1
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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2
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Leroy EC, Perry TN, Renault TT, Innis CA. Tetracenomycin X sequesters peptidyl-tRNA during translation of QK motifs. Nat Chem Biol 2023; 19:1091-1096. [PMID: 37322159 DOI: 10.1038/s41589-023-01343-0] [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] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Accepted: 04/18/2023] [Indexed: 06/17/2023]
Abstract
As antimicrobial resistance threatens our ability to treat common bacterial infections, new antibiotics with limited cross-resistance are urgently needed. In this regard, natural products that target the bacterial ribosome have the potential to be developed into potent drugs through structure-guided design, provided their mechanisms of action are well understood. Here we use inverse toeprinting coupled to next-generation sequencing to show that the aromatic polyketide tetracenomycin X primarily inhibits peptide bond formation between an incoming aminoacyl-tRNA and a terminal Gln-Lys (QK) motif in the nascent polypeptide. Using cryogenic electron microscopy, we reveal that translation inhibition at QK motifs occurs via an unusual mechanism involving sequestration of the 3' adenosine of peptidyl-tRNALys in the drug-occupied nascent polypeptide exit tunnel of the ribosome. Our study provides mechanistic insights into the mode of action of tetracenomycin X on the bacterial ribosome and suggests a path forward for the development of novel aromatic polyketide antibiotics.
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Affiliation(s)
- 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, Pessac, France
- Human Technopole, Milan, Italy
| | - Thomas N Perry
- 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, Pessac, France
- Human Technopole, Milan, Italy
| | - Thibaud T Renault
- 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, Pessac, France.
| | - 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, Pessac, France.
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3
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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4
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Manteca A, Gadea A, Van Assche D, Cossard P, Gillard-Bocquet M, Beneyton T, Innis CA, Baret JC. Directed Evolution in Drops: Molecular Aspects and Applications. ACS Synth Biol 2021; 10:2772-2783. [PMID: 34677942 PMCID: PMC8609573 DOI: 10.1021/acssynbio.1c00313] [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] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Indexed: 11/29/2022]
Abstract
The process of optimizing the properties of biological molecules is paramount for many industrial and medical applications. Directed evolution is a powerful technique for modifying and improving biomolecules such as proteins or nucleic acids (DNA or RNA). Mimicking the mechanism of natural evolution, one can enhance a desired property by applying a suitable selection pressure and sorting improved variants. Droplet-based microfluidic systems offer a high-throughput solution to this approach by helping to overcome the limiting screening steps and allowing the analysis of variants within increasingly complex libraries. Here, we review cases where successful evolution of biomolecules was achieved using droplet-based microfluidics, focusing on the molecular processes involved and the incorporation of microfluidics to the workflow. We highlight the advantages and limitations of these microfluidic systems compared to low-throughput methods and show how the integration of these systems into directed evolution workflows can open new avenues to discover or improve biomolecules according to user-defined conditions.
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Affiliation(s)
- Aitor Manteca
- Univ.
Bordeaux, Institut National de la Santé et de la Recherche
Médicale, Centre National de la Recherche Scientifique, ARNA,
U1212, UMR 5320, Institut Européen de Chimie et Biologie, F-33600 Pessac, France
| | - Alejandra Gadea
- Univ.
Bordeaux, CNRS, CRPP, UMR 5031, F-33610, Pessac, France
| | | | - Pauline Cossard
- Univ.
Bordeaux, Institut National de la Santé et de la Recherche
Médicale, Centre National de la Recherche Scientifique, ARNA,
U1212, UMR 5320, Institut Européen de Chimie et Biologie, F-33600 Pessac, France
| | - Mélanie Gillard-Bocquet
- Univ.
Bordeaux, Institut National de la Santé et de la Recherche
Médicale, Centre National de la Recherche Scientifique, ARNA,
U1212, UMR 5320, Institut Européen de Chimie et Biologie, F-33600 Pessac, France
| | - Thomas Beneyton
- Univ.
Bordeaux, CNRS, CRPP, UMR 5031, F-33610, Pessac, France
| | - C. Axel Innis
- Univ.
Bordeaux, Institut National de la Santé et de la Recherche
Médicale, Centre National de la Recherche Scientifique, ARNA,
U1212, UMR 5320, Institut Européen de Chimie et Biologie, F-33600 Pessac, France
| | - Jean-Christophe Baret
- Univ.
Bordeaux, CNRS, CRPP, UMR 5031, F-33610, Pessac, France
- Institut
Universitaire de France, F-75231 Paris, France
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5
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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: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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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6
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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7
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Cytryńska M, Rahnamaeian M, Zdybicka-Barabas A, Dobslaff K, Züchner T, Sacheau G, Innis CA, Vilcinskas A. Proline-Rich Antimicrobial Peptides in Medicinal Maggots of Lucilia sericata Interact With Bacterial DnaK But Do Not Inhibit Protein Synthesis. Front Pharmacol 2020; 11:532. [PMID: 32390853 PMCID: PMC7194015 DOI: 10.3389/fphar.2020.00532] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [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: 11/11/2019] [Accepted: 04/06/2020] [Indexed: 11/13/2022] Open
Abstract
In the search for new antibiotics to combat multidrug-resistant microbes, insects offer a rich source of novel anti-infectives, including a remarkably diverse array of antimicrobial peptides (AMPs) with broad activity against a wide range of species. Larvae of the common green bottle fly Lucilia sericata are used for maggot debridement therapy, and their effectiveness in part reflects the large panel of AMPs they secrete into the wound. To investigate the activity of these peptides in more detail, we selected two structurally different proline rich peptides (Lser-PRP2 and Lser-PRP3) in addition to the α-helical peptide Lser-stomoxyn. We investigated the mechanism of anti-Escherichia coli action of the PRPs in vitro and found that neither of them interfered with protein synthesis but both were able to bind the bacterial chaperone DnaK and are therefore likely to inhibit protein folding. However, unlike Lser-stomoxyn that permeabilized the bacterial membrane by 1% at the low concentration (0.25 µM) neither of the PRPs alone was able to permeabilize E. coli membrane. In the presence of this Lser-stomoxyn concentration significant increase in anti-E. coli activity of Lser-PRP2 was observed, indicating that this peptide needs specific membrane permeabilizing agents to exert its antibacterial activity. We then examined the AMPs-treated bacterial surface and observed detrimental structural changes in the bacterial cell envelope in response to combined AMPs. The functional analysis of insect AMPs will help select optimal combinations for targeted antimicrobial therapy.
