1
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Bastet L, Korepanov A, Jagodnik J, Grondin J, Lamontagne AM, Guillier M, Lafontaine D. Riboswitch and small RNAs modulate btuB translation initiation in Escherichia coli and trigger distinct mRNA regulatory mechanisms. Nucleic Acids Res 2024; 52:5852-5865. [PMID: 38742638 PMCID: PMC11162775 DOI: 10.1093/nar/gkae347] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Revised: 03/19/2024] [Accepted: 04/29/2024] [Indexed: 05/16/2024] Open
Abstract
Small RNAs (sRNAs) and riboswitches represent distinct classes of RNA regulators that control gene expression upon sensing metabolic or environmental variations. While sRNAs and riboswitches regulate gene expression by affecting mRNA and protein levels, existing studies have been limited to the characterization of each regulatory system in isolation, suggesting that sRNAs and riboswitches target distinct mRNA populations. We report that the expression of btuB in Escherichia coli, which is regulated by an adenosylcobalamin (AdoCbl) riboswitch, is also controlled by the small RNAs OmrA and, to a lesser extent, OmrB. Strikingly, we find that the riboswitch and sRNAs reduce mRNA levels through distinct pathways. Our data show that while the riboswitch triggers Rho-dependent transcription termination, sRNAs rely on the degradosome to modulate mRNA levels. Importantly, OmrA pairs with the btuB mRNA through its central region, which is not conserved in OmrB, indicating that these two sRNAs may have specific targets in addition to their common regulon. In contrast to canonical sRNA regulation, we find that OmrA repression of btuB is lost using an mRNA binding-deficient Hfq variant. Together, our study demonstrates that riboswitch and sRNAs modulate btuB expression, providing an example of cis- and trans-acting RNA-based regulatory systems maintaining cellular homeostasis.
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Affiliation(s)
- Laurène Bastet
- Department of Biology, Faculty of Science, Université de Sherbrooke, Sherbrooke, Quebec J1K 2R1, Canada
| | - Alexey P Korepanov
- Expression Génétique Microbienne, UMR8261 CNRS, Université Paris Cité, Institut de Biologie Physico-Chimique, 75005Paris, France
| | - Jonathan Jagodnik
- Expression Génétique Microbienne, UMR8261 CNRS, Université Paris Cité, Institut de Biologie Physico-Chimique, 75005Paris, France
| | - Jonathan P Grondin
- Department of Biology, Faculty of Science, Université de Sherbrooke, Sherbrooke, Quebec J1K 2R1, Canada
| | - Anne-Marie Lamontagne
- Department of Biology, Faculty of Science, Université de Sherbrooke, Sherbrooke, Quebec J1K 2R1, Canada
| | - Maude Guillier
- Expression Génétique Microbienne, UMR8261 CNRS, Université Paris Cité, Institut de Biologie Physico-Chimique, 75005Paris, France
| | - Daniel A Lafontaine
- Department of Biology, Faculty of Science, Université de Sherbrooke, Sherbrooke, Quebec J1K 2R1, Canada
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2
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Marina VI, Bidzhieva M, Tereshchenkov AG, Orekhov D, Sagitova VE, Sumbatyan NV, Tashlitsky VN, Ferberg AS, Maviza TP, Kasatsky P, Tolicheva O, Paleskava A, Polshakov VI, Osterman IA, Dontsova OA, Konevega AL, Sergiev PV. An easy tool to monitor the elemental steps of in vitro translation via gel electrophoresis of fluorescently labeled small peptides. RNA (NEW YORK, N.Y.) 2024; 30:298-307. [PMID: 38164606 PMCID: PMC10870375 DOI: 10.1261/rna.079766.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Accepted: 11/22/2023] [Indexed: 01/03/2024]
Abstract
Several methods are available to visualize and assess the kinetics and efficiency of elemental steps of protein biosynthesis. However, each of these methods has its own limitations. Here, we present a novel, simple and convenient tool for monitoring stepwise in vitro translation initiated by BODIPY-Met-tRNA. Synthesis and release of very short, 1-7 amino acids, BODIPY-labeled peptides, can be monitored using urea-polyacrylamide gel electrophoresis. Very short BODIPY-labeled oligopeptides might be resolved this way, in contrast to widely used Tris-tricine gel electrophoresis, which is suitable to separate peptides larger than 1 kDa. The method described in this manuscript allows one to monitor the steps of translation initiation, peptide transfer, translocation, and termination as well as their inhibition at an unprecedented single amino acid resolution.
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Affiliation(s)
- Valeriya I Marina
- Center for Molecular and Cellular Biology, Skolkovo Institute of Science and Technology, Skolkovo 121205, Russia
- Department of Chemistry, Lomonosov Moscow State University, Moscow 119991, Russia
| | - Medina Bidzhieva
- Molecular and Radiation Biophysics Division, Petersburg Nuclear Physics Institute named by B.P. Konstantinov of NRC "Kurchatov Institute," Gatchina 188300, Russia
- Institute of Biomedical Systems and Biotechnologies, Peter the Great St. Petersburg Polytechnic University, Saint Petersburg 195251, Russia
| | - Andrey G Tereshchenkov
- Department of Chemistry, Lomonosov Moscow State University, Moscow 119991, Russia
- A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow 119991, Russia
| | - Dmitry Orekhov
- R&D Department, VIC Animal Health, Severny, Belgorod Region 308519, Russia
| | | | - Nataliya V Sumbatyan
- Department of Chemistry, Lomonosov Moscow State University, Moscow 119991, Russia
| | - Vadim N Tashlitsky
- Department of Chemistry, Lomonosov Moscow State University, Moscow 119991, Russia
- A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow 119991, Russia
| | - Artem S Ferberg
- Department of Chemistry, Lomonosov Moscow State University, Moscow 119991, Russia
| | - Tinashe P Maviza
- Center for Molecular and Cellular Biology, Skolkovo Institute of Science and Technology, Skolkovo 121205, Russia
| | - Pavel Kasatsky
- Molecular and Radiation Biophysics Division, Petersburg Nuclear Physics Institute named by B.P. Konstantinov of NRC "Kurchatov Institute," Gatchina 188300, Russia
| | - Olga Tolicheva
- Molecular and Radiation Biophysics Division, Petersburg Nuclear Physics Institute named by B.P. Konstantinov of NRC "Kurchatov Institute," Gatchina 188300, Russia
| | - Alena Paleskava
- Molecular and Radiation Biophysics Division, Petersburg Nuclear Physics Institute named by B.P. Konstantinov of NRC "Kurchatov Institute," Gatchina 188300, Russia
- Institute of Biomedical Systems and Biotechnologies, Peter the Great St. Petersburg Polytechnic University, Saint Petersburg 195251, Russia
| | - Vladimir I Polshakov
- Faculty of Fundamental Medicine, Lomonosov Moscow State University Moscow, Moscow 119991, Russia
| | - Ilya A Osterman
- Center for Molecular and Cellular Biology, Skolkovo Institute of Science and Technology, Skolkovo 121205, Russia
| | - Olga A Dontsova
- Center for Molecular and Cellular Biology, Skolkovo Institute of Science and Technology, Skolkovo 121205, Russia
- Department of Chemistry, Lomonosov Moscow State University, Moscow 119991, Russia
- A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow 119991, Russia
- Department of Functioning of Living Systems, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow 117997, Russia
| | - Andrey L Konevega
- Molecular and Radiation Biophysics Division, Petersburg Nuclear Physics Institute named by B.P. Konstantinov of NRC "Kurchatov Institute," Gatchina 188300, Russia
- Institute of Biomedical Systems and Biotechnologies, Peter the Great St. Petersburg Polytechnic University, Saint Petersburg 195251, Russia
| | - Petr V Sergiev
- Center for Molecular and Cellular Biology, Skolkovo Institute of Science and Technology, Skolkovo 121205, Russia
- Department of Chemistry, Lomonosov Moscow State University, Moscow 119991, Russia
- A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow 119991, Russia
- Institute of Functional Genomics, Lomonosov Moscow State University, Moscow 119991, Russia
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3
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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] [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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4
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Koller TO, Morici M, Berger M, Safdari HA, Lele DS, Beckert B, Kaur KJ, Wilson DN. Structural basis for translation inhibition by the glycosylated drosocin peptide. Nat Chem Biol 2023; 19:1072-1081. [PMID: 36997646 PMCID: PMC10449632 DOI: 10.1038/s41589-023-01293-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Accepted: 02/14/2023] [Indexed: 04/07/2023]
Abstract
The proline-rich antimicrobial peptide (PrAMP) drosocin is produced by Drosophila species to combat bacterial infection. Unlike many PrAMPs, drosocin is O-glycosylated at threonine 11, a post-translation modification that enhances its antimicrobial activity. Here we demonstrate that the O-glycosylation not only influences cellular uptake of the peptide but also interacts with its intracellular target, the ribosome. Cryogenic electron microscopy structures of glycosylated drosocin on the ribosome at 2.0-2.8-Å resolution reveal that the peptide interferes with translation termination by binding within the polypeptide exit tunnel and trapping RF1 on the ribosome, reminiscent of that reported for the PrAMP apidaecin. The glycosylation of drosocin enables multiple interactions with U2609 of the 23S rRNA, leading to conformational changes that break the canonical base pair with A752. Collectively, our study reveals novel molecular insights into the interaction of O-glycosylated drosocin with the ribosome, which provide a structural basis for future development of this class of antimicrobials.
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Affiliation(s)
- Timm O Koller
- Institute for Biochemistry and Molecular Biology, University of Hamburg, Hamburg, Germany
| | - Martino Morici
- Institute for Biochemistry and Molecular Biology, University of Hamburg, Hamburg, Germany
| | - Max Berger
- Institute for Biochemistry and Molecular Biology, University of Hamburg, Hamburg, Germany
| | - Haaris A Safdari
- Institute for Biochemistry and Molecular Biology, University of Hamburg, Hamburg, Germany
| | - Deepti S Lele
- National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi, India
| | - Bertrand Beckert
- Dubochet Center for Imaging (DCI) at EPFL, EPFL SB IPHYS DCI, Lausanne, Switzerland
| | - Kanwal J Kaur
- National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi, India
| | - Daniel N Wilson
- Institute for Biochemistry and Molecular Biology, University of Hamburg, Hamburg, Germany.
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5
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Scheller D, Becker F, Wimbert A, Meggers D, Pienkoß S, Twittenhoff C, Knoke LR, Leichert LI, Narberhaus F. The oxidative stress response, in particular the katY gene, is temperature-regulated in Yersinia pseudotuberculosis. PLoS Genet 2023; 19:e1010669. [PMID: 37428814 PMCID: PMC10358904 DOI: 10.1371/journal.pgen.1010669] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Accepted: 06/12/2023] [Indexed: 07/12/2023] Open
Abstract
Pathogenic bacteria, such as Yersinia pseudotuberculosis encounter reactive oxygen species (ROS) as one of the first lines of defense in the mammalian host. In return, the bacteria react by mounting an oxidative stress response. Previous global RNA structure probing studies provided evidence for temperature-modulated RNA structures in the 5'-untranslated region (5'-UTR) of various oxidative stress response transcripts, suggesting that opening of these RNA thermometer (RNAT) structures at host-body temperature relieves translational repression. Here, we systematically analyzed the transcriptional and translational regulation of ROS defense genes by RNA-sequencing, qRT-PCR, translational reporter gene fusions, enzymatic RNA structure probing and toeprinting assays. Transcription of four ROS defense genes was upregulated at 37°C. The trxA gene is transcribed into two mRNA isoforms, of which the most abundant short one contains a functional RNAT. Biochemical assays validated temperature-responsive RNAT-like structures in the 5'-UTRs of sodB, sodC and katA. However, they barely conferred translational repression in Y. pseudotuberculosis at 25°C suggesting partially open structures available to the ribosome in the living cell. Around the translation initiation region of katY we discovered a novel, highly efficient RNAT that was primarily responsible for massive induction of KatY at 37°C. By phenotypic characterization of catalase mutants and through fluorometric real-time measurements of the redox-sensitive roGFP2-Orp1 reporter in these strains, we revealed KatA as the primary H2O2 scavenger. Consistent with the upregulation of katY, we observed an improved protection of Y. pseudotuberculosis at 37°C. Our findings suggest a multilayered regulation of the oxidative stress response in Yersinia and an important role of RNAT-controlled katY expression at host body temperature.
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Affiliation(s)
- Daniel Scheller
- Ruhr University Bochum, Faculty of Biology and Biotechnology, Microbial Biology, Bochum, Germany
| | - Franziska Becker
- Ruhr University Bochum, Faculty of Biology and Biotechnology, Microbial Biology, Bochum, Germany
| | - Andrea Wimbert
- Ruhr University Bochum, Faculty of Biology and Biotechnology, Microbial Biology, Bochum, Germany
| | - Dominik Meggers
- Ruhr University Bochum, Faculty of Biology and Biotechnology, Microbial Biology, Bochum, Germany
| | - Stephan Pienkoß
- Ruhr University Bochum, Faculty of Biology and Biotechnology, Microbial Biology, Bochum, Germany
| | - Christian Twittenhoff
- Ruhr University Bochum, Faculty of Biology and Biotechnology, Microbial Biology, Bochum, Germany
| | - Lisa R Knoke
- Ruhr University Bochum, Faculty of Medicine, Institute of Biochemistry and Pathobiochemistry, Microbial Biochemistry, Bochum, Germany
| | - Lars I Leichert
- Ruhr University Bochum, Faculty of Medicine, Institute of Biochemistry and Pathobiochemistry, Microbial Biochemistry, Bochum, Germany
| | - Franz Narberhaus
- Ruhr University Bochum, Faculty of Biology and Biotechnology, Microbial Biology, Bochum, Germany
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6
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Fostier CR, Ousalem F, Leroy EC, Ngo S, Soufari H, Innis CA, Hashem Y, Boël G. Regulation of the macrolide resistance ABC-F translation factor MsrD. Nat Commun 2023; 14:3891. [PMID: 37393329 PMCID: PMC10314930 DOI: 10.1038/s41467-023-39553-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Accepted: 06/19/2023] [Indexed: 07/03/2023] Open
Abstract
Antibiotic resistance ABC-Fs (ARE ABC-Fs) are translation factors that provide resistance against clinically important ribosome-targeting antibiotics which are proliferating among pathogens. Here, we combine genetic and structural approaches to determine the regulation of streptococcal ARE ABC-F gene msrD in response to macrolide exposure. We show that binding of cladinose-containing macrolides to the ribosome prompts insertion of the leader peptide MsrDL into a crevice of the ribosomal exit tunnel, which is conserved throughout bacteria and eukaryotes. This leads to a local rearrangement of the 23 S rRNA that prevents peptide bond formation and accommodation of release factors. The stalled ribosome obstructs the formation of a Rho-independent terminator structure that prevents msrD transcriptional attenuation. Erythromycin induction of msrD expression via MsrDL, is suppressed by ectopic expression of mrsD, but not by mutants which do not provide antibiotic resistance, showing correlation between MsrD function in antibiotic resistance and its action on this stalled complex.
