
Abstract
The functional significance of ribosomal proteins is still relatively unclear. Here, we examined the role of small subunit protein S20 in translation using both in vivo and in vitro techniques. By means of lambda red recombineering, the rpsT gene, encoding S20, was removed from the chromosome of Salmonella enterica var. Typhimurium LT2 to produce a DeltaS20 strain that grew markedly slower than the wild type while maintaining a wild-type rate of peptide elongation. Removal of S20 conferred a significant reduction in growth rate that was eliminated upon expression of the rpsT gene on a high-copy-number plasmid. The in vitro phenotype of mutant ribosomes was investigated using a translation system composed of highly active, purified components from Escherichia coli. Deletion of S20 conferred two types of initiation defects to the 30S subunit: (i) a significant reduction in the rate of mRNA binding and (ii) a drastic decrease in the yield of 70S complexes caused by an impairment in association with the 50S subunit. Both of these impairments were partially relieved by an extended incubation time with mRNA, fMet-tRNA(fMet), and initiation factors, indicating that absence of S20 disturbs the structural integrity of 30S subunits. Considering the topographical location of S20 in complete 30S subunits, the molecular mechanism by which it affects mRNA binding and subunit docking is not entirely obvious. We speculate that its interaction with helix 44 of the 16S ribosomal RNA is crucial for optimal ribosome function.
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Affiliation(s)
- Christina Tobin
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
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Ederth J, Mandava CS, Dasgupta S, Sanyal S. A single-step method for purification of active His-tagged ribosomes from a genetically engineered Escherichia coli. Nucleic Acids Res 2008; 37:e15. [PMID: 19074194 PMCID: PMC2632923 DOI: 10.1093/nar/gkn992] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
With the rapid development of the ribosome field in recent years a quick, simple and high-throughput method for purification of the bacterial ribosome is in demand. We have designed a new strain of Escherichia coli (JE28) by an in-frame fusion of a nucleotide sequence encoding a hexa-histidine affinity tag at the 3′-end of the single copy rplL gene (encoding the ribosomal protein L12) at the chromosomal site of the wild-type strain MG1655. As a result, JE28 produces a homogeneous population of ribosomes (His)6-tagged at the C-termini of all four L12 proteins. Furthermore, we have developed a single-step, high-throughput method for purification of tetra-(His)6-tagged 70S ribosomes from this strain using affinity chromatography. These ribosomes, when compared with the conventionally purified ones in sucrose gradient centrifugation, 2D-gel, dipeptide formation and a full-length protein synthesis assay showed higher yield and activity. We further describe how this method can be adapted for purification of ribosomal subunits and mutant ribosomes. These methodologies could, in principle, also be used to purify any functional multimeric complex from the bacterial cell.
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Affiliation(s)
- Josefine Ederth
- Department of Cell and Molecular Biology, Uppsala University, S-751 24 Uppsala, Sweden
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