1
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Huang W, Baliga C, Vázquez-Laslop N, Mankin AS. Sequence diversity of apidaecin-like peptides arresting the terminating ribosome. Nucleic Acids Res 2024:gkae567. [PMID: 38953159 DOI: 10.1093/nar/gkae567] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2024] [Revised: 05/31/2024] [Accepted: 06/22/2024] [Indexed: 07/03/2024] Open
Abstract
The Proline-rich Antimicrobial Peptide (PrAMP) apidaecin (Api) inhibits translation by binding in the ribosomal nascent peptide exit tunnel, trapping release factors RF1 or RF2, and arresting ribosomes at stop codons. To explore the extent of sequence variations of the native 18-amino acid Api that allows it to preserve its activity, we screened a library of synthetic mutant Api genes expressed in bacterial cells, resulting in nearly 350000 peptide variants with multiple substitutions. By applying orthogonal negative and positive selection strategies, we identified a number of multi-substituted Api variants capable of arresting ribosomes at stop codons. Our findings underscore the critical contribution of specific amino acid residues of the peptide for its on-target function while significantly expanding the variety of PrAMPs acting on the terminating ribosome. Additionally, some of the tested synthesized multi-substituted Api variants exhibit improved antibacterial activity compared to that of the wild type PrAMP and may constitute the starting point to develop clinically useful antimicrobials.
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Affiliation(s)
- Weiping Huang
- Department of Pharmaceutical Sciences and Center for Biomolecular Sciences, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Chetana Baliga
- Department of Pharmaceutical Sciences and Center for Biomolecular Sciences, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Nora Vázquez-Laslop
- Department of Pharmaceutical Sciences and Center for Biomolecular Sciences, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Alexander S Mankin
- Department of Pharmaceutical Sciences and Center for Biomolecular Sciences, University of Illinois at Chicago, Chicago, IL 60607, USA
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2
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Koller TO, Berger MJ, Morici M, Paternoga H, Bulatov T, Di Stasi A, Dang T, Mainz A, Raulf K, Crowe-McAuliffe C, Scocchi M, Mardirossian M, Beckert B, Vázquez-Laslop N, Mankin A, Süssmuth RD, Wilson DN. Paenilamicins from the honey bee pathogen Paenibacillus larvae are context-specific translocation inhibitors of protein synthesis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.21.595107. [PMID: 38826346 PMCID: PMC11142091 DOI: 10.1101/2024.05.21.595107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2024]
Abstract
The paenilamicins are a group of hybrid non-ribosomal peptide-polyketide compounds produced by the honey bee pathogen Paenibacillus larvae that display activity against Gram-positive pathogens, such as Staphylococcus aureus. While paenilamicins have been shown to inhibit protein synthesis, their mechanism of action has remained unclear. Here, we have determined structures of the paenilamicin PamB2 stalled ribosomes, revealing a unique binding site on the small 30S subunit located between the A- and P-site tRNAs. In addition to providing a precise description of interactions of PamB2 with the ribosome, the structures also rationalize the resistance mechanisms utilized by P. larvae. We could further demonstrate that PamB2 interferes with the translocation of mRNA and tRNAs through the ribosome during translation elongation, and that this inhibitory activity is influenced by the presence of modifications at position 37 of the A-site tRNA. Collectively, our study defines the paenilamicins as a new class of context-specific translocation inhibitors.
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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
| | - Max J. Berger
- Institute for Biochemistry and Molecular Biology, University of Hamburg, Martin-Luther-King-Platz 6, 20146 Hamburg, Germany
| | - Martino Morici
- Institute for Biochemistry and Molecular Biology, University of Hamburg, Martin-Luther-King-Platz 6, 20146 Hamburg, Germany
| | - Helge Paternoga
- Institute for Biochemistry and Molecular Biology, University of Hamburg, Martin-Luther-King-Platz 6, 20146 Hamburg, Germany
| | - Timur Bulatov
- Institut für Chemie, Technische Universität Berlin, 10623 Berlin, Germany
| | - Adriana Di Stasi
- Department of Life Sciences, University of Trieste, 34127 Trieste, Italy
| | - Tam Dang
- Institut für Chemie, Technische Universität Berlin, 10623 Berlin, Germany
| | - Andi Mainz
- Institut für Chemie, Technische Universität Berlin, 10623 Berlin, Germany
| | - Karoline Raulf
- Institute for Biochemistry and Molecular Biology, University of Hamburg, Martin-Luther-King-Platz 6, 20146 Hamburg, Germany
| | - Caillan Crowe-McAuliffe
- Institute for Biochemistry and Molecular Biology, University of Hamburg, Martin-Luther-King-Platz 6, 20146 Hamburg, Germany
| | - Marco Scocchi
- Department of Life Sciences, University of Trieste, 34127 Trieste, Italy
| | - Mario Mardirossian
- Department of Life Sciences, University of Trieste, 34127 Trieste, Italy
| | - Bertrand Beckert
- Dubochet Center for Imaging (DCI) at EPFL, EPFL SB IPHYS DCI, Lausanne, Switzerland
| | - Nora Vázquez-Laslop
- Center for Biomolecular Sciences, University of Illinois at Chicago, Chicago, IL 60607
| | - Alexander Mankin
- Center for Biomolecular Sciences, University of Illinois at Chicago, Chicago, IL 60607
| | | | - Daniel N. Wilson
- Institute for Biochemistry and Molecular Biology, University of Hamburg, Martin-Luther-King-Platz 6, 20146 Hamburg, Germany
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3
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Bhattacharya A, Renault TT, Innis CA. The ribosome as a small-molecule sensor. Curr Opin Microbiol 2024; 77:102418. [PMID: 38159358 DOI: 10.1016/j.mib.2023.102418] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Revised: 12/04/2023] [Accepted: 12/05/2023] [Indexed: 01/03/2024]
Abstract
Sensing small molecules is crucial for microorganisms to adapt their genetic programs to changes in their environment. Arrest peptides encoded by short regulatory open reading frames program the ribosomes that translate them to undergo translational arrest in response to specific metabolites. Ribosome stalling in turn controls the expression of downstream genes on the same messenger RNA by translational or transcriptional means. In this review, we present our current understanding of the mechanisms by which ribosomes translating arrest peptides sense different metabolites, such as antibiotics or amino acids, to control gene expression.
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Affiliation(s)
- Arunima Bhattacharya
- Univ. Bordeaux, Centre National de la Recherche Scientifique, Institut National de la Santé et de la Recherche Médicale, ARNA, UMR 5320, U1212, Institut Européen de Chimie et Biologie, F-33600 Pessac, France
| | - Thibaud T Renault
- Univ. Bordeaux, Centre National de la Recherche Scientifique, Institut National de la Santé et de la Recherche Médicale, ARNA, UMR 5320, U1212, Institut Européen de Chimie et Biologie, F-33600 Pessac, France
| | - C Axel Innis
- Univ. Bordeaux, Centre National de la Recherche Scientifique, Institut National de la Santé et de la Recherche Médicale, ARNA, UMR 5320, U1212, Institut Européen de Chimie et Biologie, F-33600 Pessac, France.
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4
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Volynkina IA, Bychkova EN, Karakchieva AO, Tikhomirov AS, Zatonsky GV, Solovieva SE, Martynov MM, Grammatikova NE, Tereshchenkov AG, Paleskava A, Konevega AL, Sergiev PV, Dontsova OA, Osterman IA, Shchekotikhin AE, Tevyashova AN. Hybrid Molecules of Azithromycin with Chloramphenicol and Metronidazole: Synthesis and Study of Antibacterial Properties. Pharmaceuticals (Basel) 2024; 17:187. [PMID: 38399402 PMCID: PMC10892836 DOI: 10.3390/ph17020187] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 01/23/2024] [Accepted: 01/25/2024] [Indexed: 02/25/2024] Open
Abstract
The sustained rise of antimicrobial resistance (AMR) causes a strong need to develop new antibacterial agents. One of the methods for addressing the problem of antibiotic resistance is through the design of hybrid antibiotics. In this work, we proposed a synthetic route for the conjugation of an azithromycin derivative with chloramphenicol and metronidazole hemisuccinates and synthesized two series of new hybrid molecules 4a-g and 5a-g. While a conjugation did not result in tangible synergy for wild-type bacterial strains, new compounds were able to overcome AMR associated with the inducible expression of the ermC gene on a model E. coli strain resistant to macrolide antibiotics. The newly developed hybrids demonstrated a tendency to induce premature ribosome stalling, which might be crucial since they will not induce a macrolide-resistant phenotype in a number of pathogenic bacterial strains. In summary, the designed structures are considered as a promising direction for the further development of hybrid molecules that can effectively circumvent AMR mechanisms to macrolide antibiotics.
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Affiliation(s)
- Inna A. Volynkina
- Department of Chemistry, Lomonosov Moscow State University, Leninskie Gory 1, 119234 Moscow, Russia; (A.O.K.); (P.V.S.); (O.A.D.); (I.A.O.)
| | - Elena N. Bychkova
- Gause Institute of New Antibiotics, B. Pirogovskaya 11, 119021 Moscow, Russia; (E.N.B.); (A.S.T.); (G.V.Z.); (S.E.S.); (M.M.M.); (N.E.G.); (A.E.S.)
| | - Anastasiia O. Karakchieva
- Department of Chemistry, Lomonosov Moscow State University, Leninskie Gory 1, 119234 Moscow, Russia; (A.O.K.); (P.V.S.); (O.A.D.); (I.A.O.)
| | - Alexander S. Tikhomirov
- Gause Institute of New Antibiotics, B. Pirogovskaya 11, 119021 Moscow, Russia; (E.N.B.); (A.S.T.); (G.V.Z.); (S.E.S.); (M.M.M.); (N.E.G.); (A.E.S.)
| | - George V. Zatonsky
- Gause Institute of New Antibiotics, B. Pirogovskaya 11, 119021 Moscow, Russia; (E.N.B.); (A.S.T.); (G.V.Z.); (S.E.S.); (M.M.M.); (N.E.G.); (A.E.S.)
| | - Svetlana E. Solovieva
- Gause Institute of New Antibiotics, B. Pirogovskaya 11, 119021 Moscow, Russia; (E.N.B.); (A.S.T.); (G.V.Z.); (S.E.S.); (M.M.M.); (N.E.G.); (A.E.S.)
| | - Maksim M. Martynov
- Gause Institute of New Antibiotics, B. Pirogovskaya 11, 119021 Moscow, Russia; (E.N.B.); (A.S.T.); (G.V.Z.); (S.E.S.); (M.M.M.); (N.E.G.); (A.E.S.)
| | - Natalia E. Grammatikova
- Gause Institute of New Antibiotics, B. Pirogovskaya 11, 119021 Moscow, Russia; (E.N.B.); (A.S.T.); (G.V.Z.); (S.E.S.); (M.M.M.); (N.E.G.); (A.E.S.)
| | - Andrey G. Tereshchenkov
- Department of Chemistry, Lomonosov Moscow State University, Leninskie Gory 1, 119234 Moscow, Russia; (A.O.K.); (P.V.S.); (O.A.D.); (I.A.O.)
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Leninskie Gory 1, 119234 Moscow, Russia
| | - Alena Paleskava
- Department of Molecular and Radiation Biophysics, Petersburg Nuclear Physics Institute Named by B.P. Konstantiniv of NRC “Kurchatov Institute”, Mkr. Orlova Roshcha 1, 188300 Gatchina, Russia; (A.P.); (A.L.K.)
- Institute of Biomedical Systems and Biotechnologies, Peter the Great St. Petersburg Polytechnic University, Khlopina 11, 195251 Saint Petersburg, Russia
| | - Andrey L. Konevega
- Department of Molecular and Radiation Biophysics, Petersburg Nuclear Physics Institute Named by B.P. Konstantiniv of NRC “Kurchatov Institute”, Mkr. Orlova Roshcha 1, 188300 Gatchina, Russia; (A.P.); (A.L.K.)
- Institute of Biomedical Systems and Biotechnologies, Peter the Great St. Petersburg Polytechnic University, Khlopina 11, 195251 Saint Petersburg, Russia
- NBICS Center, NRC “Kurchatov Institute”, Kurchatov Square 1, 123182 Moscow, Russia
| | - Petr V. Sergiev
- Department of Chemistry, Lomonosov Moscow State University, Leninskie Gory 1, 119234 Moscow, Russia; (A.O.K.); (P.V.S.); (O.A.D.); (I.A.O.)
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Leninskie Gory 1, 119234 Moscow, Russia
- Institute of Functional Genomics, Lomonosov Moscow State University, Leninskie Gory 1, 119234 Moscow, Russia
| | - Olga A. Dontsova
- Department of Chemistry, Lomonosov Moscow State University, Leninskie Gory 1, 119234 Moscow, Russia; (A.O.K.); (P.V.S.); (O.A.D.); (I.A.O.)
