1
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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.
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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
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2
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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.
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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
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3
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Nakamoto JA, Evangelista W, Vinogradova DS, Konevega A, Spurio R, Fabbretti A, Milón P. The dynamic cycle of bacterial translation initiation factor IF3. Nucleic Acids Res 2021; 49:6958-6970. [PMID: 34161576 PMCID: PMC8266586 DOI: 10.1093/nar/gkab522] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Revised: 06/01/2021] [Accepted: 06/09/2021] [Indexed: 11/14/2022] Open
Abstract
Initiation factor IF3 is an essential protein that enhances the fidelity and speed of bacterial mRNA translation initiation. Here, we describe the dynamic interplay between IF3 domains and their alternative binding sites using pre-steady state kinetics combined with molecular modelling of available structures of initiation complexes. Our results show that IF3 accommodates its domains at velocities ranging over two orders of magnitude, responding to the binding of each 30S ligand. IF1 and IF2 promote IF3 compaction and the movement of the C-terminal domain (IF3C) towards the P site. Concomitantly, the N-terminal domain (IF3N) creates a pocket ready to accept the initiator tRNA. Selection of the initiator tRNA is accompanied by a transient accommodation of IF3N towards the 30S platform. Decoding of the mRNA start codon displaces IF3C away from the P site and rate limits translation initiation. 70S initiation complex formation brings IF3 domains in close proximity to each other prior to dissociation and recycling of the factor for a new round of translation initiation. Altogether, our results describe the kinetic spectrum of IF3 movements and highlight functional transitions of the factor that ensure accurate mRNA translation initiation.
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Affiliation(s)
- Jose A Nakamoto
- Laboratory of Applied Biophysics and Biochemistry, Centre for Research and Innovation, Health Sciences Faculty, Universidad Peruana de Ciencias Aplicadas (UPC), Lima 15023, Peru
| | - Wilfredo Evangelista
- Laboratory of Applied Biophysics and Biochemistry, Centre for Research and Innovation, Health Sciences Faculty, Universidad Peruana de Ciencias Aplicadas (UPC), Lima 15023, Peru
| | - Daria S Vinogradova
- Petersburg Nuclear Physics Institute, NRC ‘Kurchatov Institute’, Gatchina 188300, Russia
- NanoTemper Technologies Rus, Saint Petersburg 191167, Russia
| | - Andrey L Konevega
- Petersburg Nuclear Physics Institute, NRC ‘Kurchatov Institute’, Gatchina 188300, Russia
- NRC ‘Kurchatov Institute’, Moscow 123182, Russia
- Peter the Great St. Petersburg Polytechnic University, Saint Petersburg 195251, Russia
| | - Roberto Spurio
- Laboratory of Genetics, School of Biosciences and Veterinary Medicine, University of Camerino, Camerino 62032, Italy
| | - Attilio Fabbretti
- Laboratory of Genetics, School of Biosciences and Veterinary Medicine, University of Camerino, Camerino 62032, Italy
| | - Pohl Milón
- Laboratory of Applied Biophysics and Biochemistry, Centre for Research and Innovation, Health Sciences Faculty, Universidad Peruana de Ciencias Aplicadas (UPC), Lima 15023, Peru
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4
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Barrenechea V, Vargas-Reyes M, Quiliano M, Milón P. A Complementary Mechanism of Bacterial mRNA Translation Inhibition by Tetracyclines. Front Microbiol 2021; 12:682682. [PMID: 34262544 PMCID: PMC8273347 DOI: 10.3389/fmicb.2021.682682] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Accepted: 05/10/2021] [Indexed: 11/26/2022] Open
Abstract