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Affiliation(s)
- Małgorzata Cytryńska
- Department of Immunobiology, Institute of Biological Sciences, Maria Curie-Sklodowska University, Lublin, Poland
| | - Mohammad Rahnamaeian
- Department of Bioresources, Fraunhofer Institute for Molecular Biology and Applied Ecology, Giessen, Germany
| | - Agnieszka Zdybicka-Barabas
- Department of Immunobiology, Institute of Biological Sciences, Maria Curie-Sklodowska University, Lublin, Poland
| | - Kristin Dobslaff
- Institute of Bioanalyticappll Chemistry, Faculty of Chemistry and Mineralogy and Center of Biotechnology and Biomedicine, University of Leipzig, Leipzig, Germany
| | - Thole Züchner
- Department of Bioanalytics and Laboratory automation, Faculty of Life Sciences, Albstadt-Sigmaringen University, Sigmaringen, Germany
| | - Guénaël Sacheau
- ARNA Laboratory, Inserm U1212, CNRS UMR 5320, Institut Européen de Chimie et Biologie, University of Bordeaux, Pessac, France
| | - C Axel Innis
- ARNA Laboratory, Inserm U1212, CNRS UMR 5320, Institut Européen de Chimie et Biologie, University of Bordeaux, Pessac, France
| | - Andreas Vilcinskas
- Department of Bioresources, Fraunhofer Institute for Molecular Biology and Applied Ecology, Giessen, Germany.,Institute for Insect Biotechnology, Justus-Liebig-University of Giessen, Giessen, Germany
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8
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Del Valle AH, Seip B, Cervera-Marzal I, Sacheau G, Seefeldt AC, Innis CA. Publisher Correction: Ornithine capture by a translating ribosome controls bacterial polyamine synthesis. Nat Microbiol 2020; 5:653-654. [PMID: 32218511 DOI: 10.1038/s41564-020-0708-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
An amendment to this paper has been published and can be accessed via a link at the top of the paper.
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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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9
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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10
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Abstract
The threat of bacteria resistant to multiple antibiotics poses a major public health problem requiring immediate and coordinated action worldwide. While infectious pathogens have become increasingly resistant to commercially available drugs, antibiotic discovery programs in major pharmaceutical companies have produced no new antibiotic scaffolds in 40 years. As a result, new strategies must be sought to obtain a steady supply of novel scaffolds capable of countering the spread of resistance. The bacterial ribosome is a major target for antimicrobials and is inhibited by more than half of the antibiotics used today. Recent studies showing that the ribosome is a target for several classes of ribosomally synthesized antimicrobial peptides point to ribosome-targeting peptides as a promising source of antibiotic scaffolds. In this Perspective, we revisit the current paradigm of antibiotic discovery by proposing that the bacterial ribosome can be used both as a target and as a tool for the production and selection of peptide-based antimicrobials. Turning the ribosome into a high-throughput platform for the directed evolution of peptide-based antibiotics could be achieved in different ways. One possibility would be to use a combination of state-of-the-art microfluidics and genetic reprogramming techniques, which we will review briefly. If it is successful, this strategy has the potential to produce new classes of antibiotics for treating multi-drug-resistant pathogens.
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Affiliation(s)
- Justine Charon
- 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), Pessac 33607, France
| | - Aitor Manteca
- 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), Pessac 33607, 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), Pessac 33607, France
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11
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Seip B, Sacheau G, Dupuy D, Innis CA. Ribosomal stalling landscapes revealed by high-throughput inverse toeprinting of mRNA libraries. Life Sci Alliance 2018; 1:e201800148. [PMID: 30456383 PMCID: PMC6238534 DOI: 10.26508/lsa.201800148] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [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] [Received: 08/07/2018] [Revised: 09/25/2018] [Accepted: 09/27/2018] [Indexed: 11/24/2022] Open
Abstract
High-throughput inverse toeprinting identifies peptide-encoding transcripts that induce ribosome stalling and allows the systematic analysis of sequence-dependent translational events. Although it is known that the amino acid sequence of a nascent polypeptide can impact its rate of translation, dedicated tools to systematically investigate this process are lacking. Here, we present high-throughput inverse toeprinting, a method to identify peptide-encoding transcripts that induce ribosomal stalling in vitro. Unlike ribosome profiling, inverse toeprinting protects the entire coding region upstream of a stalled ribosome, making it possible to work with random or focused transcript libraries that efficiently sample the sequence space. We used inverse toeprinting to characterize the stalling landscapes of free and drug-bound Escherichia coli ribosomes, obtaining a comprehensive list of arrest motifs that were validated in vivo, along with a quantitative measure of their pause strength. Thanks to the modest sequencing depth and small amounts of material required, inverse toeprinting provides a highly scalable and versatile tool to study sequence-dependent translational processes.