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Affiliation(s)
- Corentin R Fostier
- Expression Génétique Microbienne, CNRS, Université Paris Cité, Institut de Biologie Physico-Chimique, 75005, Paris, France
| | - Farès Ousalem
- Expression Génétique Microbienne, CNRS, Université Paris Cité, Institut de Biologie Physico-Chimique, 75005, Paris, France
| | - Elodie C Leroy
- ARNA Laboratory, UMR 5320, U1212, Institut Européen de Chimie et Biologie, Univ. Bordeaux, Centre National de la Recherche Scientifique, Institut National de la Santé et de la Recherche Médicale, 33607, Pessac, France
| | - Saravuth Ngo
- Expression Génétique Microbienne, CNRS, Université Paris Cité, Institut de Biologie Physico-Chimique, 75005, Paris, France
| | - Heddy Soufari
- ARNA Laboratory, UMR 5320, U1212, Institut Européen de Chimie et Biologie, Univ. Bordeaux, Centre National de la Recherche Scientifique, Institut National de la Santé et de la Recherche Médicale, 33607, Pessac, France
- SPT Labtech Ltd., SG8 6HB, Melbourn, United Kingdom
| | - C Axel Innis
- ARNA Laboratory, UMR 5320, U1212, Institut Européen de Chimie et Biologie, Univ. Bordeaux, Centre National de la Recherche Scientifique, Institut National de la Santé et de la Recherche Médicale, 33607, Pessac, France
| | - Yaser Hashem
- ARNA Laboratory, UMR 5320, U1212, Institut Européen de Chimie et Biologie, Univ. Bordeaux, Centre National de la Recherche Scientifique, Institut National de la Santé et de la Recherche Médicale, 33607, Pessac, France.
| | - Grégory Boël
- Expression Génétique Microbienne, CNRS, Université Paris Cité, Institut de Biologie Physico-Chimique, 75005, Paris, France.
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7
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Paranjpe M, Marina V, Grachev A, Maviza T, Tolicheva O, Paleskava A, Osterman I, Sergiev P, Konevega A, Polikanov Y, Gagnon M. Insights into the molecular mechanism of translation inhibition by the ribosome-targeting antibiotic thermorubin. Nucleic Acids Res 2023; 51:449-462. [PMID: 36546783 PMCID: PMC9841432 DOI: 10.1093/nar/gkac1189] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 11/11/2022] [Accepted: 12/19/2022] [Indexed: 12/24/2022] Open
Abstract
Thermorubin (THR) is an aromatic anthracenopyranone antibiotic active against both Gram-positive and Gram-negative bacteria. It is known to bind to the 70S ribosome at the intersubunit bridge B2a and was thought to inhibit factor-dependent initiation of translation and obstruct the accommodation of tRNAs into the A site. Here, we show that thermorubin causes ribosomes to stall in vivo and in vitro at internal and termination codons, thereby allowing the ribosome to initiate protein synthesis and translate at least a few codons before stalling. Our biochemical data show that THR affects multiple steps of translation elongation with a significant impact on the binding stability of the tRNA in the A site, explaining premature cessation of translation. Our high-resolution crystal and cryo-EM structures of the 70S-THR complex show that THR can co-exist with P- and A-site tRNAs, explaining how ribosomes can elongate in the presence of the drug. Remarkable is the ability of THR to arrest ribosomes at the stop codons. Our data suggest that by causing structural re-arrangements in the decoding center, THR interferes with the accommodation of tRNAs or release factors into the ribosomal A site.
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Affiliation(s)
- Madhura N Paranjpe
- Department of Biological Sciences, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Valeria I Marina
- Department of Chemistry and Institute of Functional Genomics, Lomonosov Moscow State University, Moscow 119992, Russia
| | - Aleksandr A Grachev
- Peter the Great St.Petersburg Polytechnic University, Saint Petersburg 195251, Russia
| | - Tinashe P Maviza
- Department of Chemistry and Institute of Functional Genomics, Lomonosov Moscow State University, Moscow 119992, Russia
| | - Olga A Tolicheva
- Peter the Great St.Petersburg Polytechnic University, Saint Petersburg 195251, Russia
| | - Alena Paleskava
- Peter the Great St.Petersburg Polytechnic University, Saint Petersburg 195251, Russia
| | - Ilya A Osterman
- Department of Chemistry and Institute of Functional Genomics, Lomonosov Moscow State University, Moscow 119992, Russia
| | - Petr V Sergiev
- Department of Chemistry and Institute of Functional Genomics, Lomonosov Moscow State University, Moscow 119992, Russia
| | - Andrey L Konevega
- Peter the Great St.Petersburg Polytechnic University, Saint Petersburg 195251, Russia
| | - Yury S Polikanov
- Department of Biological Sciences, University of Illinois at Chicago, Chicago, IL 60607, USA
- Department of Pharmaceutical Sciences, University of Illinois at Chicago, Chicago, IL 60607, USA
- Center for Biomolecular Sciences, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Matthieu G Gagnon
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX77555, USA
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX 77555, USA
- Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, TX 77555, USA
- Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, TX 77555, USA
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8
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Koller TO, Scheid U, Kösel T, Herrmann J, Krug D, Boshoff HIM, Beckert B, Evans JC, Schlemmer J, Sloan B, Weiner DM, Via LE, Moosa A, Ioerger TR, Graf M, Zinshteyn B, Abdelshahid M, Nguyen F, Arenz S, Gille F, Siebke M, Seedorf T, Plettenburg O, Green R, Warnke AL, Ullrich J, Warrass R, Barry CE, Warner DF, Mizrahi V, Kirschning A, Wilson DN, Müller R. The Myxobacterial Antibiotic Myxovalargin: Biosynthesis, Structural Revision, Total Synthesis, and Molecular Characterization of Ribosomal Inhibition. J Am Chem Soc 2023; 145:851-863. [PMID: 36603206 PMCID: PMC9853869 DOI: 10.1021/jacs.2c08816] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Resistance of bacterial pathogens against antibiotics is declared by WHO as a major global health threat. As novel antibacterial agents are urgently needed, we re-assessed the broad-spectrum myxobacterial antibiotic myxovalargin and found it to be extremely potent against Mycobacterium tuberculosis. To ensure compound supply for further development, we studied myxovalargin biosynthesis in detail enabling production via fermentation of a native producer. Feeding experiments as well as functional genomics analysis suggested a structural revision, which was eventually corroborated by the development of a concise total synthesis. The ribosome was identified as the molecular target based on resistant mutant sequencing, and a cryo-EM structure revealed that myxovalargin binds within and completely occludes the exit tunnel, consistent with a mode of action to arrest translation during a late stage of translation initiation. These studies open avenues for structure-based scaffold improvement toward development as an antibacterial agent.
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Affiliation(s)
- Timm O. Koller
- Institute
for Biochemistry and Molecular Biology, University of Hamburg, Martin-Luther-King-Platz 6, 20146 Hamburg, Germany
| | - Ullrich Scheid
- Helmholtz
Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Center
for Infection Research (HZI), Saarland University Campus, 66123 Saarbrücken, Germany
| | - Teresa Kösel
- Leibniz
Universität Hannover, Institute of
Organic Chemistry and Center for Biomolecular Drug Research (BMWZ), Schneiderberg 1B, 30167 Hannover, Germany
| | - Jennifer Herrmann
- Helmholtz
Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Center
for Infection Research (HZI), Saarland University Campus, 66123 Saarbrücken, Germany,German
Center for Infection Research (DZIF), partner site Hannover-Braunschweig, 38124 Braunschweig, Germany
| | - Daniel Krug
- Helmholtz
Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Center
for Infection Research (HZI), Saarland University Campus, 66123 Saarbrücken, Germany,Department
of Pharmacy, Saarland University, 66123 Saarbrücken, Germany,German
Center for Infection Research (DZIF), partner site Hannover-Braunschweig, 38124 Braunschweig, Germany
| | - Helena I. M. Boshoff
- Tuberculosis
Research Section, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Disease,
National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Bertrand Beckert
- Institute
for Biochemistry and Molecular Biology, University of Hamburg, Martin-Luther-King-Platz 6, 20146 Hamburg, Germany
| | - Joanna C. Evans
- SAMRC/NHLS/UCT
Molecular Mycobacteriology Research Unit & DST/NRF Centre of Excellence
for Biomedical TB Research, Institute of Infectious Disease and Molecular
Medicine and Department of Pathology, University
of Cape Town, Rondebosch 7700, South Africa
| | - Jan Schlemmer
- Helmholtz
Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Center
for Infection Research (HZI), Saarland University Campus, 66123 Saarbrücken, Germany,German
Center for Infection Research (DZIF), partner site Hannover-Braunschweig, 38124 Braunschweig, Germany
| | - Becky Sloan
- Tuberculosis
Research Section, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Disease,
National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Danielle M. Weiner
- Tuberculosis
Research Section, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Disease,
National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Laura E. Via
- Tuberculosis
Research Section, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Disease,
National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Atica Moosa
- SAMRC/NHLS/UCT
Molecular Mycobacteriology Research Unit & DST/NRF Centre of Excellence
for Biomedical TB Research, Institute of Infectious Disease and Molecular
Medicine and Department of Pathology, University
of Cape Town, Rondebosch 7700, South Africa
| | - Thomas R. Ioerger
- Department
of Computer Science and Engineering, Texas
A&M University, College
Station, Texas 77843, United States
| | - Michael Graf
- Institute
for Biochemistry and Molecular Biology, University of Hamburg, Martin-Luther-King-Platz 6, 20146 Hamburg, Germany
| | - Boris Zinshteyn
- Department
of Molecular Biology and Genetics, Johns Hopkins University, Baltimore,
Maryland 21205, United States; Howard Hughes Medical Institute, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, United States
| | - Maha Abdelshahid
- Institute
for Biochemistry and Molecular Biology, University of Hamburg, Martin-Luther-King-Platz 6, 20146 Hamburg, Germany
| | - Fabian Nguyen
- Institute
for Biochemistry and Molecular Biology, University of Hamburg, Martin-Luther-King-Platz 6, 20146 Hamburg, Germany
| | - Stefan Arenz
- Institute
for Biochemistry and Molecular Biology, University of Hamburg, Martin-Luther-King-Platz 6, 20146 Hamburg, Germany
| | - Franziska Gille
- Leibniz
Universität Hannover, Institute of
Organic Chemistry and Center for Biomolecular Drug Research (BMWZ), Schneiderberg 1B, 30167 Hannover, Germany
| | - Maik Siebke
- Leibniz
Universität Hannover, Institute of
Organic Chemistry and Center for Biomolecular Drug Research (BMWZ), Schneiderberg 1B, 30167 Hannover, Germany,Institute
of Medicinal Chemistry, Helmholtz Zentrum
München, German Research Center for Environmental Health (GmbH), Ingolstaedter Landstr. 1, 85764 Neuherberg, Germany
| | - Tim Seedorf
- Leibniz
Universität Hannover, Institute of
Organic Chemistry and Center for Biomolecular Drug Research (BMWZ), Schneiderberg 1B, 30167 Hannover, Germany
| | - Oliver Plettenburg
- Leibniz
Universität Hannover, Institute of
Organic Chemistry and Center for Biomolecular Drug Research (BMWZ), Schneiderberg 1B, 30167 Hannover, Germany,Institute
of Medicinal Chemistry, Helmholtz Zentrum
München, German Research Center for Environmental Health (GmbH), Ingolstaedter Landstr. 1, 85764 Neuherberg, Germany
| | - Rachel Green
- Department
of Molecular Biology and Genetics, Johns Hopkins University, Baltimore,
Maryland 21205, United States; Howard Hughes Medical Institute, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, United States
| | - Anna-Luisa Warnke
- Leibniz
Universität Hannover, Institute of
Organic Chemistry and Center for Biomolecular Drug Research (BMWZ), Schneiderberg 1B, 30167 Hannover, Germany,Institute
of Medicinal Chemistry, Helmholtz Zentrum
München, German Research Center for Environmental Health (GmbH), Ingolstaedter Landstr. 1, 85764 Neuherberg, Germany
| | - Joachim Ullrich
- MSD
Animal Health Innovation GmbH, Zur Propstei, 55270 Schwabenheim, Germany
| | - Ralf Warrass
- MSD
Animal Health Innovation GmbH, Zur Propstei, 55270 Schwabenheim, Germany
| | - Clifton E. Barry
- Tuberculosis
Research Section, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Disease,
National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Digby F. Warner
- SAMRC/NHLS/UCT
Molecular Mycobacteriology Research Unit & DST/NRF Centre of Excellence
for Biomedical TB Research, Institute of Infectious Disease and Molecular
Medicine and Department of Pathology, University
of Cape Town, Rondebosch 7700, South Africa
| | - Valerie Mizrahi
- SAMRC/NHLS/UCT
Molecular Mycobacteriology Research Unit & DST/NRF Centre of Excellence
for Biomedical TB Research, Institute of Infectious Disease and Molecular
Medicine and Department of Pathology, University
of Cape Town, Rondebosch 7700, South Africa
| | - Andreas Kirschning
- Leibniz
Universität Hannover, Institute of
Organic Chemistry and Center for Biomolecular Drug Research (BMWZ), Schneiderberg 1B, 30167 Hannover, Germany,
| | - Daniel N. Wilson
- Institute
for Biochemistry and Molecular Biology, University of Hamburg, Martin-Luther-King-Platz 6, 20146 Hamburg, Germany,
| | - Rolf Müller
- Helmholtz
Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Center
for Infection Research (HZI), Saarland University Campus, 66123 Saarbrücken, Germany,Department
of Pharmacy, Saarland University, 66123 Saarbrücken, Germany,German
Center for Infection Research (DZIF), partner site Hannover-Braunschweig, 38124 Braunschweig, Germany,
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9
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Hör J, Jung J, Ðurica-Mitić S, Barquist L, Vogel J. INRI-seq enables global cell-free analysis of translation initiation and off-target effects of antisense inhibitors. Nucleic Acids Res 2022; 50:e128. [PMID: 36229039 PMCID: PMC9825163 DOI: 10.1093/nar/gkac838] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Revised: 09/11/2022] [Accepted: 09/19/2022] [Indexed: 01/29/2023] Open
Abstract
Ribosome profiling (Ribo-seq) is a powerful method for the transcriptome-wide assessment of protein synthesis rates and the study of translational control mechanisms. Yet, Ribo-seq also has limitations. These include difficulties with the analysis of translation-modulating molecules such as antibiotics, which are often toxic or challenging to deliver into living cells. Here, we have developed in vitro Ribo-seq (INRI-seq), a cell-free method to analyze the translational landscape of a fully customizable synthetic transcriptome. Using Escherichia coli as an example, we show how INRI-seq can be used to analyze the translation initiation sites of a transcriptome of interest. We also study the global impact of direct translation inhibition by antisense peptide nucleic acid (PNA) to analyze PNA off-target effects. Overall, INRI-seq presents a scalable, sensitive method to study translation initiation in a transcriptome-wide manner without the potentially confounding effects of extracting ribosomes from living cells.
