1
|
Owens SL, Ahmed SR, Lang Harman RM, Stewart LE, Mori S. Natural Products That Contain Higher Homologated Amino Acids. Chembiochem 2024; 25:e202300822. [PMID: 38487927 DOI: 10.1002/cbic.202300822] [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: 12/04/2023] [Revised: 03/13/2024] [Indexed: 04/11/2024]
Abstract
This review focuses on discussing natural products (NPs) that contain higher homologated amino acids (homoAAs) in the structure as well as the proposed and characterized biosynthesis of these non-proteinogenic amino acids. Homologation of amino acids includes the insertion of a methylene group into its side chain. It is not a very common modification found in NP biosynthesis as approximately 450 homoAA-containing NPs have been isolated from four bacterial phyla (Cyanobacteria, Actinomycetota, Myxococcota, and Pseudomonadota), two fungal phyla (Ascomycota and Basidiomycota), and one animal phylum (Porifera), except for a few examples. Amino acids that are found to be homologated and incorporated in the NP structures include the following ten amino acids: alanine, arginine, cysteine, isoleucine, glutamic acid, leucine, phenylalanine, proline, serine, and tyrosine, where isoleucine, leucine, phenylalanine, and tyrosine share the comparable enzymatic pathway. Other amino acids have their individual homologation pathway (arginine, proline, and glutamic acid for bacteria), likely utilize the primary metabolic pathway (alanine and glutamic acid for fungi), or have not been reported (cysteine and serine). Despite its possible high potential in the drug discovery field, the biosynthesis of homologated amino acids has a large room to explore for future combinatorial biosynthesis and metabolic engineering purpose.
Collapse
Affiliation(s)
- Skyler L Owens
- Department of Chemistry and Biochemistry, Augusta University, 1120 15th Street, Augusta, GA 30912
| | - Shopno R Ahmed
- Department of Chemistry and Biochemistry, Augusta University, 1120 15th Street, Augusta, GA 30912
| | - Rebecca M Lang Harman
- Department of Chemistry and Biochemistry, Augusta University, 1120 15th Street, Augusta, GA 30912
| | - Laura E Stewart
- Department of Chemistry and Biochemistry, Augusta University, 1120 15th Street, Augusta, GA 30912
| | - Shogo Mori
- Department of Chemistry and Biochemistry, Augusta University, 1120 15th Street, Augusta, GA 30912
| |
Collapse
|
2
|
Schuler SMM, Jürjens G, Marker A, Hemmann U, Rey A, Yvon S, Lagrevol M, Hamiti M, Nguyen F, Hirsch R, Pöverlein C, Vilcinskas A, Hammann P, Wilson DN, Mourez M, Coyne S, Bauer A. Full Profiling of GE81112A, an Underexplored Tetrapeptide Antibiotic with Activity against Gram-Negative Pathogens. Microbiol Spectr 2023; 11:e0224722. [PMID: 37140391 PMCID: PMC10269895 DOI: 10.1128/spectrum.02247-22] [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: 01/13/2023] [Accepted: 01/19/2023] [Indexed: 05/05/2023] Open
Abstract
After the first total synthesis combined with structure revision, we performed thorough in vitro and in vivo profiling of the underexplored tetrapeptide GE81112A. From the determination of the biological activity spectrum and physicochemical and early absorption-distribution-metabolism-excretion-toxicity (eADMET) properties, as well as in vivo data regarding tolerability and pharmacokinetics (PK) in mice and efficacy in an Escherichia coli-induced septicemia model, we were able to identify the critical and limiting parameters of the original hit compound. Thus, the generated data will serve as the basis for further compound optimization programs and developability assessments to identify candidates for preclinical/clinical development derived from GE81112A as the lead structure. IMPORTANCE The spread of antimicrobial resistance (AMR) is becoming a more and more important global threat to human health. With regard to current medical needs, penetration into the site of infection represents the major challenge in the treatment of infections caused by Gram-positive bacteria. Considering infections associated with Gram-negative bacteria, resistance is a major issue. Obviously, novel scaffolds for the design of new antibacterials in this arena are urgently needed to overcome this crisis. Such a novel potential lead structure is represented by the GE81112 compounds, which inhibit protein synthesis by interacting with the small 30S ribosomal subunit using a binding site distinct from that of other known ribosome-targeting antibiotics. Therefore, the tetrapeptide antibiotic GE81112A was chosen for further exploration as a potential lead for the development of antibiotics with a new mode of action against Gram-negative bacteria.
Collapse
Affiliation(s)
- Sören M. M. Schuler
- Branch Bioresources of the Fraunhofer Institute for Molecular Biology and Applied Ecology, Giessen, Germany
| | - Gerrit Jürjens
- Branch Bioresources of the Fraunhofer Institute for Molecular Biology and Applied Ecology, Giessen, Germany
| | | | | | - Astrid Rey
- Sanofi R&D, Therapeutic Area Infectious Diseases, Marcy L’Etoile, France
| | - Stéphane Yvon
- Sanofi R&D, Therapeutic Area Infectious Diseases, Marcy L’Etoile, France
| | - Marjorie Lagrevol
- Sanofi R&D, Therapeutic Area Infectious Diseases, Marcy L’Etoile, France
| | - Mohamed Hamiti
- Sanofi R&D, Therapeutic Area Infectious Diseases, Marcy L’Etoile, France
| | - Fabian Nguyen
- Gene Center, Department for Biochemistry and Center for Protein Science Munich, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Rolf Hirsch
- Branch Bioresources of the Fraunhofer Institute for Molecular Biology and Applied Ecology, Giessen, Germany
| | | | - Andreas Vilcinskas
- Branch Bioresources of the Fraunhofer Institute for Molecular Biology and Applied Ecology, Giessen, Germany
- Institute for Insect Biotechnology, Justus-Liebig University of Giessen, Giessen, Germany
| | | | - Daniel N. Wilson
- Gene Center, Department for Biochemistry and Center for Protein Science Munich, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Michael Mourez
- Sanofi R&D, Therapeutic Area Infectious Diseases, Marcy L’Etoile, France
| | - Sebastien Coyne
- Sanofi R&D, Therapeutic Area Infectious Diseases, Marcy L’Etoile, France
| | - Armin Bauer
- Sanofi-Aventis Deutschland GmbH, Frankfurt, Germany
| |
Collapse
|
3
|
Fayad S, Jafari A, Schuler SMM, Kurz M, Plettenburg O, Hammann PE, Bauer A, Jürjens G, Pöverlein C. Total Synthesis of GE81112A: An Orthoester-Based Approach. J Org Chem 2023; 88:5597-5608. [PMID: 37023463 PMCID: PMC10167690 DOI: 10.1021/acs.joc.3c00094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/08/2023]
Abstract
The GE81112 series, consisting of three naturally occurring tetrapeptides and synthetic derivatives, is evaluated as a potential lead structure for the development of a new antibacterial drug. Although the first total synthesis of GE81112A reported by our group provided sufficient amounts of material for an initial in depth biological profiling of the compound, improvements of the routes toward the key building blocks were needed for further upscaling and structure-activity relationship studies. The major challenges identified were poor stereoselectivity in the synthesis of the C-terminal β-hydroxy histidine intermediate and a concise access to all four isomers of the 3-hydroxy pipecolic acid. Herein, we report a second-generation synthesis of GE81112A, which is also applicable to access further representatives of this series. Based on Lajoie's ortho-ester-protected serine aldehydes as key building blocks, the described route provides both a satisfactory improvement in stereoselectivity of the β-hydroxy histidine intermediate synthesis and a stereoselective approach toward both orthogonally protected cis and trans-3-hydroxy pipecolic acid.