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Leninskie Gory 1, 119234 Moscow, Russia
- Department of Functioning of Living Systems, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Miklukho-Maklaya 16/10, 117997 Moscow, Russia
| | - Ilya A. Osterman
- Department of Chemistry, Lomonosov Moscow State University, Leninskie Gory 1, 119234 Moscow, Russia; (A.O.K.); (P.V.S.); (O.A.D.); (I.A.O.)
| | - Andrey E. Shchekotikhin
- Gause Institute of New Antibiotics, B. Pirogovskaya 11, 119021 Moscow, Russia; (E.N.B.); (A.S.T.); (G.V.Z.); (S.E.S.); (M.M.M.); (N.E.G.); (A.E.S.)
| | - Anna N. Tevyashova
- Gause Institute of New Antibiotics, B. Pirogovskaya 11, 119021 Moscow, Russia; (E.N.B.); (A.S.T.); (G.V.Z.); (S.E.S.); (M.M.M.); (N.E.G.); (A.E.S.)
- School of Science, Constructor University, Campus Ring 1, 28759 Bremen, Germany
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5
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Shields KE, Ranava D, Tan Y, Zhang D, Yap MNF. Epitranscriptional m6A modification of rRNA negatively impacts translation and host colonization in Staphylococcus aureus. PLoS Pathog 2024; 20:e1011968. [PMID: 38252661 PMCID: PMC10833563 DOI: 10.1371/journal.ppat.1011968] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Revised: 02/01/2024] [Accepted: 01/12/2024] [Indexed: 01/24/2024] Open
Abstract
Macrolides, lincosamides, and streptogramin B (MLS) are structurally distinct molecules that are among the safest antibiotics for prophylactic use and for the treatment of bacterial infections. The family of erythromycin resistance methyltransferases (Erm) invariantly install either one or two methyl groups onto the N6,6-adenosine of 2058 nucleotide (m6A2058) of the bacterial 23S rRNA, leading to bacterial cross-resistance to all MLS antibiotics. Despite extensive structural studies on the mechanism of Erm-mediated MLS resistance, how the m6A epitranscriptomic mark affects ribosome function and bacterial physiology is not well understood. Here, we show that Staphylococcus aureus cells harboring m6A2058 ribosomes are outcompeted by cells carrying unmodified ribosomes during infections and are severely impaired in colonization in the absence of an unmodified counterpart. The competitive advantage of m6A2058 ribosomes is manifested only upon antibiotic challenge. Using ribosome profiling (Ribo-Seq) and a dual-fluorescence reporter to measure ribosome occupancy and translational fidelity, we found that specific genes involved in host interactions, metabolism, and information processing are disproportionally deregulated in mRNA translation. This dysregulation is linked to a substantial reduction in translational capacity and fidelity in m6A2058 ribosomes. These findings point to a general "inefficient translation" mechanism of trade-offs associated with multidrug-resistant ribosomes.
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Affiliation(s)
- Kathryn E. Shields
- Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, Saint Louis, Missouri, United States of America
| | - David Ranava
- Department of Microbiology-Immunology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, United States of America
| | - Yongjun Tan
- Department of Biology, College of Arts and Sciences, Saint Louis University, St. Louis, Missouri, United States of America
| | - Dapeng Zhang
- Department of Biology, College of Arts and Sciences, Saint Louis University, St. Louis, Missouri, United States of America
- Program of Bioinformatics and Computational Biology, College of Arts and Sciences, St. Louis, Missouri, United States of America
| | - Mee-Ngan F. Yap
- Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, Saint Louis, Missouri, United States of America
- Department of Microbiology-Immunology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, United States of America
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6
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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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7
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Zhang Z, Dou H, Yuan Q, Shi D, Wan R, Tu P, Xin D, Guo S. Proteomic and Phenotypic Studies of Mycoplasma pneumoniae Revealed Macrolide-Resistant Mutation (A2063G) Associated Changes in Protein Composition and Pathogenicity of Type I Strains. Microbiol Spectr 2023; 11:e0461322. [PMID: 37378520 PMCID: PMC10434051 DOI: 10.1128/spectrum.04613-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Accepted: 05/24/2023] [Indexed: 06/29/2023] Open
Abstract
Mycoplasma pneumoniae (MP) is an important respiratory pathogen, the prevalence of macrolide-resistant MP (mainly containing A2063G mutation in 23S rRNA) increased in recent years. Epidemiological studies suggest a higher prevalence of type I resistant (IR) strains than corresponding sensitive (IS/IIS) strains, but not type II resistant (IIR) strains. Here, we aimed to analyze the factors underlying the altered prevalence of IR strains. First, proteomic analyses exhibit the protein compositions were type specific, while more differential proteins were detected between IS and IR (227) than IIS and IIR strains (81). mRNA level detection suggested posttranscriptional regulation of these differential proteins. Differential protein-related phenotypic changes were also detected: (i) P1 abundance was different between genotypes (I < II, IR < IS), the adhesion of MPs showed accordance to P1 abundance within IS and IIS strains; (ii) type I, especially IR, strains had a higher proliferation rate, which is potentially associated with differential proteins participating in glycolysis and one carbon pool metabolisms; (iii) A549 cells infected with IR strains had lower activity of caspase-3 and higher levels IL-8, but the differences were not significant between groups (P > 0.05). Correlations of P1 abundance to caspase-3 activity and proliferation rate to the level of IL-8 were obtained. These results suggest changes in protein composition influenced the pathogenicity of MP, especially in IR strains, which may impact the prevalence of MP strains of different genotypes. IMPORTANCE The prevalence of macrolide-resistant MPs increased the difficulty in treatment of MP infections and posed potential threats to children's health. Epidemiological studies showed a high prevalence of IR-resistant strains (mainly A2063G in 23S rRNA) in these years. However, the trigger mechanisms for this phenomenon are not clear. In this paper, proteomic and phenotypic studies suggest that IR strains have reduced levels of multiple adhesion proteins and increased proliferation rate, which may lead to higher transmission rate of IR strains in the population. This suggests that we should pay attention to the prevalence of IR strains.
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Affiliation(s)
- Zhikun Zhang
- Beijing Tropical Medicine Research Institute, Beijing Friendship Hospital, Capital Medical University, Beijing, China
- Department of Pathogenic Biology, School of Basic Medicine Southwest Medical University, Luzhou, China
| | - Haiwei Dou
- Beijing Tropical Medicine Research Institute, Beijing Friendship Hospital, Capital Medical University, Beijing, China
| | - Qing Yuan
- Beijing Tropical Medicine Research Institute, Beijing Friendship Hospital, Capital Medical University, Beijing, China
| | - Dawei Shi
- Beijing Tropical Medicine Research Institute, Beijing Friendship Hospital, Capital Medical University, Beijing, China
| | - Ruijie Wan
- Beijing Tropical Medicine Research Institute, Beijing Friendship Hospital, Capital Medical University, Beijing, China
| | - Peng Tu
- Beijing Tropical Medicine Research Institute, Beijing Friendship Hospital, Capital Medical University, Beijing, China
| | - Deli Xin
- Beijing Tropical Medicine Research Institute, Beijing Friendship Hospital, Capital Medical University, Beijing, China
| | - Shuilong Guo
- Department of Science and Technology, Beijing Friendship Hospital, Capital Medical University, Beijing, China
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8
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Chen CW, Leimer N, Syroegin EA, Dunand C, Bulman ZP, Lewis K, Polikanov YS, Svetlov MS. Structural insights into the mechanism of overcoming Erm-mediated resistance by macrolides acting together with hygromycin-A. Nat Commun 2023; 14:4196. [PMID: 37452045 PMCID: PMC10349075 DOI: 10.1038/s41467-023-39653-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Accepted: 06/22/2023] [Indexed: 07/18/2023] Open
Abstract
The ever-growing rise of antibiotic resistance among bacterial pathogens is one of the top healthcare threats today. Although combination antibiotic therapies represent a potential approach to more efficiently combat infections caused by susceptible and drug-resistant bacteria, only a few known drug pairs exhibit synergy/cooperativity in killing bacteria. Here, we discover that well-known ribosomal antibiotics, hygromycin A (HygA) and macrolides, which target peptidyl transferase center and peptide exit tunnel, respectively, can act cooperatively against susceptible and drug-resistant bacteria. Remarkably, HygA slows down macrolide dissociation from the ribosome by 60-fold and enhances the otherwise weak antimicrobial activity of the newest-generation macrolide drugs known as ketolides against macrolide-resistant bacteria. By determining a set of high-resolution X-ray crystal structures of drug-sensitive wild-type and macrolide-resistant Erm-methylated 70S ribosomes in complex with three HygA-macrolide pairs, we provide a structural rationale for the binding cooperativity of these drugs and also uncover the molecular mechanism of overcoming Erm-type resistance by macrolides acting together with hygromycin A. Altogether our structural, biochemical, and microbiological findings lay the foundation for the subsequent development of synergistic antibiotic tandems with improved bactericidal properties against drug-resistant pathogens, including those expressing erm genes.
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Affiliation(s)
- Chih-Wei Chen
- Department of Biological Sciences, University of Illinois at Chicago, Chicago, IL, 60607, USA
| | - Nadja Leimer
- Department of Biology, Northeastern University, Boston, MA, 02115, USA
| | - Egor A Syroegin
- Department of Biological Sciences, University of Illinois at Chicago, Chicago, IL, 60607, USA
| | - Clémence Dunand
- Center for Biomolecular Sciences, University of Illinois at Chicago, Chicago, IL, 60607, USA
| | - Zackery P Bulman
- Department of Pharmacy Practice, University of Illinois at Chicago, Chicago, IL, 60612, USA
| | - Kim Lewis
- Department of Biology, Northeastern University, Boston, MA, 02115, USA
| | - Yury S Polikanov
- Department of Biological Sciences, University of Illinois at Chicago, Chicago, IL, 60607, USA.
- Center for Biomolecular Sciences, University of Illinois at Chicago, Chicago, IL, 60607, USA.
- Department of Pharmaceutical Sciences, University of Illinois at Chicago, Chicago, IL, 60607, USA.
| | - Maxim S Svetlov
- Center for Biomolecular Sciences, University of Illinois at Chicago, Chicago, IL, 60607, USA.
- Department of Pharmaceutical Sciences, University of Illinois at Chicago, Chicago, IL, 60607, USA.
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9
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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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10
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Nagao A, Nakanishi Y, Yamaguchi Y, Mishina Y, Karoji M, Toya T, Fujita T, Iwasaki S, Miyauchi K, Sakaguchi Y, Suzuki T. Quality control of protein synthesis in the early elongation stage. Nat Commun 2023; 14:2704. [PMID: 37198183 PMCID: PMC10192219 DOI: 10.1038/s41467-023-38077-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Accepted: 04/14/2023] [Indexed: 05/19/2023] Open
Abstract
In the early stage of bacterial translation, peptidyl-tRNAs frequently dissociate from the ribosome (pep-tRNA drop-off) and are recycled by peptidyl-tRNA hydrolase. Here, we establish a highly sensitive method for profiling of pep-tRNAs using mass spectrometry, and successfully detect a large number of nascent peptides from pep-tRNAs accumulated in Escherichia coli pthts strain. Based on molecular mass analysis, we found about 20% of the peptides bear single amino-acid substitutions of the N-terminal sequences of E. coli ORFs. Detailed analysis of individual pep-tRNAs and reporter assay revealed that most of the substitutions take place at the C-terminal drop-off site and that the miscoded pep-tRNAs rarely participate in the next round of elongation but dissociate from the ribosome. These findings suggest that pep-tRNA drop-off is an active mechanism by which the ribosome rejects miscoded pep-tRNAs in the early elongation, thereby contributing to quality control of protein synthesis after peptide bond formation.
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Affiliation(s)
- Asuteka Nagao
- Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, Bunkyo-ku, Tokyo, 113-8656, Japan.
| | - Yui Nakanishi
- Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, Bunkyo-ku, Tokyo, 113-8656, Japan
| | - Yutaro Yamaguchi
- Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, Bunkyo-ku, Tokyo, 113-8656, Japan
| | - Yoshifumi Mishina
- Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, Bunkyo-ku, Tokyo, 113-8656, Japan
| | - Minami Karoji
- Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, Bunkyo-ku, Tokyo, 113-8656, Japan
| | - Takafumi Toya
- Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, Bunkyo-ku, Tokyo, 113-8656, Japan
| | - Tomoya Fujita
- RNA Systems Biochemistry Laboratory, RIKEN Cluster for Pioneering Research, Wako, Saitama, 351-0198, Japan
| | - Shintaro Iwasaki
- RNA Systems Biochemistry Laboratory, RIKEN Cluster for Pioneering Research, Wako, Saitama, 351-0198, Japan
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, 277-8561, Japan
| | - Kenjyo Miyauchi
- Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, Bunkyo-ku, Tokyo, 113-8656, Japan
| | - Yuriko Sakaguchi
- Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, Bunkyo-ku, Tokyo, 113-8656, Japan
| | - Tsutomu Suzuki
- Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, Bunkyo-ku, Tokyo, 113-8656, Japan.