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Affiliation(s)
- Jens Hör
- Institute for Molecular Infection Biology, University of Würzburg, D-97080 Würzburg, Germany
| | - Jakob Jung
- Institute for Molecular Infection Biology, University of Würzburg, D-97080 Würzburg, Germany
| | - Svetlana Ðurica-Mitić
- Institute for Molecular Infection Biology, University of Würzburg, D-97080 Würzburg, Germany
| | - Lars Barquist
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Center for Infection Research (HZI), D-97080 Würzburg, Germany
- Faculty of Medicine, University of Würzburg, D-97080 Würzburg, Germany
| | - Jörg Vogel
- Institute for Molecular Infection Biology, University of Würzburg, D-97080 Würzburg, Germany
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Center for Infection Research (HZI), D-97080 Würzburg, Germany
- Faculty of Medicine, University of Würzburg, D-97080 Würzburg, Germany
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10
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Shi JJ, Cao Y, Lang QH, Dong Y, Huang LY, Yang LJ, Li JJ, Zhang XX, Wang DY. The effect of the nucleotides immediately upstream of the AUG start codon on the efficiency of translation initiation in sperm cells. PLANT REPRODUCTION 2022; 35:221-231. [PMID: 35674836 DOI: 10.1007/s00497-022-00442-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Accepted: 05/09/2022] [Indexed: 06/15/2023]
Abstract
It is widely known that an optimal nucleotide sequence context immediately upstream of the AUG start codon greatly improves the efficiency of translation initiation of mRNA in mammalian and plant somatic cells, which in turn increases protein levels. However, it is still unclear whether a similar regulatory mechanism is also present in highly differentiated cells. Here, we surveyed this issue in Arabidopsis thaliana sperm cells and found that the sequence context-mediated regulation of translation initiation in sperm cells is generally similar to that in somatic cells. A simple motif of four adenine nucleotides at positions - 1 to - 4 greatly improved the efficiency of translation initiation, and when the motif was present there, translation was even initiated at some non-AUG codons in sperm cells. However, unlike that in mammalian cells, a mainly effective nucleotide site to regulate the efficiency of translation initiation was not present at positions - 1 to - 4 in sperm cells. Meanwhile, different from somatic cells, sperm cells did not use eukaryotic translation initiation factor 1 to regulate the efficiency in a poor context consisting of the lowest frequency nucleotides. All these results contribute to our understanding of the cytoplasmic event of translation initiation in highly differentiated sperm cells.
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Affiliation(s)
- Jiao-Jiao Shi
- Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), College of Life Science, Northwest University, Xi'an, 710069, China
| | - Yuan Cao
- Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), College of Life Science, Northwest University, Xi'an, 710069, China
| | - Qiu-Hua Lang
- Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), College of Life Science, Northwest University, Xi'an, 710069, China
| | - Yao Dong
- Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), College of Life Science, Northwest University, Xi'an, 710069, China
| | - Liu-Yuan Huang
- Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), College of Life Science, Northwest University, Xi'an, 710069, China
| | - Liu-Jie Yang
- Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), College of Life Science, Northwest University, Xi'an, 710069, China
| | - Jing-Jing Li
- Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), College of Life Science, Northwest University, Xi'an, 710069, China
| | - Xue-Xin Zhang
- Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), College of Life Science, Northwest University, Xi'an, 710069, China
| | - Dan-Yang Wang
- Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), College of Life Science, Northwest University, Xi'an, 710069, China.
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11
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RNA thermometer-coordinated assembly of the Yersinia injectisome. J Mol Biol 2022; 434:167667. [PMID: 35667470 DOI: 10.1016/j.jmb.2022.167667] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Revised: 05/20/2022] [Accepted: 05/30/2022] [Indexed: 11/21/2022]
Abstract
The type III secretion system (T3SS) is indispensable for successful host cell infection by many Gram-negative pathogens. The molecular syringe delivers effector proteins that suppress the host immune response. Synthesis of T3SS components in Yersinia pseudotuberculosis relies on host body temperature, which induces the RNA thermometer (RNAT)-controlled translation of lcrF coding for a virulence master regulator that activates transcription of the T3SS regulon. The assembly of the secretion machinery follows a strict coordinated succession referred to as outside-in assembly, in which the membrane ring complex and the export apparatus represent the nucleation points. Two components essential for the initial assembly are YscJ and YscT. While YscJ connects the membrane ring complex with the export apparatus in the inner membrane, YscT is required for a functional export apparatus. Previous transcriptome-wide RNA structuromics data suggested the presence of unique intercistronic RNATs upstream of yscJ and yscT. Here, we show by reporter gene fusions that both upstream regions confer translational control. Moreover, we demonstrate the temperature-induced opening of the Shine-Dalgarno region, which facilitates ribosome binding, by in vitro structure probing and toeprinting methods. Rationally designed thermostable RNAT variants of the yscJ and yscT thermometers confirmed their physiological relevance with respect to T3SS assembly and host infection. Since we have shown in a recent study that YopN, the gatekeeper of type III secretion, also is under RNAT control, it appears that the synthesis, assembly and functionality of the Yersinia T3S machinery is coordinated by RNA-based temperature sensors at multiple levels.
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12
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Syroegin EA, Flemmich L, Klepacki D, Vazquez-Laslop N, Micura R, Polikanov YS. Structural basis for the context-specific action of the classic peptidyl transferase inhibitor chloramphenicol. Nat Struct Mol Biol 2022; 29:152-161. [DOI: 10.1038/s41594-022-00720-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Accepted: 12/23/2021] [Indexed: 02/06/2023]
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13
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The context of the ribosome binding site in mRNAs defines specificity of action of kasugamycin, an inhibitor of translation initiation. Proc Natl Acad Sci U S A 2022; 119:2118553119. [PMID: 35064089 PMCID: PMC8794815 DOI: 10.1073/pnas.2118553119] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/21/2021] [Indexed: 11/18/2022] Open
Abstract
Several antibiotics targeting the large ribosomal subunit interfere with translation in a context-specific manner, preventing ribosomes from polymerizing specific amino acid sequences. Here, we reveal kasugamycin as a small ribosomal subunit-targeting antibiotic whose action depends on the sequence context of the untranslated messenger RNA (mRNA) segments. We show that kasugamycin-induced ribosomal arrest at the start codons of the genes and the resulting inhibition of gene expression depend on the nature of the mRNA nucleotide immediately preceding the start codon and on the proximity of the stop codon of the upstream cistron. Our findings underlie the importance of mRNA context for the action of protein synthesis inhibitors and might help to guide the development of better antibiotics. Kasugamycin (KSG) is an aminoglycoside antibiotic widely used in agriculture and exhibits considerable medical potential. Previous studies suggested that KSG interferes with translation by blocking binding of canonical messenger RNA (mRNA) and initiator transfer tRNA (tRNA) to the small ribosomal subunit, thereby preventing initiation of protein synthesis. Here, by using genome-wide approaches, we show that KSG can interfere with translation even after the formation of the 70S initiation complex on mRNA, as the extent of KSG-mediated translation inhibition correlates with increased occupancy of start codons by 70S ribosomes. Even at saturating concentrations, KSG does not completely abolish translation, allowing for continuing expression of some Escherichia coli proteins. Differential action of KSG significantly depends on the nature of the mRNA residue immediately preceding the start codon, with guanine in this position being the most conducive to inhibition by the drug. In addition, the activity of KSG is attenuated by translational coupling as genes whose start codons overlap with the coding regions or the stop codons of the upstream cistrons tend to be less susceptible to drug-mediated inhibition. Altogether, our findings reveal KSG as an example of a small ribosomal subunit-targeting antibiotic with a well-pronounced context specificity of action.
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14
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Abstract
Toeprint assays are primer extension inhibition assays that can detect the 3' end of an RNA secondary structure, the position of a bound RNA binding protein, as well as the position of a bound 30S ribosomal subunit or a stalled ribosome. Here we describe how this assay was used to identify an RNA hairpin that sequesters a Shine-Dalgarno sequence, how the RNA-binding protein CsrA can alter RNA structure and affect 30S ribosomal subunit binding, and how the macrolide antibiotic tylosin can induce ribosome stalling.
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Affiliation(s)
- Helen Yakhnin
- Department of Biochemistry and Molecular Biology, Center for RNA Molecular Biology, The Pennsylvania State University, University Park, PA, USA
| | - Paul Babitzke
- Department of Biochemistry and Molecular Biology, Center for RNA Molecular Biology, The Pennsylvania State University, University Park, PA, USA.
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15
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Pienkoß S, Javadi S, Chaoprasid P, Nolte T, Twittenhoff C, Dersch P, Narberhaus F. The gatekeeper of Yersinia type III secretion is under RNA thermometer control. PLoS Pathog 2021; 17:e1009650. [PMID: 34767606 PMCID: PMC8612567 DOI: 10.1371/journal.ppat.1009650] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Revised: 11/24/2021] [Accepted: 10/27/2021] [Indexed: 01/03/2023] Open
Abstract
Many bacterial pathogens use a type III secretion system (T3SS) as molecular syringe to inject effector proteins into the host cell. In the foodborne pathogen Yersinia pseudotuberculosis, delivery of the secreted effector protein cocktail through the T3SS depends on YopN, a molecular gatekeeper that controls access to the secretion channel from the bacterial cytoplasm. Here, we show that several checkpoints adjust yopN expression to virulence conditions. A dominant cue is the host body temperature. A temperature of 37°C is known to induce the RNA thermometer (RNAT)-dependent synthesis of LcrF, a transcription factor that activates expression of the entire T3SS regulon. Here, we uncovered a second layer of temperature control. We show that another RNAT silences translation of the yopN mRNA at low environmental temperatures. The long and short 5’-untranslated region of both cellular yopN isoforms fold into a similar secondary structure that blocks ribosome binding. The hairpin structure with an internal loop melts at 37°C and thereby permits formation of the translation initiation complex as shown by mutational analysis, in vitro structure probing and toeprinting methods. Importantly, we demonstrate the physiological relevance of the RNAT in the faithful control of type III secretion by using a point-mutated thermostable RNAT variant with a trapped SD sequence. Abrogated YopN production in this strain led to unrestricted effector protein secretion into the medium, bacterial growth arrest and delayed translocation into eukaryotic host cells. Cumulatively, our results show that substrate delivery by the Yersinia T3SS is under hierarchical surveillance of two RNATs. Temperature serves as reliable external cue for pathogenic bacteria to recognize the entry into or exit from a warm-blooded host. At the molecular level, a temperature of 37°C induces various virulence-related processes that manipulate host cell physiology. Here, we demonstrate the temperature-dependent synthesis of the secretion regulator YopN in the foodborne pathogen Yersinia pseudotuberculosis, a close relative of Yersinia pestis. YopN blocks secretion of effector proteins through the type III secretion system unless host cell contact is established. Temperature-specific regulation relies on an RNA structure in the 5’-untranslated region of the yopN mRNA, referred to as RNA thermometer, which allows ribosome binding and thus translation initiation only at an infection-relevant temperature of 37°C. A mutated variant of the thermosensor resulting in a closed conformation prevented synthesis of the molecular gatekeeper YopN and led to permanent secretion and defective translocation of virulence factors into host cells. We suggest that the RNA thermometer plays a critical role in adjusting the optimal cellular concentration of a surveillance factor that maintains the controlled translocation of virulence factors.
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Affiliation(s)
| | - Soheila Javadi
- Microbial Biology, Ruhr University Bochum, Bochum, Germany
| | - Paweena Chaoprasid
- Institute of Infectiology, Center for Molecular Biology of Inflammation (ZMBE), University of Münster, Münster, Germany
| | - Thomas Nolte
- Microbial Biology, Ruhr University Bochum, Bochum, Germany
| | - Christian Twittenhoff
- Microbial Biology, Ruhr University Bochum, Bochum, Germany.,Rottendorf Pharma GmbH, Ennigerloh, Germany
| | - Petra Dersch
- Institute of Infectiology, Center for Molecular Biology of Inflammation (ZMBE), University of Münster, Münster, Germany
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16
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Kim Y, Eggers C, Shvetsova E, Kleemann L, Sin O, Leidel SA. Analysis of codon-specific translation by ribosome profiling. Methods Enzymol 2021; 658:191-223. [PMID: 34517947 DOI: 10.1016/bs.mie.2021.06.025] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Chemical modifications of RNA molecules can affect translation in multiple ways. Therefore, it is critical to understand how their absence changes cellular translation dynamics and in particular codon-specific translation. In this chapter, we discuss the application of ribosome profiling to analyze changes in codon-specific translation and differential translation in Saccharomyces cerevisiae and human cells.
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Affiliation(s)
- Yeji Kim
- University of Bern, Department of Chemistry, Biochemistry and Pharmaceutical Sciences, Bern, Switzerland
| | - Cristian Eggers
- University of Bern, Department of Chemistry, Biochemistry and Pharmaceutical Sciences, Bern, Switzerland
| | - Ekaterina Shvetsova
- University of Bern, Department of Chemistry, Biochemistry and Pharmaceutical Sciences, Bern, Switzerland
| | - Leon Kleemann
- University of Bern, Department of Chemistry, Biochemistry and Pharmaceutical Sciences, Bern, Switzerland
| | - Olga Sin
- University of Bern, Department of Chemistry, Biochemistry and Pharmaceutical Sciences, Bern, Switzerland
| | - Sebastian A Leidel
- University of Bern, Department of Chemistry, Biochemistry and Pharmaceutical Sciences, Bern, Switzerland.
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17
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Scheller D, Twittenhoff C, Becker F, Holler M, Narberhaus F. OmpA, a Common Virulence Factor, Is Under RNA Thermometer Control in Yersinia pseudotuberculosis. Front Microbiol 2021; 12:687260. [PMID: 34220779 PMCID: PMC8245352 DOI: 10.3389/fmicb.2021.687260] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Accepted: 04/21/2021] [Indexed: 11/13/2022] Open
Abstract
The outer membrane protein OmpA is a virulence factor in many mammalian pathogens. In previous global RNA structure probing studies, we found evidence for a temperature-modulated RNA structure in the 5'-untranslated region (5'-UTR) of the Yersinia pseudotuberculosis ompA transcript suggesting that opening of the structure at host-body temperature might relieve translational repression. Here, we support this hypothesis by quantitative reverse transcription PCR, translational reporter gene fusions, enzymatic RNA structure probing, and toeprinting assays. While ompA transcript levels decreased at 37°C compared to 25°C, translation of the transcript increased with increasing temperature. Biochemical experiments show that this is due to melting of the RNA structure, which permits ribosome binding to the 5'-UTR. A point mutation that locks the RNA structure in a closed conformation prevents translation by impairing ribosome access. Our findings add another common virulence factor to the growing list of pathogen-associated genes that are under RNA thermometer control.