Collapse
Affiliation(s)
- Scherin Fayad
- Sanofi-Aventis Deutschland GmbH, R&D, Integrated Drug Discovery, Industriepark Hoechst, 65926 Frankfurt am Main, Germany
- Helmholtz Zentrum München, Deutsches Forschungszentrum für Gesundheit und Umwelt (GmbH), Institut für Medizinalchemie, 30167 Hannover, Germany
| | - Ardalan Jafari
- Helmholtz Zentrum München, Deutsches Forschungszentrum für Gesundheit und Umwelt (GmbH), Institut für Medizinalchemie, 30167 Hannover, Germany
| | - Sören M M Schuler
- Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Branch for Bioresources, 35392 Giessen, Germany
- Evotec International GmbH, 37079 Göttingen, Germany
| | - Michael Kurz
- Sanofi-Aventis Deutschland GmbH, R&D, Integrated Drug Discovery, Industriepark Hoechst, 65926 Frankfurt am Main, Germany
| | - Oliver Plettenburg
- Helmholtz Zentrum München, Deutsches Forschungszentrum für Gesundheit und Umwelt (GmbH), Institut für Medizinalchemie, 30167 Hannover, Germany
| | - Peter E Hammann
- Evotec International GmbH, 37079 Göttingen, Germany
- Sanofi-Aventis Deutschland GmbH, R&D, Infectious Diseases, Industriepark Hoechst, 65926 Frankfurt am Main, Germany
| | - Armin Bauer
- Sanofi-Aventis Deutschland GmbH, R&D, Integrated Drug Discovery, Industriepark Hoechst, 65926 Frankfurt am Main, Germany
| | - Gerrit Jürjens
- Helmholtz Zentrum München, Deutsches Forschungszentrum für Gesundheit und Umwelt (GmbH), Institut für Medizinalchemie, 30167 Hannover, Germany
- Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Branch for Bioresources, 35392 Giessen, Germany
| | - Christoph Pöverlein
- Sanofi-Aventis Deutschland GmbH, R&D, Integrated Drug Discovery, Industriepark Hoechst, 65926 Frankfurt am Main, Germany
| |
Collapse
|
4
|
Wee LM, Tong AB, Florez Ariza AJ, Cañari-Chumpitaz C, Grob P, Nogales E, Bustamante CJ. A trailing ribosome speeds up RNA polymerase at the expense of transcript fidelity via force and allostery. Cell 2023; 186:1244-1262.e34. [PMID: 36931247 PMCID: PMC10135430 DOI: 10.1016/j.cell.2023.02.008] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Revised: 11/14/2022] [Accepted: 02/06/2023] [Indexed: 03/18/2023]
Abstract
In prokaryotes, translation can occur on mRNA that is being transcribed in a process called coupling. How the ribosome affects the RNA polymerase (RNAP) during coupling is not well understood. Here, we reconstituted the E. coli coupling system and demonstrated that the ribosome can prevent pausing and termination of RNAP and double the overall transcription rate at the expense of fidelity. Moreover, we monitored single RNAPs coupled to ribosomes and show that coupling increases the pause-free velocity of the polymerase and that a mechanical assisting force is sufficient to explain the majority of the effects of coupling. Also, by cryo-EM, we observed that RNAPs with a terminal mismatch adopt a backtracked conformation, while a coupled ribosome allosterically induces these polymerases toward a catalytically active anti-swiveled state. Finally, we demonstrate that prolonged RNAP pausing is detrimental to cell viability, which could be prevented by polymerase reactivation through a coupled ribosome.
Collapse
Affiliation(s)
- Liang Meng Wee
- QB3-Berkeley, Berkeley, CA, USA; Howard Hughes Medical Institute, University of California Berkeley, Berkeley, CA, USA
| | - Alexander B Tong
- QB3-Berkeley, Berkeley, CA, USA; Department of Chemistry, University of California Berkeley, Berkeley, CA, USA
| | - Alfredo Jose Florez Ariza
- QB3-Berkeley, Berkeley, CA, USA; Biophysics Graduate Group, University of California Berkeley, Berkeley, CA, USA
| | - Cristhian Cañari-Chumpitaz
- QB3-Berkeley, Berkeley, CA, USA; Department of Chemistry, University of California Berkeley, Berkeley, CA, USA; Howard Hughes Medical Institute, University of California Berkeley, Berkeley, CA, USA
| | - Patricia Grob
- QB3-Berkeley, Berkeley, CA, USA; Howard Hughes Medical Institute, University of California Berkeley, Berkeley, CA, USA; Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, CA, USA
| | - Eva Nogales
- QB3-Berkeley, Berkeley, CA, USA; Biophysics Graduate Group, University of California Berkeley, Berkeley, CA, USA; Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, CA, USA; Howard Hughes Medical Institute, University of California Berkeley, Berkeley, CA, USA; Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
| | - Carlos J Bustamante
- QB3-Berkeley, Berkeley, CA, USA; Biophysics Graduate Group, University of California Berkeley, Berkeley, CA, USA; Department of Chemistry, University of California Berkeley, Berkeley, CA, USA; Department of Physics, University of California Berkeley, Berkeley, CA, USA; Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, CA, USA; Kavli Energy Nanoscience Institute, Berkeley, CA, USA; Howard Hughes Medical Institute, University of California Berkeley, Berkeley, CA, USA; Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
| |
Collapse
|
5
|
Giuliodori AM, Belardinelli R, Duval M, Garofalo R, Schenckbecher E, Hauryliuk V, Ennifar E, Marzi S. Escherichia coli CspA stimulates translation in the cold of its own mRNA by promoting ribosome progression. Front Microbiol 2023; 14:1118329. [PMID: 36846801 PMCID: PMC9947658 DOI: 10.3389/fmicb.2023.1118329] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Accepted: 01/06/2023] [Indexed: 02/11/2023] Open
Abstract
Escherichia coli CspA is an RNA binding protein that accumulates during cold-shock and stimulates translation of several mRNAs-including its own. Translation in the cold of cspA mRNA involves a cis-acting thermosensor element, which enhances ribosome binding, and the trans-acting action of CspA. Using reconstituted translation systems and probing experiments we show that, at low temperature, CspA specifically promotes the translation of the cspA mRNA folded in the conformation less accessible to the ribosome, which is formed at 37°C but is retained upon cold shock. CspA interacts with its mRNA without inducing large structural rearrangements, but allowing the progression of the ribosomes during the transition from translation initiation to translation elongation. A similar structure-dependent mechanism may be responsible for the CspA-dependent translation stimulation observed with other probed mRNAs, for which the transition to the elongation phase is progressively facilitated during cold acclimation with the accumulation of CspA.