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11
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Lomakin IB, Devarkar SC, Patel S, Grada A, Bunick C. Sarecycline inhibits protein translation in Cutibacterium acnes 70S ribosome using a two-site mechanism. Nucleic Acids Res 2023; 51:2915-2930. [PMID: 36864821 PMCID: PMC10085706 DOI: 10.1093/nar/gkad103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Revised: 02/01/2023] [Accepted: 02/07/2023] [Indexed: 03/04/2023] Open
Abstract
Acne vulgaris is a chronic disfiguring skin disease affecting ∼1 billion people worldwide, often having persistent negative effects on physical and mental health. The Gram-positive anaerobe, Cutibacterium acnes is implicated in acne pathogenesis and is, therefore, a main target for antibiotic-based acne therapy. We determined a 2.8-Å resolution structure of the 70S ribosome of Cutibacterium acnes by cryogenic electron microscopy and discovered that sarecycline, a narrow-spectrum antibiotic against Cutibacterium acnes, may inhibit two active sites of this bacterium's ribosome in contrast to the one site detected previously on the model ribosome of Thermus thermophilus. Apart from the canonical binding site at the mRNA decoding center, the second binding site for sarecycline exists at the nascent peptide exit tunnel, reminiscent of the macrolides class of antibiotics. The structure also revealed Cutibacterium acnes-specific features of the ribosomal RNA and proteins. Unlike the ribosome of the Gram-negative bacterium Escherichia coli, Cutibacterium acnes ribosome has two additional proteins, bS22 and bL37, which are also present in the ribosomes of Mycobacterium smegmatis and Mycobacterium tuberculosis. We show that bS22 and bL37 have antimicrobial properties and may be involved in maintaining the healthy homeostasis of the human skin microbiome.
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Affiliation(s)
- Ivan B Lomakin
- Department of Dermatology, Yale University School of Medicine, New Haven, CT06520, USA
| | - Swapnil C Devarkar
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT06520, USA
| | - Shivali Patel
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT06520, USA
| | - Ayman Grada
- Department of Dermatology, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Christopher G Bunick
- Department of Dermatology, Yale University School of Medicine, New Haven, CT06520, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT06520, USA
- Program in Translational Biomedicine, Yale University School of Medicine, New Haven, CT 06520, USA
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12
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Zhang J, Lair C, Roubert C, Amaning K, Barrio MB, Benedetti Y, Cui Z, Xing Z, Li X, Franzblau SG, Baurin N, Bordon-Pallier F, Cantalloube C, Sans S, Silve S, Blanc I, Fraisse L, Rak A, Jenner LB, Yusupova G, Yusupov M, Zhang J, Kaneko T, Yang TJ, Fotouhi N, Nuermberger E, Tyagi S, Betoudji F, Upton A, Sacchettini JC, Lagrange S. Discovery of natural-product-derived sequanamycins as potent oral anti-tuberculosis agents. Cell 2023; 186:1013-1025.e24. [PMID: 36827973 PMCID: PMC9994261 DOI: 10.1016/j.cell.2023.01.043] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Revised: 08/03/2022] [Accepted: 01/27/2023] [Indexed: 02/25/2023]
Abstract
The emergence of drug-resistant tuberculosis has created an urgent need for new anti-tubercular agents. Here, we report the discovery of a series of macrolides called sequanamycins with outstanding in vitro and in vivo activity against Mycobacterium tuberculosis (Mtb). Sequanamycins are bacterial ribosome inhibitors that interact with the ribosome in a similar manner to classic macrolides like erythromycin and clarithromycin, but with binding characteristics that allow them to overcome the inherent macrolide resistance of Mtb. Structures of the ribosome with bound inhibitors were used to optimize sequanamycin to produce the advanced lead compound SEQ-9. SEQ-9 was efficacious in mouse models of acute and chronic TB as a single agent, and it demonstrated bactericidal activity in a murine TB infection model in combination with other TB drugs. These results support further investigation of this series as TB clinical candidates, with the potential for use in new regimens against drug-susceptible and drug-resistant TB.
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Affiliation(s)
- Jidong Zhang
- Sanofi R&D, Integrated Drug Discovery, CRVA, 94403 Vitry-sur-Seine, France
| | - Christine Lair
- Evotec ID (LYON) SAS, Lyon, France; Sanofi R&D, Infectious Diseases TSU, 31036 Toulouse, France
| | - Christine Roubert
- Evotec ID (LYON) SAS, Lyon, France; Sanofi R&D, Infectious Diseases TSU, 31036 Toulouse, France
| | - Kwame Amaning
- Sanofi R&D, Integrated Drug Discovery, CRVA, 94403 Vitry-sur-Seine, France
| | | | - Yannick Benedetti
- Sanofi R&D, Integrated Drug Discovery, CRVA, 94403 Vitry-sur-Seine, France
| | - Zhicheng Cui
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, USA
| | - Zhongliang Xing
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, USA
| | - Xiaojun Li
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, USA
| | - Scott G Franzblau
- Institute for Tuberculosis Research, College of Pharmacy, University of Illinois at Chicago, Chicago, IL 60612, USA
| | - Nicolas Baurin
- Sanofi R&D, Integrated Drug Discovery, CRVA, 94403 Vitry-sur-Seine, France
| | | | | | - Stephanie Sans
- Evotec ID (LYON) SAS, Lyon, France; Sanofi R&D, Infectious Diseases TSU, 31036 Toulouse, France
| | - Sandra Silve
- Evotec ID (LYON) SAS, Lyon, France; Sanofi R&D, Infectious Diseases TSU, 31036 Toulouse, France
| | - Isabelle Blanc
- Evotec ID (LYON) SAS, Lyon, France; Sanofi R&D, Infectious Diseases TSU, 31036 Toulouse, France
| | - Laurent Fraisse
- Evotec ID (LYON) SAS, Lyon, France; Sanofi R&D, Infectious Diseases TSU, 31036 Toulouse, France
| | - Alexey Rak
- Sanofi R&D, Integrated Drug Discovery, CRVA, 94403 Vitry-sur-Seine, France
| | | | | | | | - Junjie Zhang
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, USA
| | - Takushi Kaneko
- Global Alliance for TB Drug Development, New York, NY, USA
| | - T J Yang
- Global Alliance for TB Drug Development, New York, NY, USA
| | - Nader Fotouhi
- Global Alliance for TB Drug Development, New York, NY, USA
| | - Eric Nuermberger
- Center for Tuberculosis Research, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Sandeep Tyagi
- Center for Tuberculosis Research, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Fabrice Betoudji
- Center for Tuberculosis Research, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Anna Upton
- Evotec ID (LYON) SAS, Lyon, France; Global Alliance for TB Drug Development, New York, NY, USA
| | - James C Sacchettini
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, USA.
| | - Sophie Lagrange
- Evotec ID (LYON) SAS, Lyon, France; Sanofi R&D, Infectious Diseases TSU, 31036 Toulouse, France
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13
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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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14
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Kohl MP, Kompatscher M, Clementi N, Holl L, Erlacher M. Initiation at AUGUG and GUGUG sequences can lead to translation of overlapping reading frames in E. coli. Nucleic Acids Res 2022; 51:271-289. [PMID: 36546769 PMCID: PMC9841429 DOI: 10.1093/nar/gkac1175] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Revised: 11/16/2022] [Accepted: 11/30/2022] [Indexed: 12/24/2022] Open
Abstract
During initiation, the ribosome is tasked to efficiently recognize open reading frames (ORFs) for accurate and fast translation of mRNAs. A critical step is start codon recognition, which is modulated by initiation factors, mRNA structure, a Shine Dalgarno (SD) sequence and the start codon itself. Within the Escherichia coli genome, we identified more than 50 annotated initiation sites harboring AUGUG or GUGUG sequence motifs that provide two canonical start codons, AUG and GUG, in immediate proximity. As these sites may challenge start codon recognition, we studied if and how the ribosome is accurately guided to the designated ORF, with a special focus on the SD sequence as well as adenine at the fourth coding sequence position (A4). By in vitro and in vivo experiments, we characterized key requirements for unambiguous start codon recognition, but also discovered initiation sites that lead to the translation of both overlapping reading frames. Our findings corroborate the existence of an ambiguous translation initiation mechanism, implicating a multitude of so far unrecognized ORFs and translation products in bacteria.
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Affiliation(s)
- Maximilian P Kohl
- Institute of Genomics and RNomics, Biocenter, Medical University of Innsbruck, 6020 Innsbruck, Austria
| | - Maria Kompatscher
- Institute of Genomics and RNomics, Biocenter, Medical University of Innsbruck, 6020 Innsbruck, Austria
| | - Nina Clementi
- Institute of Genomics and RNomics, Biocenter, Medical University of Innsbruck, 6020 Innsbruck, Austria
| | - Lena Holl
- Institute of Genomics and RNomics, Biocenter, Medical University of Innsbruck, 6020 Innsbruck, Austria
| | - Matthias D Erlacher
- To whom correspondence should be addressed. Tel: +43 512900370256; Fax: +43 512900373100;
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15
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He W, Jiang K, Qiu H, Liao L, Wang S. 16-membered ring macrolides and erythromycin induce ermB expression by different mechanisms. BMC Microbiol 2022; 22:152. [PMID: 35681117 PMCID: PMC9178857 DOI: 10.1186/s12866-022-02565-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2022] [Accepted: 06/01/2022] [Indexed: 11/24/2022] Open
Abstract
Background Ribosome stalling on ermBL at the tenth codon (Asp) and mRNA stabilization are believed to be mechanisms by which erythromycin (Ery) induces ermB expression. Expression of ermB is also induced by 16-membered ring macrolides (tylosin, josamycin and spiramycin), but the mechanism underlying this induction is unknown. Methods We introduced premature termination codons, alanine-scanning mutagenesis and amino acid mutations in ermBL and ermBL2. Results In this paper, we demonstrated that 16-membered ring macrolides can induce ermB expression but not ermC expression. The truncated mutants of the ermB-coding sequence indicate that the regulatory regions of ermB whose expression is induced by Ery and 16-membered ring macrolides are different. We proved that translation of the N-terminal region of ermBL is key for the induction of ermB expression by Ery, spiramycin (Spi) and tylosin (Tyl). We also demonstrated that ermBL2 is critical for the induction of ermB expression by erythromycin but not by 16-membered ring macrolides. Conclusions The translation of ermBL and the RNA sequence of the C-terminus of ermBL are critical for the induction of ermB expression by Spi and Tyl. Supplementary Information The online version contains supplementary material available at 10.1186/s12866-022-02565-3.
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Affiliation(s)
- Weizhi He
- Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism (Ministry of Science and Technology), Shanghai Medical College of Fudan University, Shanghai, 200032, China.
| | - Kai Jiang
- Department of Biobank, Renji Hospital, School of Medicine, Shanghai JiaoTong University, Shanghai, China
| | - Hua Qiu
- Department of General Surgery, The First Affiliated Hospital of Nanchang University, No.17 Yongwai Zheng Street, Nanchang, 330006, Jiangxi Province, China
| | - Lijun Liao
- Department of Anesthesiology and Pain Management, Shanghai East Hospital, School of Medicine, Tongji University, Shanghai, 200120, China.
| | - Shasha Wang
- Department of Anesthesiology and Pain Management, Shanghai East Hospital, School of Medicine, Tongji University, Shanghai, 200120, China.
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16
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Tsai K, Stojković V, Lee DJ, Young ID, Szal T, Klepacki D, Vázquez-Laslop N, Mankin AS, Fraser JS, Fujimori DG. Structural basis for context-specific inhibition of translation by oxazolidinone antibiotics. Nat Struct Mol Biol 2022; 29:162-171. [DOI: 10.1038/s41594-022-00723-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Accepted: 01/05/2022] [Indexed: 01/02/2023]
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17
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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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18
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Jia B, Wang T, Lehmann J. Peptidyl transferase center decompaction and structural constraints during early protein elongation on the ribosome. Sci Rep 2021; 11:24061. [PMID: 34911999 PMCID: PMC8674327 DOI: 10.1038/s41598-021-02985-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2021] [Accepted: 11/15/2021] [Indexed: 11/09/2022] Open
Abstract
Peptide bond formation on the ribosome requires that aminoacyl-tRNAs and peptidyl-tRNAs are properly positioned on the A site and the P site of the peptidyl transferase center (PTC) so that nucleophilic attack can occur. Here we analyse some constraints associated with the induced-fit mechanism of the PTC, that promotes this positioning through a compaction around the aminoacyl ester orchestrated by U2506. The physical basis of PTC decompaction, that allows the elongated peptidyl-tRNA to free itself from that state and move to the P site of the PTC, is still unclear. From thermodynamics considerations and an analysis of published ribosome structures, the present work highlights the rational of this mechanism, in which the free-energy released by the new peptide bond is used to kick U2506 away from the reaction center. Furthermore, we show the evidence that decompaction is impaired when the nascent peptide is not yet anchored inside the exit tunnel, which may contribute to explain why the first rounds of elongation are inefficient, an issue that has attracted much interest for about two decades. Results in this field are examined in the light of the present analysis and a physico-chemical correlation in the genetic code, which suggest that elementary constraints associated with the size of the side-chain of the amino acids penalize early elongation events.
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Affiliation(s)
- Bin Jia
- Department of Anesthesiology, Xuanwu Hospital, Capital Medical University, Beijing, China
| | - Tianlong Wang
- Department of Anesthesiology, Xuanwu Hospital, Capital Medical University, Beijing, China.
| | - Jean Lehmann
- CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), University of Paris-Saclay, 91198, Gif-sur-Yvette, France.