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Affiliation(s)
- Daniel Scheller
- Department of Microbial Biology, Ruhr University Bochum, Bochum, Germany
| | | | - Franziska Becker
- Department of Microbial Biology, Ruhr University Bochum, Bochum, Germany
| | - Marcel Holler
- Department of Microbial Biology, Ruhr University Bochum, Bochum, Germany
| | - Franz Narberhaus
- Department of Microbial Biology, Ruhr University Bochum, Bochum, Germany
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18
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Pavlova JA, Khairullina ZZ, Tereshchenkov AG, Nazarov PA, Lukianov DA, Volynkina IA, Skvortsov DA, Makarov GI, Abad E, Murayama SY, Kajiwara S, Paleskava A, Konevega AL, Antonenko YN, Lyakhovich A, Osterman IA, Bogdanov AA, Sumbatyan NV. Triphenilphosphonium Analogs of Chloramphenicol as Dual-Acting Antimicrobial and Antiproliferating Agents. Antibiotics (Basel) 2021; 10:antibiotics10050489. [PMID: 33922611 PMCID: PMC8145938 DOI: 10.3390/antibiotics10050489] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 04/19/2021] [Accepted: 04/19/2021] [Indexed: 02/06/2023] Open
Abstract
In the current work, in continuation of our recent research, we synthesized and studied new chimeric compounds, including the ribosome-targeting antibiotic chloramphenicol (CHL) and the membrane-penetrating cation triphenylphosphonium (TPP), which are linked by alkyl groups of different lengths. Using various biochemical assays, we showed that these CAM-Cn-TPP compounds bind to the bacterial ribosome, inhibit protein synthesis in vitro and in vivo in a way similar to that of the parent CHL, and significantly reduce membrane potential. Similar to CAM-C4-TPP, the mode of action of CAM-C10-TPP and CAM-C14-TPP in bacterial ribosomes differs from that of CHL. By simulating the dynamics of CAM-Cn-TPP complexes with bacterial ribosomes, we proposed a possible explanation for the specificity of the action of these analogs in the translation process. CAM-C10-TPP and CAM-C14-TPP more strongly inhibit the growth of the Gram-positive bacteria, as compared to CHL, and suppress some CHL-resistant bacterial strains. Thus, we have shown that TPP derivatives of CHL are dual-acting compounds targeting both the ribosomes and cellular membranes of bacteria. The TPP fragment of CAM-Cn-TPP compounds has an inhibitory effect on bacteria. Moreover, since the mitochondria of eukaryotic cells possess qualities similar to those of their prokaryotic ancestors, we demonstrate the possibility of targeting chemoresistant cancer cells with these compounds.
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Affiliation(s)
- Julia A. Pavlova
- Department of Chemistry, Lomonosov Moscow State University, Leninskie Gory 1, 119991 Moscow, Russia; (J.A.P.); (Z.Z.K.); (D.A.S.); (A.A.B.)
| | - Zimfira Z. Khairullina
- Department of Chemistry, Lomonosov Moscow State University, Leninskie Gory 1, 119991 Moscow, Russia; (J.A.P.); (Z.Z.K.); (D.A.S.); (A.A.B.)
| | - Andrey G. Tereshchenkov
- A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Leninskie Gory 1, 119992 Moscow, Russia; (A.G.T.); (P.A.N.); (Y.N.A.)
| | - Pavel A. Nazarov
- A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Leninskie Gory 1, 119992 Moscow, Russia; (A.G.T.); (P.A.N.); (Y.N.A.)
- Laboratory of Molecular Genetics, Moscow Institute of Physics and Technology, 141700 Dolgoprudny, Russia
| | - Dmitrii A. Lukianov
- Center of Life Sciences, Skolkovo Institute of Science and Technology, 143028 Skolkovo, Russia;
| | - Inna A. Volynkina
- School of Bioengineering and Bioinformatics, Lomonosov Moscow State University, 119992 Moscow, Russia;
| | - Dmitry A. Skvortsov
- Department of Chemistry, Lomonosov Moscow State University, Leninskie Gory 1, 119991 Moscow, Russia; (J.A.P.); (Z.Z.K.); (D.A.S.); (A.A.B.)
| | - Gennady I. Makarov
- Laboratory of the Multiscale Modeling of Multicomponent Materials, South Ural State University, 454080 Chelyabinsk, Russia;
| | - Etna Abad
- Department of Experimental and Health Sciences, Universitat Pompeu Fabra, 08003 Barcelona, Spain;
| | - Somay Y. Murayama
- Department of Chemotherapy and Mycoses, National Institute of Infectious Diseases, 1-23-1 Toyama, Shinjuku-ku, Tokyo 162-8340, Japan;
| | - Susumu Kajiwara
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Kanagawa 226-8501, Japan;
| | - Alena Paleskava
- Petersburg Nuclear Physics Institute, NRC “Kurchatov Institute”, 188300 Gatchina, Russia; (A.P.); (A.L.K.)
- Peter the Great St. Petersburg Polytechnic University, 195251 Saint Petersburg, Russia
| | - Andrey L. Konevega
- Petersburg Nuclear Physics Institute, NRC “Kurchatov Institute”, 188300 Gatchina, Russia; (A.P.); (A.L.K.)
- Peter the Great St. Petersburg Polytechnic University, 195251 Saint Petersburg, Russia
- NRC “Kurchatov Institute”, 123182 Moscow, Russia
| | - Yuri N. Antonenko
- A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Leninskie Gory 1, 119992 Moscow, Russia; (A.G.T.); (P.A.N.); (Y.N.A.)
| | - Alex Lyakhovich
- Institute of Molecular Biology and Biophysics, Federal Research Center of Fundamental and Translational Medicine, 630117 Novosibirsk, Russia;
- Vall D’Hebron Institut de Recerca, 08035 Barcelona, Spain
| | - Ilya A. Osterman
- Department of Chemistry, Lomonosov Moscow State University, Leninskie Gory 1, 119991 Moscow, Russia; (J.A.P.); (Z.Z.K.); (D.A.S.); (A.A.B.)
- Center of Life Sciences, Skolkovo Institute of Science and Technology, 143028 Skolkovo, Russia;
- Genetics and Life Sciences Research Center, Sirius University of Science and Technology, 1 Olympic Ave, 354340 Sochi, Russia
- Correspondence: (I.A.O.); (N.V.S.)
| | - Alexey A. Bogdanov
- Department of Chemistry, Lomonosov Moscow State University, Leninskie Gory 1, 119991 Moscow, Russia; (J.A.P.); (Z.Z.K.); (D.A.S.); (A.A.B.)
- A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Leninskie Gory 1, 119992 Moscow, Russia; (A.G.T.); (P.A.N.); (Y.N.A.)
| | - Natalia V. Sumbatyan
- Department of Chemistry, Lomonosov Moscow State University, Leninskie Gory 1, 119991 Moscow, Russia; (J.A.P.); (Z.Z.K.); (D.A.S.); (A.A.B.)
- A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Leninskie Gory 1, 119992 Moscow, Russia; (A.G.T.); (P.A.N.); (Y.N.A.)
- Correspondence: (I.A.O.); (N.V.S.)
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19
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Chen CW, Pavlova JA, Lukianov DA, Tereshchenkov AG, Makarov GI, Khairullina ZZ, Tashlitsky VN, Paleskava A, Konevega AL, Bogdanov AA, Osterman IA, Sumbatyan NV, Polikanov YS. Binding and Action of Triphenylphosphonium Analog of Chloramphenicol upon the Bacterial Ribosome. Antibiotics (Basel) 2021; 10:390. [PMID: 33916420 PMCID: PMC8066774 DOI: 10.3390/antibiotics10040390] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2021] [Revised: 03/30/2021] [Accepted: 03/30/2021] [Indexed: 12/20/2022] Open
Abstract
Chloramphenicol (CHL) is a ribosome-targeting antibiotic that binds to the peptidyl transferase center (PTC) of the bacterial ribosome and inhibits peptide bond formation. As an approach for modifying and potentially improving the properties of this inhibitor, we explored ribosome binding and inhibitory properties of a semi-synthetic triphenylphosphonium analog of CHL-CAM-C4-TPP. Our data demonstrate that this compound exhibits a ~5-fold stronger affinity for the bacterial ribosome and higher potency as an in vitro protein synthesis inhibitor compared to CHL. The X-ray crystal structure of the Thermus thermophilus 70S ribosome in complex with CAM-C4-TPP reveals that, while its amphenicol moiety binds at the PTC in a fashion identical to CHL, the C4-TPP tail adopts an extended propeller-like conformation within the ribosome exit tunnel where it establishes multiple hydrophobic Van der Waals interactions with the rRNA. The synthesized compound represents a promising chemical scaffold for further development by medicinal chemists because it simultaneously targets the two key functional centers of the bacterial ribosome-PTC and peptide exit tunnel.
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Affiliation(s)
- Chih-Wei Chen
- Department of Biological Sciences, University of Illinois at Chicago, Chicago, IL 60607, USA;
| | - Julia A. Pavlova
- Department of Chemistry, Lomonosov Moscow State University, 119991 Moscow, Russia; (J.A.P.); (Z.Z.K.); (V.N.T.); (A.A.B.)
| | - Dmitrii A. Lukianov
- Center of Life Sciences, Skolkovo Institute of Science and Technology, 143028 Skolkovo, Russia;
| | - Andrey G. Tereshchenkov
- A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119991 Moscow, Russia;
| | - Gennady I. Makarov
- Laboratory of Multiscale Modeling of Multicomponent Materials, South Ural State University, 454080 Chelyabinsk, Russia;
| | - Zimfira Z. Khairullina
- Department of Chemistry, Lomonosov Moscow State University, 119991 Moscow, Russia; (J.A.P.); (Z.Z.K.); (V.N.T.); (A.A.B.)
| | - Vadim N. Tashlitsky
- Department of Chemistry, Lomonosov Moscow State University, 119991 Moscow, Russia; (J.A.P.); (Z.Z.K.); (V.N.T.); (A.A.B.)
| | - Alena Paleskava
- Petersburg Nuclear Physics Institute, National Research Center (NRC) “Kurchatov Institute”, 188300 Gatchina, Russia; (A.P.); (A.L.K.)
- Peter the Great St.Petersburg Polytechnic University, 195251 Saint Petersburg, Russia
| | - Andrey L. Konevega
- Petersburg Nuclear Physics Institute, National Research Center (NRC) “Kurchatov Institute”, 188300 Gatchina, Russia; (A.P.); (A.L.K.)
- Peter the Great St.Petersburg Polytechnic University, 195251 Saint Petersburg, Russia
- National Research Center (NRC) “Kurchatov Institute”, 123182 Moscow, Russia
| | - Alexey A. Bogdanov
- Department of Chemistry, Lomonosov Moscow State University, 119991 Moscow, Russia; (J.A.P.); (Z.Z.K.); (V.N.T.); (A.A.B.)
- A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119991 Moscow, Russia;
| | - Ilya A. Osterman
- Department of Chemistry, Lomonosov Moscow State University, 119991 Moscow, Russia; (J.A.P.); (Z.Z.K.); (V.N.T.); (A.A.B.)
- Center of Life Sciences, Skolkovo Institute of Science and Technology, 143028 Skolkovo, Russia;
| | - Natalia V. Sumbatyan
- Department of Chemistry, Lomonosov Moscow State University, 119991 Moscow, Russia; (J.A.P.); (Z.Z.K.); (V.N.T.); (A.A.B.)
- A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119991 Moscow, Russia;
| | - Yury S. Polikanov
- Department of Biological Sciences, University of Illinois at Chicago, Chicago, IL 60607, USA;
- Department of Pharmaceutical Sciences, University of Illinois at Chicago, Chicago, IL 60607, USA
- Center for Biomolecular Sciences, University of Illinois at Chicago, Chicago, IL 60607, USA
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20
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ATP-Independent Initiation during Cap-Independent Translation of m 6A-Modified mRNA. Int J Mol Sci 2021; 22:ijms22073662. [PMID: 33915887 PMCID: PMC8036370 DOI: 10.3390/ijms22073662] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2021] [Revised: 03/21/2021] [Accepted: 03/26/2021] [Indexed: 11/16/2022] Open
Abstract
The methylation of adenosine in the N6 position (m6A) is a widely used modification of eukaryotic mRNAs. Its importance for the regulation of mRNA translation was put forward recently, essentially due to the ability of methylated mRNA to be translated in conditions of inhibited cap-dependent translation initiation, e.g., under stress. However, the peculiarities of translation initiation on m6A-modified mRNAs are not fully known. In this study, we used toeprinting and translation in a cell-free system to confirm that m6A-modified mRNAs can be translated in conditions of suppressed cap-dependent translation. We show for the first time that m6A-modified mRNAs display not only decreased elongation, but also a lower efficiency of translation initiation. Additionally, we report relative resistance of m6A-mRNA translation initiation in the absence of ATP and inhibited eIF4A activity. Our novel findings indicate that the scanning of m6A-modified leader sequences is performed by a noncanonical mechanism.
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21
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Brewer SM, Twittenhoff C, Kortmann J, Brubaker SW, Honeycutt J, Massis LM, Pham THM, Narberhaus F, Monack DM. A Salmonella Typhi RNA thermosensor regulates virulence factors and innate immune evasion in response to host temperature. PLoS Pathog 2021; 17:e1009345. [PMID: 33651854 PMCID: PMC7954313 DOI: 10.1371/journal.ppat.1009345] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2020] [Revised: 03/12/2021] [Accepted: 01/28/2021] [Indexed: 12/20/2022] Open
Abstract
Sensing and responding to environmental signals is critical for bacterial pathogens to successfully infect and persist within hosts. Many bacterial pathogens sense temperature as an indication they have entered a new host and must alter their virulence factor expression to evade immune detection. Using secondary structure prediction, we identified an RNA thermosensor (RNAT) in the 5' untranslated region (UTR) of tviA encoded by the typhoid fever-causing bacterium Salmonella enterica serovar Typhi (S. Typhi). Importantly, tviA is a transcriptional regulator of the critical virulence factors Vi capsule, flagellin, and type III secretion system-1 expression. By introducing point mutations to alter the mRNA secondary structure, we demonstrate that the 5' UTR of tviA contains a functional RNAT using in vitro expression, structure probing, and ribosome binding methods. Mutational inhibition of the RNAT in S. Typhi causes aberrant virulence factor expression, leading to enhanced innate immune responses during infection. In conclusion, we show that S. Typhi regulates virulence factor expression through an RNAT in the 5' UTR of tviA. Our findings demonstrate that limiting inflammation through RNAT-dependent regulation in response to host body temperature is important for S. Typhi's "stealthy" pathogenesis.
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Affiliation(s)
- Susan M. Brewer
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California, United States of America
| | | | - Jens Kortmann
- Genentech, Inc., South San Francisco, California, United States of America
| | - Sky W. Brubaker
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California, United States of America
| | - Jared Honeycutt
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California, United States of America
| | - Liliana Moura Massis
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California, United States of America
| | - Trung H. M. Pham
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California, United States of America
| | | | - Denise M. Monack
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California, United States of America
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22
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Sawyer EB, Phelan JE, Clark TG, Cortes T. A snapshot of translation in Mycobacterium tuberculosis during exponential growth and nutrient starvation revealed by ribosome profiling. Cell Rep 2021; 34:108695. [PMID: 33535039 PMCID: PMC7856553 DOI: 10.1016/j.celrep.2021.108695] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Revised: 11/20/2020] [Accepted: 01/05/2021] [Indexed: 12/15/2022] Open
Abstract
Mycobacterium tuberculosis, which causes tuberculosis, can undergo prolonged periods of non-replicating persistence in the host. The mechanisms underlying this are not fully understood, but translational regulation is thought to play a role. A large proportion of mRNA transcripts expressed in M. tuberculosis lack canonical bacterial translation initiation signals, but little is known about the implications of this for fine-tuning of translation. Here, we perform ribosome profiling to characterize the translational landscape of M. tuberculosis under conditions of exponential growth and nutrient starvation. Our data reveal robust, widespread translation of non-canonical transcripts and point toward different translation initiation mechanisms compared to canonical Shine-Dalgarno transcripts. During nutrient starvation, patterns of ribosome recruitment vary, suggesting that regulation of translation in this pathogen is more complex than originally thought. Our data represent a rich resource for others seeking to understand translational regulation in bacterial pathogens.