Collapse
Affiliation(s)
- Anna Maria Giuliodori
- School of Biosciences and Veterinary Medicine, University of Camerino, Camerino, Italy,*Correspondence: Anna Maria Giuliodori, ✉
| | - Riccardo Belardinelli
- Architecture et Réactivité de l’ARN, CNRS 9002, Université de Strasbourg, Strasbourg, France
| | - Melodie Duval
- Architecture et Réactivité de l’ARN, CNRS 9002, Université de Strasbourg, Strasbourg, France
| | - Raffaella Garofalo
- Architecture et Réactivité de l’ARN, CNRS 9002, Université de Strasbourg, Strasbourg, France
| | - Emma Schenckbecher
- Architecture et Réactivité de l’ARN, CNRS 9002, Université de Strasbourg, Strasbourg, France
| | - Vasili Hauryliuk
- Department of Experimental Medical Science, Lund University, Lund, Sweden,Institute of Technology, University of Tartu, Tartu, Estonia
| | - Eric Ennifar
- Architecture et Réactivité de l’ARN, CNRS 9002, Université de Strasbourg, Strasbourg, France
| | - Stefano Marzi
- Architecture et Réactivité de l’ARN, CNRS 9002, Université de Strasbourg, Strasbourg, France,Stefano Marzi, ✉
| |
Collapse
|
6
|
Neis N, Xie F, Krug D, Zhao H, Siebert A, Binz T, Fu C, Müller R, Kazmaier U. Stereoselective Syntheses of Deuterated Pipecolic Acids as Tools to Investigate the Stereoselectivity of the Hydroxylase GetF. European J Org Chem 2022. [DOI: 10.1002/ejoc.202200162] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Nadine Neis
- Saarland University: Universitat des Saarlandes Organic Chemistry GERMANY
| | - Feng Xie
- Helmholtz Centre for Infection Research: Helmholtz-Zentrum fur Infektionsforschung GmbH Microbial Natural Products GERMANY
| | - Daniel Krug
- Helmholtz Centre for Infection Research: Helmholtz-Zentrum fur Infektionsforschung GmbH Microbial Natural Products GERMANY
| | - Haowen Zhao
- Helmholtz Centre for Infection Research: Helmholtz-Zentrum fur Infektionsforschung GmbH Microbial Natural Products GERMANY
| | - Andreas Siebert
- Saarland University: Universitat des Saarlandes Organic Chemistry GERMANY
| | - Tina Binz
- Helmholtz-Zentrum für Infektionsforschung GmbH: Helmholtz-Zentrum fur Infektionsforschung GmbH Microbial Natural Products GERMANY
| | - Chengzhang Fu
- Helmholtz-Zentrum für Infektionsforschung GmbH: Helmholtz-Zentrum fur Infektionsforschung GmbH Microbial Natural Products GERMANY
| | - Rolf Müller
- Helmholtz-Zentrum für Infektionsforschung GmbH: Helmholtz-Zentrum fur Infektionsforschung GmbH Microbial Natural Products GERMANY
| | - Uli Kazmaier
- Saarland University Organic Chemistry Campus, Bldg. C4.2 66123 Saarbrücken GERMANY
| |
Collapse
|
7
|
Zwick CR, Sosa MB, Renata H. Modular Chemoenzymatic Synthesis of GE81112 B1 and Related Analogues Enables Elucidation of Its Key Pharmacophores. J Am Chem Soc 2021; 143:1673-1679. [PMID: 33416325 DOI: 10.1021/jacs.0c13424] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The GE81112 complex has garnered much interest due to its broad antimicrobial properties and unique ability to inhibit bacterial translation initiation. Herein we report the use of a chemoenzymatic strategy to complete the first total synthesis of GE81112 B1. By pairing iron and α-ketoglutarate dependent hydroxylases found in GE81112 biosynthesis with traditional synthetic methodology, we were able to access the natural product in 11 steps (longest linear sequence). Following this strategy, 10 GE81112 B1 analogues were synthesized, allowing for identification of its key pharmacophores. A key feature of our medicinal chemistry effort is the incorporation of additional biocatalytic hydroxylations in modular analogue synthesis to rapidly enable exploration of relevant chemical space.
Collapse
Affiliation(s)
- Christian R Zwick
- Department of Chemistry, The Scripps Research Institute, 130 Scripps Way, Jupiter, Florida 33458, United States
| | - Max B Sosa
- Department of Chemistry, The Scripps Research Institute, 130 Scripps Way, Jupiter, Florida 33458, United States
| | - Hans Renata
- Department of Chemistry, The Scripps Research Institute, 130 Scripps Way, Jupiter, Florida 33458, United States
| |
Collapse
|
8
|
Renata H. Exploration of Iron- and a-Ketoglutarate-Dependent Dioxygenases as Practical Biocatalysts in Natural Product Synthesis. Synlett 2021; 32:775-784. [PMID: 34413574 PMCID: PMC8372184 DOI: 10.1055/s-0040-1707320] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Catalytic C─H oxidation is a powerful transformation with enormous promise to streamline access to complex molecules. In recent years, biocatalytic C─H oxidation strategies have received tremendous attention due to their potential to address unmet regio- and stereoselectivity challenges that are often encountered with the use of small-molecule-based catalysts. This Account provides an overview of recent contributions from our laboratory in this area, specifically in the use of iron- and α-ketoglutarate-dependent dioxygenases in the chemoenzymatic synthesis of complex natural products.
Collapse
Affiliation(s)
- Hans Renata
- Department of Chemistry, The Scripps Research Institute, 130 Scripps Way, Jupiter, FL, 33458, USA
| |
Collapse
|
9
|
Zwick CR, Sosa MB, Renata H. Characterization of a Citrulline 4-Hydroxylase from Nonribosomal Peptide GE81112 Biosynthesis and Engineering of Its Substrate Specificity for the Chemoenzymatic Synthesis of Enduracididine. Angew Chem Int Ed Engl 2019; 58:18854-18858. [PMID: 31610076 PMCID: PMC6917913 DOI: 10.1002/anie.201910659] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Revised: 10/06/2019] [Indexed: 12/15/2022]
Abstract
The GE81112 tetrapeptides are a small family of unusual nonribosomal peptide congeners with potent inhibitory activity against prokaryotic translation initiation. With the exception of the 3-hydroxy-l-pipecolic acid unit, little is known about the biosynthetic origins of the non-proteinogenic amino acid monomers of the natural product family. Here, we elucidate the biogenesis of the 4-hydroxy-l-citrulline unit and establish the role of an iron- and α-ketoglutarate-dependent enzyme (Fe/αKG) in the pathway. Homology modelling and sequence alignment analysis further facilitate the rational engineering of this enzyme to become a specific 4-arginine hydroxylase. We subsequently demonstrate the utility of this engineered enzyme in the synthesis of a dipeptide fragment of the antibiotic enduracidin. This work highlights the value of applying a bioinformatics-guided approach in the discovery of novel enzymes and engineering of new catalytic activity into existing ones.