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19
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Zeng F, Li X, Pires-Alves M, Chen X, Hawk CW, Jin H. Conserved heterodimeric GTPase Rbg1/Tma46 promotes efficient translation in eukaryotic cells. Cell Rep 2021; 37:109877. [PMID: 34706231 DOI: 10.1016/j.celrep.2021.109877] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Revised: 06/21/2021] [Accepted: 09/30/2021] [Indexed: 11/19/2022] Open
Abstract
Conserved developmentally regulated guanosine triphosphate (GTP)-binding proteins (Drgs) and their binding partner Drg family regulatory proteins (Dfrps) are important for embryonic development, cellular growth control, differentiation, and proliferation. Here, we report that the yeast Drg1/Dfrp1 ortholog Rbg1/Tma46 facilitates translational initiation, elongation, and termination by suppressing prolonged ribosome pausing. Consistent with the genome-wide observations, deletion of Rbg1 exacerbates the growth defect resulting from translation stalling, and Rbg1 stabilizes mRNAs against no-go decay. Furthermore, we provide a cryoelectron microscopy (cryo-EM) structure of the 80S ribosome bound with Rbg1/Tma46 that reveals the molecular interactions responsible for Rbg1/Tma46 function. The Rbg1 subunit binds to the GTPase association center of the ribosome and the A-tRNA, and the N-terminal zinc finger domain of the Tma46 subunit binds to the 40S, establishing an interaction critical for the ribosomal association. Our results answer the fundamental question of how a paused ribosome resumes translation and show that Drg1/Dfrp1 play a critical role in ensuring orderly translation.
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Affiliation(s)
- Fuxing Zeng
- Department of Biochemistry, University of Illinois at Urbana-Champaign, 600 S. Mathews Avenue, Urbana, IL 61801, USA; Department of Biology, School of Life Sciences, Southern University of Science and Technology, No. 1088 Xueyuan Blvd., Shenzhen 518055, People's Republic of China
| | - Xin Li
- Department of Biology, School of Life Sciences, Southern University of Science and Technology, No. 1088 Xueyuan Blvd., Shenzhen 518055, People's Republic of China
| | - Melissa Pires-Alves
- Department of Biochemistry, University of Illinois at Urbana-Champaign, 600 S. Mathews Avenue, Urbana, IL 61801, USA
| | - Xin Chen
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, 600 S. Mathews Avenue, Urbana, IL 61801, USA
| | - Christopher W Hawk
- Department of Biochemistry, University of Illinois at Urbana-Champaign, 600 S. Mathews Avenue, Urbana, IL 61801, USA
| | - Hong Jin
- Department of Biochemistry, University of Illinois at Urbana-Champaign, 600 S. Mathews Avenue, Urbana, IL 61801, USA; Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, 600 S. Mathews Avenue, Urbana, IL 61801, USA; Carl R. Woese Institute for Genomic Biology, 1206 West Gregory Drive, University of Illinois at Urbana-Champaign, 600 S. Mathews Avenue, Urbana, IL 61801, USA.
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20
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Lee JH, Lee EJ, Roe JH. uORF-mediated riboregulation controls transcription of whiB7/wblC antibiotic resistance gene. Mol Microbiol 2021; 117:179-192. [PMID: 34687261 DOI: 10.1111/mmi.14834] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Revised: 10/05/2021] [Accepted: 10/19/2021] [Indexed: 11/27/2022]
Abstract
WhiB7/WblC is a transcriptional factor of actinomycetes conferring intrinsic resistance to multiple translation-inhibitory antibiotics. It positively autoregulates its own transcription in response to the same antibiotics. The presence of a uORF and a potential Rho-independent transcription terminator in the 5' leader region has suggested a possibility that the whiB7/wblC gene is regulated via a uORF-mediated transcription attenuation. However, experimental evidence for the molecular mechanism to explain how antibiotic stress suppresses the attenuator, if any, and induces transcription of the whiB7/wblC gene has been lacking. Here we report that the 5' leader sequences of the whiB7/wblC genes in sub-clades of actinomycetes include conserved antiterminator RNA structures. We confirmed that the putative antiterminator in the whiB7/wblC leader sequences of both Streptomyces and Mycobacterium indeed suppresses Rho-independent transcription terminator and facilitates transcription readthrough, which is required for WhiB7/WblC-mediated antibiotic resistance. The antibiotic-mediated suppression of the attenuator can be recapitulated by amino acid starvation, indicating that translational inhibition of uORF by multiple signals is a key to induce whiB7/wblC expression. Our findings of a mechanism leading to intrinsic antibiotic resistance could provide an alternative to treat drug-resistant mycobacteria.
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Affiliation(s)
- Ju-Hyung Lee
- School of Biological Sciences, and Institute of Microbiology, Seoul National University, Seoul, Korea
| | - Eun-Jin Lee
- Department of Life Sciences, Korea University, Seoul, Korea
| | - Jung-Hye Roe
- School of Biological Sciences, and Institute of Microbiology, Seoul National University, Seoul, Korea
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21
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Leimer N, Wu X, Imai Y, Morrissette M, Pitt N, Favre-Godal Q, Iinishi A, Jain S, Caboni M, Leus IV, Bonifay V, Niles S, Bargabos R, Ghiglieri M, Corsetti R, Krumpoch M, Fox G, Son S, Klepacki D, Polikanov YS, Freliech CA, McCarthy JE, Edmondson DG, Norris SJ, D'Onofrio A, Hu LT, Zgurskaya HI, Lewis K. A selective antibiotic for Lyme disease. Cell 2021; 184:5405-5418.e16. [PMID: 34619078 DOI: 10.1016/j.cell.2021.09.011] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Revised: 07/22/2021] [Accepted: 09/08/2021] [Indexed: 12/11/2022]
Abstract
Lyme disease is on the rise. Caused by a spirochete Borreliella burgdorferi, it affects an estimated 500,000 people in the United States alone. The antibiotics currently used to treat Lyme disease are broad spectrum, damage the microbiome, and select for resistance in non-target bacteria. We therefore sought to identify a compound acting selectively against B. burgdorferi. A screen of soil micro-organisms revealed a compound highly selective against spirochetes, including B. burgdorferi. Unexpectedly, this compound was determined to be hygromycin A, a known antimicrobial produced by Streptomyces hygroscopicus. Hygromycin A targets the ribosomes and is taken up by B. burgdorferi, explaining its selectivity. Hygromycin A cleared the B. burgdorferi infection in mice, including animals that ingested the compound in a bait, and was less disruptive to the fecal microbiome than clinically relevant antibiotics. This selective antibiotic holds the promise of providing a better therapeutic for Lyme disease and eradicating it in the environment.
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Affiliation(s)
- Nadja Leimer
- Antimicrobial Discovery Center, Department of Biology, Northeastern University, Boston, MA 02115, USA
| | - Xiaoqian Wu
- Antimicrobial Discovery Center, Department of Biology, Northeastern University, Boston, MA 02115, USA
| | - Yu Imai
- Antimicrobial Discovery Center, Department of Biology, Northeastern University, Boston, MA 02115, USA
| | - Madeleine Morrissette
- Antimicrobial Discovery Center, Department of Biology, Northeastern University, Boston, MA 02115, USA
| | - Norman Pitt
- Antimicrobial Discovery Center, Department of Biology, Northeastern University, Boston, MA 02115, USA
| | - Quentin Favre-Godal
- Antimicrobial Discovery Center, Department of Biology, Northeastern University, Boston, MA 02115, USA
| | - Akira Iinishi
- Antimicrobial Discovery Center, Department of Biology, Northeastern University, Boston, MA 02115, USA
| | - Samta Jain
- Antimicrobial Discovery Center, Department of Biology, Northeastern University, Boston, MA 02115, USA
| | - Mariaelena Caboni
- Antimicrobial Discovery Center, Department of Biology, Northeastern University, Boston, MA 02115, USA
| | - Inga V Leus
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, OK 73019, USA
| | - Vincent Bonifay
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, OK 73019, USA
| | - Samantha Niles
- Antimicrobial Discovery Center, Department of Biology, Northeastern University, Boston, MA 02115, USA
| | - Rachel Bargabos
- Antimicrobial Discovery Center, Department of Biology, Northeastern University, Boston, MA 02115, USA
| | - Meghan Ghiglieri
- Antimicrobial Discovery Center, Department of Biology, Northeastern University, Boston, MA 02115, USA
| | - Rachel Corsetti
- Antimicrobial Discovery Center, Department of Biology, Northeastern University, Boston, MA 02115, USA
| | - Megan Krumpoch
- Antimicrobial Discovery Center, Department of Biology, Northeastern University, Boston, MA 02115, USA
| | - Gabriel Fox
- Antimicrobial Discovery Center, Department of Biology, Northeastern University, Boston, MA 02115, USA
| | - Sangkeun Son
- Antimicrobial Discovery Center, Department of Biology, Northeastern University, Boston, MA 02115, USA
| | - Dorota Klepacki
- Center for Biomolecular Sciences, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Yury S Polikanov
- Department of Biological Sciences, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Cecily A Freliech
- Division of Geographic Medicine and Infectious Diseases, Tufts Medical Center, Boston, MA 02111, USA
| | - Julie E McCarthy
- Division of Geographic Medicine and Infectious Diseases, Tufts Medical Center, Boston, MA 02111, USA
| | - Diane G Edmondson
- Department of Pathology and Laboratory Medicine, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX 77225, USA
| | - Steven J Norris
- Department of Pathology and Laboratory Medicine, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX 77225, USA
| | - Anthony D'Onofrio
- Antimicrobial Discovery Center, Department of Biology, Northeastern University, Boston, MA 02115, USA
| | - Linden T Hu
- Division of Geographic Medicine and Infectious Diseases, Tufts Medical Center, Boston, MA 02111, USA
| | - Helen I Zgurskaya
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, OK 73019, USA
| | - Kim Lewis
- Antimicrobial Discovery Center, Department of Biology, Northeastern University, Boston, MA 02115, USA.
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22
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Zhang J, Liu G, Zhang X, Chang Y, Wang S, He W, Sun W, Chen D, Murchie AIH. Aminoglycoside riboswitch control of the expression of integron associated aminoglycoside resistance adenyltransferases. Virulence 2021; 11:1432-1442. [PMID: 33103573 PMCID: PMC7588185 DOI: 10.1080/21505594.2020.1836910] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022] Open
Abstract
The proliferation of antibiotic resistance has its origins in horizontal gene transfer. The class 1 integrons mediate gene transfer by assimilating antibiotic-resistance genes through site-specific recombination. For the class 1 integrons the first assimilated gene normally encodes an aminoglycoside antibiotic resistance protein which is either an aminoglycoside acetyltransferase (AAC), nucleotidyltransferase - (ANT), or adenyl transferase (AAD). An aminoglycoside-sensing riboswitch RNA in the leader RNA of AAC/AAD that controls the expression of aminoglycoside resistance genes has been previously described. Here we explore the relationship between the recombinant products of integron recombination and a series of candidate riboswitch RNAs in the 5' UTR of aad (aminoglycoside adenyltransferases) genes. The RNA sequences from the 5' UTR of the aad genes from pathogenic strains that are the products of site-specific DNA recombination by class 1 integrons were investigated. Reporter assays, MicroScale Thermophoresis (MST) and covariance analysis revealed that a functional aminoglycoside-sensing riboswitch was selected at the DNA level through integron-mediated site-specific recombination. This study explains the close association between integron recombination and the aminoglycoside-sensing riboswitch RNA.
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Affiliation(s)
- Jun Zhang
- Key Laboratory of Medical Epigenetics and Metabolism, Fudan University Pudong Medical Center, Institutes of Biomedical Sciences, Fudan University , Shanghai, PR China.,Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, School of Basic Medical Sciences, Fudan University , Shanghai, PR China
| | - Getong Liu
- Key Laboratory of Medical Epigenetics and Metabolism, Fudan University Pudong Medical Center, Institutes of Biomedical Sciences, Fudan University , Shanghai, PR China.,Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, School of Basic Medical Sciences, Fudan University , Shanghai, PR China
| | - Xuhui Zhang
- Key Laboratory of Medical Epigenetics and Metabolism, Fudan University Pudong Medical Center, Institutes of Biomedical Sciences, Fudan University , Shanghai, PR China.,Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, School of Basic Medical Sciences, Fudan University , Shanghai, PR China
| | - Yaowen Chang
- Key Laboratory of Medical Epigenetics and Metabolism, Fudan University Pudong Medical Center, Institutes of Biomedical Sciences, Fudan University , Shanghai, PR China.,Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, School of Basic Medical Sciences, Fudan University , Shanghai, PR China
| | - Shasha Wang
- Key Laboratory of Medical Epigenetics and Metabolism, Fudan University Pudong Medical Center, Institutes of Biomedical Sciences, Fudan University , Shanghai, PR China.,Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, School of Basic Medical Sciences, Fudan University , Shanghai, PR China
| | - Weizhi He
- Key Laboratory of Medical Epigenetics and Metabolism, Fudan University Pudong Medical Center, Institutes of Biomedical Sciences, Fudan University , Shanghai, PR China.,Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, School of Basic Medical Sciences, Fudan University , Shanghai, PR China
| | - Wenxia Sun
- Key Laboratory of Medical Epigenetics and Metabolism, Fudan University Pudong Medical Center, Institutes of Biomedical Sciences, Fudan University , Shanghai, PR China.,Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, School of Basic Medical Sciences, Fudan University , Shanghai, PR China
| | - Dongrong Chen
- Key Laboratory of Medical Epigenetics and Metabolism, Fudan University Pudong Medical Center, Institutes of Biomedical Sciences, Fudan University , Shanghai, PR China.,Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, School of Basic Medical Sciences, Fudan University , Shanghai, PR China
| | - Alastair I H Murchie
- Key Laboratory of Medical Epigenetics and Metabolism, Fudan University Pudong Medical Center, Institutes of Biomedical Sciences, Fudan University , Shanghai, PR China.,Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, School of Basic Medical Sciences, Fudan University , Shanghai, PR China
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23
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Dmitriev SE, Vladimirov DO, Lashkevich KA. A Quick Guide to Small-Molecule Inhibitors of Eukaryotic Protein Synthesis. BIOCHEMISTRY (MOSCOW) 2021; 85:1389-1421. [PMID: 33280581 PMCID: PMC7689648 DOI: 10.1134/s0006297920110097] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Eukaryotic ribosome and cap-dependent translation are attractive targets in the antitumor, antiviral, anti-inflammatory, and antiparasitic therapies. Currently, a broad array of small-molecule drugs is known that specifically inhibit protein synthesis in eukaryotic cells. Many of them are well-studied ribosome-targeting antibiotics that block translocation, the peptidyl transferase center or the polypeptide exit tunnel, modulate the binding of translation machinery components to the ribosome, and induce miscoding, premature termination or stop codon readthrough. Such inhibitors are widely used as anticancer, anthelmintic and antifungal agents in medicine, as well as fungicides in agriculture. Chemicals that affect the accuracy of stop codon recognition are promising drugs for the nonsense suppression therapy of hereditary diseases and restoration of tumor suppressor function in cancer cells. Other compounds inhibit aminoacyl-tRNA synthetases, translation factors, and components of translation-associated signaling pathways, including mTOR kinase. Some of them have antidepressant, immunosuppressive and geroprotective properties. Translation inhibitors are also used in research for gene expression analysis by ribosome profiling, as well as in cell culture techniques. In this article, we review well-studied and less known inhibitors of eukaryotic protein synthesis (with the exception of mitochondrial and plastid translation) classified by their targets and briefly describe the action mechanisms of these compounds. We also present a continuously updated database (http://eupsic.belozersky.msu.ru/) that currently contains information on 370 inhibitors of eukaryotic protein synthesis.