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Affiliation(s)
- Elizabeth B Sawyer
- TB Centre and Department of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 7HT, UK
| | - Jody E Phelan
- TB Centre and Department of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 7HT, UK
| | - Taane G Clark
- TB Centre and Department of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 7HT, UK; Department of Infectious Disease Epidemiology, Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 7HT, UK
| | - Teresa Cortes
- TB Centre and Department of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 7HT, UK.
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23
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Correia Santos S, Bischler T, Westermann AJ, Vogel J. MAPS integrates regulation of actin-targeting effector SteC into the virulence control network of Salmonella small RNA PinT. Cell Rep 2021; 34:108722. [PMID: 33535041 DOI: 10.1016/j.celrep.2021.108722] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Revised: 11/25/2020] [Accepted: 01/13/2021] [Indexed: 10/22/2022] Open
Abstract
A full understanding of the contribution of small RNAs (sRNAs) to bacterial virulence demands knowledge of their target suites under infection-relevant conditions. Here, we take an integrative approach to capturing targets of the Hfq-associated sRNA PinT, a known post-transcriptional timer of the two major virulence programs of Salmonella enterica. Using MS2 affinity purification and RNA sequencing (MAPS), we identify PinT ligands in bacteria under in vitro conditions mimicking specific stages of the infection cycle and in bacteria growing inside macrophages. This reveals PinT-mediated translational inhibition of the secreted effector kinase SteC, which had gone unnoticed in previous target searches. Using genetic, biochemical, and microscopic assays, we provide evidence for PinT-mediated repression of steC mRNA, eventually delaying actin rearrangements in infected host cells. Our findings support the role of PinT as a central post-transcriptional regulator in Salmonella virulence and illustrate the need for complementary methods to reveal the full target suites of sRNAs.
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Affiliation(s)
- Sara Correia Santos
- Institute for Molecular Infection Biology, University of Würzburg, Würzburg, Germany
| | - Thorsten Bischler
- Core Unit Systems Medicine, University of Würzburg, Würzburg, Germany
| | - Alexander J Westermann
- Institute for Molecular Infection Biology, University of Würzburg, Würzburg, Germany; Helmholtz Institute for RNA-Based Infection Research, Helmholtz Centre for Infection Research, Würzburg, Germany.
| | - Jörg Vogel
- Institute for Molecular Infection Biology, University of Würzburg, Würzburg, Germany; Helmholtz Institute for RNA-Based Infection Research, Helmholtz Centre for Infection Research, Würzburg, Germany.
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24
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Niblett D, Nelson C, Leung CS, Rexroad G, Cozy J, Zhou J, Lancaster L, Noller HF. Mutations in domain IV of elongation factor EF-G confer -1 frameshifting. RNA (NEW YORK, N.Y.) 2021; 27:40-53. [PMID: 33008838 PMCID: PMC7749637 DOI: 10.1261/rna.077339.120] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Accepted: 09/24/2020] [Indexed: 05/25/2023]
Abstract
A recent crystal structure of a ribosome complex undergoing partial translocation in the absence of elongation factor EF-G showed disruption of codon-anticodon pairing and slippage of the reading frame by -1, directly implicating EF-G in preservation of the translational reading frame. Among mutations identified in a random screen for dominant-lethal mutations of EF-G were a cluster of six that map to the tip of domain IV, which has been shown to contact the codon-anticodon duplex in trapped translocation intermediates. In vitro synthesis of a full-length protein using these mutant EF-Gs revealed dramatically increased -1 frameshifting, providing new evidence for a role for domain IV of EF-G in maintaining the reading frame. These mutations also caused decreased rates of mRNA translocation and rotational movement of the head and body domains of the 30S ribosomal subunit during translocation. Our results are in general agreement with recent findings from Rodnina and coworkers based on in vitro translation of an oligopeptide using EF-Gs containing mutations at two positions in domain IV, who found an inverse correlation between the degree of frameshifting and rates of translocation. Four of our six mutations are substitutions at positions that interact with the translocating tRNA, in each case contacting the RNA backbone of the anticodon loop. We suggest that EF-G helps to preserve the translational reading frame by preventing uncoupled movement of the tRNA through these contacts; a further possibility is that these interactions may stabilize a conformation of the anticodon that favors base-pairing with its codon.
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Affiliation(s)
- Dustin Niblett
- Center for Molecular Biology of RNA and Department of Molecular, Cell and Developmental Biology, University of California at Santa Cruz, Santa Cruz, California 95064, USA
| | - Charlotte Nelson
- Center for Molecular Biology of RNA and Department of Molecular, Cell and Developmental Biology, University of California at Santa Cruz, Santa Cruz, California 95064, USA
| | - Calvin S Leung
- Center for Molecular Biology of RNA and Department of Molecular, Cell and Developmental Biology, University of California at Santa Cruz, Santa Cruz, California 95064, USA
| | - Gillian Rexroad
- Center for Molecular Biology of RNA and Department of Molecular, Cell and Developmental Biology, University of California at Santa Cruz, Santa Cruz, California 95064, USA
| | - Jake Cozy
- Center for Molecular Biology of RNA and Department of Molecular, Cell and Developmental Biology, University of California at Santa Cruz, Santa Cruz, California 95064, USA
| | - Jie Zhou
- Center for Molecular Biology of RNA and Department of Molecular, Cell and Developmental Biology, University of California at Santa Cruz, Santa Cruz, California 95064, USA
| | - Laura Lancaster
- Center for Molecular Biology of RNA and Department of Molecular, Cell and Developmental Biology, University of California at Santa Cruz, Santa Cruz, California 95064, USA
| | - Harry F Noller
- Center for Molecular Biology of RNA and Department of Molecular, Cell and Developmental Biology, University of California at Santa Cruz, Santa Cruz, California 95064, USA
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25
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Hör J, Di Giorgio S, Gerovac M, Venturini E, Förstner KU, Vogel J. Grad-seq shines light on unrecognized RNA and protein complexes in the model bacterium Escherichia coli. Nucleic Acids Res 2020; 48:9301-9319. [PMID: 32813020 PMCID: PMC7498339 DOI: 10.1093/nar/gkaa676] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2020] [Revised: 07/29/2020] [Accepted: 08/14/2020] [Indexed: 12/21/2022] Open
Abstract
Stable protein complexes, including those formed with RNA, are major building blocks of every living cell. Escherichia coli has been the leading bacterial organism with respect to global protein-protein networks. Yet, there has been no global census of RNA/protein complexes in this model species of microbiology. Here, we performed Grad-seq to establish an RNA/protein complexome, reconstructing sedimentation profiles in a glycerol gradient for ∼85% of all E. coli transcripts and ∼49% of the proteins. These include the majority of small noncoding RNAs (sRNAs) detectable in this bacterium as well as the general sRNA-binding proteins, CsrA, Hfq and ProQ. In presenting use cases for utilization of these RNA and protein maps, we show that a stable association of RyeG with 30S ribosomes gives this seemingly noncoding RNA of prophage origin away as an mRNA of a toxic small protein. Similarly, we show that the broadly conserved uncharacterized protein YggL is a 50S subunit factor in assembled 70S ribosomes. Overall, this study crucially extends our knowledge about the cellular interactome of the primary model bacterium E. coli through providing global RNA/protein complexome information and should facilitate functional discovery in this and related species.
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Affiliation(s)
- Jens Hör
- Institute of Molecular Infection Biology, University of Würzburg, D-97080 Würzburg, Germany
| | - Silvia Di Giorgio
- Institute of Molecular Infection Biology, University of Würzburg, D-97080 Würzburg, Germany.,ZB MED - Information Centre for Life Sciences, D-50931 Cologne, Germany
| | - Milan Gerovac
- Institute of Molecular Infection Biology, University of Würzburg, D-97080 Würzburg, Germany
| | - Elisa Venturini
- Institute of Molecular Infection Biology, University of Würzburg, D-97080 Würzburg, Germany
| | - Konrad U Förstner
- ZB MED - Information Centre for Life Sciences, D-50931 Cologne, Germany.,TH Köln, Faculty of Information Science and Communication Studies, D-50678 Cologne, Germany
| | - Jörg Vogel
- Institute of Molecular Infection Biology, University of Würzburg, D-97080 Würzburg, Germany.,Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), D-97080 Würzburg, Germany
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26
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Limbrick EM, Graf M, Derewacz DK, Nguyen F, Spraggins JM, Wieland M, Ynigez-Gutierrez AE, Reisman BJ, Zinshteyn B, McCulloch KM, Iverson TM, Green R, Wilson DN, Bachmann BO. Bifunctional Nitrone-Conjugated Secondary Metabolite Targeting the Ribosome. J Am Chem Soc 2020; 142:18369-18377. [PMID: 32709196 DOI: 10.1021/jacs.0c04675] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Many microorganisms possess the capacity for producing multiple antibiotic secondary metabolites. In a few notable cases, combinations of secondary metabolites produced by the same organism are used in important combination therapies for treatment of drug-resistant bacterial infections. However, examples of conjoined roles of bioactive metabolites produced by the same organism remain uncommon. During our genetic functional analysis of oxidase-encoding genes in the everninomicin producer Micromonospora carbonacea var. aurantiaca, we discovered previously uncharacterized antibiotics everninomicin N and O, comprised of an everninomicin fragment conjugated to the macrolide rosamicin via a rare nitrone moiety. These metabolites were determined to be hydrolysis products of everninomicin P, a nitrone-linked conjugate likely the result of nonenzymatic condensation of the rosamicin aldehyde and the octasaccharide everninomicin F, possessing a hydroxylamino sugar moiety. Rosamicin binds the erythromycin macrolide binding site approximately 60 Å from the orthosomycin binding site of everninomicins. However, while individual ribosomal binding sites for each functional half of everninomicin P are too distant for bidentate binding, ligand displacement studies demonstrated that everninomicin P competes with rosamicin for ribosomal binding. Chemical protection studies and structural analysis of everninomicin P revealed that everninomicin P occupies both the macrolide- and orthosomycin-binding sites on the 70S ribosome. Moreover, resistance mutations within each binding site were overcome by the inhibition of the opposite functional antibiotic moiety binding site. These data together demonstrate a strategy for coupling orthogonal antibiotic pharmacophores, a surprising tolerance for substantial covalent modification of each antibiotic, and a potential beneficial strategy to combat antibiotic resistance.
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Affiliation(s)
- Emilianne M Limbrick
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Michael Graf
- Institute of Biochemistry and Molecular Biology, University of Hamburg, Hamburg 20146, Germany
| | - Dagmara K Derewacz
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Fabian Nguyen
- Department of Biochemistry, University of Munich, 81377 Munich, Germany
| | - Jeffrey M Spraggins
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States.,Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37205, United States.,Mass Spectrometry Research Center, Vanderbilt University School of Medicine, Nashville, Tennessee 37232, United States
| | - Maximiliane Wieland
- Institute of Biochemistry and Molecular Biology, University of Hamburg, Hamburg 20146, Germany
| | | | - Benjamin J Reisman
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Boris Zinshteyn
- Department of Molecular Biology and Genetics, Johns Hopkins University. Baltimore, Maryland 21205, United States
| | - Kathryn M McCulloch
- Department of Pharmacology, Vanderbilt University, Nashville, Tennessee 37232, United States
| | - T M Iverson
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37205, United States.,Department of Pharmacology, Vanderbilt University, Nashville, Tennessee 37232, United States.,Vanderbilt Center for Structural Biology, Nashville, Tennessee 37232, United States
| | - Rachel Green
- Department of Molecular Biology and Genetics, Johns Hopkins University. Baltimore, Maryland 21205, United States.,Howard Hughes Medical Institute, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, United States
| | - Daniel N Wilson
- Institute of Biochemistry and Molecular Biology, University of Hamburg, Hamburg 20146, Germany
| | - Brian O Bachmann
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States.,Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37205, United States.,Department of Pharmacology, Vanderbilt University, Nashville, Tennessee 37232, United States.,Vanderbilt Institute of Chemical Biology, Nashville, Tennessee 37205, United States
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27
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Ovchinnikov SV, Bikmetov D, Livenskyi A, Serebryakova M, Wilcox B, Mangano K, Shiriaev DI, Osterman IA, Sergiev PV, Borukhov S, Vazquez-Laslop N, Mankin AS, Severinov K, Dubiley S. Mechanism of translation inhibition by type II GNAT toxin AtaT2. Nucleic Acids Res 2020; 48:8617-8625. [PMID: 32597957 PMCID: PMC7470980 DOI: 10.1093/nar/gkaa551] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2020] [Revised: 06/05/2020] [Accepted: 06/17/2020] [Indexed: 12/25/2022] Open
Abstract
Type II toxin–antitoxins systems are widespread in prokaryotic genomes. Typically, they comprise two proteins, a toxin, and an antitoxin, encoded by adjacent genes and forming a complex in which the enzymatic activity of the toxin is inhibited. Under stress conditions, the antitoxin is degraded liberating the active toxin. Though thousands of various toxin–antitoxins pairs have been predicted bioinformatically, only a handful has been thoroughly characterized. Here, we describe the AtaT2 toxin from a toxin–antitoxin system from Escherichia coli O157:H7. We show that AtaT2 is the first GNAT (Gcn5-related N-acetyltransferase) toxin that specifically targets charged glycyl tRNA. In vivo, the AtaT2 activity induces ribosome stalling at all four glycyl codons but does not evoke a stringent response. In vitro, AtaT2 acetylates the aminoacyl moiety of isoaccepting glycyl tRNAs, thus precluding their participation in translation. Our study broadens the known target specificity of GNAT toxins beyond the earlier described isoleucine and formyl methionine tRNAs, and suggest that various GNAT toxins may have evolved to specificaly target other if not all individual aminoacyl tRNAs.
