51
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Mangano K, Florin T, Shao X, Klepacki D, Chelysheva I, Ignatova Z, Gao Y, Mankin AS, Vázquez-Laslop N. Genome-wide effects of the antimicrobial peptide apidaecin on translation termination in bacteria. eLife 2020; 9:e62655. [PMID: 33031031 PMCID: PMC7544508 DOI: 10.7554/elife.62655] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Accepted: 09/20/2020] [Indexed: 12/16/2022] Open
Abstract
Biochemical studies suggested that the antimicrobial peptide apidaecin (Api) inhibits protein synthesis by binding in the nascent peptide exit tunnel and trapping the release factor associated with a terminating ribosome. The mode of Api action in bacterial cells had remained unknown. Here genome-wide analysis reveals that in bacteria, Api arrests translating ribosomes at stop codons and causes pronounced queuing of the trailing ribosomes. By sequestering the available release factors, Api promotes pervasive stop codon bypass, leading to the expression of proteins with C-terminal extensions. Api-mediated translation arrest leads to the futile activation of the ribosome rescue systems. Understanding the unique mechanism of Api action in living cells may facilitate the development of new medicines and research tools for genome exploration.
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Affiliation(s)
- Kyle Mangano
- Center for Biomolecular Sciences, University of Illinois at ChicagoChicagoUnited States
- Department of Pharmaceutical Sciences, University of Illinois at ChicagoChicagoUnited States
| | - Tanja Florin
- Center for Biomolecular Sciences, University of Illinois at ChicagoChicagoUnited States
| | - Xinhao Shao
- Department of Pharmaceutical Sciences, University of Illinois at ChicagoChicagoUnited States
| | - Dorota Klepacki
- Center for Biomolecular Sciences, University of Illinois at ChicagoChicagoUnited States
| | - Irina Chelysheva
- Institute of Biochemistry and Molecular Biology, University of HamburgHamburgGermany
| | - Zoya Ignatova
- Institute of Biochemistry and Molecular Biology, University of HamburgHamburgGermany
| | - Yu Gao
- Department of Pharmaceutical Sciences, University of Illinois at ChicagoChicagoUnited States
| | - Alexander S Mankin
- Center for Biomolecular Sciences, University of Illinois at ChicagoChicagoUnited States
- Department of Pharmaceutical Sciences, University of Illinois at ChicagoChicagoUnited States
| | - Nora Vázquez-Laslop
- Center for Biomolecular Sciences, University of Illinois at ChicagoChicagoUnited States
- Department of Pharmaceutical Sciences, University of Illinois at ChicagoChicagoUnited States
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52
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Sola R, Mardirossian M, Beckert B, Sanghez De Luna L, Prickett D, Tossi A, Wilson DN, Scocchi M. Characterization of Cetacean Proline-Rich Antimicrobial Peptides Displaying Activity against ESKAPE Pathogens. Int J Mol Sci 2020; 21:E7367. [PMID: 33036159 PMCID: PMC7582929 DOI: 10.3390/ijms21197367] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Revised: 09/28/2020] [Accepted: 09/29/2020] [Indexed: 12/27/2022] Open
Abstract
Proline-rich antimicrobial peptides (PrAMPs) may be a valuable weapon against multi-drug resistant pathogens, combining potent antimicrobial activity with low cytotoxicity. We have identified novel PrAMPs from five cetacean species (cePrAMPs), and characterized their potency, mechanism of action and in vitro cytotoxicity. Despite the homology between the N-terminal of cePrAMPs and the bovine PrAMP Bac7, some differences emerged in their sequence, activity spectrum and mode of action. CePrAMPs with the highest similarity with the Bac7(1-35) fragment inhibited bacterial protein synthesis without membrane permeabilization, while a second subgroup of cePrAMPs was more membrane-active but less efficient at inhibiting bacterial translation. Such differences may be ascribable to differences in presence and positioning of Trp residues and of a conserved motif seemingly required for translation inhibition. Unlike Bac7(1-35), which requires the peptide transporter SbmA for its uptake, the activity of cePrAMPs was mostly independent of SbmA, regardless of their mechanism of action. Two peptides displayed a promisingly broad spectrum of activity, with minimal inhibiting concentration MIC ≤ 4 µM against several bacteria of the ESKAPE group, including Pseudomonas aeruginosa and Enterococcus faecium. Our approach has led us to discover several new peptides; correlating their sequences and mechanism of action will provide useful insights for designing optimized future peptide-based antibiotics.
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Affiliation(s)
- Riccardo Sola
- Department of Life Sciences, University of Trieste, 34127 Trieste, Italy; (R.S.); (L.S.D.L.); (D.P.); (A.T.); mscocchi.units.it (M.S.)
| | - Mario Mardirossian
- Department of Medical Sciences, University of Trieste, 34125 Trieste, Italy;
| | - Bertrand Beckert
- Institute for Biochemistry and Molecular Biology, University of Hamburg, 20146 Hamburg, Germany; (B.B.); (D.N.W.)
| | - Laura Sanghez De Luna
- Department of Life Sciences, University of Trieste, 34127 Trieste, Italy; (R.S.); (L.S.D.L.); (D.P.); (A.T.); mscocchi.units.it (M.S.)
| | - Dennis Prickett
- Department of Life Sciences, University of Trieste, 34127 Trieste, Italy; (R.S.); (L.S.D.L.); (D.P.); (A.T.); mscocchi.units.it (M.S.)
| | - Alessandro Tossi
- Department of Life Sciences, University of Trieste, 34127 Trieste, Italy; (R.S.); (L.S.D.L.); (D.P.); (A.T.); mscocchi.units.it (M.S.)
| | - Daniel N. Wilson
- Institute for Biochemistry and Molecular Biology, University of Hamburg, 20146 Hamburg, Germany; (B.B.); (D.N.W.)
| | - Marco Scocchi
- Department of Life Sciences, University of Trieste, 34127 Trieste, Italy; (R.S.); (L.S.D.L.); (D.P.); (A.T.); mscocchi.units.it (M.S.)
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53
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Arbour CA, Mendoza LG, Stockdill JL. Recent advances in the synthesis of C-terminally modified peptides. Org Biomol Chem 2020; 18:7253-7272. [PMID: 32914156 PMCID: PMC9508648 DOI: 10.1039/d0ob01417f] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/10/2023]
Abstract
C-Terminally modified peptides are important for the development and delivery of peptide-based pharmaceuticals because they impact peptide activity, stability, hydrophobicity, and membrane permeability. Additionally, the vulnerability of C-terminal esters to cleavage by endogenous esterases makes them excellent pro-drugs. Methods for post-SPPS C-terminal functionalization potentially enable access to libraries of modified peptides, facilitating tailoring of their solubility, potency, toxicity, and uptake pathway. Apparently minor structural changes can significantly impact the binding, folding, and pharmacokinetics of the peptide. This review summarizes developments in chemical methods for C-terminal modification of peptides published since the last review on this topic in 2003.
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Affiliation(s)
- Christine A Arbour
- Wayne State University, Department of Chemistry, Detroit, Michigan, USA.
| | - Lawrence G Mendoza
- Wayne State University, Department of Chemistry, Detroit, Michigan, USA.