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Affiliation(s)
- S E Dmitriev
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119234, Russia. .,Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, 119234, Russia.,Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, 119991, Russia
| | - D O Vladimirov
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, 119234, Russia
| | - K A Lashkevich
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119234, Russia
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24
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Osterman IA, Dontsova OA, Sergiev PV. rRNA Methylation and Antibiotic Resistance. BIOCHEMISTRY (MOSCOW) 2021; 85:1335-1349. [PMID: 33280577 DOI: 10.1134/s000629792011005x] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Methylation of nucleotides in rRNA is one of the basic mechanisms of bacterial resistance to protein synthesis inhibitors. The genes for corresponding methyltransferases have been found in producer strains and clinical isolates of pathogenic bacteria. In some cases, rRNA methylation by housekeeping enzymes is, on the contrary, required for the action of antibiotics. The effects of rRNA modifications associated with antibiotic efficacy may be cooperative or mutually exclusive. Evolutionary relationships between the systems of rRNA modification by housekeeping enzymes and antibiotic resistance-related methyltransferases are of particular interest. In this review, we discuss the above topics in detail.
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Affiliation(s)
- I A Osterman
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Skolkovo, 143028, Russia.,Faculty of Chemistry, Lomonosov Moscow State University, Moscow, 119991, Russia
| | - O A Dontsova
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Skolkovo, 143028, Russia.,Faculty of Chemistry, Lomonosov Moscow State University, Moscow, 119991, Russia.,Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia
| | - P V Sergiev
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Skolkovo, 143028, Russia. .,Faculty of Chemistry, Lomonosov Moscow State University, Moscow, 119991, Russia.,Institute of Functional Genomics, Lomonosov Moscow State University, Moscow, 119991, Russia
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25
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Wang S, Jiang K, Du X, Lu Y, Liao L, He Z, He W. Translational Attenuation Mechanism of ErmB Induction by Erythromycin Is Dependent on Two Leader Peptides. Front Microbiol 2021; 12:690744. [PMID: 34262551 PMCID: PMC8274638 DOI: 10.3389/fmicb.2021.690744] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2021] [Accepted: 06/03/2021] [Indexed: 11/13/2022] Open
Abstract
Ribosome stalling on ermBL at the tenth codon (Asp) is believed to be a major mechanism of ermB induction by erythromycin (Ery). In this study, we demonstrated that the mechanism of ermB induction by Ery depends not only on ermBL expression but also on previously unreported ermBL2 expression. Introducing premature termination codons in ermBL, we proved that translation of the N-terminal region of ermBL is the key component for ermB induced by Ery, whereas translation of the C-terminal region of ermBL did not affect Ery-induced ermB. Mutation of the tenth codon (Asp10) of ermBL with other amino acids showed that the degree of induction in vivo was not completely consistent with the data from the in vitro toe printing assay. Alanine-scanning mutagenesis of ermBL demonstrated that both N-terminal residues (R7-K11) and the latter part of ermBL (K20-K27) are critical for Ery induction of ermB. The frameshifting reporter plasmid showed that a new leader peptide, ermBL2, exists in the ermB regulatory region. Further, introducing premature termination mutation and alanine-scanning mutagenesis of ermBL2 demonstrated that the N-terminus of ermBL2 is essential for induction by Ery. Therefore, the detailed function of ermBL2 requires further study.
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Affiliation(s)
- Shasha Wang
- Institute for Regenerative Medicine, Shanghai East Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, China.,Department of Anesthesiology and Pain Management, Shanghai East Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Kai Jiang
- Department of Biobank, Renji Hospital, School of Medicine, Shanghai JiaoTong University, Shanghai, China
| | - Xinyue Du
- Institute for Regenerative Medicine, Shanghai East Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Yanli Lu
- Institute for Regenerative Medicine, Shanghai East Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Lijun Liao
- Department of Anesthesiology and Pain Management, Shanghai East Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Zhiying He
- Institute for Regenerative Medicine, Shanghai East Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, China.,Shanghai Engineering Research Center of Stem Cells Translational Medicine, Shanghai, China
| | - Weizhi He
- Institute for Regenerative Medicine, Shanghai East Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, China
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26
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Abstract
Folding of polypeptides begins during their synthesis on ribosomes. This process has evolved as a means for the cell to maintain proteostasis, by mitigating the risk of protein misfolding and aggregation. The capacity to now depict this cellular feat at increasingly higher resolution is providing insight into the mechanistic determinants that promote successful folding. Emerging from these studies is the intimate interplay between protein translation and folding, and within this the ribosome particle is the key player. Its unique structural properties provide a specialized scaffold against which nascent polypeptides can begin to form structure in a highly coordinated, co-translational manner. Here, we examine how, as a macromolecular machine, the ribosome modulates the intrinsic dynamic properties of emerging nascent polypeptide chains and guides them toward their biologically active structures.
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Affiliation(s)
- Anaïs M E Cassaignau
- Institute of Structural and Molecular Biology, University College London and Birkbeck College, London WC1E 7HX, United Kingdom; , ,
| | - Lisa D Cabrita
- Institute of Structural and Molecular Biology, University College London and Birkbeck College, London WC1E 7HX, United Kingdom; , ,
| | - John Christodoulou
- Institute of Structural and Molecular Biology, University College London and Birkbeck College, London WC1E 7HX, United Kingdom; , ,
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27
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Seefeldt AC, Aguirre Rivera J, Johansson M. Direct Measurements of Erythromycin's Effect on Protein Synthesis Kinetics in Living Bacterial Cells. J Mol Biol 2021; 433:166942. [PMID: 33744313 DOI: 10.1016/j.jmb.2021.166942] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Revised: 03/09/2021] [Accepted: 03/09/2021] [Indexed: 10/21/2022]
Abstract
Macrolide antibiotics, such as erythromycin, bind to the nascent peptide exit tunnel (NPET) of the bacterial ribosome and modulate protein synthesis depending on the nascent peptide sequence. Whereas in vitro biochemical and structural methods have been instrumental in dissecting and explaining the molecular details of macrolide-induced peptidyl-tRNA drop-off and ribosome stalling, the dynamic effects of the drugs on ongoing protein synthesis inside live bacterial cells are far less explored. In the present study, we used single-particle tracking of dye-labeled tRNAs to study the kinetics of mRNA translation in the presence of erythromycin, directly inside live Escherichia coli cells. In erythromycin-treated cells, we find that the dwells of elongator tRNAPhe on ribosomes extend significantly, but they occur much more seldom. In contrast, the drug barely affects the ribosome binding events of the initiator tRNAfMet. By overexpressing specific short peptides, we further find context-specific ribosome binding dynamics of tRNAPhe, underscoring the complexity of erythromycin's effect on protein synthesis in bacterial cells.
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Affiliation(s)
| | | | - Magnus Johansson
- Department of Cell and Molecular Biology, Uppsala University, Sweden.
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28
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Aung MS, Urushibara N, Kawaguchiya M, Hirose M, Ike M, Ito M, Kobayashi N. Distribution of Virulence Factors and Resistance Determinants in Three Genotypes of Staphylococcus argenteus Clinical Isolates in Japan. Pathogens 2021; 10:pathogens10020163. [PMID: 33546443 PMCID: PMC7913748 DOI: 10.3390/pathogens10020163] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Revised: 01/29/2021] [Accepted: 02/01/2021] [Indexed: 11/16/2022] Open
Abstract
Staphylococcus argenteus, a novel staphylococcal species independent of S. aureus, causes a wide spectrum of infectious diseases. As detection of this species from humans and animals has been increasingly reported worldwide, its growing virulence and drug resistance via external genetic determinants has become concerning. In this study, the prevalence and genetic characteristics of virulence factors and drug resistance determinants were investigated for 82 S. argenteus clinical isolates in Hokkaido, Japan, for a one-year period starting in August 2019. These S. argenteus isolates corresponded to 0.66% of the total number of S. aureus isolates collected in the same period. The most prevalent genotype was sequence type (ST) 2250 and staphylocoagulase (coa) genotype XId (45.1%, n = 37), followed by ST1223-coa XV (30.5%, n = 25) and ST2198-coa XIV (24.4%, n = 20). Panton-Valentine leukocidin genes (lukS-PV-lukF-PV) were identified in a single ST2250 isolate. Only ST1223 isolates had the enterotoxin gene cluster (egc-2), seb, and selw (detection rate; 100%, 60%, and 84%, respectively), while sec, sey, sel26-sel27, tst-1 were only detected in ST2250 isolates (detection rate; 10.8%, 100%, 67.6%, and 10.8%, respectively). ST2198 isolates harbored selx at a significantly higher rate (60%) than isolates of other STs. Although most of S. argenteus isolates were susceptible to antimicrobials examined, ST2198 showed higher resistance rates to penicillin, macrolides, and aminoglycosides than other STs, and it harbored various resistance genes such as blaZ, erm(C), msr(A), lnuA, and aac(6′)-Ie-aph(2″)-Ia. Only one ST2250 isolate possessed SCCmec-IVc, showing resistance to oxacillin. blaZ was the most prevalent determinant of resistance in the three STs and belonged to two plasmid groups and a chromosomal group, suggesting its diverse origin. lnu(A) in ST2198 isolates was assigned to a major cluster with various staphylococcal species. The present study indicates that the prevalence of virulence factors and drug resistance profile/determinants differ depending on the lineage (ST) of S. argenteus.
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Affiliation(s)
- Meiji Soe Aung
- Department of Hygiene, Sapporo Medical University School of Medicine, Hokkaido, Sapporo 060-8556, Japan; (N.U.); (M.K.); (N.K.)
- Correspondence: ; Tel.: +81-11-611-2111
| | - Noriko Urushibara
- Department of Hygiene, Sapporo Medical University School of Medicine, Hokkaido, Sapporo 060-8556, Japan; (N.U.); (M.K.); (N.K.)
| | - Mitsuyo Kawaguchiya
- Department of Hygiene, Sapporo Medical University School of Medicine, Hokkaido, Sapporo 060-8556, Japan; (N.U.); (M.K.); (N.K.)
| | - Mina Hirose
- Division of Pediatric Dentistry, Department of Oral Growth and Development, School of Dentistry, Health Sciences University of Hokkaido, Ishikari-Tobetsu 061-0293, Japan;
| | - Miyo Ike
- Sapporo Clinical Laboratory, Incorporated, Hokkaido, Sapporo 060-0005, Japan; (M.I.); (M.I.)
| | - Masahiko Ito
- Sapporo Clinical Laboratory, Incorporated, Hokkaido, Sapporo 060-0005, Japan; (M.I.); (M.I.)
| | - Nobumichi Kobayashi
- Department of Hygiene, Sapporo Medical University School of Medicine, Hokkaido, Sapporo 060-8556, Japan; (N.U.); (M.K.); (N.K.)