Collapse
Affiliation(s)
- Christian R. Zwick
- Department of Chemistry The Scripps Research Institute 130 Scripps Way, Jupiter, FL 33458
| | - Max B. Sosa
- Department of Chemistry The Scripps Research Institute 130 Scripps Way, Jupiter, FL 33458
| | - Hans Renata
- Department of Chemistry The Scripps Research Institute 130 Scripps Way, Jupiter, FL 33458
| |
Collapse
|
10
|
Zwick CR, Sosa MB, Renata H. Characterization of a Citrulline 4‐Hydroxylase from Nonribosomal Peptide GE81112 Biosynthesis and Engineering of Its Substrate Specificity for the Chemoenzymatic Synthesis of Enduracididine. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201910659] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Christian R. Zwick
- Department of ChemistryThe Scripps Research Institute 130 Scripps Way Jupiter FL 33458 USA
| | - Max B. Sosa
- Department of ChemistryThe Scripps Research Institute 130 Scripps Way Jupiter FL 33458 USA
| | - Hans Renata
- Department of ChemistryThe Scripps Research Institute 130 Scripps Way Jupiter FL 33458 USA
| |
Collapse
|
11
|
O'Sullivan ME, Poitevin F, Sierra RG, Gati C, Dao EH, Rao Y, Aksit F, Ciftci H, Corsepius N, Greenhouse R, Hayes B, Hunter MS, Liang M, McGurk A, Mbgam P, Obrinsky T, Pardo-Avila F, Seaberg MH, Cheng AG, Ricci AJ, DeMirci H. Aminoglycoside ribosome interactions reveal novel conformational states at ambient temperature. Nucleic Acids Res 2019; 46:9793-9804. [PMID: 30113694 PMCID: PMC6182148 DOI: 10.1093/nar/gky693] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2018] [Accepted: 07/19/2018] [Indexed: 11/21/2022] Open
Abstract
The bacterial 30S ribosomal subunit is a primary antibiotic target. Despite decades of discovery, the mechanisms by which antibiotic binding induces ribosomal dysfunction are not fully understood. Ambient temperature crystallographic techniques allow more biologically relevant investigation of how local antibiotic binding site interactions trigger global subunit rearrangements that perturb protein synthesis. Here, the structural effects of 2-deoxystreptamine (paromomycin and sisomicin), a novel sisomicin derivative, N1-methyl sulfonyl sisomicin (N1MS) and the non-deoxystreptamine (streptomycin) aminoglycosides on the ribosome at ambient and cryogenic temperatures were examined. Comparative studies led to three main observations. First, individual aminoglycoside–ribosome interactions in the decoding center were similar for cryogenic versus ambient temperature structures. Second, analysis of a highly conserved GGAA tetraloop of h45 revealed aminoglycoside-specific conformational changes, which are affected by temperature only for N1MS. We report the h44–h45 interface in varying states, i.e. engaged, disengaged and in equilibrium. Third, we observe aminoglycoside-induced effects on 30S domain closure, including a novel intermediary closure state, which is also sensitive to temperature. Analysis of three ambient and five cryogenic crystallography datasets reveal a correlation between h44–h45 engagement and domain closure. These observations illustrate the role of ambient temperature crystallography in identifying dynamic mechanisms of ribosomal dysfunction induced by local drug-binding site interactions. Together, these data identify tertiary ribosomal structural changes induced by aminoglycoside binding that provides functional insight and targets for drug design.
Collapse
Affiliation(s)
- Mary E O'Sullivan
- Department of Otolaryngology-Head and Neck Surgery, Stanford University School of Medicine, Palo Alto, CA, USA, 94305
| | - Frédéric Poitevin
- Department of Structural Biology, Stanford University, Palo Alto, CA, USA, 94305.,Stanford PULSE Institute, SLAC National Laboratory, Menlo Park, CA, USA, 94025
| | - Raymond G Sierra
- Linac Coherent Light Source, SLAC National Laboratory, Menlo Park, CA, USA, 94025
| | - Cornelius Gati
- Department of Structural Biology, Stanford University, Palo Alto, CA, USA, 94305.,Biosciences Division, SLAC National Laboratory, Menlo Park, CA, USA, 94025
| | - E Han Dao
- Stanford PULSE Institute, SLAC National Laboratory, Menlo Park, CA, USA, 94025
| | - Yashas Rao
- Linac Coherent Light Source, SLAC National Laboratory, Menlo Park, CA, USA, 94025
| | - Fulya Aksit
- Linac Coherent Light Source, SLAC National Laboratory, Menlo Park, CA, USA, 94025
| | - Halilibrahim Ciftci
- Linac Coherent Light Source, SLAC National Laboratory, Menlo Park, CA, USA, 94025
| | - Nicholas Corsepius
- Department of Structural Biology, Stanford University, Palo Alto, CA, USA, 94305
| | - Robert Greenhouse
- Department of Otolaryngology-Head and Neck Surgery, Stanford University School of Medicine, Palo Alto, CA, USA, 94305
| | - Brandon Hayes
- Linac Coherent Light Source, SLAC National Laboratory, Menlo Park, CA, USA, 94025
| | - Mark S Hunter
- Linac Coherent Light Source, SLAC National Laboratory, Menlo Park, CA, USA, 94025
| | - Mengling Liang
- Linac Coherent Light Source, SLAC National Laboratory, Menlo Park, CA, USA, 94025
| | - Alex McGurk
- Linac Coherent Light Source, SLAC National Laboratory, Menlo Park, CA, USA, 94025
| | - Paul Mbgam
- Linac Coherent Light Source, SLAC National Laboratory, Menlo Park, CA, USA, 94025
| | - Trevor Obrinsky
- Linac Coherent Light Source, SLAC National Laboratory, Menlo Park, CA, USA, 94025
| | - Fátima Pardo-Avila
- Department of Structural Biology, Stanford University, Palo Alto, CA, USA, 94305
| | - Matthew H Seaberg
- Linac Coherent Light Source, SLAC National Laboratory, Menlo Park, CA, USA, 94025
| | - Alan G Cheng