Tetracycline has positively impacted human health as well as the farming and animal industries. Its extensive usage and versatility led to the spread of resistance mechanisms followed by the development of new variants of the antibiotic. Tetracyclines inhibit bacterial growth by impeding the binding of elongator tRNAs to the ribosome. However, a small number of reports indicated that Tetracyclines could also inhibit translation initiation, yet the molecular mechanism remained unknown. Here, we use biochemical and computational methods to study how Oxytetracycline (Otc), Demeclocycline (Dem), and Tigecycline (Tig) affect the translation initiation phase of protein synthesis. Our results show that all three Tetracyclines induce Initiation Factor IF3 to adopt a compact conformation on the 30S ribosomal subunit, similar to that induced by Initiation Factor IF1. This compaction was faster for Tig than Dem or Otc. Furthermore, all three tested tetracyclines affected IF1-bound 30S complexes. The dissociation rate constant of IF1 in early 30S complexes was 14-fold slower for Tig than Dem or Otc. Late 30S initiation complexes (30S pre-IC or IC) exhibited greater IF1 stabilization by Tig than for Dem and Otc. Tig and Otc delayed 50S joining to 30S initiation complexes (30S ICs). Remarkably, the presence of Tig considerably slowed the progression to translation elongation and retained IF1 in the resulting 70S initiation complex (70S IC). Molecular modeling of Tetracyclines bound to the 30S pre-IC and 30S IC indicated that the antibiotics binding site topography fluctuates along the initiation pathway. Mainly, 30S complexes show potential contacts between Dem or Tig with IF1, providing a structural rationale for the enhanced affinity of the antibiotics in the presence of the factor. Altogether, our data indicate that Tetracyclines inhibit translation initiation by allosterically perturbing the IF3 layout on the 30S, retaining IF1 during 70S IC formation, and slowing the transition toward translation elongation. Thus, this study describes a new complementary mechanism by which Tetracyclines may inhibit bacterial protein synthesis.
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Affiliation(s)
- Victor Barrenechea
- Faculty of Health Sciences, Centre for Research and Innovation, Universidad Peruana de Ciencias Aplicadas (UPC), Lima, Peru.,Postgraduate Unit, Medicine Faculty, Universidad Nacional Mayor de San Marcos, Lima, Peru
| | - Maryhory Vargas-Reyes
- Faculty of Health Sciences, Centre for Research and Innovation, Universidad Peruana de Ciencias Aplicadas (UPC), Lima, Peru
| | - Miguel Quiliano
- Faculty of Health Sciences, Centre for Research and Innovation, Universidad Peruana de Ciencias Aplicadas (UPC), Lima, Peru
| | - Pohl Milón
- Faculty of Health Sciences, Centre for Research and Innovation, Universidad Peruana de Ciencias Aplicadas (UPC), Lima, Peru
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5
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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.
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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
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6
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Tharp JM, Krahn N, Varshney U, Söll D. Hijacking Translation Initiation for Synthetic Biology. Chembiochem 2020; 21:1387-1396. [PMID: 32023356 PMCID: PMC7237318 DOI: 10.1002/cbic.202000017] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Indexed: 12/17/2022]
Abstract
Genetic code expansion (GCE) has revolutionized the field of protein chemistry. Over the past several decades more than 150 different noncanonical amino acids (ncAAs) have been co-translationally installed into proteins within various host organisms. The vast majority of these ncAAs have been incorporated between the start and stop codons within an open reading frame. This requires that the ncAA be able to form a peptide bond at the α-amine, limiting the types of molecules that can be genetically encoded. In contrast, the α-amine of the initiating amino acid is not required for peptide bond formation. Therefore, including the initiator position in GCE allows for co-translational insertion of more diverse molecules that are modified, or completely lacking an α-amine. This review explores various methods which have been used to initiate protein synthesis with diverse molecules both in vitro and in vivo.