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54
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Muthunayake NS, Islam R, Inutan ED, Colangelo W, Trimpin S, Cunningham PR, Chow CS. Expression and In Vivo Characterization of the Antimicrobial Peptide Oncocin and Variants Binding to Ribosomes. Biochemistry 2020; 59:3380-3391. [PMID: 32840100 DOI: 10.1021/acs.biochem.0c00600] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Peptides have important biomedical applications, but poor correlation between in vitro and in vivo activities can limit their development for clinical use. The ability to generate peptides and monitor their expression with new mass spectrometric methods and biological activities in vivo would be an advantage for the discovery and improvement of peptide-based drugs. In this study, a plasmid-based system was used to express the ribosome-targeting peptide oncocin (19 amino acids, VDKPPYLPRPRPPRRIYNR) and to determine its direct antibacterial effects on Escherichia coli. Previous biochemical and structure studies showed that oncocin targets the bacterial ribosome. The oncocin peptide generated in vivo strongly inhibits bacterial growth. In vivo dimethyl sulfate footprinting of oncocin on the rRNA gives results that are consistent with those of in vitro studies but reveals additional binding interactions with E. coli ribosomes. Furthermore, expression of truncated or mutated peptides reveals which amino acids are important for antimicrobial activity. Overall, the in vivo peptide expression system can be used to investigate biological activities and interactions of peptides with their targets within the cellular environment and to separate contributions of the sequence to cellular transport. This strategy has future applications for improving the effectiveness of existing peptides and developing new peptide-based drugs.
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Affiliation(s)
- Nisansala S Muthunayake
- Department of Chemistry, Wayne State University, Detroit, Michigan 48202, United States.,Department of Biological Sciences, Wayne State University, Detroit, Michigan 48202, United States
| | - Rabiul Islam
- Department of Chemistry, Wayne State University, Detroit, Michigan 48202, United States
| | - Ellen D Inutan
- Department of Chemistry, Mindanao State University-Iligan Institute of Technology, Iligan 9200, Philippines
| | - Wesley Colangelo
- Department of Biological Sciences, Wayne State University, Detroit, Michigan 48202, United States
| | - Sarah Trimpin
- Department of Chemistry, Wayne State University, Detroit, Michigan 48202, United States
| | - Philip R Cunningham
- Department of Biological Sciences, Wayne State University, Detroit, Michigan 48202, United States
| | - Christine S Chow
- Department of Chemistry, Wayne State University, Detroit, Michigan 48202, United States
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55
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Kolano L, Knappe D, Volke D, Sträter N, Hoffmann R. Ribosomal Target-Binding Sites of Antimicrobial Peptides Api137 and Onc112 Are Conserved among Pathogens Indicating New Lead Structures To Develop Novel Broad-Spectrum Antibiotics. Chembiochem 2020; 21:2628-2634. [PMID: 32293093 PMCID: PMC7540576 DOI: 10.1002/cbic.202000109] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Indexed: 12/13/2022]
Abstract
Proline-rich antimicrobial peptides expressed in insects are primarily active against Enterobacteriaceae. Mechanistically, they target the bacterial (70S) ribosome after partially transporter-based cellular uptake, as revealed for Api137 and Onc112 on Escherichia coli. Following molecular modeling indicating that the Onc112 contact site is conserved among the ribosomes of high-priority pathogens, the ribosome binding of Api137 and Onc112 was studied. The dissociation constants (Kd ) of Onc112 were ∼75 nmol/L for Escherichia coli, Klebsiella pneumoniae, and Acinetobacter baumannii, 36 nmol/L for Pseudomonas aeruginosa, and 102 nmol/L for Staphylococcus aureus, thus indicating a very promising lead structure for developing broad-spectrum antibiotics. Api137 bound weaker with Kd values ranging from 155 nmol/L to 13 μmol/L. For most bacteria, the antibacterial activities were lower than predicted from the Kd values, which was only partially explained by their ability to enter bacterial cells. Other factors limiting the activity expected from the ribosome binding might be off-target binding.
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Affiliation(s)
- Lisa Kolano
- Faculty of Chemistry and MineralogyInstitute of Bioanalytical ChemistryDeutscher Platz 504103LeipzigGermany
- Center for Biotechnology and Biomedicine (BBZ)Deutscher Platz 504103LeipzigGermany
| | - Daniel Knappe
- Faculty of Chemistry and MineralogyInstitute of Bioanalytical ChemistryDeutscher Platz 504103LeipzigGermany
- Center for Biotechnology and Biomedicine (BBZ)Deutscher Platz 504103LeipzigGermany
- EnBiotix GmbHLeipzigDeutscher Platz 5E04103LeipzigGermany
| | - Daniela Volke
- Faculty of Chemistry and MineralogyInstitute of Bioanalytical ChemistryDeutscher Platz 504103LeipzigGermany
- Center for Biotechnology and Biomedicine (BBZ)Deutscher Platz 504103LeipzigGermany
| | - Norbert Sträter
- Faculty of Chemistry and MineralogyInstitute of Bioanalytical ChemistryDeutscher Platz 504103LeipzigGermany
- Center for Biotechnology and Biomedicine (BBZ)Deutscher Platz 504103LeipzigGermany
| | - Ralf Hoffmann
- Faculty of Chemistry and MineralogyInstitute of Bioanalytical ChemistryDeutscher Platz 504103LeipzigGermany
- Center for Biotechnology and Biomedicine (BBZ)Deutscher Platz 504103LeipzigGermany
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56
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Mardirossian M, Sola R, Beckert B, Valencic E, Collis DWP, Borišek J, Armas F, Di Stasi A, Buchmann J, Syroegin EA, Polikanov YS, Magistrato A, Hilpert K, Wilson DN, Scocchi M. Peptide Inhibitors of Bacterial Protein Synthesis with Broad Spectrum and SbmA-Independent Bactericidal Activity against Clinical Pathogens. J Med Chem 2020; 63:9590-9602. [PMID: 32787108 DOI: 10.1021/acs.jmedchem.0c00665] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Proline-rich antimicrobial peptides (PrAMPs) are promising lead compounds for developing new antimicrobials; however, their narrow spectrum of action is limiting. PrAMPs kill bacteria binding to their ribosomes and inhibiting protein synthesis. In this study, 133 derivatives of the PrAMP Bac7(1-16) were synthesized to identify the crucial residues for ribosome inactivation and antimicrobial activity. Then, five new Bac7(1-16) derivatives were conceived and characterized by antibacterial and membrane permeabilization assays, X-ray crystallography, and molecular dynamics simulations. Some derivatives displayed broad spectrum activity, encompassing Escherichia coli, Klebsiella pneumoniae, Acinetobacter baumanii, Pseudomonas aeruginosa, and Staphylococcus aureus. Two peptides out of five acquired a weak membrane-perturbing activity while maintaining the ability to inhibit protein synthesis. These derivatives became independent of the SbmA transporter, commonly used by native PrAMPs, suggesting that they obtained a novel route to enter bacterial cells. PrAMP-derived compounds could become new-generation antimicrobials to combat antibiotic-resistant pathogens.