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Affiliation(s)
- Stepan V Ovchinnikov
- Centre for Life Sciences, Skolkovo Institute of Science and Technology, Skolkovo 143025, Russia
| | - Dmitry Bikmetov
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology, Russian Academy of Sciences, 119334 Moscow, Russia.,Institute of Gene Biology, Russian Academy of Science, 119334 Moscow, Russia
| | - Alexei Livenskyi
- Institute of Gene Biology, Russian Academy of Science, 119334 Moscow, Russia.,Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow 119992, Russia
| | - Marina Serebryakova
- Institute of Gene Biology, Russian Academy of Science, 119334 Moscow, Russia.,Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow 119992, Russia
| | - Brendan Wilcox
- Centre for Life Sciences, Skolkovo Institute of Science and Technology, Skolkovo 143025, Russia
| | - Kyle Mangano
- Center for Biomolecular Sciences, University of Illinois, Chicago, IL 60607, USA.,Department of Pharmaceutical Sciences, University of Illinois, Chicago, IL 60607, USA
| | - Dmitrii I Shiriaev
- Department of Chemistry, Lomonosov Moscow State University, Moscow 119992, Russia
| | - Ilya A Osterman
- Centre for Life Sciences, Skolkovo Institute of Science and Technology, Skolkovo 143025, Russia.,Department of Chemistry, Lomonosov Moscow State University, Moscow 119992, Russia
| | - Petr V Sergiev
- Centre for Life Sciences, Skolkovo Institute of Science and Technology, Skolkovo 143025, Russia.,Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow 119992, Russia
| | - Sergei Borukhov
- Department of Cell Biology and Neuroscience, Rowan University School of Osteopathic Medicine, Stratford, NJ 08084-1489, USA
| | - Nora Vazquez-Laslop
- Center for Biomolecular Sciences, University of Illinois, Chicago, IL 60607, USA.,Department of Pharmaceutical Sciences, University of Illinois, Chicago, IL 60607, USA
| | - Alexander S Mankin
- Center for Biomolecular Sciences, University of Illinois, Chicago, IL 60607, USA.,Department of Pharmaceutical Sciences, University of Illinois, Chicago, IL 60607, USA
| | - Konstantin Severinov
- Centre for Life Sciences, Skolkovo Institute of Science and Technology, Skolkovo 143025, Russia.,Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology, Russian Academy of Sciences, 119334 Moscow, Russia.,Waksman Institute for Microbiology, Piscataway, NJ 08854-8020, USA
| | - Svetlana Dubiley
- Centre for Life Sciences, Skolkovo Institute of Science and Technology, Skolkovo 143025, Russia.,Institute of Gene Biology, Russian Academy of Science, 119334 Moscow, Russia
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28
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Sarecycline interferes with tRNA accommodation and tethers mRNA to the 70S ribosome. Proc Natl Acad Sci U S A 2020; 117:20530-20537. [PMID: 32817463 PMCID: PMC7456112 DOI: 10.1073/pnas.2008671117] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Sarecycline is the first narrow-spectrum tetracycline-class antibiotic that was recently approved by the FDA for the clinical treatment of acne vulgaris. In this work, we determined two (2.8-Å and 3.0-Å) X-ray crystal structures of sarecycline bound to the initiation complex of the bacterial 70S ribosome and found that this antibiotic inhibits bacterial ribosome in part using a mechanism of direct mRNA contact, which has not been reported for any other tetracyclines so far. Moreover, our structural analysis rationalizes why sarecycline is able to overcome one of the most common mechanisms of resistance to tetracyclines among pathogenic bacteria. Thus, this work provides mechanistic insights into the function of the tetracycline class of antibiotics on the ribosome with direct clinical relevance. Sarecycline is a new narrow-spectrum tetracycline-class antibiotic approved for the treatment of acne vulgaris. Tetracyclines share a common four-ring naphthacene core and inhibit protein synthesis by interacting with the 70S bacterial ribosome. Sarecycline is distinguished chemically from other tetracyclines because it has a 7-[[methoxy(methyl)amino]methyl] group attached at the C7 position of ring D. To investigate the functional role of this C7 moiety, we determined the X-ray crystal structure of sarecycline bound to the Thermus thermophilus 70S ribosome. Our 2.8-Å resolution structure revealed that sarecycline binds at the canonical tetracycline binding site located in the decoding center of the small ribosomal subunit. Importantly, unlike other tetracyclines, the unique C7 extension of sarecycline extends into the messenger RNA (mRNA) channel to form a direct interaction with the A-site codon to possibly interfere with mRNA movement through the channel and/or disrupt A-site codon–anticodon interaction. Based on our biochemical studies, sarecycline appears to be a more potent initiation inhibitor compared to other tetracyclines, possibly due to drug interactions with the mRNA, thereby blocking accommodation of the first aminoacyl transfer RNA (tRNA) into the A site. Overall, our structural and biochemical findings rationalize the role of the unique C7 moiety of sarecycline in antibiotic action.
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Sakharov PA, Sogorin EA, Agalarov SC, Kolb VA. Modification of the 5' End of mRNA Leader Sequence Alters the Set of Initiation Factors Essential for Initiation of Translation. Mol Biol 2020. [DOI: 10.1134/s0026893320030140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Aleksashin NA, Szal T, d'Aquino AE, Jewett MC, Vázquez-Laslop N, Mankin AS. A fully orthogonal system for protein synthesis in bacterial cells. Nat Commun 2020; 11:1858. [PMID: 32313034 PMCID: PMC7170887 DOI: 10.1038/s41467-020-15756-1] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Accepted: 03/12/2020] [Indexed: 02/06/2023] Open
Abstract
Ribosome engineering is a powerful approach for expanding the catalytic potential of the protein synthesis apparatus. Due to the potential detriment the properties of the engineered ribosome may have on the cell, the designer ribosome needs to be functionally isolated from the translation machinery synthesizing cellular proteins. One solution to this problem was offered by Ribo-T, an engineered ribosome with tethered subunits which, while producing a desired protein, could be excluded from general translation. Here, we provide a conceptually different design of a cell with two orthogonal protein synthesis systems, where Ribo-T produces the proteome, while the dissociable ribosome is committed to the translation of a specific mRNA. The utility of this system is illustrated by generating a comprehensive collection of mutants with alterations at every rRNA nucleotide of the peptidyl transferase center and isolating gain-of-function variants that enable the ribosome to overcome the translation termination blockage imposed by an arrest peptide.
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Affiliation(s)
- Nikolay A Aleksashin
- Center for Biomolecular Sciences, University of Illinois at Chicago, Chicago, IL, 60607, USA.,Department of Pharmaceutical Sciences, University of Illinois at Chicago, Chicago, IL, 60612, USA
| | - Teresa Szal
- Center for Biomolecular Sciences, University of Illinois at Chicago, Chicago, IL, 60607, USA
| | - Anne E d'Aquino
- Interdisciplinary Biological Science Program, Northwestern University, 2145 Sheridan Rd, Evanston, IL, 60208, USA.,Department of Chemical and Biological Engineering, Northwestern University, 2145 Sheridan Rd, Evanston, IL, 60208, USA
| | - Michael C Jewett
- Department of Chemical and Biological Engineering, Northwestern University, 2145 Sheridan Rd, Evanston, IL, 60208, USA.,Center for Synthetic Biology, Northwestern University, 2145 Sheridan Rd, Evanston, IL, 60208, USA
| | - Nora Vázquez-Laslop
- Center for Biomolecular Sciences, University of Illinois at Chicago, Chicago, IL, 60607, USA.,Department of Pharmaceutical Sciences, University of Illinois at Chicago, Chicago, IL, 60612, USA
| | - Alexander S Mankin
- Center for Biomolecular Sciences, University of Illinois at Chicago, Chicago, IL, 60607, USA. .,Department of Pharmaceutical Sciences, University of Illinois at Chicago, Chicago, IL, 60612, USA.
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31
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Romilly C, Hoekzema M, Holmqvist E, Wagner EGH. Small RNAs OmrA and OmrB promote class III flagellar gene expression by inhibiting the synthesis of anti-Sigma factor FlgM. RNA Biol 2020; 17:872-880. [PMID: 32133913 PMCID: PMC7549644 DOI: 10.1080/15476286.2020.1733801] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
Bacteria can move by a variety of mechanisms, the best understood being flagella-mediated motility. Flagellar genes are organized in a three-tiered cascade allowing for temporally regulated expression that involves both transcriptional and post-transcriptional control. The class I operon encodes the master regulator FlhDC that drives class II gene transcription. Class II genes include fliA and flgM, which encode the Sigma factor σ28, required for class III transcription, and the anti-Sigma factor FlgM, which inhibits σ28 activity, respectively. The flhDC mRNA is regulated by several small regulatory RNAs (sRNAs). Two of these, the sequence-related OmrA and OmrB RNAs, inhibit FlhD synthesis. Here, we report on a second layer of sRNA-mediated control downstream of FhlDC in the flagella pathway. By mutational analysis, we confirm that a predicted interaction between the conserved 5ʹ seed sequences of OmrA/B and the early coding sequence in flgM mRNA reduces FlgM expression. Regulation is dependent on the global RNA-binding protein Hfq. In vitro experiments support a canonical mechanism: binding of OmrA/B prevents ribosome loading and decreases FlgM protein synthesis. Simultaneous inhibition of both FlhD and FlgM synthesis by OmrA/B complicated an assessment of how regulation of FlgM alone impacts class III gene transcription. Using a combinatorial mutation strategy, we were able to uncouple these two targets and demonstrate that OmrA/B-dependent inhibition of FlgM synthesis liberates σ28 to ultimately promote higher expression of the class III flagellin gene fliC.
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Affiliation(s)
- Cédric Romilly
- Department of Cell and Molecular Biology, Biomedical Center, Uppsala University , Uppsala, Sweden
| | - Mirthe Hoekzema
- Department of Cell and Molecular Biology, Biomedical Center, Uppsala University , Uppsala, Sweden
| | - Erik Holmqvist
- Department of Cell and Molecular Biology, Biomedical Center, Uppsala University , Uppsala, Sweden
| | - E Gerhart H Wagner
- Department of Cell and Molecular Biology, Biomedical Center, Uppsala University , Uppsala, Sweden
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The 5' NAD Cap of RNAIII Modulates Toxin Production in Staphylococcus aureus Isolates. J Bacteriol 2020; 202:JB.00591-19. [PMID: 31871032 DOI: 10.1128/jb.00591-19] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Accepted: 12/18/2019] [Indexed: 01/14/2023] Open
Abstract
Nicotinamide adenosine dinucleotide (NAD) has been found to be covalently attached to the 5' ends of specific RNAs in many different organisms, but the physiological consequences of this modification are largely unknown. Here, we report the occurrence of several NAD-RNAs in the opportunistic pathogen Staphylococcus aureus Most prominently, RNAIII, a central quorum-sensing regulator of this bacterium's physiology, was found to be 5' NAD capped in a range from 10 to 35%. NAD incorporation efficiency into RNAIII was found to depend in vivo on the -1 position of the P3 promoter. An increase in RNAIII's NAD content led to a decreased expression of alpha- and delta-toxins, resulting in reduced cytotoxicity of the modified strains. These effects seem to be caused neither by changes in RNAIII's secondary structure nor by a different translatability upon NAD attachment, as indicated by unaltered patterns in in vitro chemical probing and toeprinting experiments. Even though we did not observe any effect of this modification on RNAIII's secondary structure or translatability in vitro, additional unidentified factors might account for the modulation of exotoxins in vivo Ultimately, the study constitutes a step forward in the discovery of new roles of the NAD molecule in bacteria.IMPORTANCE Numerous organisms, including bacteria, are endowed with a 5' NAD cap in specific RNAs. While the presence of the 5' NAD cap modulates the stability of the modified RNA species, a significant biological function and phenotype have not been assigned so far. Here, we show the presence of a 5' NAD cap in RNAIII from S. aureus, a dual-function regulatory RNA involved in quorum-sensing processes and regulation of virulence factor expression. We also demonstrate that altering the natural NAD modification ratio of RNAIII leads to a decrease in exotoxin production, thereby modulating the bacterium's virulence. Our work unveils a new layer of regulation of RNAIII and the agr system that might be linked to the redox state of the NAD molecule in the cell.
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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: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Accepted: 01/10/2020] [Indexed: 02/06/2023]
Abstract
Polyamines are essential metabolites that play an important role in cell growth, stress adaptation, and microbial virulence1–3. In order to survive and multiply within a human host, pathogenic bacteria adjust the expression and activity of polyamine biosynthetic enzymes in response to different environmental stresses and metabolic cues2. Here, we show that ornithine capture by the ribosome and the nascent peptide SpeFL controls polyamine synthesis in γ-proteobacteria by inducing the expression of the ornithine decarboxylase SpeF4, via a mechanism involving ribosome stalling and transcription antitermination. In addition, we present the cryo-EM structure of an Escherichia coli (E. coli) ribosome stalled during translation of speFL in the presence of ornithine. The structure shows how the ribosome and the SpeFL sensor domain form a highly selective binding pocket that accommodates a single ornithine molecule but excludes near-cognate ligands. Ornithine pre-associates with the ribosome and is then held in place by the sensor domain, leading to the compaction of the SpeFL effector domain and blocking the action of release factor RF1. Thus, our study not only reveals basic strategies by which nascent peptides assist the ribosome in detecting a specific metabolite, but also provides a framework for assessing how ornithine promotes virulence in several human pathogens.
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Affiliation(s)
- Alba Herrero Del Valle
- Institut Européen de Chimie et Biologie, Université de Bordeaux, Pessac, France.,Institut National de la Santé et de la Recherche Médicale (U1212), Bordeaux, France.,Centre National de la Recherche Scientifique (UMR 5320), Bordeaux, France
| | - Britta Seip
- Institut Européen de Chimie et Biologie, Université de Bordeaux, Pessac, France.,Institut National de la Santé et de la Recherche Médicale (U1212), Bordeaux, France.,Centre National de la Recherche Scientifique (UMR 5320), Bordeaux, France.,Evotec International GmbH, Göttingen, Germany
| | - Iñaki Cervera-Marzal
- Institut Européen de Chimie et Biologie, Université de Bordeaux, Pessac, France.,Institut National de la Santé et de la Recherche Médicale (U1212), Bordeaux, France.,Centre National de la Recherche Scientifique (UMR 5320), Bordeaux, France.,Aix Marseille Université, CNRS, INSERM, CIML, Centre d'Immunologie de Marseille-Luminy, Marseille, France
| | - Guénaël Sacheau
- Institut Européen de Chimie et Biologie, Université de Bordeaux, Pessac, France.,Institut National de la Santé et de la Recherche Médicale (U1212), Bordeaux, France.,Centre National de la Recherche Scientifique (UMR 5320), Bordeaux, France.,Sopra Steria, Saint-Herblain, France
| | - A Carolin Seefeldt
- Institut Européen de Chimie et Biologie, Université de Bordeaux, Pessac, France.,Institut National de la Santé et de la Recherche Médicale (U1212), Bordeaux, France.,Centre National de la Recherche Scientifique (UMR 5320), Bordeaux, France.,Department of Cell and Molecular Biology, Biomedical Center, Uppsala University, Uppsala, Sweden
| | - C Axel Innis
- Institut Européen de Chimie et Biologie, Université de Bordeaux, Pessac, France. .,Institut National de la Santé et de la Recherche Médicale (U1212), Bordeaux, France. .,Centre National de la Recherche Scientifique (UMR 5320), Bordeaux, France.