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Affiliation(s)
- Jeffery M Tharp
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06520, USA
| | - Natalie Krahn
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06520, USA
| | - Umesh Varshney
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, 560012, India
| | - Dieter Söll
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06520, USA
- Department of Chemistry, Yale University, New Haven, CT, 06520, USA
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7
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Sharma IM, Woodson SA. RbfA and IF3 couple ribosome biogenesis and translation initiation to increase stress tolerance. Nucleic Acids Res 2020; 48:359-372. [PMID: 31728529 PMCID: PMC7145577 DOI: 10.1093/nar/gkz1065] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Revised: 10/09/2019] [Accepted: 11/04/2019] [Indexed: 12/12/2022] Open
Abstract
Bacterial ribosome biogenesis and translation occur in the same cellular compartment. Therefore, a biochemical gate-keeping step is required to prevent error-prone immature ribosomes from engaging in protein synthesis. Here, we provide evidence for a previously unknown quality control mechanism in which the abundant ribosome assembly factor, RbfA, suppresses protein synthesis by immature Escherichia coli 30S subunits. After 30S maturation, RbfA is displaced by initiation factor 3 (IF3), which promotes translation initiation. Genetic interactions between RbfA and IF3 show that RbfA release by IF3 is important during logarithmic growth as well as during stress encountered during stationary phase, low nutrition, low temperature, and antibiotics. By gating the transition from 30S biogenesis to translation initiation, RbfA and IF3 maintain the fidelity of bacterial protein synthesis.
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Affiliation(s)
- Indra Mani Sharma
- T. C. Jenkins Department of Biophysics, Johns Hopkins University, 3400 N. Charles St., Baltimore, MD 21218, USA
| | - Sarah A Woodson
- T. C. Jenkins Department of Biophysics, Johns Hopkins University, 3400 N. Charles St., Baltimore, MD 21218, USA
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8
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Tomsic J, Smorlesi A, Caserta E, Giuliodori AM, Pon CL, Gualerzi CO. Disparate Phenotypes Resulting from Mutations of a Single Histidine in Switch II of Geobacillus stearothermophilus Translation Initiation Factor IF2. Int J Mol Sci 2020; 21:ijms21030735. [PMID: 31979156 PMCID: PMC7037019 DOI: 10.3390/ijms21030735] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2019] [Revised: 01/20/2020] [Accepted: 01/20/2020] [Indexed: 11/16/2022] Open
Abstract
The conserved Histidine 301 in switch II of Geobacillus stearothermophilus IF2 G2 domain was substituted with Ser, Gln, Arg, Leu and Tyr to generate mutants displaying different phenotypes. Overexpression of IF2H301S, IF2H301L and IF2H301Y in cells expressing wtIF2, unlike IF2H301Q and IF2H301R, caused a dominant lethal phenotype, inhibiting in vivo translation and drastically reducing cell viability. All mutants bound GTP but, except for IF2H301Q, were inactive in ribosome-dependent GTPase for different reasons. All mutants promoted 30S initiation complex (30S IC) formation with wild type (wt) efficiency but upon 30S IC association with the 50S subunit, the fMet-tRNA reacted with puromycin to different extents depending upon the IF2 mutant present in the complex (wtIF2 ≥ to IF2H301Q > IF2H301R >>> IF2H301S, IF2H301L and IF2H301Y) whereas only fMet-tRNA 30S-bound with IF2H301Q retained some ability to form initiation dipeptide fMet-Phe. Unlike wtIF2, all mutants, regardless of their ability to hydrolyze GTP, displayed higher affinity for the ribosome and failed to dissociate from the ribosomes upon 50S docking to 30S IC. We conclude that different amino acids substitutions of His301 cause different structural alterations of the factor, resulting in disparate phenotypes with no direct correlation existing between GTPase inactivation and IF2 failure to dissociate from ribosomes.