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29
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Jednačak T, Mikulandra I, Novak P. Advanced Methods for Studying Structure and Interactions of Macrolide Antibiotics. Int J Mol Sci 2020; 21:E7799. [PMID: 33096889 PMCID: PMC7589898 DOI: 10.3390/ijms21207799] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2020] [Revised: 10/09/2020] [Accepted: 10/19/2020] [Indexed: 11/17/2022] Open
Abstract
Macrolide antibiotics are macrocyclic compounds that are clinically used and prescribed for the treatment of upper and lower respiratory tract infections. They inhibit the synthesis of bacterial proteins by reversible binding to the 23S rRNA at or near the peptidyl transferase center. However, their excellent antibacterial profile was largely compromised by the emergence of bacterial resistance. Today, fighting resistance to antibiotics is one of the greatest challenges in medicinal chemistry. Considering various physicochemical properties of macrolides, understanding their structure and interactions with macromolecular targets is crucial for the design of new antibiotics efficient against resistant pathogens. The solid-state structures of some macrolide-ribosome complexes have recently been solved, throwing new light on the macrolide binding mechanisms. On the other hand, a combination of NMR spectroscopy and molecular modeling calculations can be applied to study free and bound conformations in solution. In this article, a description of advanced physicochemical methods for elucidating the structure and interactions of macrolide antibiotics in solid state and solution will be provided, and their principal advantages and drawbacks will be discussed.
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Affiliation(s)
- Tomislav Jednačak
- Department of Chemistry, Faculty of Science, University of Zagreb, Horvatovac 102a, HR-10000 Zagreb, Croatia;
| | | | - Predrag Novak
- Department of Chemistry, Faculty of Science, University of Zagreb, Horvatovac 102a, HR-10000 Zagreb, Croatia;
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30
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Ribosome-Mediated Attenuation of vga(A) Expression Is Shaped by the Antibiotic Resistance Specificity of Vga(A) Protein Variants. Antimicrob Agents Chemother 2020; 64:AAC.00666-20. [PMID: 32816732 DOI: 10.1128/aac.00666-20] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Accepted: 08/10/2020] [Indexed: 01/29/2023] Open
Abstract
Vga(A) protein variants confer different levels of resistance to lincosamides, streptogramin A, and pleuromutilins (LSAP) by displacing antibiotics from the ribosome. Here, we show that expression of vga(A) variants from Staphylococcus haemolyticus is regulated by cis-regulatory RNA in response to the LSAP antibiotics by the mechanism of ribosome-mediated attenuation. The specificity of induction depends on Vga(A)-mediated resistance rather than on the sequence of the riboregulator. Fine tuning between Vga(A) activity and its expression in response to the antibiotics may contribute to the selection of more potent Vga(A) variants because newly acquired mutation can be immediately phenotypically manifested.
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31
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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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32
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Mangano K, Florin T, Shao X, Klepacki D, Chelysheva I, Ignatova Z, Gao Y, Mankin AS, Vázquez-Laslop N. Genome-wide effects of the antimicrobial peptide apidaecin on translation termination in bacteria. eLife 2020; 9:e62655. [PMID: 33031031 PMCID: PMC7544508 DOI: 10.7554/elife.62655] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Accepted: 09/20/2020] [Indexed: 12/16/2022] Open
Abstract
Biochemical studies suggested that the antimicrobial peptide apidaecin (Api) inhibits protein synthesis by binding in the nascent peptide exit tunnel and trapping the release factor associated with a terminating ribosome. The mode of Api action in bacterial cells had remained unknown. Here genome-wide analysis reveals that in bacteria, Api arrests translating ribosomes at stop codons and causes pronounced queuing of the trailing ribosomes. By sequestering the available release factors, Api promotes pervasive stop codon bypass, leading to the expression of proteins with C-terminal extensions. Api-mediated translation arrest leads to the futile activation of the ribosome rescue systems. Understanding the unique mechanism of Api action in living cells may facilitate the development of new medicines and research tools for genome exploration.
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Affiliation(s)
- Kyle Mangano
- Center for Biomolecular Sciences, University of Illinois at ChicagoChicagoUnited States
- Department of Pharmaceutical Sciences, University of Illinois at ChicagoChicagoUnited States
| | - Tanja Florin
- Center for Biomolecular Sciences, University of Illinois at ChicagoChicagoUnited States
| | - Xinhao Shao
- Department of Pharmaceutical Sciences, University of Illinois at ChicagoChicagoUnited States
| | - Dorota Klepacki
- Center for Biomolecular Sciences, University of Illinois at ChicagoChicagoUnited States
| | - Irina Chelysheva
- Institute of Biochemistry and Molecular Biology, University of HamburgHamburgGermany
| | - Zoya Ignatova
- Institute of Biochemistry and Molecular Biology, University of HamburgHamburgGermany
| | - Yu Gao
- Department of Pharmaceutical Sciences, University of Illinois at ChicagoChicagoUnited States
| | - Alexander S Mankin
- Center for Biomolecular Sciences, University of Illinois at ChicagoChicagoUnited States
- Department of Pharmaceutical Sciences, University of Illinois at ChicagoChicagoUnited States
| | - Nora Vázquez-Laslop
- Center for Biomolecular Sciences, University of Illinois at ChicagoChicagoUnited States
- Department of Pharmaceutical Sciences, University of Illinois at ChicagoChicagoUnited States
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33
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Guzel P, Yildirim HZ, Yuce M, Kurkcuoglu O. Exploring Allosteric Signaling in the Exit Tunnel of the Bacterial Ribosome by Molecular Dynamics Simulations and Residue Network Model. Front Mol Biosci 2020; 7:586075. [PMID: 33102529 PMCID: PMC7545307 DOI: 10.3389/fmolb.2020.586075] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Accepted: 09/08/2020] [Indexed: 11/25/2022] Open
Abstract
The bacterial ribosomal tunnel is equipped with numerous sites highly sensitive to the course of the translation process. This study investigates allosteric pathways linking distant functional sites that collaboratively play a role either in translation regulation or recruitment of chaperones. We apply perturbation response scanning (PRS) analysis to 700 ns long and 500 ns long coarse-grained molecular dynamics simulations of E. coli and T. thermophilus large subunits, respectively, to reveal nucleotides/residues with the ability to transmit perturbations by dynamic rationale. We also use the residue network model with the k-shortest pathways method to calculate suboptimal pathways based on the contact topology of the ribosomal tunnel of E. coli crystal structure and 101 ClustENM generated conformers of T. thermophilus large subunit. In the upper part of the tunnel, results suggest that A2062 and A2451 can communicate in both directions for translation stalling, mostly through dynamically coupled C2063, C2064, and A2450. For a similar purpose, U2585 and U2586 are coupled with A2062, while they are also sensitive to uL4 and uL22 at the constriction region through two different pathways at the opposite sides of the tunnel wall. In addition, the constriction region communicates with the chaperone binding site on uL23 at the solvent side but through few nucleotides. Potential allosteric communication pathways between the lower part of the tunnel and chaperone binding site mostly use the flexible loop of uL23, while A1336–G1339 provide a suboptimal pathway. Both species seem to employ similar mechanisms in the long tunnel, where a non-conserved cavity at the bacterial uL23 and 23S rRNA interface is proposed as a novel drug target.
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Affiliation(s)
- Pelin Guzel
- Department of Chemical Engineering, Istanbul Technical University, Istanbul, Turkey.,Science and Advanced Technology Research and Application Center, Istanbul Medeniyet University, Istanbul, Turkey
| | - Hatice Zeynep Yildirim
- Polymer Research Center and Graduate Program in Computational Science and Engineering, Bogazici University, Istanbul, Turkey
| | - Merve Yuce
- Department of Chemical Engineering, Istanbul Technical University, Istanbul, Turkey
| | - Ozge Kurkcuoglu
- Department of Chemical Engineering, Istanbul Technical University, Istanbul, Turkey
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34
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Hew B, Tan QW, Goh W, Ng JWX, Mutwil M. LSTrAP-Crowd: prediction of novel components of bacterial ribosomes with crowd-sourced analysis of RNA sequencing data. BMC Biol 2020; 18:114. [PMID: 32883264 PMCID: PMC7470450 DOI: 10.1186/s12915-020-00846-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Accepted: 08/12/2020] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Bacterial resistance to antibiotics is a growing health problem that is projected to cause more deaths than cancer by 2050. Consequently, novel antibiotics are urgently needed. Since more than half of the available antibiotics target the structurally conserved bacterial ribosomes, factors involved in protein synthesis are thus prime targets for the development of novel antibiotics. However, experimental identification of these potential antibiotic target proteins can be labor-intensive and challenging, as these proteins are likely to be poorly characterized and specific to few bacteria. Here, we use a bioinformatics approach to identify novel components of protein synthesis. RESULTS In order to identify these novel proteins, we established a Large-Scale Transcriptomic Analysis Pipeline in Crowd (LSTrAP-Crowd), where 285 individuals processed 26 terabytes of RNA-sequencing data of the 17 most notorious bacterial pathogens. In total, the crowd processed 26,269 RNA-seq experiments and used the data to construct gene co-expression networks, which were used to identify more than a hundred uncharacterized genes that were transcriptionally associated with protein synthesis. We provide the identity of these genes together with the processed gene expression data. CONCLUSIONS We identified genes related to protein synthesis in common bacterial pathogens and thus provide a resource of potential antibiotic development targets for experimental validation. The data can be used to explore additional vulnerabilities of bacteria, while our approach demonstrates how the processing of gene expression data can be easily crowd-sourced.
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Affiliation(s)
- Benedict Hew
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore
| | - Qiao Wen Tan
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore
| | - William Goh
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore
| | - Jonathan Wei Xiong Ng
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore
| | - Marek Mutwil
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore.
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35
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Dever TE, Ivanov IP, Sachs MS. Conserved Upstream Open Reading Frame Nascent Peptides That Control Translation. Annu Rev Genet 2020; 54:237-264. [PMID: 32870728 DOI: 10.1146/annurev-genet-112618-043822] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Cells utilize transcriptional and posttranscriptional mechanisms to alter gene expression in response to environmental cues. Gene-specific controls, including changing the translation of specific messenger RNAs (mRNAs), provide a rapid means to respond precisely to different conditions. Upstream open reading frames (uORFs) are known to control the translation of mRNAs. Recent studies in bacteria and eukaryotes have revealed the functions of evolutionarily conserved uORF-encoded peptides. Some of these uORF-encoded nascent peptides enable responses to specific metabolites to modulate the translation of their mRNAs by stalling ribosomes and through ribosome stalling may also modulate the level of their mRNAs. In this review, we highlight several examples of conserved uORF nascent peptides that stall ribosomes to regulate gene expression in response to specific metabolites in bacteria, fungi, mammals, and plants.
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Affiliation(s)
- Thomas E Dever
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892, USA; ,
| | - Ivaylo P Ivanov
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892, USA; ,
| | - Matthew S Sachs
- Department of Biology, Texas A&M University, College Station, Texas 77843, USA;
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36
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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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37
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Pichkur EB, Paleskava A, Tereshchenkov AG, Kasatsky P, Komarova ES, Shiriaev DI, Bogdanov AA, Dontsova OA, Osterman IA, Sergiev PV, Polikanov YS, Myasnikov AG, Konevega AL. Insights into the improved macrolide inhibitory activity from the high-resolution cryo-EM structure of dirithromycin bound to the E. coli 70S ribosome. RNA (NEW YORK, N.Y.) 2020; 26:715-723. [PMID: 32144191 PMCID: PMC7266154 DOI: 10.1261/rna.073817.119] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Accepted: 12/27/2019] [Indexed: 05/05/2023]
Abstract
Macrolides are one of the most successful and widely used classes of antibacterials, which kill or stop the growth of pathogenic bacteria by binding near the active site of the ribosome and interfering with protein synthesis. Dirithromycin is a derivative of the prototype macrolide erythromycin with additional hydrophobic side chain. In our recent study, we have discovered that the side chain of dirithromycin forms lone pair-π stacking interaction with the aromatic imidazole ring of the His69 residue in ribosomal protein uL4 of the Thermus thermophilus 70S ribosome. In the current work, we found that neither the presence of the side chain, nor the additional contact with the ribosome, improve the binding affinity of dirithromycin to the ribosome. Nevertheless, we found that dirithromycin is a more potent inhibitor of in vitro protein synthesis in comparison with its parent compound, erythromycin. Using high-resolution cryo-electron microscopy, we determined the structure of the dirithromycin bound to the translating Escherichia coli 70S ribosome, which suggests that the better inhibitory properties of the drug could be rationalized by the side chain of dirithromycin pointing into the lumen of the nascent peptide exit tunnel, where it can interfere with the normal passage of the growing polypeptide chain.