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Affiliation(s)
- Mario Mardirossian
- Department of Medical Sciences, University of Trieste, 34125 Trieste, Italy
| | - Riccardo Sola
- Department of Life Sciences, University of Trieste, 34127 Trieste, Italy
| | - Bertrand Beckert
- Institut für Biochemie und Molekularbiologie, University of Hamburg, 20146 Hamburg, Germany
| | - Erica Valencic
- Institute for Maternal and Child Health-IRCCS "Burlo Garofolo", 30137 Trieste, Italy
| | | | | | - Federica Armas
- Department of Life Sciences, University of Trieste, 34127 Trieste, Italy
| | - Adriana Di Stasi
- Department of Life Sciences, University of Trieste, 34127 Trieste, Italy
| | - Jan Buchmann
- Institut für Biochemie und Molekularbiologie, University of Hamburg, 20146 Hamburg, Germany.,Department of Biological Sciences, University of Illinois at Chicago, Chicago, Illinois 60607, United States
| | - Egor A Syroegin
- Department of Biological Sciences, University of Illinois at Chicago, Chicago, Illinois 60607, United States
| | - Yury S Polikanov
- Department of Biological Sciences, University of Illinois at Chicago, Chicago, Illinois 60607, United States.,Department of Pharmaceutical Sciences, University of Illinois at Chicago, Chicago, Illinois 60607, United States
| | | | - Kai Hilpert
- Institute of Infection and Immunology, St. George's, University of London, SW 17 0RE London, U.K
| | - Daniel N Wilson
- Institut für Biochemie und Molekularbiologie, University of Hamburg, 20146 Hamburg, Germany
| | - Marco Scocchi
- Department of Life Sciences, University of Trieste, 34127 Trieste, Italy
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57
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André C, Veillard F, Wolff P, Lobstein AM, Compain G, Monsarrat C, Reichhart JM, Noûs C, Burnouf DY, Guichard G, Wagner JE. Antibacterial activity of a dual peptide targeting the Escherichia coli sliding clamp and the ribosome. RSC Chem Biol 2020; 1:137-147. [PMID: 34458754 PMCID: PMC8341878 DOI: 10.1039/d0cb00060d] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Revised: 07/06/2021] [Accepted: 07/06/2020] [Indexed: 12/20/2022] Open
Abstract
The bacterial processivity factor, or sliding clamp (SC), is a target of choice for new antibacterial drugs development. We have previously developed peptides that target Escherichia coli SC and block its interaction with DNA polymerases in vitro. Here, one such SC binding peptide was fused to a Proline-rich AntiMicrobial Peptide (PrAMP) to allow its internalization into E. coli cells. Co-immunoprecipitation assays with a N-terminally modified bifunctional peptide that still enters the bacteria but fails to interact with the bacterial ribosome, the major target of PrAMPs, demonstrate that it actually interacts with the bacterial SC. Moreover, when compared to SC non-binding controls, this peptide induces a ten-fold higher antibacterial activity against E. coli, showing that the observed antimicrobial activity is linked to SC binding. Finally, an unmodified bifunctional compound significantly increases the survival of Drosophila melanogaster flies challenged by an E. coli infection. Our study demonstrates the potential of PrAMPs to transport antibiotics into the bacterial cytoplasm and validates the development of drugs targeting the bacterial processivity factor of Gram-negative bacteria as a promising new class of antibiotics. Bifunctional peptides targeting both the translation and the replication machineries have been developed and shown to act as new antimicrobials.![]()
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Affiliation(s)
- Christophe André
- Univ. Bordeaux, CNRS, Bordeaux INP, CBMN, UMR 5248, Institut Européen de Chimie et Biologie 2 rue Robert Escarpit F-33607 Pessac France
| | - Florian Veillard
- Insect Models of Innate Immunity, UPR 9022-CNRS, Institut de Biologie Moléculaire et Cellulaire 67000 Strasbourg France
| | - Philippe Wolff
- CNRS, Architecture et Réactivité de l'ARN, UPR 9002, Institut de Biologie Moléculaire et Cellulaire 67000 Strasbourg France
| | - Anne-Marie Lobstein
- CNRS, Architecture et Réactivité de l'ARN, UPR 9002, Institut de Biologie Moléculaire et Cellulaire 67000 Strasbourg France
| | - Guillaume Compain
- Univ. Bordeaux, CNRS, Bordeaux INP, CBMN, UMR 5248, Institut Européen de Chimie et Biologie 2 rue Robert Escarpit F-33607 Pessac France
| | - Clément Monsarrat
- Univ. Bordeaux, CNRS, Bordeaux INP, CBMN, UMR 5248, Institut Européen de Chimie et Biologie 2 rue Robert Escarpit F-33607 Pessac France
| | - Jean-Marc Reichhart
- Insect Models of Innate Immunity, UPR 9022-CNRS, Institut de Biologie Moléculaire et Cellulaire 67000 Strasbourg France
| | - Camille Noûs
- Laboratoire Cogitamus 1 3/4 rue Descartes 75005 Paris France
| | - Dominique Y Burnouf
- CNRS, Architecture et Réactivité de l'ARN, UPR 9002, Institut de Biologie Moléculaire et Cellulaire 67000 Strasbourg France
| | - Gilles Guichard
- Univ. Bordeaux, CNRS, Bordeaux INP, CBMN, UMR 5248, Institut Européen de Chimie et Biologie 2 rue Robert Escarpit F-33607 Pessac France
| | - Jérôme E Wagner
- Université de Strasbourg, CNRS, Biotechnologie et Signalisation Cellulaire, UMR 7242, Ecole Supérieure de Biotechnologie de Strasbourg 67400 Illkirch France
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58
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Zhu Y, Weisshaar JC, Mustafi M. Long-term effects of the proline-rich antimicrobial peptide Oncocin112 on the Escherichia coli translation machinery. J Biol Chem 2020; 295:13314-13325. [PMID: 32727850 DOI: 10.1074/jbc.ra120.013587] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Revised: 07/23/2020] [Indexed: 11/06/2022] Open
Abstract
Proline-rich antimicrobial peptides (PrAMPs) are cationic antimicrobial peptides unusual for their ability to penetrate bacterial membranes and kill cells without causing membrane permeabilization. Structural studies show that many such PrAMPs bind deep in the peptide exit channel of the ribosome, near the peptidyl transfer center. Biochemical studies of the particular synthetic PrAMP oncocin112 (Onc112) suggest that on reaching the cytoplasm, the peptide occupies its binding site prior to the transition from initiation to the elongation phase of translation, thus blocking further initiation events. We present a superresolution fluorescence microscopy study of the long-term effects of Onc112 on ribosome, elongation factor-Tu (EF-Tu), and DNA spatial distributions and diffusive properties in intact Escherichia coli cells. The new data corroborate earlier mechanistic inferences from studies in vitro Comparisons with the diffusive behavior induced by the ribosome-binding antibiotics chloramphenicol and kasugamycin show how the specific location of each agent's ribosomal binding site affects the long-term distribution of ribosomal species between 30S and 50S subunits versus 70S polysomes. Analysis of the single-step displacements from ribosome and EF-Tu diffusive trajectories before and after Onc112 treatment suggests that the act of codon testing of noncognate ternary complexes (TCs) at the ribosomal A-site enhances the dissociation rate of such TCs from their L7/L12 tethers. Testing and rejection of noncognate TCs on a sub-ms timescale is essential to enable incorporation of the rare cognate amino acids into the growing peptide chain at a rate of ∼20 aa/s.