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Affiliation(s)
- Britta Seip
- Institut Européen de Chimie et Biologie, Université de Bordeaux, Institut National de la Santé et de la Recherche Médicale and Centre National de la Recherche Scientifique, Pessac, France
| | - Guénaël Sacheau
- Institut Européen de Chimie et Biologie, Université de Bordeaux, Institut National de la Santé et de la Recherche Médicale and Centre National de la Recherche Scientifique, Pessac, France
| | - Denis Dupuy
- Institut Européen de Chimie et Biologie, Université de Bordeaux, Institut National de la Santé et de la Recherche Médicale and Centre National de la Recherche Scientifique, Pessac, France
| | - C Axel Innis
- Institut Européen de Chimie et Biologie, Université de Bordeaux, Institut National de la Santé et de la Recherche Médicale and Centre National de la Recherche Scientifique, Pessac, France
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12
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Mardirossian M, Pérébaskine N, Benincasa M, Gambato S, Hofmann S, Huter P, Müller C, Hilpert K, Innis CA, Tossi A, Wilson DN. The Dolphin Proline-Rich Antimicrobial Peptide Tur1A Inhibits Protein Synthesis by Targeting the Bacterial Ribosome. Cell Chem Biol 2018; 25:530-539.e7. [PMID: 29526712 PMCID: PMC6219704 DOI: 10.1016/j.chembiol.2018.02.004] [Citation(s) in RCA: 75] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2017] [Revised: 01/08/2018] [Accepted: 02/05/2018] [Indexed: 12/22/2022]
Abstract
Proline-rich antimicrobial peptides (PrAMPs) internalize into susceptible bacteria using specific transporters and interfere with protein synthesis and folding. To date, mammalian PrAMPs have so far been identified only in artiodactyls. Since cetaceans are co-phyletic with artiodactyls, we mined the genome of the bottlenose dolphin Tursiops truncatus, leading to the identification of two PrAMPs, Tur1A and Tur1B. Tur1A, which is orthologous to the bovine PrAMP Bac7, is internalized into Escherichia coli, without damaging the membranes, using the inner membrane transporters SbmA and YjiL/MdM. Furthermore, like Bac7, Tur1A also inhibits bacterial protein synthesis by binding to the ribosome and blocking the transition from the initiation to the elongation phase. By contrast, Tur1B is a poor inhibitor of protein synthesis and may utilize another mechanism of action. An X-ray structure of Tur1A bound within the ribosomal exit tunnel provides a basis to develop these peptides as novel antimicrobial agents.
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Affiliation(s)
- Mario Mardirossian
- Gene Center, Department for Biochemistry and Center for Integrated Protein Sciences, Munich (CiPSM), University of Munich, 81377 Munich, Germany
| | - Natacha Pérébaskine
- ARNA Laboratory, University of Bordeaux, Inserm U1212, CNRS UMR 5320, IECB, 33607 Pessac, France
| | - Monica Benincasa
- Antimicrobial Peptides Laboratory, Department of Life Sciences, University of Trieste, 34127 Trieste, Italy
| | - Stefano Gambato
- Antimicrobial Peptides Laboratory, Department of Life Sciences, University of Trieste, 34127 Trieste, Italy
| | - Sven Hofmann
- Institute of Infection and Immunity, St George's, University of London, SW17 0RE London, UK
| | - Paul Huter
- Gene Center, Department for Biochemistry and Center for Integrated Protein Sciences, Munich (CiPSM), University of Munich, 81377 Munich, Germany; Institute for Biochemistry and Molecular Biology, University of Hamburg, Martin-Luther-King-Platz 6, 20146 Hamburg, Germany
| | - Claudia Müller
- Gene Center, Department for Biochemistry and Center for Integrated Protein Sciences, Munich (CiPSM), University of Munich, 81377 Munich, Germany; Institute for Biochemistry and Molecular Biology, University of Hamburg, Martin-Luther-King-Platz 6, 20146 Hamburg, Germany
| | - Kai Hilpert
- Institute of Infection and Immunity, St George's, University of London, SW17 0RE London, UK
| | - C Axel Innis
- ARNA Laboratory, University of Bordeaux, Inserm U1212, CNRS UMR 5320, IECB, 33607 Pessac, France
| | - Alessandro Tossi
- Antimicrobial Peptides Laboratory, Department of Life Sciences, University of Trieste, 34127 Trieste, Italy
| | - Daniel N Wilson
- Gene Center, Department for Biochemistry and Center for Integrated Protein Sciences, Munich (CiPSM), University of Munich, 81377 Munich, Germany; Institute for Biochemistry and Molecular Biology, University of Hamburg, Martin-Luther-King-Platz 6, 20146 Hamburg, Germany.
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13
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Affiliation(s)
- Daniel N Wilson
- Institut Européen de Chimie et Biologie, INSERM U869, Pessac, France.,Université de Bordeaux, Talence, France
| | - Gilles Guichard
- Institut Européen de Chimie et Biologie, INSERM U869, Pessac, France.,Université de Bordeaux, Talence, France
| | - C Axel Innis
- Institut Européen de Chimie et Biologie, INSERM U869, Pessac, France.,Université de Bordeaux, Talence, France
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14
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Graf M, Mardirossian M, Nguyen F, Seefeldt AC, Guichard G, Scocchi M, Innis CA, Wilson DN. Proline-rich antimicrobial peptides targeting protein synthesis. Nat Prod Rep 2017; 34:702-711. [DOI: 10.1039/c7np00020k] [Citation(s) in RCA: 97] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Proline-rich antimicrobial peptides (PrAMPs) bind within the exit tunnel of the ribosome and inhibit translation elongation. Structures of ribosome-bound PrAMPs reveal the interactions with ribosomal components and could pave the way for the development of novel peptide-based antimicrobial agents.