- Department of Otolaryngology-Head and Neck Surgery, Stanford University School of Medicine, Palo Alto, CA, USA, 94305
| | - Anthony J Ricci
- Department of Otolaryngology-Head and Neck Surgery, Stanford University School of Medicine, Palo Alto, CA, USA, 94305
| | - Hasan DeMirci
- Department of Structural Biology, Stanford University, Palo Alto, CA, USA, 94305.,Stanford PULSE Institute, SLAC National Laboratory, Menlo Park, CA, USA, 94025.,Biosciences Division, SLAC National Laboratory, Menlo Park, CA, USA, 94025
| |
Collapse
|
12
|
Giuliodori AM, Fabbretti A, Gualerzi C. Cold-Responsive Regions of Paradigm Cold-Shock and Non-Cold-Shock mRNAs Responsible for Cold Shock Translational Bias. Int J Mol Sci 2019; 20:E457. [PMID: 30678142 PMCID: PMC6386945 DOI: 10.3390/ijms20030457] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Revised: 01/12/2019] [Accepted: 01/16/2019] [Indexed: 01/16/2023] Open
Abstract
In Escherichia coli, the mRNA transcribed from the main cold-shock gene cspA is a thermosensor, which at low temperature adopts a conformation particularly suitable for translation in the cold. Unlike cspA, its paralogue cspD is expressed only at 37 °C, is toxic so cannot be hyper-expressed in E. coli and is poorly translated in vitro, especially at low temperature. In this work, chimeric mRNAs consisting of different segments of cspA and cspD were constructed to determine if parts of cspA could confer cold-responsive properties to cspD to improve its expression. The activities of these chimeric mRNAs in translation and in partial steps of translation initiation such as formation of 30S initiation complexes and 50S subunits docking to 30S complexes to yield 70S initiation complexes were analyzed. We show that the 5' untranslated region (5'UTR) of cspA mRNA is sufficient to improve the translation of cspD mRNA at 37 °C whereas both the 5'UTR and the region immediately downstream the cspA mRNA initiation triplet are essential for translation at low temperature. Furthermore, the translational apparatus of cold-stressed cells contains trans-active elements targeting both 5'UTR and downstream regions of cspA mRNA, thereby improving translation of specific chimeric constructs at both 15 and 37 °C.
Collapse
Affiliation(s)
| | - Attilio Fabbretti
- Laboratory of Genetics, University of Camerino, 62032 Camerino, Italy.
| | - Claudio Gualerzi
- Laboratory of Genetics, University of Camerino, 62032 Camerino, Italy.
| |
Collapse
|
13
|
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.
Collapse
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
| |
Collapse
|
14
|
Jürjens G, Schuler SMM, Kurz M, Petit S, Couturier C, Jeannot F, Nguyen F, Wende RC, Hammann PE, Wilson DN, Bacqué E, Pöverlein C, Bauer A. Totalsynthese und Strukturkorrektur des antibiotisch wirksamen Tetrapeptids GE81112A. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201805901] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Affiliation(s)
- Gerrit Jürjens
- Fraunhofer IME; Projektgruppe Bioressourcen; Gießen Deutschland
- Helmholtz Zentrum München; Institut für Medizinalchemie; Hannover Deutschland
| | | | - Michael Kurz
- R&D Integrated Drug Discovery; Sanofi-Aventis Deutschland GmbH; Industriepark Höchst 65926 Frankfurt am Main Deutschland
| | - Sylvain Petit
- Therapeutic Area Infectious Diseases; Sanofi R&D; Marcy L'Etoile Frankreich
- Derzeitige Adresse: UCB Pharma SA; Braine-L'Alleud Belgien
| | - Cédric Couturier
- Therapeutic Area Infectious Diseases; Sanofi R&D; Marcy L'Etoile Frankreich
| | - Frédéric Jeannot
- Therapeutic Area Infectious Diseases; Sanofi R&D; Marcy L'Etoile Frankreich
| | - Fabian Nguyen
- Gene Center; Department for Biochemistry and Center for Protein Science Munich (CiPSM); Ludwig-Maximilians-Universität München; Deutschland
- Derzeitige Adresse: Institut für Biochemie und Molekularbiologie; Universität Hamburg; Deutschland
| | | | - Peter E. Hammann
- R&D Therapeutic Area Infectious Diseases; Sanofi-Aventis Deutschland GmbH; Industriepark Höchst 65926 Frankfurt am Main Deutschland
| | - Daniel N. Wilson
- Gene Center; Department for Biochemistry and Center for Protein Science Munich (CiPSM); Ludwig-Maximilians-Universität München; Deutschland
- Derzeitige Adresse: Institut für Biochemie und Molekularbiologie; Universität Hamburg; Deutschland
| | - Eric Bacqué
- Therapeutic Area Infectious Diseases; Sanofi R&D; Marcy L'Etoile Frankreich
| | - Christoph Pöverlein
- R&D Integrated Drug Discovery; Sanofi-Aventis Deutschland GmbH; Industriepark Höchst 65926 Frankfurt am Main Deutschland
| | - Armin Bauer
- R&D Therapeutic Area Infectious Diseases; Sanofi-Aventis Deutschland GmbH; Industriepark Höchst 65926 Frankfurt am Main Deutschland
| |
Collapse
|
15
|
Jürjens G, Schuler SMM, Kurz M, Petit S, Couturier C, Jeannot F, Nguyen F, Wende RC, Hammann PE, Wilson DN, Bacqué E, Pöverlein C, Bauer A. Total Synthesis and Structural Revision of the Antibiotic Tetrapeptide GE81112A. Angew Chem Int Ed Engl 2018; 57:12157-12161. [PMID: 30004165 DOI: 10.1002/anie.201805901] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2018] [Indexed: 01/14/2023]
Abstract
The total synthesis of the naturally occurring antibiotic GE81112A, a densely functionalized tetrapeptide, is reported. Comparison of spectral data with those of the natural product and the lack of biological activity of the synthesized compound led us to revise the published configuration of the 3-hydroxypipecolic acid moiety. This hypothesis was fully validated by the synthesis of the corresponding epimer.