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Affiliation(s)
- Yanyu Zhu
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - James C Weisshaar
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Mainak Mustafi
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA.
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59
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Glaub A, Huptas C, Neuhaus K, Ardern Z. Recommendations for bacterial ribosome profiling experiments based on bioinformatic evaluation of published data. J Biol Chem 2020; 295:8999-9011. [PMID: 32385111 PMCID: PMC7335797 DOI: 10.1074/jbc.ra119.012161] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Revised: 05/05/2020] [Indexed: 02/03/2023] Open
Abstract
Ribosome profiling (RIBO-Seq) has improved our understanding of bacterial translation, including finding many unannotated genes. However, protocols for RIBO-Seq and corresponding data analysis are not yet standardized. Here, we analyzed 48 RIBO-Seq samples from nine studies of Escherichia coli K12 grown in lysogeny broth medium and particularly focused on the size-selection step. We show that for conventional expression analysis, a size range between 22 and 30 nucleotides is sufficient to obtain protein-coding fragments, which has the advantage of removing many unwanted rRNA and tRNA reads. More specific analyses may require longer reads and a corresponding improvement in rRNA/tRNA depletion. There is no consensus about the appropriate sequencing depth for RIBO-Seq experiments in prokaryotes, and studies vary significantly in total read number. Our analysis suggests that 20 million reads that are not mapping to rRNA/tRNA are required for global detection of translated annotated genes. We also highlight the influence of drug-induced ribosome stalling, which causes bias at translation start sites. The resulting accumulation of reads at the start site may be especially useful for detecting weakly expressed genes. As different methods suit different questions, it may not be possible to produce a "one-size-fits-all" ribosome profiling data set. Therefore, experiments should be carefully designed in light of the scientific questions of interest. We propose some basic characteristics that should be reported with any new RIBO-Seq data sets. Careful attention to the factors discussed should improve prokaryotic gene detection and the comparability of ribosome profiling data sets.
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Affiliation(s)
- Alina Glaub
- Chair for Microbial Ecology, Technical University of Munich, Freising, Germany
| | - Christopher Huptas
- Chair for Microbial Ecology, Technical University of Munich, Freising, Germany
| | - Klaus Neuhaus
- Chair for Microbial Ecology, Technical University of Munich, Freising, Germany; Core Facility Microbiome, ZIEL Institute for Food and Health, Technical University of Munich, Freising, Germany
| | - Zachary Ardern
- Chair for Microbial Ecology, Technical University of Munich, Freising, Germany.
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60
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Cytryńska M, Rahnamaeian M, Zdybicka-Barabas A, Dobslaff K, Züchner T, Sacheau G, Innis CA, Vilcinskas A. Proline-Rich Antimicrobial Peptides in Medicinal Maggots of Lucilia sericata Interact With Bacterial DnaK But Do Not Inhibit Protein Synthesis. Front Pharmacol 2020; 11:532. [PMID: 32390853 PMCID: PMC7194015 DOI: 10.3389/fphar.2020.00532] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Accepted: 04/06/2020] [Indexed: 11/13/2022] Open
Abstract
In the search for new antibiotics to combat multidrug-resistant microbes, insects offer a rich source of novel anti-infectives, including a remarkably diverse array of antimicrobial peptides (AMPs) with broad activity against a wide range of species. Larvae of the common green bottle fly Lucilia sericata are used for maggot debridement therapy, and their effectiveness in part reflects the large panel of AMPs they secrete into the wound. To investigate the activity of these peptides in more detail, we selected two structurally different proline rich peptides (Lser-PRP2 and Lser-PRP3) in addition to the α-helical peptide Lser-stomoxyn. We investigated the mechanism of anti-Escherichia coli action of the PRPs in vitro and found that neither of them interfered with protein synthesis but both were able to bind the bacterial chaperone DnaK and are therefore likely to inhibit protein folding. However, unlike Lser-stomoxyn that permeabilized the bacterial membrane by 1% at the low concentration (0.25 µM) neither of the PRPs alone was able to permeabilize E. coli membrane. In the presence of this Lser-stomoxyn concentration significant increase in anti-E. coli activity of Lser-PRP2 was observed, indicating that this peptide needs specific membrane permeabilizing agents to exert its antibacterial activity. We then examined the AMPs-treated bacterial surface and observed detrimental structural changes in the bacterial cell envelope in response to combined AMPs. The functional analysis of insect AMPs will help select optimal combinations for targeted antimicrobial therapy.
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Affiliation(s)
- Małgorzata Cytryńska
- Department of Immunobiology, Institute of Biological Sciences, Maria Curie-Sklodowska University, Lublin, Poland
| | - Mohammad Rahnamaeian
- Department of Bioresources, Fraunhofer Institute for Molecular Biology and Applied Ecology, Giessen, Germany
| | - Agnieszka Zdybicka-Barabas
- Department of Immunobiology, Institute of Biological Sciences, Maria Curie-Sklodowska University, Lublin, Poland
| | - Kristin Dobslaff
- Institute of Bioanalyticappll Chemistry, Faculty of Chemistry and Mineralogy and Center of Biotechnology and Biomedicine, University of Leipzig, Leipzig, Germany
| | - Thole Züchner
- Department of Bioanalytics and Laboratory automation, Faculty of Life Sciences, Albstadt-Sigmaringen University, Sigmaringen, Germany
| | - Guénaël Sacheau
- ARNA Laboratory, Inserm U1212, CNRS UMR 5320, Institut Européen de Chimie et Biologie, University of Bordeaux, Pessac, France
| | - C Axel Innis
- ARNA Laboratory, Inserm U1212, CNRS UMR 5320, Institut Européen de Chimie et Biologie, University of Bordeaux, Pessac, France
| | - Andreas Vilcinskas
- Department of Bioresources, Fraunhofer Institute for Molecular Biology and Applied Ecology, Giessen, Germany.,Institute for Insect Biotechnology, Justus-Liebig-University of Giessen, Giessen, Germany
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61
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Bam complex-mediated assembly of bacterial outer membrane proteins synthesized in an in vitro translation system. Sci Rep 2020; 10:4557. [PMID: 32165713 PMCID: PMC7067875 DOI: 10.1038/s41598-020-61431-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Accepted: 02/21/2020] [Indexed: 02/01/2023] Open
Abstract
Bacterial outer membrane proteins (OMPs) contain a unique "β barrel" segment that is inserted into the membrane by the barrel assembly machinery (Bam) complex by an unknown mechanism. OMP assembly has been reconstituted in vitro, but assembly reactions have involved the use of urea-denatured protein purified from inclusion bodies. Here we show that the E. coli Bam complex catalyzes the efficient assembly of OMPs synthesized de novo in a coupled in vitro transcription/translation system. Interestingly, the in vitro translated forms of the OMPs we analyzed were assembled more rapidly and were effectively engaged by fewer periplasmic chaperones than their urea-denatured counterparts. Taken together, our results strongly suggest that the mode of production influences the conformational states sampled by OMPs and thereby affects their recognition by both chaperones and the Bam complex. Besides providing insights into OMP biogenesis, our work describes a novel, streamlined method to reconstitute OMP assembly in vitro.