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Regulation of OmpA Translation and Shigella dysenteriae Virulence by an RNA Thermometer. Infect Immun 2020; 88:IAI.00871-19. [PMID: 31792074 DOI: 10.1128/iai.00871-19] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Accepted: 11/25/2019] [Indexed: 12/20/2022] Open
Abstract
RNA thermometers are cis-acting riboregulators that mediate the posttranscriptional regulation of gene expression in response to environmental temperature. Such regulation is conferred by temperature-responsive structural changes within the RNA thermometer that directly result in differential ribosomal binding to the regulated transcript. The significance of RNA thermometers in controlling bacterial physiology and pathogenesis is becoming increasingly clear. This study combines in silico, molecular genetics, and biochemical analyses to characterize both the structure and function of a newly identified RNA thermometer within the ompA transcript of Shigella dysenteriae First identified by in silico structural predictions, genetic analyses have demonstrated that the ompA RNA thermometer is a functional riboregulator sufficient to confer posttranscriptional temperature-dependent regulation, with optimal expression observed at the host-associated temperature of 37°C. Structural studies and ribosomal binding analyses have revealed both increased exposure of the ribosomal binding site and increased ribosomal binding to the ompA transcript at permissive temperatures. The introduction of site-specific mutations predicted to alter the temperature responsiveness of the ompA RNA thermometer has predictable consequences for both the structure and function of the regulatory element. Finally, in vitro tissue culture-based analyses implicate the ompA RNA thermometer as a bona fide S. dysenteriae virulence factor in this bacterial pathogen. Given that ompA is highly conserved among Gram-negative pathogens, these studies not only provide insight into the significance of riboregulation in controlling Shigella virulence, but they also have the potential to facilitate further understanding of the physiology and/or pathogenesis of a wide range of bacterial species.
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Twittenhoff C, Heroven AK, Mühlen S, Dersch P, Narberhaus F. An RNA thermometer dictates production of a secreted bacterial toxin. PLoS Pathog 2020; 16:e1008184. [PMID: 31951643 PMCID: PMC6992388 DOI: 10.1371/journal.ppat.1008184] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Revised: 01/30/2020] [Accepted: 11/01/2019] [Indexed: 02/06/2023] Open
Abstract
Frequent transitions of bacterial pathogens between their warm-blooded host and external reservoirs are accompanied by abrupt temperature shifts. A temperature of 37°C serves as reliable signal for ingestion by a mammalian host, which induces a major reprogramming of bacterial gene expression and metabolism. Enteric Yersiniae are Gram-negative pathogens accountable for self-limiting gastrointestinal infections. Among the temperature-regulated virulence genes of Yersinia pseudotuberculosis is cnfY coding for the cytotoxic necrotizing factor (CNFY), a multifunctional secreted toxin that modulates the host’s innate immune system and contributes to the decision between acute infection and persistence. We report that the major determinant of temperature-regulated cnfY expression is a thermo-labile RNA structure in the 5’-untranslated region (5’-UTR). Various translational gene fusions demonstrated that this region faithfully regulates translation initiation regardless of the transcription start site, promoter or reporter strain. RNA structure probing revealed a labile stem-loop structure, in which the ribosome binding site is partially occluded at 25°C but liberated at 37°C. Consistent with translational control in bacteria, toeprinting (primer extension inhibition) experiments in vitro showed increased ribosome binding at elevated temperature. Point mutations locking the 5’-UTR in its 25°C structure impaired opening of the stem loop, ribosome access and translation initiation at 37°C. To assess the in vivo relevance of temperature control, we used a mouse infection model. Y. pseudotuberculosis strains carrying stabilized RNA thermometer variants upstream of cnfY were avirulent and attenuated in their ability to disseminate into mesenteric lymph nodes and spleen. We conclude with a model, in which the RNA thermometer acts as translational roadblock in a two-layered regulatory cascade that tightly controls provision of the CNFY toxin during acute infection. Similar RNA structures upstream of various cnfY homologs suggest that RNA thermosensors dictate the production of secreted toxins in a wide range of pathogens. Bacterial pathogens closely survey the ambient conditions and induce virulence genes only at appropriate conditions. Upon host contact, many pathogens secrete toxins in order to subvert host defense systems. We find that such a secreted toxin in enteropathogenic Yersinia pseudotuberculosis is produced only at host body temperature. This regulation depends on a temperature-responsive RNA structure, an RNA thermometer, in the 5’-untranslated region of the toxin mRNA, which prevents translation at low temperatures when the bacterium is outside the host. Preventing melting of the RNA structure at 37°C by nucleotide substitutions that stabilize base pairing resulted in avirulent Yersinia strains unable to infect mice. Given that similar RNA thermometer-like structures exist upstream of related toxin genes in various bacterial pathogens, we propose that RNA thermometer-mediated toxin production is an evolutionary conserved mechanism. Interfering with opening of such regulatory structures might thus be a promising strategy targeting a broad spectrum of bacterial pathogens.
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Affiliation(s)
| | - Ann Kathrin Heroven
- Department of Molecular Infection Biology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Sabrina Mühlen
- Department of Molecular Infection Biology, Helmholtz Centre for Infection Research, Braunschweig, Germany
- Institute of Infectiology, Center for Molecular Biology of Inflammation, University of Münster, Münster, Germany
| | - Petra Dersch
- Department of Molecular Infection Biology, Helmholtz Centre for Infection Research, Braunschweig, Germany
- Institute of Infectiology, Center for Molecular Biology of Inflammation, University of Münster, Münster, Germany
| | - Franz Narberhaus
- Microbial Biology, Ruhr University Bochum, Bochum, Germany
- * E-mail:
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Herzog R, Peschek N, Fröhlich KS, Schumacher K, Papenfort K. Three autoinducer molecules act in concert to control virulence gene expression in Vibrio cholerae. Nucleic Acids Res 2019; 47:3171-3183. [PMID: 30649554 PMCID: PMC6451090 DOI: 10.1093/nar/gky1320] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2018] [Revised: 12/21/2018] [Accepted: 12/28/2018] [Indexed: 12/24/2022] Open
Abstract
Bacteria use quorum sensing to monitor cell density and coordinate group behaviours. In Vibrio cholerae, the causative agent of the diarrheal disease cholera, quorum sensing is connected to virulence gene expression via the two autoinducer molecules, AI-2 and CAI-1. Both autoinducers share one signal transduction pathway to control the production of AphA, a key transcriptional activator of biofilm formation and virulence genes. In this study, we demonstrate that the recently identified autoinducer, DPO, also controls AphA production in V. cholerae. DPO, functioning through the transcription factor VqmA and the VqmR small RNA, reduces AphA levels at the post-transcriptional level and consequently inhibits virulence gene expression. VqmR-mediated repression of AphA provides an important link between the AI-2/CAI-1 and DPO-dependent quorum sensing pathways in V. cholerae. Transcriptome analyses comparing the effect of single autoinducers versus autoinducer combinations show that quorum sensing controls the expression of ∼400 genes in V. cholerae and that all three autoinducers are required for a full quorum sensing response. Together, our data provide a global view on autoinducer interplay in V. cholerae and highlight the importance of RNA-based gene control for collective functions in this major human pathogen.
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Affiliation(s)
- Roman Herzog
- Faculty of Biology I, Department of Microbiology, Ludwig-Maximilians-University of Munich, 82152 Martinsried, Germany
| | - Nikolai Peschek
- Faculty of Biology I, Department of Microbiology, Ludwig-Maximilians-University of Munich, 82152 Martinsried, Germany.,Munich Center for Integrated Protein Science (CIPSM), Germany
| | - Kathrin S Fröhlich
- Faculty of Biology I, Department of Microbiology, Ludwig-Maximilians-University of Munich, 82152 Martinsried, Germany
| | - Kilian Schumacher
- Faculty of Biology I, Department of Microbiology, Ludwig-Maximilians-University of Munich, 82152 Martinsried, Germany
| | - Kai Papenfort
- Faculty of Biology I, Department of Microbiology, Ludwig-Maximilians-University of Munich, 82152 Martinsried, Germany.,Munich Center for Integrated Protein Science (CIPSM), Germany
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Wilcox B, Osterman I, Serebryakova M, Lukyanov D, Komarova E, Gollan B, Morozova N, Wolf YI, Makarova KS, Helaine S, Sergiev P, Dubiley S, Borukhov S, Severinov K. Escherichia coli ItaT is a type II toxin that inhibits translation by acetylating isoleucyl-tRNAIle. Nucleic Acids Res 2019; 46:7873-7885. [PMID: 29931259 PMCID: PMC6125619 DOI: 10.1093/nar/gky560] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2018] [Accepted: 06/07/2018] [Indexed: 11/14/2022] Open
Abstract
Prokaryotic toxin-antitoxin (TA) modules are highly abundant and are involved in stress response and drug tolerance. The most common type II TA modules consist of two interacting proteins. The type II toxins are diverse enzymes targeting various essential intracellular targets. The antitoxin binds to cognate toxin and inhibits its function. Recently, TA modules whose toxins are GNAT-family acetyltransferases were described. For two such systems, the target of acetylation was shown to be aminoacyl-tRNA: the TacT toxin targets aminoacylated elongator tRNAs, while AtaT targets the amino acid moiety of initiating tRNAMet. We show that the itaRT gene pair from Escherichia coli encodes a TA module with acetyltransferase toxin ItaT that specifically and exclusively acetylates Ile-tRNAIle thereby blocking translation and inhibiting cell growth. ItaT forms a tight complex with the ItaR antitoxin, which represses the transcription of itaRT operon. A comprehensive bioinformatics survey of GNAT acetyltransferases reveals that enzymes encoded by validated or putative TA modules are common and form a distinct branch of the GNAT family tree. We speculate that further functional analysis of such TA modules will result in identification of enzymes capable of specifically targeting many, perhaps all, aminoacyl tRNAs.
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Affiliation(s)
- Brendan Wilcox
- Centre for Life Sciences, Skolkovo Institute of Science and Technology, Skolkovo 143025, Russia
| | - Ilya Osterman
- Centre for Life Sciences, Skolkovo Institute of Science and Technology, Skolkovo 143025, Russia.,Lomonosov Moscow State University, A.N. Belozersky Institute of Physico-Chemical Biology, Moscow 119992, Russia
| | - Marina Serebryakova
- Centre for Life Sciences, Skolkovo Institute of Science and Technology, Skolkovo 143025, Russia.,Lomonosov Moscow State University, A.N. Belozersky Institute of Physico-Chemical Biology, Moscow 119992, Russia
| | - Dmitry Lukyanov
- Lomonosov Moscow State University, A.N. Belozersky Institute of Physico-Chemical Biology, Moscow 119992, Russia
| | - Ekaterina Komarova
- Centre for Life Sciences, Skolkovo Institute of Science and Technology, Skolkovo 143025, Russia.,Lomonosov Moscow State University, A.N. Belozersky Institute of Physico-Chemical Biology, Moscow 119992, Russia
| | - Bridget Gollan
- MRC Centre for Molecular Bacteriology and Infection, Flowers Building, Armstrong Road, Imperial College London, London SW7 2AZ, UK
| | - Natalia Morozova
- Centre for Life Sciences, Skolkovo Institute of Science and Technology, Skolkovo 143025, Russia.,Peter the Great St. Petersburg State Polytechnic University, St. Petersburg, Russia
| | - Yuri I Wolf
- National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD 20894, USA
| | - Kira S Makarova
- National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD 20894, USA
| | - Sophie Helaine
- MRC Centre for Molecular Bacteriology and Infection, Flowers Building, Armstrong Road, Imperial College London, London SW7 2AZ, UK
| | - Petr Sergiev
- Centre for Life Sciences, Skolkovo Institute of Science and Technology, Skolkovo 143025, Russia.,Lomonosov Moscow State University, A.N. Belozersky Institute of Physico-Chemical Biology, Moscow 119992, Russia
| | - Svetlana Dubiley
- Centre for Life Sciences, Skolkovo Institute of Science and Technology, Skolkovo 143025, Russia.,Institute of Gene Biology of the Russian Academy of Sciences, Moscow 119334, Russia
| | - Sergei Borukhov
- Department of Cell Biology, Rowan University School of Osteopathic Medicine at Stratford, Stratford, NJ 08084-1489, USA
| | - Konstantin Severinov
- Centre for Life Sciences, Skolkovo Institute of Science and Technology, Skolkovo 143025, Russia.,Institute of Gene Biology of the Russian Academy of Sciences, Moscow 119334, Russia.,Waksman Institute for Microbiology, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
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Toribio R, Díaz-López I, Boskovic J, Ventoso I. Translation initiation of alphavirus mRNA reveals new insights into the topology of the 48S initiation complex. Nucleic Acids Res 2019; 46:4176-4187. [PMID: 29415133 PMCID: PMC5934618 DOI: 10.1093/nar/gky071] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2017] [Accepted: 02/01/2018] [Indexed: 02/02/2023] Open
Abstract
The topology and dynamics of the scanning ribosomal 43S pre-initiation complex (PIC) bound to mRNA and initiation factors (eIFs) are probably the least understood aspects of translation initiation in eukaryotes. Recently, we described a trapping mechanism in alphavirus that stalls the PIC during scanning of viral mRNA. Using this model, we were able to snapshot for the first time the eIF4A helicase bound to mRNA in a 48S initiation complex assembled in vitro. This interaction was only detected in the presence of the natural stem loop structure (DLP) located downstream from the AUG in viral mRNA that promoted stalling of the PIC, suggesting that DLP stability was enough to jam the helicase activity of eIF4A in a fraction of assembled 48S complexes. However, a substantial proportion of DLP mRNA molecules were effectively unwound by eIF4A in vitro, an activity that alphaviruses counteract in infected cells by excluding eIF4A from viral factories. Our data indicated that eIF4A–mRNA contact occurred in (or near) the ES6S region of the 40S subunit, suggesting that incoming mRNA sequences penetrate through the ES6S region during the scanning process. We propose a topological model of the scanning PIC and how some viruses have exploited this topology to translate their mRNAs with fewer eIF requirements.
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Affiliation(s)
- René Toribio
- Centro de Biología Molecular 'Severo Ochoa' (CSIC-UAM), Departamento de Biología Molecular, Universidad Autónoma de Madrid (UAM), 28049 Madrid, Spain
| | - Irene Díaz-López
- Centro de Biología Molecular 'Severo Ochoa' (CSIC-UAM), Departamento de Biología Molecular, Universidad Autónoma de Madrid (UAM), 28049 Madrid, Spain
| | - Jasminka Boskovic
- Structural Biology Programme, Electron Microscopy Unit, Spanish National Cancer Research Center (CNIO), 28029 Madrid, Spain
| | - Iván Ventoso
- Centro de Biología Molecular 'Severo Ochoa' (CSIC-UAM), Departamento de Biología Molecular, Universidad Autónoma de Madrid (UAM), 28049 Madrid, Spain
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Monestier A, Lazennec-Schurdevin C, Coureux PD, Mechulam Y, Schmitt E. Role of aIF1 in Pyrococcus abyssi translation initiation. Nucleic Acids Res 2019; 46:11061-11074. [PMID: 30239976 PMCID: PMC6237735 DOI: 10.1093/nar/gky850] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2018] [Accepted: 09/11/2018] [Indexed: 01/06/2023] Open
Abstract
In archaeal translation initiation, a preinitiation complex (PIC) made up of aIF1, aIF1A, the ternary complex (TC, e/aIF2-GTP-Met-tRNAiMet) and mRNA bound to the small ribosomal subunit is responsible for start codon selection. Many archaeal mRNAs contain a Shine-Dalgarno (SD) sequence allowing the PIC to be prepositioned in the vicinity of the start codon. Nevertheless, cryo-EM studies have suggested local scanning to definitely establish base pairing of the start codon with the tRNA anticodon. Here, using fluorescence anisotropy, we show that aIF1 and mRNA have synergistic binding to the Pyrococcus abyssi 30S. Stability of 30S:mRNA:aIF1 strongly depends on the SD sequence. Further, toeprinting experiments show that aIF1-containing PICs display a dynamic conformation with the tRNA not firmly accommodated in the P site. AIF1-induced destabilization of the PIC is favorable for proofreading erroneous initiation complexes. After aIF1 departure, the stability of the PIC increases reflecting initiator tRNA fully base-paired to the start codon. Altogether, our data support the idea that some of the main events governing start codon selection in eukaryotes and archaea occur within a common structural and functional core. However, idiosyncratic features in loop 1 sequence involved in 30S:mRNA binding suggest adjustments of e/aIF1 functioning in the two domains.