Collapse
Affiliation(s)
- Gerrit Jürjens
- Fraunhofer IME, Projektgruppe Bioressourcen, Gießen, Germany.,Helmholtz Zentrum München, Institut für Medizinalchemie, Hannover, Germany
| | | | - Michael Kurz
- R&D Integrated Drug Discovery, Sanofi-Aventis Deutschland GmbH, Industriepark Höchst, 65926, Frankfurt am Main, Germany
| | - Sylvain Petit
- Therapeutic Area Infectious Diseases, Sanofi R&D, Marcy L'Etoile, France.,Present address: UCB Pharma SA, Braine-L'Alleud, Belgium
| | - Cédric Couturier
- Therapeutic Area Infectious Diseases, Sanofi R&D, Marcy L'Etoile, France
| | - Frédéric Jeannot
- Therapeutic Area Infectious Diseases, Sanofi R&D, Marcy L'Etoile, France
| | - Fabian Nguyen
- Gene Center, Department for Biochemistry and Center for Protein Science Munich (CiPSM), Ludwig-Maximilians-Universität, München, Germany.,Present address: Institut für Biochemie und Molekularbiologie, Universität Hamburg, Germany
| | - Raffael C Wende
- Fraunhofer IME, Projektgruppe Bioressourcen, Gießen, Germany
| | - Peter E Hammann
- R&D Therapeutic Area Infectious Diseases, Sanofi-Aventis Deutschland GmbH, Industriepark Höchst, 65926, Frankfurt am Main, Germany
| | - Daniel N Wilson
- Gene Center, Department for Biochemistry and Center for Protein Science Munich (CiPSM), Ludwig-Maximilians-Universität, München, Germany.,Present address: Institut für Biochemie und Molekularbiologie, Universität Hamburg, Germany
| | - Eric Bacqué
- Therapeutic Area Infectious Diseases, Sanofi R&D, Marcy L'Etoile, France
| | - Christoph Pöverlein
- R&D Integrated Drug Discovery, Sanofi-Aventis Deutschland GmbH, Industriepark Höchst, 65926, Frankfurt am Main, Germany
| | - Armin Bauer
- R&D Therapeutic Area Infectious Diseases, Sanofi-Aventis Deutschland GmbH, Industriepark Höchst, 65926, Frankfurt am Main, Germany
| |
Collapse
|
16
|
Polikanov YS, Aleksashin NA, Beckert B, Wilson DN. The Mechanisms of Action of Ribosome-Targeting Peptide Antibiotics. Front Mol Biosci 2018; 5:48. [PMID: 29868608 PMCID: PMC5960728 DOI: 10.3389/fmolb.2018.00048] [Citation(s) in RCA: 67] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2018] [Accepted: 04/23/2018] [Indexed: 12/31/2022] Open
Abstract
The ribosome is one of the major targets in the cell for clinically used antibiotics. However, the increase in multidrug resistant bacteria is rapidly reducing the effectiveness of our current arsenal of ribosome-targeting antibiotics, highlighting the need for the discovery of compounds with new scaffolds that bind to novel sites on the ribosome. One possible avenue for the development of new antimicrobial agents is by characterization and optimization of ribosome-targeting peptide antibiotics. Biochemical and structural data on ribosome-targeting peptide antibiotics illustrates the large diversity of scaffolds, binding interactions with the ribosome as well as mechanism of action to inhibit translation. The availability of high-resolution structures of ribosomes in complex with peptide antibiotics opens the way to structure-based design of these compounds as novel antimicrobial agents.
Collapse
Affiliation(s)
- Yury S Polikanov
- Department of Biological Sciences, University of Illinois at Chicago, Chicago, IL, United States.,Department of Medicinal Chemistry and Pharmacognosy, University of Illinois at Chicago, Chicago, IL, United States
| | - Nikolay A Aleksashin
- Center for Biomolecular Sciences, University of Illinois at Chicago, Chicago, IL, United States
| | - Bertrand Beckert
- Institute for Biochemistry and Molecular Biology, University of Hamburg, Hamburg, Germany
| | - Daniel N Wilson
- Institute for Biochemistry and Molecular Biology, University of Hamburg, Hamburg, Germany
| |
Collapse
|
17
|
Lin J, Zhou D, Steitz TA, Polikanov YS, Gagnon MG. Ribosome-Targeting Antibiotics: Modes of Action, Mechanisms of Resistance, and Implications for Drug Design. Annu Rev Biochem 2018; 87:451-478. [PMID: 29570352 DOI: 10.1146/annurev-biochem-062917-011942] [Citation(s) in RCA: 161] [Impact Index Per Article: 26.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Genetic information is translated into proteins by the ribosome. Structural studies of the ribosome and of its complexes with factors and inhibitors have provided invaluable information on the mechanism of protein synthesis. Ribosome inhibitors are among the most successful antimicrobial drugs and constitute more than half of all medicines used to treat infections. However, bacterial infections are becoming increasingly difficult to treat because the microbes have developed resistance to the most effective antibiotics, creating a major public health care threat. This has spurred a renewed interest in structure-function studies of protein synthesis inhibitors, and in few cases, compounds have been developed into potent therapeutic agents against drug-resistant pathogens. In this review, we describe the modes of action of many ribosome-targeting antibiotics, highlight the major resistance mechanisms developed by pathogenic bacteria, and discuss recent advances in structure-assisted design of new molecules.
Collapse
Affiliation(s)
- Jinzhong Lin
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai 200438, China;
| | - Dejian Zhou
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai 200438, China;
| | - Thomas A Steitz
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520, USA; .,Department of Chemistry, Yale University, New Haven, Connecticut 06520, USA.,Howard Hughes Medical Institute, Yale University, New Haven, Connecticut 06520, USA
| | - Yury S Polikanov
- Department of Biological Sciences, and Department of Medicinal Chemistry and Pharmacognosy, University of Illinois at Chicago, Chicago, Illinois 60607, USA;
| | - Matthieu G Gagnon
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520, USA; .,Howard Hughes Medical Institute, Yale University, New Haven, Connecticut 06520, USA.,Current affiliation: Department of Microbiology and Immunology, and Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, Texas 77555, USA;
| |
Collapse
|
18
|
López-Alonso JP, Kaminishi T, Kikuchi T, Hirata Y, Iturrioz I, Dhimole N, Schedlbauer A, Hase Y, Goto S, Kurita D, Muto A, Zhou S, Naoe C, Mills DJ, Gil-Carton D, Takemoto C, Himeno H, Fucini P, Connell SR. RsgA couples the maturation state of the 30S ribosomal decoding center to activation of its GTPase pocket. Nucleic Acids Res 2017; 45:6945-6959. [PMID: 28482099 PMCID: PMC5499641 DOI: 10.1093/nar/gkx324] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2017] [Accepted: 04/19/2017] [Indexed: 01/18/2023] Open
Abstract
During 30S ribosomal subunit biogenesis, assembly factors are believed to prevent accumulation of misfolded intermediate states of low free energy that slowly convert into mature 30S subunits, namely, kinetically trapped particles. Among the assembly factors, the circularly permuted GTPase, RsgA, plays a crucial role in the maturation of the 30S decoding center. Here, directed hydroxyl radical probing and single particle cryo-EM are employed to elucidate RsgA΄s mechanism of action. Our results show that RsgA destabilizes the 30S structure, including late binding r-proteins, providing a structural basis for avoiding kinetically trapped assembly intermediates. Moreover, RsgA exploits its distinct GTPase pocket and specific interactions with the 30S to coordinate GTPase activation with the maturation state of the 30S subunit. This coordination validates the architecture of the decoding center and facilitates the timely release of RsgA to control the progression of 30S biogenesis.