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62
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Chu Y, Huang J, Ma G, Cui T, Yan X, Li H, Wang N. An Upstream Open Reading Frame Represses Translation of Chicken PPARγ Transcript Variant 1. Front Genet 2020; 11:165. [PMID: 32184808 PMCID: PMC7058706 DOI: 10.3389/fgene.2020.00165] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Accepted: 02/12/2020] [Indexed: 11/20/2022] Open
Abstract
Peroxisome proliferator-activated receptor γ (PPARγ) is a master regulator of adipogenesis. The PPARγ gene produces various transcripts with different 5'-untranslated regions (5' UTRs) because of alternative promoter usage and splicing. The 5' UTR plays important roles in posttranscriptional gene regulation. However, to date, the regulatory role and underlying mechanism of 5' UTRs in the posttranscriptional regulation of PPARγ expression remain largely unclear. In this study, we investigated the effects of 5' UTRs on posttranscriptional regulation using reporter assays. Our results showed that the five PPARγ 5' UTRs exerted different effects on reporter gene activity. Bioinformatics analysis showed that chicken PPARγ transcript 1 (PPARγ1) possessed an upstream open reading frame (uORF) in its 5' UTR. Mutation analysis showed that a mutation in the uORF led to increased Renilla luciferase activity and PPARγ protein expression, but decreased Renilla luciferase and PPARγ1 mRNA expression. mRNA stability analysis using real-time RT-PCR showed that the uORF mutation did not interfere with mRNA stability, but promoter activity analysis of the cloned 5' UTR showed that the uORF mutation reduced promoter activity. Furthermore, in vitro transcription/translation assays demonstrated that the uORF mutation markedly increased the translation of PPARγ1 mRNA. Collectively, our results indicate that the uORF represses the translation of chicken PPARγ1 mRNA.
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Affiliation(s)
- Yankai Chu
- Key Laboratory of Chicken Genetics and Breeding, Ministry of Agriculture and Rural Affairs, Harbin, China
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Education Department of Heilongjiang Province, Harbin, China
- College of Animal Science and Technology, Northeast Agricultural University, Harbin, China
| | - Jiaxin Huang
- Key Laboratory of Chicken Genetics and Breeding, Ministry of Agriculture and Rural Affairs, Harbin, China
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Education Department of Heilongjiang Province, Harbin, China
- College of Animal Science and Technology, Northeast Agricultural University, Harbin, China
| | - Guangwei Ma
- Key Laboratory of Chicken Genetics and Breeding, Ministry of Agriculture and Rural Affairs, Harbin, China
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Education Department of Heilongjiang Province, Harbin, China
- College of Animal Science and Technology, Northeast Agricultural University, Harbin, China
| | - Tingting Cui
- Key Laboratory of Chicken Genetics and Breeding, Ministry of Agriculture and Rural Affairs, Harbin, China
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Education Department of Heilongjiang Province, Harbin, China
- College of Animal Science and Technology, Northeast Agricultural University, Harbin, China
| | - Xiaohong Yan
- Key Laboratory of Chicken Genetics and Breeding, Ministry of Agriculture and Rural Affairs, Harbin, China
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Education Department of Heilongjiang Province, Harbin, China
- College of Animal Science and Technology, Northeast Agricultural University, Harbin, China
| | - Hui Li
- Key Laboratory of Chicken Genetics and Breeding, Ministry of Agriculture and Rural Affairs, Harbin, China
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Education Department of Heilongjiang Province, Harbin, China
- College of Animal Science and Technology, Northeast Agricultural University, Harbin, China
| | - Ning Wang
- Key Laboratory of Chicken Genetics and Breeding, Ministry of Agriculture and Rural Affairs, Harbin, China
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Education Department of Heilongjiang Province, Harbin, China
- College of Animal Science and Technology, Northeast Agricultural University, Harbin, China
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63
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Herrero Del Valle A, Seip B, Cervera-Marzal I, Sacheau G, Seefeldt AC, Innis CA. Ornithine capture by a translating ribosome controls bacterial polyamine synthesis. Nat Microbiol 2020; 5:554-561. [PMID: 32094585 PMCID: PMC7250644 DOI: 10.1038/s41564-020-0669-1] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Accepted: 01/10/2020] [Indexed: 02/06/2023]
Abstract
Polyamines are essential metabolites that play an important role in cell growth, stress adaptation, and microbial virulence1–3. In order to survive and multiply within a human host, pathogenic bacteria adjust the expression and activity of polyamine biosynthetic enzymes in response to different environmental stresses and metabolic cues2. Here, we show that ornithine capture by the ribosome and the nascent peptide SpeFL controls polyamine synthesis in γ-proteobacteria by inducing the expression of the ornithine decarboxylase SpeF4, via a mechanism involving ribosome stalling and transcription antitermination. In addition, we present the cryo-EM structure of an Escherichia coli (E. coli) ribosome stalled during translation of speFL in the presence of ornithine. The structure shows how the ribosome and the SpeFL sensor domain form a highly selective binding pocket that accommodates a single ornithine molecule but excludes near-cognate ligands. Ornithine pre-associates with the ribosome and is then held in place by the sensor domain, leading to the compaction of the SpeFL effector domain and blocking the action of release factor RF1. Thus, our study not only reveals basic strategies by which nascent peptides assist the ribosome in detecting a specific metabolite, but also provides a framework for assessing how ornithine promotes virulence in several human pathogens.
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Affiliation(s)
- Alba Herrero Del Valle
- Institut Européen de Chimie et Biologie, Université de Bordeaux, Pessac, France.,Institut National de la Santé et de la Recherche Médicale (U1212), Bordeaux, France.,Centre National de la Recherche Scientifique (UMR 5320), Bordeaux, France
| | - Britta Seip
- Institut Européen de Chimie et Biologie, Université de Bordeaux, Pessac, France.,Institut National de la Santé et de la Recherche Médicale (U1212), Bordeaux, France.,Centre National de la Recherche Scientifique (UMR 5320), Bordeaux, France.,Evotec International GmbH, Göttingen, Germany
| | - Iñaki Cervera-Marzal
- Institut Européen de Chimie et Biologie, Université de Bordeaux, Pessac, France.,Institut National de la Santé et de la Recherche Médicale (U1212), Bordeaux, France.,Centre National de la Recherche Scientifique (UMR 5320), Bordeaux, France.,Aix Marseille Université, CNRS, INSERM, CIML, Centre d'Immunologie de Marseille-Luminy, Marseille, France
| | - Guénaël Sacheau
- Institut Européen de Chimie et Biologie, Université de Bordeaux, Pessac, France.,Institut National de la Santé et de la Recherche Médicale (U1212), Bordeaux, France.,Centre National de la Recherche Scientifique (UMR 5320), Bordeaux, France.,Sopra Steria, Saint-Herblain, France
| | - A Carolin Seefeldt
- Institut Européen de Chimie et Biologie, Université de Bordeaux, Pessac, France.,Institut National de la Santé et de la Recherche Médicale (U1212), Bordeaux, France.,Centre National de la Recherche Scientifique (UMR 5320), Bordeaux, France.,Department of Cell and Molecular Biology, Biomedical Center, Uppsala University, Uppsala, Sweden
| | - C Axel Innis
- Institut Européen de Chimie et Biologie, Université de Bordeaux, Pessac, France. .,Institut National de la Santé et de la Recherche Médicale (U1212), Bordeaux, France. .,Centre National de la Recherche Scientifique (UMR 5320), Bordeaux, France.