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Affiliation(s)
- Evgeny B Pichkur
- Petersburg Nuclear Physics Institute named by B.P. Konstantinov of NRC "Kurchatov Institute," Gatchina, 188300, Russia
- National Research Center "Kurchatov Institute," Moscow, 123182, Russia
| | - Alena Paleskava
- Petersburg Nuclear Physics Institute named by B.P. Konstantinov of NRC "Kurchatov Institute," Gatchina, 188300, Russia
- Peter the Great St. Petersburg Polytechnic University, Saint Petersburg, 195251, Russia
| | - Andrey G Tereshchenkov
- Department of Chemistry and A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119992, Russia
| | - Pavel Kasatsky
- Petersburg Nuclear Physics Institute named by B.P. Konstantinov of NRC "Kurchatov Institute," Gatchina, 188300, Russia
| | - Ekaterina S Komarova
- Department of Bioengineering and Bioinformatics and A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119992, Russia
- Skolkovo Institute of Science and Technology, Skolkovo, Moscow region, 143025, Russia
| | - Dmitrii I Shiriaev
- Department of Chemistry and A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119992, Russia
| | - Alexey A Bogdanov
- Department of Chemistry and A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119992, Russia
| | - Olga A Dontsova
- Department of Chemistry and A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119992, Russia
- Skolkovo Institute of Science and Technology, Skolkovo, Moscow region, 143025, Russia
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia
| | - Ilya A Osterman
- Department of Chemistry and A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119992, Russia
- Skolkovo Institute of Science and Technology, Skolkovo, Moscow region, 143025, Russia
| | - Petr V Sergiev
- Department of Chemistry and A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119992, Russia
- Skolkovo Institute of Science and Technology, Skolkovo, Moscow region, 143025, Russia
| | - Yury S Polikanov
- Departments of Biological Sciences and Pharmaceutical Sciences, University of Illinois at Chicago, Chicago, Illinois 60607, USA
- Center for Biomolecular Sciences, University of Illinois at Chicago, Chicago, Illinois 60607, USA
| | - Alexander G Myasnikov
- Petersburg Nuclear Physics Institute named by B.P. Konstantinov of NRC "Kurchatov Institute," Gatchina, 188300, Russia
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, USA
- Centre for Integrative Biology, IGBMC, CNRS, Inserm, Université de Strasbourg, Illkirch, 67404, France
| | - Andrey L Konevega
- Petersburg Nuclear Physics Institute named by B.P. Konstantinov of NRC "Kurchatov Institute," Gatchina, 188300, Russia
- National Research Center "Kurchatov Institute," Moscow, 123182, Russia
- Peter the Great St. Petersburg Polytechnic University, Saint Petersburg, 195251, Russia
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38
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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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39
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Chu Y, Huang J, Ma G, Cui T, Yan X, Li H, Wang N. An Upstream Open Reading Frame Represses Translation of Chicken PPARγ Transcript Variant 1. Front Genet 2020; 11:165. [PMID: 32184808 PMCID: PMC7058706 DOI: 10.3389/fgene.2020.00165] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Accepted: 02/12/2020] [Indexed: 11/20/2022] Open
Abstract
Peroxisome proliferator-activated receptor γ (PPARγ) is a master regulator of adipogenesis. The PPARγ gene produces various transcripts with different 5'-untranslated regions (5' UTRs) because of alternative promoter usage and splicing. The 5' UTR plays important roles in posttranscriptional gene regulation. However, to date, the regulatory role and underlying mechanism of 5' UTRs in the posttranscriptional regulation of PPARγ expression remain largely unclear. In this study, we investigated the effects of 5' UTRs on posttranscriptional regulation using reporter assays. Our results showed that the five PPARγ 5' UTRs exerted different effects on reporter gene activity. Bioinformatics analysis showed that chicken PPARγ transcript 1 (PPARγ1) possessed an upstream open reading frame (uORF) in its 5' UTR. Mutation analysis showed that a mutation in the uORF led to increased Renilla luciferase activity and PPARγ protein expression, but decreased Renilla luciferase and PPARγ1 mRNA expression. mRNA stability analysis using real-time RT-PCR showed that the uORF mutation did not interfere with mRNA stability, but promoter activity analysis of the cloned 5' UTR showed that the uORF mutation reduced promoter activity. Furthermore, in vitro transcription/translation assays demonstrated that the uORF mutation markedly increased the translation of PPARγ1 mRNA. Collectively, our results indicate that the uORF represses the translation of chicken PPARγ1 mRNA.
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Affiliation(s)
- Yankai Chu
- Key Laboratory of Chicken Genetics and Breeding, Ministry of Agriculture and Rural Affairs, Harbin, China
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Education Department of Heilongjiang Province, Harbin, China
- College of Animal Science and Technology, Northeast Agricultural University, Harbin, China
| | - Jiaxin Huang
- Key Laboratory of Chicken Genetics and Breeding, Ministry of Agriculture and Rural Affairs, Harbin, China
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Education Department of Heilongjiang Province, Harbin, China
- College of Animal Science and Technology, Northeast Agricultural University, Harbin, China
| | - Guangwei Ma
- Key Laboratory of Chicken Genetics and Breeding, Ministry of Agriculture and Rural Affairs, Harbin, China
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Education Department of Heilongjiang Province, Harbin, China
- College of Animal Science and Technology, Northeast Agricultural University, Harbin, China
| | - Tingting Cui
- Key Laboratory of Chicken Genetics and Breeding, Ministry of Agriculture and Rural Affairs, Harbin, China
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Education Department of Heilongjiang Province, Harbin, China
- College of Animal Science and Technology, Northeast Agricultural University, Harbin, China
| | - Xiaohong Yan
- Key Laboratory of Chicken Genetics and Breeding, Ministry of Agriculture and Rural Affairs, Harbin, China
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Education Department of Heilongjiang Province, Harbin, China
- College of Animal Science and Technology, Northeast Agricultural University, Harbin, China
| | - Hui Li
- Key Laboratory of Chicken Genetics and Breeding, Ministry of Agriculture and Rural Affairs, Harbin, China
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Education Department of Heilongjiang Province, Harbin, China
- College of Animal Science and Technology, Northeast Agricultural University, Harbin, China
| | - Ning Wang
- Key Laboratory of Chicken Genetics and Breeding, Ministry of Agriculture and Rural Affairs, Harbin, China
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Education Department of Heilongjiang Province, Harbin, China
- College of Animal Science and Technology, Northeast Agricultural University, Harbin, China
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40
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Pletnev P, Guseva E, Zanina A, Evfratov S, Dzama M, Treshin V, Pogorel'skaya A, Osterman I, Golovina A, Rubtsova M, Serebryakova M, Pobeguts OV, Govorun VM, Bogdanov AA, Dontsova OA, Sergiev PV. Comprehensive Functional Analysis of Escherichia coli Ribosomal RNA Methyltransferases. Front Genet 2020; 11:97. [PMID: 32174967 PMCID: PMC7056703 DOI: 10.3389/fgene.2020.00097] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Accepted: 01/29/2020] [Indexed: 11/13/2022] Open
Abstract
Ribosomal RNAs in all organisms are methylated. The functional role of the majority of modified nucleotides is unknown. We systematically questioned the influence of rRNA methylation in Escherichia coli on a number of characteristics of bacterial cells with the help of a set of rRNA methyltransferase (MT) gene knockout strains from the Keio collection. Analysis of ribosomal subunits sedimentation profiles of the knockout strains revealed a surprisingly small number of rRNA MT that significantly affected ribosome assembly. Accumulation of the assembly intermediates was observed only for the rlmE knockout strain whose growth was retarded most significantly among other rRNA MT knockout strains. Accumulation of the 17S rRNA precursor was observed for rsmA(ksgA) knockout cells as well as for cells devoid of functional rsmB and rlmC genes. Significant differences were found among the WT and the majority of rRNA MT knockout strains in their ability to sustain exogenous protein overexpression. While the majority of the rRNA MT knockout strains supported suboptimal reporter gene expression, the strain devoid of the rsmF gene demonstrated a moderate increase in the yield of ectopic gene expression. Comparative 2D protein gel analysis of rRNA MT knockout strains revealed only minor perturbations of the proteome.
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Affiliation(s)
- Philipp Pletnev
- Department of Chemistry, Lomonosov Moscow State University, Moscow, Russia.,Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, Russia.,Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
| | - Ekaterina Guseva
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia
| | - Anna Zanina
- Department of Chemistry, Lomonosov Moscow State University, Moscow, Russia
| | - Sergey Evfratov
- Department of Chemistry, Lomonosov Moscow State University, Moscow, Russia
| | - Margarita Dzama
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia
| | - Vsevolod Treshin
- Department of Chemistry, Lomonosov Moscow State University, Moscow, Russia
| | - Alexandra Pogorel'skaya
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia
| | - Ilya Osterman
- Department of Chemistry, Lomonosov Moscow State University, Moscow, Russia.,Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, Russia
| | - Anna Golovina
- Belozersky Institute of Physico-Chemical Biololgy, Lomonosov Moscow State University, Moscow, Russia
| | - Maria Rubtsova
- Department of Chemistry, Lomonosov Moscow State University, Moscow, Russia.,Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, Russia
| | - Marina Serebryakova
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, Russia.,Belozersky Institute of Physico-Chemical Biololgy, Lomonosov Moscow State University, Moscow, Russia
| | - Olga V Pobeguts
- Federal Research and Clinical Centre of Physical-Chemical Medicine, Moscow, Russia
| | - Vadim M Govorun
- Federal Research and Clinical Centre of Physical-Chemical Medicine, Moscow, Russia
| | - Alexey A Bogdanov
- Department of Chemistry, Lomonosov Moscow State University, Moscow, Russia.,Belozersky Institute of Physico-Chemical Biololgy, Lomonosov Moscow State University, Moscow, Russia
| | - Olga A Dontsova
- Department of Chemistry, Lomonosov Moscow State University, Moscow, Russia.,Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, Russia.,Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia.,Belozersky Institute of Physico-Chemical Biololgy, Lomonosov Moscow State University, Moscow, Russia
| | - Petr V Sergiev
- Department of Chemistry, Lomonosov Moscow State University, Moscow, Russia.,Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, Russia.,Belozersky Institute of Physico-Chemical Biololgy, Lomonosov Moscow State University, Moscow, Russia.,Institute of Functional Genomics, Lomonosov Moscow State University, Moscow, Russia
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41
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Herrero Del Valle A, Seip B, Cervera-Marzal I, Sacheau G, Seefeldt AC, Innis CA. Ornithine capture by a translating ribosome controls bacterial polyamine synthesis. Nat Microbiol 2020; 5:554-561. [PMID: 32094585 PMCID: PMC7250644 DOI: 10.1038/s41564-020-0669-1] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Accepted: 01/10/2020] [Indexed: 02/06/2023]
Abstract
Polyamines are essential metabolites that play an important role in cell growth, stress adaptation, and microbial virulence1–3. In order to survive and multiply within a human host, pathogenic bacteria adjust the expression and activity of polyamine biosynthetic enzymes in response to different environmental stresses and metabolic cues2. Here, we show that ornithine capture by the ribosome and the nascent peptide SpeFL controls polyamine synthesis in γ-proteobacteria by inducing the expression of the ornithine decarboxylase SpeF4, via a mechanism involving ribosome stalling and transcription antitermination. In addition, we present the cryo-EM structure of an Escherichia coli (E. coli) ribosome stalled during translation of speFL in the presence of ornithine. The structure shows how the ribosome and the SpeFL sensor domain form a highly selective binding pocket that accommodates a single ornithine molecule but excludes near-cognate ligands. Ornithine pre-associates with the ribosome and is then held in place by the sensor domain, leading to the compaction of the SpeFL effector domain and blocking the action of release factor RF1. Thus, our study not only reveals basic strategies by which nascent peptides assist the ribosome in detecting a specific metabolite, but also provides a framework for assessing how ornithine promotes virulence in several human pathogens.
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Affiliation(s)
- Alba Herrero Del Valle
- Institut Européen de Chimie et Biologie, Université de Bordeaux, Pessac, France.,Institut National de la Santé et de la Recherche Médicale (U1212), Bordeaux, France.,Centre National de la Recherche Scientifique (UMR 5320), Bordeaux, France
| | - Britta Seip
- Institut Européen de Chimie et Biologie, Université de Bordeaux, Pessac, France.,Institut National de la Santé et de la Recherche Médicale (U1212), Bordeaux, France.,Centre National de la Recherche Scientifique (UMR 5320), Bordeaux, France.,Evotec International GmbH, Göttingen, Germany
| | - Iñaki Cervera-Marzal
- Institut Européen de Chimie et Biologie, Université de Bordeaux, Pessac, France.,Institut National de la Santé et de la Recherche Médicale (U1212), Bordeaux, France.,Centre National de la Recherche Scientifique (UMR 5320), Bordeaux, France.,Aix Marseille Université, CNRS, INSERM, CIML, Centre d'Immunologie de Marseille-Luminy, Marseille, France
| | - Guénaël Sacheau
- Institut Européen de Chimie et Biologie, Université de Bordeaux, Pessac, France.,Institut National de la Santé et de la Recherche Médicale (U1212), Bordeaux, France.,Centre National de la Recherche Scientifique (UMR 5320), Bordeaux, France.,Sopra Steria, Saint-Herblain, France
| | - A Carolin Seefeldt
- Institut Européen de Chimie et Biologie, Université de Bordeaux, Pessac, France.,Institut National de la Santé et de la Recherche Médicale (U1212), Bordeaux, France.,Centre National de la Recherche Scientifique (UMR 5320), Bordeaux, France.,Department of Cell and Molecular Biology, Biomedical Center, Uppsala University, Uppsala, Sweden
| | - C Axel Innis
- Institut Européen de Chimie et Biologie, Université de Bordeaux, Pessac, France. .,Institut National de la Santé et de la Recherche Médicale (U1212), Bordeaux, France. .,Centre National de la Recherche Scientifique (UMR 5320), Bordeaux, France.