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Affiliation(s)
- Michael Graf
- Gene Center
- Department for Biochemistry and Center for Integrated Protein Sciences Munich (CiPS-M)
- University of Munich
- 81377 Munich
- Germany
| | - Mario Mardirossian
- Gene Center
- Department for Biochemistry and Center for Integrated Protein Sciences Munich (CiPS-M)
- University of Munich
- 81377 Munich
- Germany
| | - Fabian Nguyen
- Gene Center
- Department for Biochemistry and Center for Integrated Protein Sciences Munich (CiPS-M)
- University of Munich
- 81377 Munich
- Germany
| | | | - Gilles Guichard
- Université de Bordeaux
- CNRS
- Institut Polytechnique de Bordeaux
- UMR 5248
- Institut de Chimie et Biologie des Membranes et des Nano-objets (CBMN)
| | - Marco Scocchi
- Department of Life Sciences
- University of Trieste
- Trieste
- Italy
| | - C. Axel Innis
- Univ. Bordeaux
- ARNA Laboratory
- Inserm U1212
- CNRS UMR 5320
- IECB
| | - Daniel N. Wilson
- Gene Center
- Department for Biochemistry and Center for Integrated Protein Sciences Munich (CiPS-M)
- University of Munich
- 81377 Munich
- Germany
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15
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Arenz S, Bock LV, Graf M, Innis CA, Beckmann R, Grubmüller H, Vaiana AC, Wilson DN. A combined cryo-EM and molecular dynamics approach reveals the mechanism of ErmBL-mediated translation arrest. Nat Commun 2016; 7:12026. [PMID: 27380950 PMCID: PMC4935803 DOI: 10.1038/ncomms12026] [Citation(s) in RCA: 85] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2016] [Accepted: 05/17/2016] [Indexed: 12/30/2022] Open
Abstract
Nascent polypeptides can induce ribosome stalling, regulating downstream genes. Stalling of ErmBL peptide translation in the presence of the macrolide antibiotic erythromycin leads to resistance in Streptococcus sanguis. To reveal this stalling mechanism we obtained 3.6-Å-resolution cryo-EM structures of ErmBL-stalled ribosomes with erythromycin. The nascent peptide adopts an unusual conformation with the C-terminal Asp10 side chain in a previously unseen rotated position. Together with molecular dynamics simulations, the structures indicate that peptide-bond formation is inhibited by displacement of the peptidyl-tRNA A76 ribose from its canonical position, and by non-productive interactions of the A-tRNA Lys11 side chain with the A-site crevice. These two effects combine to perturb peptide-bond formation by increasing the distance between the attacking Lys11 amine and the Asp10 carbonyl carbon. The interplay between drug, peptide and ribosome uncovered here also provides insight into the fundamental mechanism of peptide-bond formation.
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Affiliation(s)
- Stefan Arenz
- Gene Center and Department for Biochemistry, University of Munich, Feodor-Lynenstrasse 25, Munich 81377, Germany
| | - Lars V. Bock
- Department of Theoretical and Computational Biophysics, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, Göttingen 37079, Germany
| | - Michael Graf
- Gene Center and Department for Biochemistry, University of Munich, Feodor-Lynenstrasse 25, Munich 81377, Germany
| | - C. Axel Innis
- Institut Européen de Chimie et Biologie, University of Bordeaux, Pessac 33607, France
- INSERM U1212, Bordeaux 33076, France
- CNRS UMR7377, Bordeaux 33076, France
| | - Roland Beckmann
- Gene Center and Department for Biochemistry, University of Munich, Feodor-Lynenstrasse 25, Munich 81377, Germany
- Center for integrated Protein Science Munich, University of Munich, Feodor-Lynenstrasse 25, Munich 81377, Germany
| | - Helmut Grubmüller
- Department of Theoretical and Computational Biophysics, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, Göttingen 37079, Germany
| | - Andrea C. Vaiana
- Department of Theoretical and Computational Biophysics, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, Göttingen 37079, Germany
| | - Daniel N. Wilson
- Gene Center and Department for Biochemistry, University of Munich, Feodor-Lynenstrasse 25, Munich 81377, Germany
- Center for integrated Protein Science Munich, University of Munich, Feodor-Lynenstrasse 25, Munich 81377, Germany
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16
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Seefeldt AC, Graf M, Pérébaskine N, Nguyen F, Arenz S, Mardirossian M, Scocchi M, Wilson DN, Innis CA. Structure of the mammalian antimicrobial peptide Bac7(1-16) bound within the exit tunnel of a bacterial ribosome. Nucleic Acids Res 2016; 44:2429-38. [PMID: 26792896 PMCID: PMC4797285 DOI: 10.1093/nar/gkv1545] [Citation(s) in RCA: 82] [Impact Index Per Article: 10.3] [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] [Received: 10/13/2015] [Accepted: 12/28/2015] [Indexed: 11/25/2022] Open
Abstract
Proline-rich antimicrobial peptides (PrAMPs) produced as part of the innate immune response of animals, insects and plants represent a vast, untapped resource for the treatment of multidrug-resistant bacterial infections. PrAMPs such as oncocin or bactenecin-7 (Bac7) interact with the bacterial ribosome to inhibit translation, but their supposed specificity as inhibitors of bacterial rather than mammalian protein synthesis remains unclear, despite being key to developing drugs with low toxicity. Here, we present crystal structures of the Thermus thermophilus 70S ribosome in complex with the first 16 residues of mammalian Bac7, as well as the insect-derived PrAMPs metalnikowin I and pyrrhocoricin. The structures reveal that the mammalian Bac7 interacts with a similar region of the ribosome as insect-derived PrAMPs. Consistently, Bac7 and the oncocin derivative Onc112 compete effectively with antibiotics, such as erythromycin, which target the ribosomal exit tunnel. Moreover, we demonstrate that Bac7 allows initiation complex formation but prevents entry into the elongation phase of translation, and show that it inhibits translation on both mammalian and bacterial ribosomes, explaining why this peptide needs to be stored as an inactive pro-peptide. These findings highlight the need to consider the specificity of PrAMP derivatives for the bacterial ribosome in future drug development efforts.