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9
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Bennison DJ, Irving SE, Corrigan RM. The Impact of the Stringent Response on TRAFAC GTPases and Prokaryotic Ribosome Assembly. Cells 2019; 8:cells8111313. [PMID: 31653044 PMCID: PMC6912228 DOI: 10.3390/cells8111313] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Revised: 10/17/2019] [Accepted: 10/23/2019] [Indexed: 12/24/2022] Open
Abstract
Many facets of ribosome biogenesis and function, including ribosomal RNA (rRNA) transcription, 70S assembly and protein translation, are negatively impacted upon induction of a nutrient stress-sensing signalling pathway termed the stringent response. This stress response is mediated by the alarmones guanosine tetra- and penta-phosphate ((p)ppGpp), the accumulation of which leads to a massive cellular response that slows growth and aids survival. The 70S bacterial ribosome is an intricate structure, with assembly both complex and highly modular. Presiding over the assembly process is a group of P-loop GTPases within the TRAFAC (Translation Factor Association) superclass that are crucial for correct positioning of both early and late stage ribosomal proteins (r-proteins) onto the rRNA. Often described as 'molecular switches', members of this GTPase superfamily readily bind and hydrolyse GTP to GDP in a cyclic manner that alters the propensity of the GTPase to carry out a function. TRAFAC GTPases are considered to act as checkpoints to ribosome assembly, involved in binding to immature sections in the GTP-bound state, preventing further r-protein association until maturation is complete. Here we review our current understanding of the impact of the stringent response and (p)ppGpp production on ribosome maturation in prokaryotic cells, focusing on the inhibition of (p)ppGpp on GTPase-mediated subunit assembly, but also touching upon the inhibition of rRNA transcription and protein translation.
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Affiliation(s)
- Daniel J Bennison
- The Florey Institute, Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield S10 2TN, UK.
| | - Sophie E Irving
- The Florey Institute, Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield S10 2TN, UK.
| | - Rebecca M Corrigan
- The Florey Institute, Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield S10 2TN, UK.
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10
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Kaledhonkar S, Fu Z, Caban K, Li W, Chen B, Sun M, Gonzalez RL, Frank J. Late steps in bacterial translation initiation visualized using time-resolved cryo-EM. Nature 2019; 570:400-404. [PMID: 31108498 PMCID: PMC7060745 DOI: 10.1038/s41586-019-1249-5] [Citation(s) in RCA: 79] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Accepted: 05/08/2019] [Indexed: 12/02/2022]
Abstract
The initiation of bacterial translation involves the tightly regulated joining of the 50S ribosomal subunit to an initiator transfer RNA (fMet-tRNAfMet)-containing 30S ribosomal initiation complex to form a 70S initiation complex, which subsequently matures into a 70S elongation-competent complex. Rapid and accurate formation of the 70S initiation complex is promoted by initiation factors, which must dissociate from the 30S initiation complex before the resulting 70S elongation-competent complex can begin the elongation of translation1. Although comparisons of the structures of the 30S2-5 and 70S4,6-8 initiation complexes have revealed that the ribosome, initiation factors and fMet-tRNAfMet can acquire different conformations in these complexes, the timing of conformational changes during formation of the 70S initiation complex, the structures of any intermediates formed during these rearrangements, and the contributions that these dynamics might make to the mechanism and regulation of initiation remain unknown. Moreover, the absence of a structure of the 70S elongation-competent complex formed via an initiation-factor-catalysed reaction has precluded an understanding of the rearrangements to the ribosome, initiation factors and fMet-tRNAfMet that occur during maturation of a 70S initiation complex into a 70S elongation-competent complex. Here, using time-resolved cryogenic electron microscopy9, we report the near-atomic-resolution view of how a time-ordered series of conformational changes drive and regulate subunit joining, initiation factor dissociation and fMet-tRNAfMet positioning during formation of the 70S elongation-competent complex. Our results demonstrate the power of time-resolved cryogenic electron microscopy to determine how a time-ordered series of conformational changes contribute to the mechanism and regulation of one of the most fundamental processes in biology.