Collapse
Affiliation(s)
- Jorge Pedro López-Alonso
- Molecular Recognition and Host-Pathogen Interactions, CIC bioGUNE, Bizkaia Technology Park, 48160 Derio, Spain
| | - Tatsuya Kaminishi
- Molecular Recognition and Host-Pathogen Interactions, CIC bioGUNE, Bizkaia Technology Park, 48160 Derio, Spain
| | - Takeshi Kikuchi
- Department of Biochemistry and Molecular Biology, Faculty of Agriculture and Life Science, Hirosaki University, Hirosaki, Aomori 036-8561, Japan
| | - Yuya Hirata
- Department of Biochemistry and Molecular Biology, Faculty of Agriculture and Life Science, Hirosaki University, Hirosaki, Aomori 036-8561, Japan
| | - Idoia Iturrioz
- Molecular Recognition and Host-Pathogen Interactions, CIC bioGUNE, Bizkaia Technology Park, 48160 Derio, Spain
| | - Neha Dhimole
- Molecular Recognition and Host-Pathogen Interactions, CIC bioGUNE, Bizkaia Technology Park, 48160 Derio, Spain
| | - Andreas Schedlbauer
- Molecular Recognition and Host-Pathogen Interactions, CIC bioGUNE, Bizkaia Technology Park, 48160 Derio, Spain
| | - Yoichi Hase
- Department of Biochemistry and Molecular Biology, Faculty of Agriculture and Life Science, Hirosaki University, Hirosaki, Aomori 036-8561, Japan
| | - Simon Goto
- Department of Biochemistry and Molecular Biology, Faculty of Agriculture and Life Science, Hirosaki University, Hirosaki, Aomori 036-8561, Japan
| | - Daisuke Kurita
- Department of Biochemistry and Molecular Biology, Faculty of Agriculture and Life Science, Hirosaki University, Hirosaki, Aomori 036-8561, Japan
| | - Akira Muto
- Department of Biochemistry and Molecular Biology, Faculty of Agriculture and Life Science, Hirosaki University, Hirosaki, Aomori 036-8561, Japan
| | - Shu Zhou
- Molecular Recognition and Host-Pathogen Interactions, CIC bioGUNE, Bizkaia Technology Park, 48160 Derio, Spain
| | - Chieko Naoe
- Division of Structural and Synthetic Biology, RIKEN Center for Life Science Technology, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan
| | - Deryck J Mills
- Max Planck Institute of Biophysics, Department of Structural Biology, Max-von-Laue-Straße 3, D-60438 Frankfurt am Main, Germany
| | - David Gil-Carton
- Molecular Recognition and Host-Pathogen Interactions, CIC bioGUNE, Bizkaia Technology Park, 48160 Derio, Spain
| | - Chie Takemoto
- Division of Structural and Synthetic Biology, RIKEN Center for Life Science Technology, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan
| | - Hyouta Himeno
- Department of Biochemistry and Molecular Biology, Faculty of Agriculture and Life Science, Hirosaki University, Hirosaki, Aomori 036-8561, Japan
| | - Paola Fucini
- Molecular Recognition and Host-Pathogen Interactions, CIC bioGUNE, Bizkaia Technology Park, 48160 Derio, Spain.,IKERBASQUE, Basque Foundation for Science, 48011 Bilbao, Spain
| | - Sean R Connell
- Molecular Recognition and Host-Pathogen Interactions, CIC bioGUNE, Bizkaia Technology Park, 48160 Derio, Spain.,IKERBASQUE, Basque Foundation for Science, 48011 Bilbao, Spain
| |
Collapse
|
19
|
Chengguang H, Sabatini P, Brandi L, Giuliodori AM, Pon CL, Gualerzi CO. Ribosomal selection of mRNAs with degenerate initiation triplets. Nucleic Acids Res 2017; 45:7309-7325. [PMID: 28575317 PMCID: PMC5499595 DOI: 10.1093/nar/gkx472] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2017] [Accepted: 05/12/2017] [Indexed: 12/27/2022] Open
Abstract
To assess the influence of degenerate initiation triplets on mRNA recruitment by ribosomes, five mRNAs identical but for their start codon (AUG, GUG, UUG, AUU and AUA) were offered to a limiting amount of ribosomes, alone or in competition with an identical AUGmRNA bearing a mutation conferring different electrophoretic mobility to the product. Translational efficiency and competitiveness of test mRNAs toward this AUGmRNA were determined quantifying the relative amounts of the electrophoretically separated wt and mutated products synthesized in vitro and found to be influenced to different extents by the nature of their initiation triplet and by parameters such as temperature and nutrient availability in the medium. The behaviors of AUAmRNA, UUGmRNA and AUGmRNA were the same between 20 and 40°C whereas the GUG and AUUmRNAs were less active and competed poorly with the AUGmRNA, especially at low temperature. Nutrient limitation and preferential inhibition by ppGpp severely affected activity and competitiveness of all mRNAs bearing non-AUG starts, the UUGmRNA being the least affected. Overall, our data indicate that beyond these effects exclusively due to the degenerate start codons within an optimized translational initiation region, an important role is played by the context in which the rare start codons are present.
Collapse
Affiliation(s)
- He Chengguang
- College of Life Sciences, Engineering Research Centre of the Chinese Ministry of Education for Bioreactor and Pharmaceutical Development, Jilin Agricultural University, Changchun 130118, Jilin, China.,Laboratory of Genetics, University of Camerino 62032 Camerino, Italy
| | - Paola Sabatini
- Laboratory of Genetics, University of Camerino 62032 Camerino, Italy
| | - Letizia Brandi
- Laboratory of Genetics, University of Camerino 62032 Camerino, Italy
| | - Anna M Giuliodori
- Laboratory of Genetics, University of Camerino 62032 Camerino, Italy
| | - Cynthia L Pon
- Laboratory of Genetics, University of Camerino 62032 Camerino, Italy
| | | |
Collapse
|
20
|
López-Alonso JP, Fabbretti A, Kaminishi T, Iturrioz I, Brandi L, Gil-Carton D, Gualerzi CO, Fucini P, Connell SR. Structure of a 30S pre-initiation complex stalled by GE81112 reveals structural parallels in bacterial and eukaryotic protein synthesis initiation pathways. Nucleic Acids Res 2017; 45:2179-2187. [PMID: 27986852 PMCID: PMC5389724 DOI: 10.1093/nar/gkw1251] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2016] [Accepted: 12/13/2016] [Indexed: 12/28/2022] Open
Abstract
In bacteria, the start site and the reading frame of the messenger RNA are selected by the small ribosomal subunit (30S) when the start codon, typically an AUG, is decoded in the P-site by the initiator tRNA in a process guided and controlled by three initiation factors. This process can be efficiently inhibited by GE81112, a natural tetrapeptide antibiotic that is highly specific toward bacteria. Here GE81112 was used to stabilize the 30S pre-initiation complex and obtain its structure by cryo-electron microscopy. The results obtained reveal the occurrence of changes in both the ribosome conformation and initiator tRNA position that may play a critical role in controlling translational fidelity. Furthermore, the structure highlights similarities with the early steps of initiation in eukaryotes suggesting that shared structural features guide initiation in all kingdoms of life.