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Affiliation(s)
- A Carolin Seefeldt
- Institut Européen de Chimie et Biologie, University of Bordeaux, Pessac 33607, France U1212, Inserm, Bordeaux 33076, France UMR 5320, CNRS, Bordeaux 33076, France
| | - Michael Graf
- Gene Center and Department for Biochemistry, University of Munich, Munich 81377, Germany
| | - Natacha Pérébaskine
- Institut Européen de Chimie et Biologie, University of Bordeaux, Pessac 33607, France U1212, Inserm, Bordeaux 33076, France UMR 5320, CNRS, Bordeaux 33076, France
| | - Fabian Nguyen
- Gene Center and Department for Biochemistry, University of Munich, Munich 81377, Germany
| | - Stefan Arenz
- Gene Center and Department for Biochemistry, University of Munich, Munich 81377, Germany
| | - Mario Mardirossian
- Department of Life Sciences, University of Trieste, Trieste 34127, Italy
| | - Marco Scocchi
- Department of Life Sciences, University of Trieste, Trieste 34127, Italy
| | - Daniel N Wilson
- Gene Center and Department for Biochemistry, University of Munich, Munich 81377, Germany Center for integrated Protein Science Munich (CiPSM), University of Munich, Munich 81377, Germany
| | - C Axel Innis
- Institut Européen de Chimie et Biologie, University of Bordeaux, Pessac 33607, France U1212, Inserm, Bordeaux 33076, France UMR 5320, CNRS, Bordeaux 33076, France
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17
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Sohmen D, Chiba S, Shimokawa-Chiba N, Innis CA, Berninghausen O, Beckmann R, Ito K, Wilson DN. Structure of the Bacillus subtilis 70S ribosome reveals the basis for species-specific stalling. Nat Commun 2015; 6:6941. [PMID: 25903689 PMCID: PMC4423224 DOI: 10.1038/ncomms7941] [Citation(s) in RCA: 83] [Impact Index Per Article: 9.2] [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] [Received: 01/12/2015] [Accepted: 03/16/2015] [Indexed: 12/23/2022] Open
Abstract
Ribosomal stalling is used to regulate gene expression and can occur in a species-specific manner. Stalling during translation of the MifM leader peptide regulates expression of the downstream membrane protein biogenesis factor YidC2 (YqjG) in Bacillus subtilis, but not in Escherichia coli. In the absence of structures of Gram-positive bacterial ribosomes, a molecular basis for species-specific stalling has remained unclear. Here we present the structure of a Gram-positive B. subtilis MifM-stalled 70S ribosome at 3.5–3.9 Å, revealing a network of interactions between MifM and the ribosomal tunnel, which stabilize a non-productive conformation of the PTC that prevents aminoacyl-tRNA accommodation and thereby induces translational arrest. Complementary genetic analyses identify a single amino acid within ribosomal protein L22 that dictates the species specificity of the stalling event. Such insights expand our understanding of how the synergism between the ribosome and the nascent chain is utilized to modulate the translatome in a species-specific manner. Ribosome stalling regulates gene expression by exposing otherwise inaccessible downstream ribosome-binding sites. Here the authors present a high-resolution Cryo-EM structure of the Bacillus subtilis MifM-stalled 70S ribosome to provide mechanistic insight into species-specific nascent peptide induced translational arrest.
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Affiliation(s)
- Daniel Sohmen
- Gene Center and Department for Biochemistry, University of Munich, Feodor-Lynen-Street 25, Munich 81377, Germany
| | - Shinobu Chiba
- 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
| | - C Axel Innis
- 1] Institut Européen de Chimie et Biologie, Université de Bordeaux, Pessac, France [2] Institut National de la Santé et de la Recherche Médicale (U869), Bordeaux, France
| | - Otto Berninghausen
- Gene Center and Department for Biochemistry, University of Munich, Feodor-Lynen-Street 25, Munich 81377, Germany
| | - Roland Beckmann
- 1] Gene Center and Department for Biochemistry, University of Munich, Feodor-Lynen-Street 25, Munich 81377, Germany [2] Center for integrated Protein Science Munich (CiPSM), University of Munich, Feodor-Lynen-Street 25, Munich 81377, Germany
| | - Koreaki Ito
- Faculty of Life Sciences, Kyoto Sangyo University, Motoyama, Kamigamo, Kita-Ku, Kyoto 603-8555, Japan
| | - Daniel N Wilson
- 1] Gene Center and Department for Biochemistry, University of Munich, Feodor-Lynen-Street 25, Munich 81377, Germany [2] Center for integrated Protein Science Munich (CiPSM), University of Munich, Feodor-Lynen-Street 25, Munich 81377, Germany
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18
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Seidelt B, Innis CA, Wilson DN, Gartmann M, Armache JP, Villa E, Trabuco LG, Becker T, Mielke T, Schulten K, Steitz TA, Beckmann R. Structural insight into nascent polypeptide chain-mediated translational stalling. Science 2009; 326:1412-5. [PMID: 19933110 DOI: 10.1126/science.1177662] [Citation(s) in RCA: 235] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Expression of the Escherichia coli tryptophanase operon depends on ribosome stalling during translation of the upstream TnaC leader peptide, a process for which interactions between the TnaC nascent chain and the ribosomal exit tunnel are critical. We determined a 5.8 angstrom-resolution cryo-electron microscopy and single-particle reconstruction of a ribosome stalled during translation of the tnaC leader gene. The nascent chain was extended within the exit tunnel, making contacts with ribosomal components at distinct sites. Upon stalling, two conserved residues within the peptidyltransferase center adopted conformations that preclude binding of release factors. We propose a model whereby interactions within the tunnel are relayed to the peptidyltransferase center to inhibit translation. Moreover, we show that nascent chains adopt distinct conformations within the ribosomal exit tunnel.