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MESH Headings
- Cryoelectron Microscopy
- Escherichia coli/chemistry
- Escherichia coli/metabolism
- Escherichia coli/ultrastructure
- Peptide Chain Elongation, Translational
- Peptide Chain Initiation, Translational
- Protein Conformation
- Ribosome Subunits, Large, Bacterial/metabolism
- Ribosome Subunits, Large, Bacterial/ultrastructure
- Ribosome Subunits, Small, Bacterial/metabolism
- Ribosome Subunits, Small, Bacterial/ultrastructure
- Ribosomes/chemistry
- Ribosomes/metabolism
- Ribosomes/ultrastructure
- Time Factors
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Affiliation(s)
- Sandip Kaledhonkar
- Department of Biochemistry & Molecular Biophysics, Columbia University, New York, NY, USA
| | - Ziao Fu
- Integrated Program in Cellular, Molecular and Biophysical Studies, Columbia University, College of Physicians and Surgeons, New York, NY, USA
| | - Kelvin Caban
- Department of Chemistry, Columbia University, New York, NY, USA
| | - Wen Li
- Department of Biochemistry & Molecular Biophysics, Columbia University, New York, NY, USA
| | - Bo Chen
- Department of Biochemistry & Molecular Biophysics, Columbia University, New York, NY, USA
| | - Ming Sun
- Department of Biological Sciences, Columbia University, New York, NY, USA
| | - Ruben L Gonzalez
- Department of Chemistry, Columbia University, New York, NY, USA.
| | - Joachim Frank
- Department of Biochemistry & Molecular Biophysics, Columbia University, New York, NY, USA.
- Department of Biological Sciences, Columbia University, New York, NY, USA.
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11
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Koripella RK, Sharma MR, Haque ME, Risteff P, Spremulli LL, Agrawal RK. Structure of Human Mitochondrial Translation Initiation Factor 3 Bound to the Small Ribosomal Subunit. iScience 2019; 12:76-86. [PMID: 30677741 PMCID: PMC6352543 DOI: 10.1016/j.isci.2018.12.030] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Revised: 12/11/2018] [Accepted: 12/27/2018] [Indexed: 11/20/2022] Open
Abstract
The human mitochondrial translational initiation factor 3 (IF3mt) carries mitochondrial-specific amino acid extensions at both its N and C termini (N- and C-terminal extensions [NTE and CTE, respectively]), when compared with its eubacterial counterpart. Here we present 3.3- to 3.5-Å-resolution cryoelectron microscopic structures of the mammalian 28S mitoribosomal subunit in complex with human IF3mt. Unique contacts observed between the 28S subunit and N-terminal domain of IF3mt explain its unusually high affinity for the 28S subunit, whereas the position of the mito-specific NTE suggests NTE's role in binding of initiator tRNA to the 28S subunit. The location of the C-terminal domain (CTD) clarifies its anti-association activity, whereas the orientation of the mito-specific CTE provides a mechanistic explanation for its role in destabilizing initiator tRNA in the absence of mRNA. Furthermore, our structure hints at a possible role of the CTD in recruiting leaderless mRNAs for translation initiation. Our findings highlight unique features of IF3mt in mitochondrial translation initiation. High-resolution cryo-EM study of the mammalian 28S mitoribosome-IF3mt complex Interaction between the 28S and IF3mt's NTD explains NTD's unusual high affinity Provides insights into role of IF3mt's N-terminal extension in initiator tRNA binding Provides insights into roles of IF3mt's CTD and C-terminal extension in mRNA sensing
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Affiliation(s)
- Ravi K Koripella
- Division of Translational Medicine, Wadsworth Center, New York State Department of Health, Albany, NY 12201-0509, USA
| | - Manjuli R Sharma
- Division of Translational Medicine, Wadsworth Center, New York State Department of Health, Albany, NY 12201-0509, USA
| | - Md Emdadul Haque
- Department of Chemistry, Campus Box 3290, University of North Carolina, Chapel Hill, NC, USA
| | - Paul Risteff
- Division of Translational Medicine, Wadsworth Center, New York State Department of Health, Albany, NY 12201-0509, USA
| | - Linda L Spremulli
- Department of Chemistry, Campus Box 3290, University of North Carolina, Chapel Hill, NC, USA
| | - Rajendra K Agrawal
- Division of Translational Medicine, Wadsworth Center, New York State Department of Health, Albany, NY 12201-0509, USA; Department of Biomedical Sciences, School of Public Health, University at Albany, SUNY, Albany, NY, USA.