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64
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Mardirossian M, Sola R, Beckert B, Collis DWP, Di Stasi A, Armas F, Hilpert K, Wilson DN, Scocchi M. Proline-Rich Peptides with Improved Antimicrobial Activity against E. coli, K. pneumoniae, and A. baumannii. ChemMedChem 2019; 14:2025-2033. [PMID: 31692278 PMCID: PMC6973051 DOI: 10.1002/cmdc.201900465] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Revised: 10/16/2019] [Indexed: 01/08/2023]
Abstract
Proline-rich antimicrobial peptides (PrAMPs) are promising agents to combat multi-drug resistant pathogens due to a high antimicrobial activity, yet low cytotoxicity. A library of derivatives of the PrAMP Bac5(1-17) was synthesized and screened to identify which residues are relevant for its activity. In this way, we discovered that two central motifs -PIRXP- cannot be modified, while residues at N- and C- termini tolerated some variations. We found five Bac5(1-17) derivatives bearing 1-5 substitutions, with an increased number of arginine and/or tryptophan residues, exhibiting improved antimicrobial activity and broader spectrum of activity while retaining low cytotoxicity toward eukaryotic cells. Transcription/translation and bacterial membrane permeabilization assays showed that these new derivatives still retained the ability to strongly inhibit bacterial protein synthesis, but also acquired permeabilizing activity to different degrees. These new Bac5(1-17) derivatives therefore show a dual mode of action which could hinder the selection of bacterial resistance against these molecules.
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Affiliation(s)
| | - Riccardo Sola
- Department of Life SciencesUniversity of Trieste34128TriesteItaly
| | - Bertrand Beckert
- Institute for Biochemistry and Molecular BiologyUniversity of Hamburg20146HamburgGermany
| | | | - Adriana Di Stasi
- Department of Life SciencesUniversity of Trieste34128TriesteItaly
| | - Federica Armas
- Department of Life SciencesUniversity of Trieste34128TriesteItaly
| | - Kai Hilpert
- St GeorgesUniversity of LondonLondonSW17 0REUK
| | - Daniel N. Wilson
- Institute for Biochemistry and Molecular BiologyUniversity of Hamburg20146HamburgGermany
| | - Marco Scocchi
- Department of Life SciencesUniversity of Trieste34128TriesteItaly
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65
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Design and Characterization of a Novel Hybrid Antimicrobial Peptide OM19R Based on Oncocin and MDAP-2. Int J Pept Res Ther 2019. [DOI: 10.1007/s10989-019-09984-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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66
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Zhang D, He Y, Ye Y, Ma Y, Zhang P, Zhu H, Xu N, Liang S. Little Antimicrobial Peptides with Big Therapeutic Roles. Protein Pept Lett 2019; 26:564-578. [PMID: 30799781 DOI: 10.2174/1573406415666190222141905] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Revised: 01/24/2019] [Accepted: 01/25/2019] [Indexed: 02/05/2023]
Abstract
Antimicrobial Peptides (AMPs) are short amphipathic biological molecules generally with less than 100 amino acids. AMPs not only present high bioactivities against bacteria, fungi or protists-induced infections, but also play important roles in anticancer activity, immune response and inflammation regulation. AMPs are classified as ribosomally synthesized, non-ribosomally synthesized and post-translationally modified, non-ribosomally synthesized ones and several synthetic or semisynthetic peptides according to their synthesis with or without the involvement of ribosomes. The molecular characterization and bioactivity action mechanisms are summarized for several ribosomally synthesized AMPs and main non-ribosomally synthesized members (cyclopeptides, lipopeptides, glycopeptides, lipoglycopeptides). We also analyze challenges and new strategies to overcome drug resistance and application limitations for AMP discovery. In conclusion, the growing novel small molecular AMPs have huge therapeutic potentials of antibacterial, antiviral, anticancer and immunoregulatory bioactivities through new techniquesdriven drug discovery strategy including bioinformatics prediction, de novo rational design and biosynthesis.
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Affiliation(s)
- Dan Zhang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University / Collaborative Innovation Center for Biotherapy, Chengdu 610041, China
| | - Yu He
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University / Collaborative Innovation Center for Biotherapy, Chengdu 610041, China
| | - Yang Ye
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University / Collaborative Innovation Center for Biotherapy, Chengdu 610041, China
| | - Yanni Ma
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University / Collaborative Innovation Center for Biotherapy, Chengdu 610041, China
| | - Peng Zhang
- Department of Urinary Surgery, West China Hospital, West China Medical School, Sichuan University, Chengdu 610041, China
| | - Hongxia Zhu
- Laboratory of Cell and Molecular Biology, State Key Laboratory of Molecular Oncology, Cancer Institute & Cancer Hospital, Chinese Academy of Medical Sciences, Beijing 100034, China
| | - Ningzhi Xu
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University / Collaborative Innovation Center for Biotherapy, Chengdu 610041, China.,Laboratory of Cell and Molecular Biology, State Key Laboratory of Molecular Oncology, Cancer Institute & Cancer Hospital, Chinese Academy of Medical Sciences, Beijing 100034, China
| | - Shufang Liang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University / Collaborative Innovation Center for Biotherapy, Chengdu 610041, China
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67
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Knappe D, Schmidt R, Adermann K, Hoffmann R. Continuous Subcutaneous Delivery of Proline-Rich Antimicrobial Peptide Api137 Provides Superior Efficacy to Intravenous Administration in a Mouse Infection Model. Front Microbiol 2019; 10:2283. [PMID: 31632382 PMCID: PMC6783563 DOI: 10.3389/fmicb.2019.02283] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Accepted: 09/18/2019] [Indexed: 01/29/2023] Open
Abstract
Apidaecins are cationic, proline-rich antimicrobial peptides originally isolated from honeybees and exhibit high Gram-negative activity by inhibiting bacterial protein translation. Pharmacokinetics of apidaecin derivative Api137 was studied using single and multiple intravenous or subcutaneous injections as well as continuous subcutaneous infusion and correlated to its efficacy in a lethal murine Escherichia coli infection model. Survival rates of infected CD-1 mice were monitored and Api137 and its metabolites were quantified in plasma of uninfected CD-1 mice and Sprague Dawley rats using reversed-phase chromatography coupled online to mass spectrometry. The highest Api137 plasma levels of 23 mg/L were obtained after a single intravenous injection of 20 mg/kg body weight, which declined fast over the next 120 min (half-life time < 30 min). In contrast, continuous subcutaneous infusion of a similar dose over an hour (19.2 mg/kg/h) lead to stable plasma levels of ∼6 mg/L, which was above the minimal inhibitory concentration against E. coli ATCC 25922 (4 mg/L). The increased exposure by continuous subcutaneous administration of Api137 at 19.2 mg/kg/h over 48 h improved efficacy in the murine intraperitoneal sepsis model with survival rates of 67% over 5 days compared to 33% after intravenous and subcutaneous administration in different dosing schemes. To the best of our knowledge, continuous subcutaneous infusion using osmotic pumps was successfully utilized for delivery of an antimicrobial peptide for the first time. Additionally, the potential of apidaecin analogs as novel antibiotics is demonstrated even in a scenario where the infection site is clearly separated from the route of administration.