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Affiliation(s)
- Birgit Seidelt
- Gene Center and Center for Integrated Protein Science Munich (CIPSM), Department for Chemistry and Biochemistry, University of Munich, Feodor-Lynen-Strasse 25, 81377 Munich, Germany
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19
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Yin FF, Bailey S, Innis CA, Ciubotaru M, Kamtekar S, Steitz TA, Schatz DG. Structure of the RAG1 nonamer binding domain with DNA reveals a dimer that mediates DNA synapsis. Nat Struct Mol Biol 2009; 16:499-508. [PMID: 19396172 PMCID: PMC2715281 DOI: 10.1038/nsmb.1593] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.6] [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] [Received: 10/15/2008] [Accepted: 03/20/2009] [Indexed: 12/23/2022]
Abstract
The products of recombination-activating genes RAG1 and RAG2 mediate the assembly of antigen receptor genes during lymphocyte development in a process known as V(D)J recombination. Lack of structural information for the RAG proteins has hindered mechanistic studies of this reaction. We report here the crystal structure of an essential DNA binding domain of the RAG1 catalytic core bound to its nonamer DNA recognition motif. The RAG1 nonamer binding domain (NBD) forms a tightly interwoven dimer that binds and synapses two nonamer elements, with each NBD making contact with both DNA molecules. Biochemical and biophysical experiments confirm that the two nonamers are in close proximity in the RAG1/2-DNA synaptic complex and demonstrate the functional importance of the protein-DNA contacts revealed in the structure. These findings reveal a previously unsuspected function for the NBD in DNA synapsis and have implications for the regulation of DNA binding and cleavage by RAG1 and RAG2.
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Affiliation(s)
- Fang Fang Yin
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, USA
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20
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Abstract
Although knowledge of a protein's functional site is a key requirement for understanding its mode of action at the molecular level, our ability to locate such sites experimentally is far exceeded by the rate at which sequence and structural information is being accumulated. siteFiNDER|3D is an online tool for the prediction of functionally important regions in proteins of known structure. At the core of the server lies the CFG analysis algorithm, which uses a moving 3D window to correlate patterns of functional/chemical group conservation in the query protein with the location of functional sites. Here, we give a general overview of the functionality offered by the siteFiNDER|3D server, along with general recommendations aimed at maximizing the accuracy and predictive value of this tool in a variety of contexts. siteFiNDER|3D can be accessed at: ‘http://sage.csb.yale.edu/sitefinder3d’ and requires, at a minimum, the atomic coordinates of a query protein in PDB format.
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Affiliation(s)
- C Axel Innis
- Howard Hughes Medical Institute/Yale University, Department of Molecular Biophysics and Biochemistry, New Haven, CT 06520-8114, USA.
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21
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Innis CA, Anand AP, Sowdhamini R. Prediction of functional sites in proteins using conserved functional group analysis. J Mol Biol 2004; 337:1053-68. [PMID: 15033369 DOI: 10.1016/j.jmb.2004.01.053] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2003] [Revised: 01/20/2004] [Accepted: 01/28/2004] [Indexed: 11/21/2022]
Abstract
A detailed knowledge of a protein's functional site is an absolute prerequisite for understanding its mode of action at the molecular level. However, the rapid pace at which sequence and structural information is being accumulated for proteins greatly exceeds our ability to determine their biochemical roles experimentally. As a result, computational methods are required which allow for the efficient processing of the evolutionary information contained in this wealth of data, in particular that related to the nature and location of functionally important sites and residues. The method presented here, referred to as conserved functional group (CFG) analysis, relies on a simplified representation of the chemical groups found in amino acid side-chains to identify functional sites from a single protein structure and a number of its sequence homologues. We show that CFG analysis can fully or partially predict the location of functional sites in approximately 96% of the 470 cases tested and that, unlike other methods available, it is able to tolerate wide variations in sequence identity. In addition, we discuss its potential in a structural genomics context, where automation, scalability and efficiency are critical, and an increasing number of protein structures are determined with no prior knowledge of function. This is exemplified by our analysis of the hypothetical protein Ydde_Ecoli, whose structure was recently solved by members of the North East Structural Genomics consortium. Although the proposed active site for this protein needs to be validated experimentally, this example illustrates the scope of CFG analysis as a general tool for the identification of residues likely to play an important role in a protein's biochemical function. Thus, our method offers a convenient solution to rapidly and automatically process the vast amounts of data that are beginning to emerge from structural genomics projects.
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Affiliation(s)
- C Axel Innis
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, UAS-GKVK Campus, Bellary Road, Bangalore 560065, India.