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42
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Guerin F, Rose S, Cattoir V, Douthwaite S. Helcococcus kunzii methyltransferase Erm(47) responsible for MLSB resistance is induced by diverse ribosome-targeting antibiotics. J Antimicrob Chemother 2020; 75:371-378. [PMID: 31670815 DOI: 10.1093/jac/dkz441] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Revised: 09/26/2019] [Accepted: 09/30/2019] [Indexed: 11/14/2022] Open
Abstract
OBJECTIVES To determine the mechanism of induction of erm(47) and its atypical expression in the Gram-positive opportunistic pathogen Helcococcus kunzii, where it confers resistance to a subset of clinically important macrolide, lincosamide and streptogramin B (MLSB) antibiotics. METHODS The resistant H. kunzii clinical isolate UCN99 was challenged with subinhibitory concentrations of a wide range of ribosome-targeting drugs. The methylation status of the H. kunzii ribosomal RNA at the MLSB binding site was then determined using an MS approach and was correlated with any increase in resistance to the drugs. RESULTS The H. kunzii erm(47) gene encodes a monomethyltransferase. Expression is induced by subinhibitory concentrations of the macrolide erythromycin, as is common for many erm genes, and surprisingly also by 16-membered macrolide, lincosamide, streptogramin, ketolide, chloramphenicol and linezolid antibiotics, all of which target the 50S ribosomal subunit. No induction was detected with spectinomycin, which targets the 30S subunit. CONCLUSIONS The structure of the erm(47) leader sequence functions as a hair trigger for the induction mechanism that expresses resistance. Consequently, translation of the erm(47) mRNA is tripped by MLSB compounds and also by drugs that target the 50S ribosomal subunit outside the MLSB site. Expression of erm(47) thus extends previous assumptions about how erm genes can be induced.
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Affiliation(s)
- François Guerin
- Service de Microbiologie, CHU de Caen, Avenue de la Côte de Nacre - CS30001 - 14033 Caen Cedex 9, France
| | - Simon Rose
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, DK-5230 Odense M, Denmark
| | - Vincent Cattoir
- Service de Bactériologie-Hygiène hospitalière & CNR de la Résistance aux Antibiotiques (laboratoire associé 'Entérocoques'), CHU de Rennes, 2 rue Henri Le Guilloux, 35033 Rennes Cedex 9, France.,Unité Inserm U1230, Université de Rennes 1, 2 avenue du Pr. Léon Bernard, 35043 Rennes, France
| | - Stephen Douthwaite
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, DK-5230 Odense M, Denmark
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43
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Dynamics of transcription–translation coordination tune bacterial indole signaling. Nat Chem Biol 2019; 16:440-449. [DOI: 10.1038/s41589-019-0430-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2019] [Accepted: 11/08/2019] [Indexed: 12/31/2022]
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44
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Dynamics of the context-specific translation arrest by chloramphenicol and linezolid. Nat Chem Biol 2019; 16:310-317. [PMID: 31844301 PMCID: PMC7036023 DOI: 10.1038/s41589-019-0423-2] [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: 06/07/2019] [Accepted: 10/30/2019] [Indexed: 12/14/2022]
Abstract
Chloramphenicol (CHL) and linezolid (LZD) are antibiotics that inhibit translation. Both were thought to block peptide bond formation between all combinations of amino acids. Yet recently, a strong nascent peptide context-dependency of CHL- and LZD-induced translation arrest was discovered. Here, we probed the mechanism of action of CHL and LZD by using single-molecule Förster resonance energy transfer spectroscopy (smFRET) to monitor translation arrest induced by antibiotics. The presence of CHL or LZD does not significantly alter dynamics of protein synthesis until the arrest-motif of the nascent peptide is generated. Inhibition of peptide-bond formation compels the fully accommodated A-site tRNA to undergo repeated rounds of dissociation and non-productive rebinding. The glycyl amino-acid moiety on the A-site Gly-tRNA manages to overcome the arrest by CHL. Our results illuminate the mechanism of CHL and LZD action through their interactions with the ribosome, the nascent peptide and the incoming amino acid, perturbing elongation dynamics.
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45
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Dao Duc K, Batra SS, Bhattacharya N, Cate JHD, Song YS. Differences in the path to exit the ribosome across the three domains of life. Nucleic Acids Res 2019; 47:4198-4210. [PMID: 30805621 PMCID: PMC6486554 DOI: 10.1093/nar/gkz106] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2019] [Accepted: 02/22/2019] [Indexed: 01/07/2023] Open
Abstract
The ribosome exit tunnel is an important structure involved in the regulation of translation and other essential functions such as protein folding. By comparing 20 recently obtained cryo-EM and X-ray crystallography structures of the ribosome from all three domains of life, we here characterize the key similarities and differences of the tunnel across species. We first show that a hierarchical clustering of tunnel shapes closely reflects the species phylogeny. Then, by analyzing the ribosomal RNAs and proteins, we explain the observed geometric variations and show direct association between the conservations of the geometry, structure and sequence. We find that the tunnel is more conserved in the upper part close to the polypeptide transferase center, while in the lower part, it is substantially narrower in eukaryotes than in bacteria. Furthermore, we provide evidence for the existence of a second constriction site in eukaryotic exit tunnels. Overall, these results have several evolutionary and functional implications, which explain certain differences between eukaryotes and prokaryotes in their translation mechanisms. In particular, they suggest that major co-translational functions of bacterial tunnels were externalized in eukaryotes, while reducing the tunnel size provided some other advantages, such as facilitating the nascent chain elongation and enabling antibiotic resistance.
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Affiliation(s)
- Khanh Dao Duc
- Computer Science Division, University of California, Berkeley, CA 94720, USA
| | - Sanjit S Batra
- Computer Science Division, University of California, Berkeley, CA 94720, USA
| | | | - Jamie H D Cate
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA.,Department of Chemistry, University of California, Berkeley, CA 94720, USA.,Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Yun S Song
- Computer Science Division, University of California, Berkeley, CA 94720, USA.,Department of Statistics, University of California, Berkeley, CA 94720, USA.,Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
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46
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Emmanuel JS, Sengupta A, Gordon ER, Noble JT, Cruz-Vera LR. The regulatory TnaC nascent peptide preferentially inhibits release factor 2-mediated hydrolysis of peptidyl-tRNA. J Biol Chem 2019; 294:19224-19235. [PMID: 31712310 DOI: 10.1074/jbc.ra119.011313] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Revised: 11/01/2019] [Indexed: 01/29/2023] Open
Abstract
The tnaC regulatory gene from the tna operon of Escherichia coli controls the transcription of its own operon through an attenuation mechanism relying on the accumulation of arrested ribosomes during inhibition of its own translation termination. This free l-Trp-dependent mechanism of inhibition of translation termination remains unclear. Here, we analyzed the inhibitory effects of l-Trp on the function of two known E. coli translation termination factors, RF1 and RF2. Using a series of reporter genes, we found that the in vivo l-Trp sensitivity of tnaC gene expression is influenced by the identity of its stop codon, with the UGA stop codon producing higher expression efficiency of the tnaA-lacZ gene construct than the UAG stop codon. In vitro TnaC-peptidyl-tRNA accumulation and toe-printing assays confirmed that in the presence of l-Trp, the UGA stop codon generates higher accumulation of both TnaC-peptidyl-tRNA and arrested ribosomes than does the UAG stop codon. RF-mediated hydrolysis assays corroborated that l-Trp blocks RF2 function more than that of RF1. Mutational analyses disclosed that amino acids substitutions at the 246 and 256 residue positions surrounding the RF2-GGQ functional motif reduce l-Trp-dependent expression of the tnaC(UGA) tnaA-lacZ construct and the ability of l-Trp to inhibit RF2-mediated cleavage of the TnaC-peptidyl-tRNA. Altogether, our results indicate that l-Trp preferentially blocks RF2 activity during translation termination of the tnaC gene. This inhibition depends on the identities of amino acid residues surrounding the RF2-GGQ functional motif.
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Affiliation(s)
| | - Arnab Sengupta
- University of Alabama in Huntsville, Huntsville, Alabama 35899
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47
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Nguyen HL, An PH, Thai NQ, Linh HQ, Li MS. Erythromycin, Cethromycin and Solithromycin display similar binding affinities to the E. coli's ribosome: A molecular simulation study. J Mol Graph Model 2019; 91:80-90. [PMID: 31200217 DOI: 10.1016/j.jmgm.2019.06.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Revised: 05/09/2019] [Accepted: 06/02/2019] [Indexed: 01/06/2023]
Abstract
Macrolide antibiotics bind to the exit tunnel of the ribosome and inhibit protein synthesis blocking its translocation. Thus, antibiotics including the known macrolide Erythromycin (ERY) are active against bacteria. However, at present, some bacteria show resistance to drugs, which requires the development of new powerful antibacterial agents. One possible way is to use the ERY structure, but change its side chains, while the size of the lactone ring can remain unchanged or change. In this work we consider Cethromycin (CET) and Solithromycin (SOL), which are ketolides with quinolylallyl group at C6 and aminophenyl at C11, respectively (both of them have the same lactone ring as ERY). Experiments have shown that these ketolides have improved efficacy against pathogens, but their binding affinity to the E. coli's ribosome is almost identical. To clarify this issue, we have studied in detail the binding mechanisms of ERY, CET and SOL using the docking and molecular dynamic simulations. In agreement with the experiments, we showed that these compounds have similar binding affinities. Desosamine and lactone ring groups play a critical role in the binding of ERY to the ribosome. In CET and SOL, the contribution of keto and alkylaryl groups is balanced by cyclic carbamate. We have demonstrated that increased fluctuations in the ribosomal residues at the binding site led to an increase in the entropic term in the free binding energy of ERY compared to SOL and CET. The alkyl-aryl arm of both ketolides strongly interacts with A752 and U2609. In addition, the presence of macrolides in the exit tunnel can alter the conformation of U2585, which is located in the peptidyl transferase center, through non-bonded interaction. Therefore, the side chain of ketolides affects not only the binding site but also other residues possibly leading to a strong effect on the protein synthesis process. We predict that to combat bacterial mutations, it is necessary either to design a bulk and charged group as a cladinose, or to use several groups with different signs of charges. This prediction can be used for the development of new efficient antibiotics.
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Affiliation(s)
- Hoang Linh Nguyen
- Institute for Computational Science and Technology, Quang Trung Software City, Tan Chanh, Hiep Ward, District 12, Ho Chi Minh City, Viet Nam; Biomedical Engineering Department, University of Technology - VNU HCM, 268 Ly Thuong Kiet Str., Distr. 10, Ho Chi Minh City, Viet Nam
| | - Pham Hong An
- Institute for Computational Science and Technology, Quang Trung Software City, Tan Chanh, Hiep Ward, District 12, Ho Chi Minh City, Viet Nam; Department of Theoretical Physics, VNUHCM-University of Science, Ho Chi Minh City, Viet Nam
| | - Nguyen Quoc Thai
- Institute for Computational Science and Technology, Quang Trung Software City, Tan Chanh, Hiep Ward, District 12, Ho Chi Minh City, Viet Nam; Biomedical Engineering Department, University of Technology - VNU HCM, 268 Ly Thuong Kiet Str., Distr. 10, Ho Chi Minh City, Viet Nam; Dong Thap University, 783 Pham Huu Lau Street, Ward 6, Cao Lanh City, Dong Thap, Viet Nam
| | - Huynh Quang Linh
- Biomedical Engineering Department, University of Technology - VNU HCM, 268 Ly Thuong Kiet Str., Distr. 10, Ho Chi Minh City, Viet Nam
| | - Mai Suan Li
- Institute of Physics, Polish Acad Sci, Al. Lotnikow 32/46, 02-668, Warsaw, Poland.
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48
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Integron-Derived Aminoglycoside-Sensing Riboswitches Control Aminoglycoside Acetyltransferase Resistance Gene Expression. Antimicrob Agents Chemother 2019; 63:AAC.00236-19. [PMID: 30936094 DOI: 10.1128/aac.00236-19] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Accepted: 03/24/2019] [Indexed: 02/06/2023] Open
Abstract
Class 1 integrons accumulate antibiotic resistance genes by site-specific recombination at aatI-1 sites. Captured genes are transcribed from a promoter located within the integron; for class 1 integrons, the first gene to be transcribed and translated normally encodes an aminoglycoside antibiotic resistance protein (either an acetyltransferase [AAC] or adenyltransferase [AAD]). The leader RNA from the Pseudomonas fluorescens class 1 integron contains an aminoglycoside-sensing riboswitch RNA that controls the expression of the downstream aminoglycoside resistance gene. Here, we explore the relationship between integron-dependent DNA recombination and potential aminoglycoside-sensing riboswitch products of recombination derived from a series of aminoglycoside-resistant clinical strains. Sequence analysis of the clinical strains identified a series of sequence variants that were associated with class I integron-derived aminoglycoside-resistant (both aac and aad) recombinants. For the aac recombinants, representative sequences showed up to 6-fold aminoglycoside-dependent regulation of reporter gene expression. Microscale thermophoresis (MST) confirmed RNA binding. Covariance analysis generated a secondary-structure model for the RNA that is an independent verification of previous models that were derived from mutagenesis and chemical probing data and that was similar to that of the P. fluorescens riboswitch RNA. The aminoglycosides were among the first antibiotics to be used clinically, and the data suggest that in an aminoglycoside-rich environment, functional riboswitch recombinants were selected during integron-mediated recombination to regulate aminoglycoside resistance. The incorporation of a functional aminoglycoside-sensing riboswitch by integron recombination confers a selective advantage for the expression of resistance genes of diverse origins.
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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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50
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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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