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Affiliation(s)
- Daniel Knappe
- Faculty of Chemistry and Mineralogy, Institute of Bioanalytical Chemistry, Leipzig University, Leipzig, Germany.,Center for Biotechnology and Biomedicine, Leipzig University, Leipzig, Germany.,AMP-Therapeutics GmbH, Leipzig, Germany
| | - Rico Schmidt
- Faculty of Chemistry and Mineralogy, Institute of Bioanalytical Chemistry, Leipzig University, Leipzig, Germany.,Center for Biotechnology and Biomedicine, Leipzig University, Leipzig, Germany
| | | | - Ralf Hoffmann
- Faculty of Chemistry and Mineralogy, Institute of Bioanalytical Chemistry, Leipzig University, Leipzig, Germany.,Center for Biotechnology and Biomedicine, Leipzig University, Leipzig, Germany
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68
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Computational screening of antimicrobial peptides for Acinetobacter baumannii. PLoS One 2019; 14:e0219693. [PMID: 31577808 PMCID: PMC6774513 DOI: 10.1371/journal.pone.0219693] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Accepted: 06/29/2019] [Indexed: 02/07/2023] Open
Abstract
Acinetobacter baumannii, has been developing resistance to even the last line of drugs. Antimicrobial peptides (AMPs) to which bacteria do not develop resistance easily may be the last hope. A few independent experimental studies have designed and studied the activity of AMPs on A. baumannii, however the number of such studies are still limited. With the goal of developing a rational approach to the screening of AMPs against A. baumannii, we carefully curated the drug activity data from 75 cationic AMPs, all measured with a similar protocol, and on the same ATCC 19606 strain. A quantitative model developed and validated with a part of the data. While the model may be used for predicting the activity of any designed AMPs, in this work, we perform an in silico screening for the entire database of naturally occurring AMPs, to provide a rational guidance in this urgently needed drug development.
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69
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Zinshteyn B, Chan D, England W, Feng C, Green R, Spitale RC. Assaying RNA structure with LASER-Seq. Nucleic Acids Res 2019; 47:43-55. [PMID: 30476193 PMCID: PMC6326810 DOI: 10.1093/nar/gky1172] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Accepted: 11/17/2018] [Indexed: 01/06/2023] Open
Abstract
Chemical probing methods are crucial to our understanding of the structure and function of RNA molecules. The majority of chemical methods used to probe RNA structure report on Watson–Crick pairing, but tertiary structure parameters such as solvent accessibility can provide an additional layer of structural information, particularly in RNA-protein complexes. Herein we report the development of Light Activated Structural Examination of RNA by high-throughput sequencing, or LASER-Seq, for measuring RNA structure in cells with deep sequencing. LASER relies on a light-generated nicotinoyl nitrenium ion to form covalent adducts with the C8 position of adenosine and guanosine. Reactivity is governed by the accessibility of C8 to the light-generated probe. We compare structure probing by RT-stop and mutational profiling (MaP), demonstrating that LASER can be integrated with both platforms for RNA structure analyses. We find that LASER reactivity correlates with solvent accessibility across the entire ribosome, and that LASER can be used to rapidly survey for ligand binding sites in an unbiased fashion. LASER has a particular advantage in this last application, as it readily modifies paired nucleotides, enabling the identification of binding sites and conformational changes in highly structured RNA.
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Affiliation(s)
- Boris Zinshteyn
- Department of Molecular Biology and Genetics, Johns Hopkins University. Baltimore, MD 21205, USA
| | - Dalen Chan
- Department of Pharmaceutical Sciences, University of California, Irvine, Irvine, CA 92697, USA
| | - Whitney England
- Department of Pharmaceutical Sciences, University of California, Irvine, Irvine, CA 92697, USA
| | - Chao Feng
- Department of Pharmaceutical Sciences, University of California, Irvine, Irvine, CA 92697, USA
| | - Rachel Green
- Department of Molecular Biology and Genetics, Johns Hopkins University. Baltimore, MD 21205, USA.,Howard Hughes Medical Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Robert C Spitale
- Department of Pharmaceutical Sciences, University of California, Irvine, Irvine, CA 92697, USA.,Department of Chemistry, University of California, Irvine, Irvine, CA 92697, USA
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70
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Large-Scale Analyses of Human Microbiomes Reveal Thousands of Small, Novel Genes. Cell 2019; 178:1245-1259.e14. [PMID: 31402174 DOI: 10.1016/j.cell.2019.07.016] [Citation(s) in RCA: 135] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Revised: 05/06/2019] [Accepted: 07/11/2019] [Indexed: 12/12/2022]
Abstract
Small proteins are traditionally overlooked due to computational and experimental difficulties in detecting them. To systematically identify small proteins, we carried out a comparative genomics study on 1,773 human-associated metagenomes from four different body sites. We describe >4,000 conserved protein families, the majority of which are novel; ∼30% of these protein families are predicted to be secreted or transmembrane. Over 90% of the small protein families have no known domain and almost half are not represented in reference genomes. We identify putative housekeeping, mammalian-specific, defense-related, and protein families that are likely to be horizontally transferred. We provide evidence of transcription and translation for a subset of these families. Our study suggests that small proteins are highly abundant and those of the human microbiome, in particular, may perform diverse functions that have not been previously reported.
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71
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Peng S, Yang M, Sun RN, Liu Y, Wang W, Xi Q, Gong H, Chen C. Mechanism of actions of Oncocin, a proline-rich antimicrobial peptide, in early elongation revealed by single-molecule FRET. Protein Cell 2019; 9:890-895. [PMID: 29256010 PMCID: PMC6160386 DOI: 10.1007/s13238-017-0495-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
Affiliation(s)
- Sijia Peng
- School of Life Sciences, Tsinghua University, Beijing, 100084, China.,Tsinghua-Peking Joint Center for Life Sciences, Tsinghua University, Beijing, 100084, China.,Beijing Advanced Innovation Center for Structural Biology, Tsinghua University, Beijing, 100084, China
| | - Mengyi Yang
- School of Life Sciences, Tsinghua University, Beijing, 100084, China.,Tsinghua-Peking Joint Center for Life Sciences, Tsinghua University, Beijing, 100084, China.,Beijing Advanced Innovation Center for Structural Biology, Tsinghua University, Beijing, 100084, China
| | - Rui Ning Sun
- School of Life Sciences, Tsinghua University, Beijing, 100084, China.,Beijing Advanced Innovation Center for Structural Biology, Tsinghua University, Beijing, 100084, China.,MOE Key Laboratory of Bioinformatics, Tsinghua University, Beijing, 100084, China
| | - Yang Liu
- School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Wenjuan Wang
- School of Life Sciences, Tsinghua University, Beijing, 100084, China.,Technology Center for Protein Sciences, Tsinghua University, Beijing, 100084, China
| | - Qiaoran Xi
- School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Haipeng Gong
- School of Life Sciences, Tsinghua University, Beijing, 100084, China.,Beijing Advanced Innovation Center for Structural Biology, Tsinghua University, Beijing, 100084, China.,MOE Key Laboratory of Bioinformatics, Tsinghua University, Beijing, 100084, China
| | - Chunlai Chen
- School of Life Sciences, Tsinghua University, Beijing, 100084, China. .,Tsinghua-Peking Joint Center for Life Sciences, Tsinghua University, Beijing, 100084, China. .,Beijing Advanced Innovation Center for Structural Biology, Tsinghua University, Beijing, 100084, China.