Collapse
Affiliation(s)
- Jorge P López-Alonso
- Structural Biology Unit, CIC bioGUNE, Parque Tecnológico de Bizkaia, 48160 Derio, Bizkaia, Spain
| | - Attilio Fabbretti
- Laboratory of Genetics, University of Camerino, 62032 Camerino, Italy
| | - Tatsuya Kaminishi
- Structural Biology Unit, CIC bioGUNE, Parque Tecnológico de Bizkaia, 48160 Derio, Bizkaia, Spain
| | - Idoia Iturrioz
- Structural Biology Unit, CIC bioGUNE, Parque Tecnológico de Bizkaia, 48160 Derio, Bizkaia, Spain
| | - Letizia Brandi
- Laboratory of Genetics, University of Camerino, 62032 Camerino, Italy
| | - David Gil-Carton
- Structural Biology Unit, CIC bioGUNE, Parque Tecnológico de Bizkaia, 48160 Derio, Bizkaia, Spain
| | | | - Paola Fucini
- Structural Biology Unit, CIC bioGUNE, Parque Tecnológico de Bizkaia, 48160 Derio, Bizkaia, Spain.,IKERBASQUE, Basque Foundation for Science, 48013 Bilbao, Spain
| | - Sean R Connell
- Structural Biology Unit, CIC bioGUNE, Parque Tecnológico de Bizkaia, 48160 Derio, Bizkaia, Spain.,IKERBASQUE, Basque Foundation for Science, 48013 Bilbao, Spain
| |
Collapse
|
21
|
Chulluncuy R, Espiche C, Nakamoto JA, Fabbretti A, Milón P. Conformational Response of 30S-bound IF3 to A-Site Binders Streptomycin and Kanamycin. Antibiotics (Basel) 2016; 5:antibiotics5040038. [PMID: 27983590 PMCID: PMC5187519 DOI: 10.3390/antibiotics5040038] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2016] [Revised: 10/22/2016] [Accepted: 12/06/2016] [Indexed: 11/16/2022] Open
Abstract
Aminoglycoside antibiotics are widely used to treat infectious diseases. Among them, streptomycin and kanamycin (and derivatives) are of importance to battle multidrug-resistant (MDR) Mycobacterium tuberculosis. Both drugs bind the small ribosomal subunit (30S) and inhibit protein synthesis. Genetic, structural, and biochemical studies indicate that local and long-range conformational rearrangements of the 30S subunit account for this inhibition. Here, we use intramolecular FRET between the C- and N-terminus domains of the flexible IF3 to monitor real-time perturbations of their binding sites on the 30S platform. Steady and pre-steady state binding experiments show that both aminoglycosides bring IF3 domains apart, promoting an elongated state of the factor. Binding of Initiation Factor IF1 triggers closure of IF3 bound to the 30S complex, while both aminoglycosides revert the IF1-dependent conformation. Our results uncover dynamic perturbations across the 30S subunit, from the A-site to the platform, and suggest that both aminoglycosides could interfere with prokaryotic translation initiation by modulating the interaction between IF3 domains with the 30S platform.
Collapse
Affiliation(s)
- Roberto Chulluncuy
- Centro de Investigación e Innovación, Faculty of Health Sciences, Universidad Peruana de Ciencias Aplicadas-UPC, Lima L-33, Peru.
| | - Carlos Espiche
- Centro de Investigación e Innovación, Faculty of Health Sciences, Universidad Peruana de Ciencias Aplicadas-UPC, Lima L-33, Peru.
| | - Jose Alberto Nakamoto
- Centro de Investigación e Innovación, Faculty of Health Sciences, Universidad Peruana de Ciencias Aplicadas-UPC, Lima L-33, Peru.
- Facultad de Ciencias y Filosofía Alberto Cazorla Talleri, Universidad Peruana Cayetano Heredia-UPCH, Lima L-31, Peru.
| | - Attilio Fabbretti
- Laboratory of Genetics, Department of Biosciences and Veterinary Medicine, University of Camerino, 62032 Camerino, Italy.
| | - Pohl Milón
- Centro de Investigación e Innovación, Faculty of Health Sciences, Universidad Peruana de Ciencias Aplicadas-UPC, Lima L-33, Peru.
| |
Collapse
|
22
|
New antibiotics from Nature’s chemical inventory. Bioorg Med Chem 2016; 24:6227-6252. [DOI: 10.1016/j.bmc.2016.09.014] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2016] [Accepted: 09/07/2016] [Indexed: 01/07/2023]
|
23
|
Maio A, Brandi L, Donadio S, Gualerzi CO. The Oligopeptide Permease Opp Mediates Illicit Transport of the Bacterial P-site Decoding Inhibitor GE81112. Antibiotics (Basel) 2016; 5:antibiotics5020017. [PMID: 27231947 PMCID: PMC4929432 DOI: 10.3390/antibiotics5020017] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2016] [Revised: 05/10/2016] [Accepted: 05/12/2016] [Indexed: 11/16/2022] Open
Abstract
GE81112 is a tetrapeptide antibiotic that binds to the 30S ribosomal subunit and specifically inhibits P-site decoding of the mRNA initiation codon by the fMet-tRNA anticodon. GE81112 displays excellent microbiological activity against some Gram-positive and Gram-negative bacteria in both minimal and complete, chemically defined, broth, but is essentially inactive in complete complex media. This is due to the presence of peptides that compete with the antibiotic for the oligopeptide permease system (Opp) responsible for its illicit transport into the bacterial cells as demonstrated in the cases of Escherichia coli and Bacillus subtilis. Mutations that inactivate the Opp system and confer GE81112 resistance arise spontaneously with a frequency of ca. 1 × 10(-6), similar to that of the mutants resistant to tri-l-ornithine, a known Opp substrate. On the contrary, cells expressing extrachromosomal copies of the opp genes are extremely sensitive to GE81112 in rich medium and GE81112-resistant mutations affecting the molecular target of the antibiotic were not detected upon examining >10⁸ cells of this type. However, some mutations introduced in the 16S rRNA to confer kasugamycin resistance were found to reduce the sensitivity of the cells to GE81112.
Collapse
Affiliation(s)
- Alessandro Maio
- Laboratory of Genetics, University of Camerino, via Gentile III da Varano, Camerino 62032 (MC), Italy.
| | - Letizia Brandi
- Laboratory of Genetics, University of Camerino, via Gentile III da Varano, Camerino 62032 (MC), Italy.
| | | | - Claudio O Gualerzi
- Laboratory of Genetics, University of Camerino, via Gentile III da Varano, Camerino 62032 (MC), Italy.
| |
Collapse
|