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Affiliation(s)
- Auriane Monestier
- Laboratoire de Biochimie, Ecole polytechnique, CNRS, Université Paris-Saclay, 91128 Palaiseau cedex, France
| | | | - Pierre-Damien Coureux
- Laboratoire de Biochimie, Ecole polytechnique, CNRS, Université Paris-Saclay, 91128 Palaiseau cedex, France
| | - Yves Mechulam
- Laboratoire de Biochimie, Ecole polytechnique, CNRS, Université Paris-Saclay, 91128 Palaiseau cedex, France
| | - Emmanuelle Schmitt
- Laboratoire de Biochimie, Ecole polytechnique, CNRS, Université Paris-Saclay, 91128 Palaiseau cedex, France
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40
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Egorova T, Sokolova E, Shuvalova E, Matrosova V, Shuvalov A, Alkalaeva E. Fluorescent toeprinting to study the dynamics of ribosomal complexes. Methods 2019; 162-163:54-59. [PMID: 31201933 DOI: 10.1016/j.ymeth.2019.06.010] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Revised: 06/08/2019] [Accepted: 06/10/2019] [Indexed: 12/20/2022] Open
Abstract
Classical toeprinting is generally used to determine the position of ribosomes on mRNA; however, it has several disadvantages. We describe a fluorescent toeprinting assay that enables easier identification of ribosomal complexes bound to mRNA in vitro. The procedure involves the use of stable and safe fluorescently labeled oligonucleotides for reverse transcription reactions as primers, followed by the analysis of cDNA products using an automatic sequencer. This procedure allows the multiplexing and simultaneous analysis of a large number of samples. Over the past ten years, fluorescent toeprinting was applied to determine the activities of eukaryotic release factors and additional proteins involved in translation termination, to study the dynamics of translation initiation and elongation complexes, and to quantitatively evaluate the observed ribosomal complexes. Because of the simplicity and small amounts of material required, fluorescent toeprinting provides a highly scalable and versatile tool to study ribosomal complexes.
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Affiliation(s)
- Tatiana Egorova
- Engelhardt Institute of Molecular Biology, The Russian Academy of Sciences, 119991 Moscow, Russia
| | - Elizaveta Sokolova
- Engelhardt Institute of Molecular Biology, The Russian Academy of Sciences, 119991 Moscow, Russia
| | - Ekaterina Shuvalova
- Engelhardt Institute of Molecular Biology, The Russian Academy of Sciences, 119991 Moscow, Russia
| | - Vera Matrosova
- Engelhardt Institute of Molecular Biology, The Russian Academy of Sciences, 119991 Moscow, Russia
| | - Alexey Shuvalov
- Engelhardt Institute of Molecular Biology, The Russian Academy of Sciences, 119991 Moscow, Russia
| | - Elena Alkalaeva
- Engelhardt Institute of Molecular Biology, The Russian Academy of Sciences, 119991 Moscow, Russia.
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Retapamulin-Assisted Ribosome Profiling Reveals the Alternative Bacterial Proteome. Mol Cell 2019; 74:481-493.e6. [PMID: 30904393 DOI: 10.1016/j.molcel.2019.02.017] [Citation(s) in RCA: 101] [Impact Index Per Article: 20.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Revised: 01/25/2019] [Accepted: 02/12/2019] [Indexed: 12/21/2022]
Abstract
The use of alternative translation initiation sites enables production of more than one protein from a single gene, thereby expanding the cellular proteome. Although several such examples have been serendipitously found in bacteria, genome-wide mapping of alternative translation start sites has been unattainable. We found that the antibiotic retapamulin specifically arrests initiating ribosomes at start codons of the genes. Retapamulin-enhanced Ribo-seq analysis (Ribo-RET) not only allowed mapping of conventional initiation sites at the beginning of the genes, but strikingly, it also revealed putative internal start sites in a number of Escherichia coli genes. Experiments demonstrated that the internal start codons can be recognized by the ribosomes and direct translation initiation in vitro and in vivo. Proteins, whose synthesis is initiated at internal in-frame and out-of-frame start sites, can be functionally important and contribute to the "alternative" bacterial proteome. The internal start sites may also play regulatory roles in gene expression.
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42
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Amiri H, Noller HF. Structural evidence for product stabilization by the ribosomal mRNA helicase. RNA (NEW YORK, N.Y.) 2019; 25:364-375. [PMID: 30552154 PMCID: PMC6380275 DOI: 10.1261/rna.068965.118] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Accepted: 12/12/2018] [Indexed: 06/09/2023]
Abstract
Protein synthesis in all organisms proceeds by stepwise translocation of the ribosome along messenger RNAs (mRNAs), during which the helicase activity of the ribosome unwinds encountered structures in the mRNA. This activity is known to occur near the mRNA tunnel entrance, which is lined by ribosomal proteins uS3, uS4, and uS5. However, the mechanism(s) of mRNA unwinding by the ribosome and the possible role of these proteins in the helicase activity are not well understood. Here, we present a crystal structure of the Escherichia coli ribosome in which single-stranded mRNA is observed beyond the tunnel entrance, interacting in an extended conformation with a positively charged patch on ribosomal protein uS3 immediately outside the entrance. This apparent binding specificity for single-stranded mRNA ahead of the tunnel entrance suggests that product stabilization may play a role in the unwinding of structured mRNA by the ribosomal helicase.
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Affiliation(s)
- Hossein Amiri
- Center for Molecular Biology of RNA and Department of Molecular, Cell and Developmental Biology, University of California at Santa Cruz, Santa Cruz, California 95064, USA
| | - Harry F Noller
- Center for Molecular Biology of RNA and Department of Molecular, Cell and Developmental Biology, University of California at Santa Cruz, Santa Cruz, California 95064, USA
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43
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Charon J, Manteca A, Innis CA. Using the Bacterial Ribosome as a Discovery Platform for Peptide-Based Antibiotics. Biochemistry 2019; 58:75-84. [PMID: 30372045 PMCID: PMC7615898 DOI: 10.1021/acs.biochem.8b00927] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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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44
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Odilorhabdins, Antibacterial Agents that Cause Miscoding by Binding at a New Ribosomal Site. Mol Cell 2019; 70:83-94.e7. [PMID: 29625040 DOI: 10.1016/j.molcel.2018.03.001] [Citation(s) in RCA: 73] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2017] [Revised: 02/01/2018] [Accepted: 02/28/2018] [Indexed: 12/31/2022]
Abstract
Growing resistance of pathogenic bacteria and shortage of antibiotic discovery platforms challenge the use of antibiotics in the clinic. This threat calls for exploration of unconventional sources of antibiotics and identification of inhibitors able to eradicate resistant bacteria. Here we describe a different class of antibiotics, odilorhabdins (ODLs), produced by the enzymes of the non-ribosomal peptide synthetase gene cluster of the nematode-symbiotic bacterium Xenorhabdus nematophila. ODLs show activity against Gram-positive and Gram-negative pathogens, including carbapenem-resistant Enterobacteriaceae, and can eradicate infections in animal models. We demonstrate that the bactericidal ODLs interfere with protein synthesis. Genetic and structural analyses reveal that ODLs bind to the small ribosomal subunit at a site not exploited by current antibiotics. ODLs induce miscoding and promote hungry codon readthrough, amino acid misincorporation, and premature stop codon bypass. We propose that ODLs' miscoding activity reflects their ability to increase the affinity of non-cognate aminoacyl-tRNAs to the ribosome.
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45
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Abstract
Ribosome profiling accesses the translational step of gene expression via deep sequencing of ribosome-protected mRNA footprints. Pairing of ribosome profiling and transcriptomics data provides a translational efficiency for each gene. Here, the translatome and transcriptome of the model cyanobacterium
Synechocystis
were compared under carbon-replete and carbon starvation conditions. The latter may be experienced when cyanobacteria are cultivated in poorly mixed bioreactors or engineered to be product-secreting cell factories. A small fraction of genes (<200), including stress response genes, showed changes in translational efficiency during carbon starvation, indicating condition-dependent translation-level regulation. We observed ribosome occupancy in untranslated regions, possibly due to an alternative translation initiation mechanism in
Synechocystis.
The higher proportion of ribosomes residing in untranslated regions during carbon starvation may be a mechanism to quickly inactivate superfluous ribosomes. This work provides the first ribosome profiling data for cyanobacteria and reveals new regulation strategies for coping with nutrient limitation.
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46
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Abstract
The ribosome is a major antibiotic target. Many types of inhibitors can stop cells from growing by binding at functional centers of the ribosome and interfering with its ability to synthesize proteins. These antibiotics were usually viewed as general protein synthesis inhibitors, which indiscriminately stop translation at every codon of every mRNA, preventing the ribosome from making any protein. However, at each step of the translation cycle, the ribosome interacts with multiple ligands (mRNAs, tRNA substrates, translation factors, etc.), and as a result, the properties of the translation complex vary from codon to codon and from gene to gene. Therefore, rather than being indiscriminate inhibitors, many ribosomal antibiotics impact protein synthesis in a context-specific manner. This review presents a snapshot of the growing body of evidence that some, and possibly most, ribosome-targeting antibiotics manifest site specificity of action, which is modulated by the nature of the nascent protein, the mRNA, or the tRNAs.
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Affiliation(s)
- Nora Vázquez-Laslop
- Center for Biomolecular Sciences, University of Illinois, Chicago, Illinois 60607, USA; ,
| | - Alexander S Mankin
- Center for Biomolecular Sciences, University of Illinois, Chicago, Illinois 60607, USA; ,
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47
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Fragments of the Nonlytic Proline-Rich Antimicrobial Peptide Bac5 Kill Escherichia coli Cells by Inhibiting Protein Synthesis. Antimicrob Agents Chemother 2018; 62:AAC.00534-18. [PMID: 29844040 DOI: 10.1128/aac.00534-18] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2018] [Accepted: 05/19/2018] [Indexed: 11/20/2022] Open
Abstract
Unlike most antimicrobial peptides (AMPs), the main mode of action of the subclass of proline-rich antimicrobial peptides (PrAMPs) is not based on disruption of the bacterial membrane. Instead, PrAMPs exploit the inner membrane transporters SbmA and YjiL/MdtM to pass through the bacterial membrane and enter the cytosol of specific Gram-negative bacteria, where they exert an inhibitory effect on protein synthesis. Despite sharing a high proline and arginine content with other characterized PrAMPs, the PrAMP Bac5 has a low sequence identity with them. Here we investigated the mode of action of three N-terminal Bac5 fragments, Bac5(1-15), Bac5(1-25), and Bac5(1-31). We show that Bac5(1-25) and Bac5(1-31) retained excellent antimicrobial activity toward Escherichia coli and low toxicity toward eukaryotic cells, whereas Bac5(1-15) was inactive. Bac5(1-25) and Bac5(1-31) inhibited bacterial protein synthesis in vitro and in vivo Competition assays suggested that the binding site of Bac5 is within the ribosomal tunnel, where it prevents the transition from the initiation to the elongation phase of translation, as reported for other PrAMPs, such as the bovine PrAMP Bac7. Surprisingly, unlike Bac7, Bac5(1-25) exhibited species-specific inhibition, being an excellent inhibitor of protein synthesis on E. coli ribosomes but a poor inhibitor on Thermus thermophilus ribosomes. This indicates that while Bac5 most likely has an overlapping binding site with Bac7, the mode of interaction is distinct, suggesting that Bac5 fragments may be interesting alternative lead compounds for the development of new antimicrobial agents.
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48
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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: 80] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [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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49
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Ross JA, Thakor N. Toeprinting Analysis of Translation Initiation Complex Formation on Mammalian mRNAs. J Vis Exp 2018. [PMID: 29806829 DOI: 10.3791/57519] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
Translation initiation is the rate-limiting step of protein synthesis and represents a key point at which cells regulate their protein output. Regulation of protein synthesis is the key to cellular stress-response, and dysregulation is central to many disease states, such as cancer. For instance, although cellular stress leads to the inhibition of global translation by attenuating cap-dependent initiation, certain stress-response proteins are selectively translated in a cap-independent manner. Discreet RNA regulatory elements, such as cellular internal ribosome entry sites (IRESes), allow for the translation of these specific mRNAs. Identification of such mRNAs, and the characterization of their regulatory mechanisms, have been a key area in molecular biology. Toeprinting is a method for the study of RNA structure and function as it pertains to translation initiation. The goal of toeprinting is to assess the ability of in vitro transcribed RNA to form stable complexes with ribosomes under a variety of conditions, in order to determine which sequences, structural elements, or accessory factors are involved in ribosome binding-a pre-cursor for efficient translation initiation. Alongside other techniques, such as western analysis and polysome profiling, toeprinting allows for a robust characterization of mechanisms for the regulation of translation initiation.
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Affiliation(s)
- Joseph A Ross
- Department of Chemistry and Biochemistry, Alberta RNA Research and Training Institute, University of Lethbridge;
| | - Nehal Thakor
- Department of Chemistry and Biochemistry, Alberta RNA Research and Training Institute, University of Lethbridge; Department of Neuroscience and the Canadian Centre for Behavioral Neuroscience (CCBN), University of Lethbridge; Arnie Charbonneau Cancer Institute, University of Calgary;
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50
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Mazzoni-Putman SM, Stepanova AN. A Plant Biologist's Toolbox to Study Translation. FRONTIERS IN PLANT SCIENCE 2018; 9:873. [PMID: 30013583 PMCID: PMC6036148 DOI: 10.3389/fpls.2018.00873] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Accepted: 06/04/2018] [Indexed: 05/03/2023]
Abstract
Across a broad range of species and biological questions, more and more studies are incorporating translation data to better assess how gene regulation occurs at the level of protein synthesis. The inclusion of translation data improves upon, and has been shown to be more accurate than, transcriptional studies alone. However, there are many different techniques available to measure translation and it can be difficult, especially for young or aspiring scientists, to determine which methods are best applied in specific situations. We have assembled this review in order to enhance the understanding and promote the utilization of translational methods in plant biology. We cover a broad range of methods to measure changes in global translation (e.g., radiolabeling, polysome profiling, or puromycylation), translation of single genes (e.g., fluorescent reporter constructs, toeprinting, or ribosome density mapping), sequencing-based methods to uncover the entire translatome (e.g., Ribo-seq or translating ribosome affinity purification), and mass spectrometry-based methods to identify changes in the proteome (e.g., stable isotope labeling by amino acids in cell culture or bioorthogonal noncanonical amino acid tagging). The benefits and limitations of each method are discussed with a particular note of how applications from other model systems might be extended for use in plants. In order to make this burgeoning field more accessible to students and newer scientists, our review includes an extensive glossary to define key terms.
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