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Opron K, Burton ZF. Ribosome Structure, Function, and Early Evolution. Int J Mol Sci 2018; 20:ijms20010040. [PMID: 30583477 PMCID: PMC6337491 DOI: 10.3390/ijms20010040] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Revised: 12/03/2018] [Accepted: 12/16/2018] [Indexed: 11/16/2022] Open
Abstract
Ribosomes are among the largest and most dynamic molecular motors. The structure and dynamics of translation initiation and elongation are reviewed. Three ribosome motions have been identified for initiation and translocation. A swivel motion between the head/beak and the body of the 30S subunit was observed. A tilting dynamic of the head/beak versus the body of the 30S subunit was detected using simulations. A reversible ratcheting motion was seen between the 30S and the 50S subunits that slide relative to one another. The 30S⁻50S intersubunit contacts regulate translocation. IF2, EF-Tu, and EF-G are homologous G-protein GTPases that cycle on and off the same site on the ribosome. The ribosome, aminoacyl-tRNA synthetase (aaRS) enzymes, transfer ribonucleic acid (tRNA), and messenger ribonucleic acid (mRNA) form the core of information processing in cells and are coevolved. Surprisingly, class I and class II aaRS enzymes, with distinct and incompatible folds, are homologs. Divergence of class I and class II aaRS enzymes and coevolution of the genetic code are described by analysis of ancient archaeal species.
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Affiliation(s)
- Kristopher Opron
- Bioinformatics Core, University of Michigan, Ann Arbor, MI 48109-0674, USA.
| | - Zachary F Burton
- Department of Biochemistry and Molecular Biology, 603 Wilson Rd., Michigan State University, MI 48824-1319, USA.
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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: 73] [Impact Index Per Article: 12.2] [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.
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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
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Complementary charge-based interaction between the ribosomal-stalk protein L7/12 and IF2 is the key to rapid subunit association. Proc Natl Acad Sci U S A 2018; 115:4649-4654. [PMID: 29686090 DOI: 10.1073/pnas.1802001115] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
The interaction between the ribosomal-stalk protein L7/12 (L12) and initiation factor 2 (IF2) is essential for rapid subunit association, but the underlying mechanism is unknown. Here, we have characterized the L12-IF2 interaction on Escherichia coli ribosomes using site-directed mutagenesis, fast kinetics, and molecular dynamics (MD) simulations. Fifteen individual point mutations were introduced into the C-terminal domain of L12 (L12-CTD) at helices 4 and 5, which constitute the common interaction site for translational GTPases. In parallel, 15 point mutations were also introduced into IF2 between the G4 and G5 motifs, which we hypothesized as the potential L12 interaction sites. The L12 and IF2 mutants were tested in ribosomal subunit association assay in a stopped-flow instrument. Those amino acids that caused defective subunit association upon substitution were identified as the molecular determinants of L12-IF2 interaction. Further, MD simulations of IF2 docked onto the L12-CTD pinpointed the exact interacting partners-all of which were positively charged on L12 and negatively charged on IF2, connected by salt bridges. Lastly, we tested two pairs of charge-reversed mutants of L12 and IF2, which significantly restored the yield and the rate of formation of the 70S initiation complex. We conclude that complementary charge-based interaction between L12-CTD and IF2 is the key for fast subunit association. Considering the homology of the G domain, similar mechanisms may apply for L12 interactions with other translational GTPases.
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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.
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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
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