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22
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Abstract
Follistatin associates with transforming growth factor-beta-like growth factors such as activin or bone morphogenetic proteins to form an inactive complex, thereby regulating processes as diverse as embryonic development and cell secretion. Although an interaction between heparan sulfate chains present at the cell surface and follistatin has been recorded, the impact of this binding reaction on the follistatin-mediated inhibition of transforming growth factor-beta-like signaling remains unclear. To gain a structural insight into this interaction, we have solved the crystal structure of the presumed heparan sulfate-binding domain of follistatin, both alone and in complex with the small heparin analogs sucrose octasulfate and D-myo-inositol hexasulfate. In addition, we have confirmed the binding of the sucrose octasulfate and D-myo-inositol hexasulfate molecules to this follistatin domain and determined the association constants and stoichiometries of both interactions in solution using isothermal titration calorimetry. Overall, our results shed light upon the structure of this follistatin domain and reveal a novel conformation for a hinge region connecting epidermal growth factor-like and Kazal-like subdomains compared with the follistatin-like domain found in the extracellular matrix protein BM-40. Moreover, the crystallographic analysis of the two protein-ligand complexes mentioned above leads us to propose a potential location for the heparan sulfate-binding site on the surface of follistatin and to suggest the involvement of residues Asn80 and Arg86 in such a follistatin-heparin interaction.
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Affiliation(s)
- C Axel Innis
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, United Kingdom
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23
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Williams MG, Shirai H, Shi J, Nagendra HG, Mueller J, Mizuguchi K, Miguel RN, Lovell SC, Innis CA, Deane CM, Chen L, Campillo N, Burke DF, Blundell TL, de Bakker PI. Sequence-structure homology recognition by iterative alignment refinement and comparative modeling. Proteins 2002; Suppl 5:92-7. [PMID: 11835486 DOI: 10.1002/prot.1169] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Our approach to fold recognition for the fourth critical assessment of techniques for protein structure prediction (CASP4) experiment involved the use of the FUGUE sequence-structure homology recognition program (http://www-cryst.bioc.cam.ac.uk/fugue), followed by model building. We treat models as hypotheses and examine these to determine whether they explain the available data. Our method depends heavily on environment-specific substitution tables derived from our database of structural alignments of homologous proteins (HOMSTRAD, http://www-cryst.bioc.cam.ac.uk/homstrad/). FUGUE uses these tables to incorporate structural information into profiles created from HOMSTRAD alignments that are matched against a profile created for the target from multiple sequence alignment. In addition, environment-specific substitution tables are used throughout the modeling procedure and as part of the model evaluation. Annotation of sequence alignments with JOY, to reflect local structural features, proved valuable, both for modifying hypotheses, and for rejecting predictions when the expected pattern of conservation is not observed. Our stringency in rejecting incorrect predictions led us to submit a relatively small number of models, including only a low number of false positives, resulting in a high average score.
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Affiliation(s)
- M G Williams
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
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Liu SS, Melmed AP, Klos JW, Innis CA. Prospective experience with a 20-gauge Tuohy needle for lumbar epidural steroid injections: Is confirmation with fluoroscopy necessary? Reg Anesth Pain Med 2001; 26:143-6. [PMID: 11251138 DOI: 10.1053/rapm.2001.21743] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
BACKGROUND AND OBJECTIVES Small (20-gauge) Tuohy needles have been introduced for epidural steroid injection to optimize patient comfort and decrease the risk of spinal headache. These needles may be less reliable for indentification of the epidural space than standard 17- or 18-gauge needles because of their small size. We prospectively examined the success rate of lumbar epidural steroid placement with loss-of-resistance (LOR) technique compared with fluoroscopy confirmation. METHODS One hundred patients without history of lumbar spine surgery were enrolled. A 20-gauge Tuohy needle was placed into the epidural space using LOR to saline. Confidence in epidural placement was recorded (Yes/No). Radiologic contrast was then injected and a fluoroscopic epidurogram interpreted by a blinded radiologist for correct placement, (Yes/No) separate from the clinical process. RESULTS Reliability of LOR was less than our "gold standard" of fluoroscopy (P <.004). Sensitivity of LOR was 99% and specificity was 27%. Positive and negative predictive values were 92% and 75%. Increased patient age (>70 years) and male sex were associated with poor reliability of LOR (P <.05). CONCLUSIONS In contrast to the reported 99% success rates for epidural placement of standard 17- or 18-gauge Tuohy needles, we observed a success rate of 92%. Small-gauge Tuohy needles are technically more difficult to use than larger needles and may require confirmation with fluoroscopy for correct epidural placement, especially in elderly male patients.
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Affiliation(s)
- S S Liu
- Department of Anesthesiology, Virginia Mason Medical Center, Seattle, Washington, USA.
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25
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Innis CA, Shi J, Blundell TL. Evolutionary trace analysis of TGF-beta and related growth factors: implications for site-directed mutagenesis. Protein Eng 2000; 13:839-47. [PMID: 11239083 DOI: 10.1093/protein/13.12.839] [Citation(s) in RCA: 121] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
The TGF-beta family of growth factors contains a large number of homologous proteins, grouped in several subfamilies on the basis of sequence identity. These subgroups can be combined into three broader groups of related cytokines, with marked specificities for their cellular receptors: the TGF-betas, the activins and the BMPs/GDFs. Although structural information is available for some members of the TGF-beta family, very little is known about the way in which these growth factors interact with the extra-cellular domains of their multiple cell surface receptors or with the specific protein inhibitors thought to modulate their activity. In this paper, we use the evolutionary trace method [Lichtarge et al. (1996) J. Mol. Biol., 257, 342-358] to locate two functional patches on the surface of TGF-beta-like growth factors. The first of these is centred on a conserved proline (P(36) in TGF-betas 1-3) and contains two amino acids which could account for the receptor specificity of TGF-betas (H(34) and E(35)). The second patch is located on the other side of the growth factor protomer and surrounds a hydrophobic cavity, large enough to accommodate the side chain of an aromatic residue. In addition to two conserved tryptophans at positions 30 and 32, the main protagonists in this potential binding interface are found at positions 31, 92, 93 and 98. Several mutagenesis studies have highlighted the importance of the C-terminal region of the growth factor molecule in TGF-betas and of residues in activin A equivalent to positions 31 and 94 of the TGF-betas for the binding of type II receptors to these ligands. These data, together with our improved knowledge of possible functional residues, can be used in future structure-function analysis experiments.
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Affiliation(s)
- C A Innis
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK
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26
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Blundell TL, Burke DF, Chirgadze D, Dhanaraj V, Hyvönen M, Innis CA, Parisini E, Pellegrini L, Sayed M, Sibanda BL. Protein-protein interactions in receptor activation and intracellular signalling. Biol Chem 2000; 381:955-9. [PMID: 11076027 DOI: 10.1515/bc.2000.117] [Citation(s) in RCA: 43] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
We review here signalling complexes that we have defined using X-ray analysis in our laboratory. They include growth factors and their receptors: nerve growth factor (NGF) and its hetero-hexameric 7S NGF storage complex, hepatocyte growth factor/scatter factor (HGF/SF) NK1 dimers and fibroblast growth factor (FGF1) in complex with its receptor (FGFR2) ectodomain and heparin. We also review our recent structural studies on intracellular signalling complexes, focusing on phosducin transducin GPry, CK2 protein kinase and its complexes, and the cyclin D-dependent kinase, Cdk6, bound to the cell cycle inhibitor p19INK4d. Comparing the structures of these complexes with others we show that the surface area buried in signalling interactions does not always give a good indication of the strength of the interactions. We show that conformational changes are often important in complexes with intermediate buried surface areas of 1500 to 2000 A2, such as Cdk6INK4 interactions. Some interactions involve recognition of continuous epitopes, where there is no necessity for a tertiary structure and very often the binding conformation is induced during the process of interaction, for example phosducin binding to the betagamma subunits (Gtbetagamma) of the heterotrimeric G protein transducin.
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Affiliation(s)
- T L Blundell
- Department of Biochemistry, University of Cambridge, UK
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27
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Abstract
RATIONALE AND OBJECTIVES The authors evaluated the perceptions of patients who underwent stereotaxic core breast biopsy before and after the procedure. METHODS By using a standard questionnaire, 58 patients undergoing stereotaxic core breast biopsy with a 14-gauge needle were interviewed immediately before, immediately after, and 24 hours and 5 days after the procedure. RESULTS Discomfort recorded by patients 24 hours after core biopsy correlated with the amount of time needed before normal activities were resumed (P = .001). Only five patients (9%) indicated severe discomfort during the procedure. Patient age, number of core biopsy samples taken, and lesion depth did not correlate with level of discomfort. Fifty-five patients (95%) resumed normal activities within 24 hours. However, 41 patients (71%) had some breast bruising as many as 5 days after the procedure. Overall, patient satisfaction with care was high; 56 patients (97%) stated they would return for another biopsy in the future. CONCLUSION The morbidity associated with stereotaxic core breast biopsy is low, although the majority of patients in this series experienced bruising lasting as long as 5 days after the procedure. Despite this, almost all patients would return for a core breast biopsy in the future, if indicated.
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Affiliation(s)
- R B Handy
- Department of Radiology, College of Medicine, University of Arizona, Tucson 85724, USA
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28
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Harvey JA, Fajardo LL, Innis CA. Previous mammograms in patients with impalpable breast carcinoma: retrospective vs blinded interpretation. 1993 ARRS President's Award. AJR Am J Roentgenol 1993; 161:1167-72. [PMID: 8249720 DOI: 10.2214/ajr.161.6.8249720] [Citation(s) in RCA: 153] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
OBJECTIVE We examined differences between blinded and retrospective reviews of screening mammograms obtained before a mammogram that resulted in the diagnosis of an impalpable breast carcinoma. MATERIALS AND METHODS We reviewed 152 previous mammograms in 73 patients in whom impalpable breast carcinomas were subsequently detected on later mammograms. The earlier studies were interpreted in two ways: (1) blindly (without knowledge that carcinoma was subsequently detected) and (2) retrospectively (with the mammogram showing the carcinoma for comparison). The two interpretations were then compared with regard to the presence of carcinoma, recommendations for biopsy, parenchymal density, histologic characteristics of the tumor, lymph node status, and film quality. RESULTS When we did a blinded review of the mammograms obtained before the diagnostic mammograms, the previous study was interpreted as showing evidence of carcinoma in 30 patients (41%). For the remaining 43 patients (59%), the findings of the most-recent previous mammogram were interpreted as normal or benign by the blinded reviewers; however, the retrospective reviewers thought evidence of cancer was visible in 25 of these patients (34%). Differences between blinded and retrospective interpretations were statistically significant. In patients in whom evidence of tumor was thought to be present on retrospective review but not on blinded review, the majority of mammographic abnormalities were asymmetric densities on the most-recent previous examination. This was true whether or not the retrospective reviewers thought that the mammographic finding warranted earlier biopsy. The histologic characteristics and lymph node status among patients in whom mammograms were interpreted retrospectively as showing evidence of tumor were no different from those among patients with no evidence of tumor. CONCLUSION Our results show that impalpable breast carcinomas are frequently evident in retrospect on previous mammograms. However, because many are manifested only as an asymmetric density, these may not necessarily be true radiologic errors. Failure to detect a retrospectively visible abnormality on a screening mammogram is not necessarily negligent, and retrospective reviews do not reflect the everyday practice of screening mammography.
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Affiliation(s)
- J A Harvey
- Department of Radiology, University of Arizona and University Medical Center, Tucson 85724
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Innis CA, Garvey KJ, Ito J. Nucleotide sequence of phage phi 29 gene 7: structure of intergenic spacer between the major early and late genes. Nucleic Acids Res 1986; 14:7129. [PMID: 3763399 PMCID: PMC311725 DOI: 10.1093/nar/14.17.7129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
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