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72
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Lai PK, Tresnak DT, Hackel BJ. Identification and elucidation of proline-rich antimicrobial peptides with enhanced potency and delivery. Biotechnol Bioeng 2019; 116:2439-2450. [PMID: 31209863 DOI: 10.1002/bit.27092] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2019] [Revised: 06/04/2019] [Accepted: 06/09/2019] [Indexed: 01/06/2023]
Abstract
Proline-rich antimicrobial peptides (PrAMPs) kill bacteria via a nonlytic mechanism in which they permeate through the outer membrane, utilize protein-mediated transport across the inner membrane, and target the ribosome to inhibit protein synthesis. We previously reported that substitutions of oncocin ( VDKPPYLPRPRPPRRIYNR - NH 2 ) with a pair of cationic residues improved the antimicrobial activity. In this study, we applied the design protocol to three other PrAMPs: apidaecin-1b, pyrrhocoricin, and bactenecin 7(1-16) and found that the substitutions (R4K and I8K/R) for apidaecin-1b improve the activity by twofold (p < .05) against nonpathogenic Escherichia coli. Moreover, the substitutions (L7K/R and R14K) for pyrrhocoricin improve the activity by 2-10-fold (p < .05) against some strains of E. coli and Salmonella Typhimurium. We also performed activity tests against inner membrane protein (SbmA or YgdD) knockout strains. The result is consistent with previous studies that SbmA is the major transporter for apidaecin-1b and pyrrhocoricin derivatives. However, bactenecin 7(1-16) functions independently of these transporters. In addition, several apidaecin-1b derivatives exhibit enhanced activity relative to wild-type only in the absence of SbmA, which is consistent with mutations that enhance transport across the inner membrane. A high performance liquid chromatography-based kinetic assay for cellular association and internalization demonstrates that the selected cationic mutations can improve cellular association in minimal media, but this enhanced association is not required for increased activity, which suggests the importance of inner membrane transport. These functional studies on cationic mutants of PrAMPs advance understanding of potency and mechanism and advance the ability to engineer improved antimicrobials as evidenced by the identification of the pyrrhocoricin mutant (L7R and R14K) with 10-fold elevated potency against pathogenic E. coli.
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Affiliation(s)
- Pin-Kuang Lai
- Department of Chemical Engineering and Materials Science, University of Minnesota, Minneapolis, Minnesota
| | - Daniel T Tresnak
- Department of Chemical Engineering and Materials Science, University of Minnesota, Minneapolis, Minnesota
| | - Benjamin J Hackel
- Department of Chemical Engineering and Materials Science, University of Minnesota, Minneapolis, Minnesota
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73
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Kaspar JR, Walker AR. Expanding the Vocabulary of Peptide Signals in Streptococcus mutans. Front Cell Infect Microbiol 2019; 9:194. [PMID: 31245303 PMCID: PMC6563777 DOI: 10.3389/fcimb.2019.00194] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Accepted: 05/21/2019] [Indexed: 12/18/2022] Open
Abstract
Streptococci, including the dental pathogen Streptococcus mutans, undergo cell-to-cell signaling that is mediated by small peptides to control critical physiological functions such as adaptation to the environment, control of subpopulation behaviors and regulation of virulence factors. One such model pathway is the regulation of genetic competence, controlled by the ComRS signaling system and the peptide XIP. However, recent research in the characterization of this pathway has uncovered novel operons and peptides that are intertwined into its regulation. These discoveries, such as cell lysis playing a critical role in XIP release and importance of bacterial self-sensing during the signaling process, have caused us to reevaluate previous paradigms and shift our views on the true purpose of these signaling systems. The finding of new peptides such as the ComRS inhibitor XrpA and the peptides of the RcrRPQ operon also suggests there may be more peptides hidden in the genomes of streptococci that could play critical roles in the physiology of these organisms. In this review, we summarize the recent findings in S. mutans regarding the integration of other circuits into the ComRS signaling pathway, the true mode of XIP export, and how the RcrRPQ operon controls competence activation. We also look at how new technologies can be used to re-annotate the genome to find new open reading frames that encode peptide signals. Together, this summary of research will allow us to reconsider how we perceive these systems to behave and lead us to expand our vocabulary of peptide signals within the genus Streptococcus.
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Affiliation(s)
- Justin R. Kaspar
- Department of Oral Biology, University of Florida, Gainesville, FL, United States
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74
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Holfeld L, Knappe D, Hoffmann R. Proline-rich antimicrobial peptides show a long-lasting post-antibiotic effect on Enterobacteriaceae and Pseudomonas aeruginosa. J Antimicrob Chemother 2019; 73:933-941. [PMID: 29309652 DOI: 10.1093/jac/dkx482] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2017] [Accepted: 11/21/2017] [Indexed: 01/28/2023] Open
Abstract
Background Proline-rich antimicrobial peptides (PrAMPs) represent a promising class of potential therapeutics to treat multiresistant infections. They inhibit bacterial protein translation at the 70S ribosome by either blocking the peptide-exit tunnel (oncocin type) or trapping release factors (apidaecin type). Objectives Besides direct concentration-dependent antibacterial effects, the post-antibiotic effect (PAE) is the second most important criterion of antimicrobial pharmacodynamics to be determined in vitro. Here, PAEs of 10 PrAMPs and three antibiotics against three Escherichia coli strains, Klebsiella pneumoniae ATCC 10031 and Pseudomonas aeruginosa ATCC 27853 were studied after 1 h of exposure. Methods A robust high-throughput screening to determine PAEs was established, i.e. liquid handling by a 96-channel pipetting system and continuous incubation and absorbance measurement in a microplate reader. Results Prolonged PAEs (≥4 h) were detected for all peptides at their MIC values against all strains; PAEs were even >10 h for Api88, Api137, Bac7(1-60) and A3-APO. The PAEs increased further at 4 × MIC. Aminoglycosides gentamicin and kanamycin usually showed lower PAEs (≤4 h) at MIC, but PAEs increased to > 10 h at 4 × MIC. Bacteriostatic chloramphenicol exhibited the shortest PAEs (<4 h). Conclusions The PAEs of PrAMPs studied against Enterobacteriaceae and P. aeruginosa for the first time were typically 4-fold stronger than for conventional antibiotics. Together with their fast and irreversible uptake by bacteria, the observed prolonged PAE of PrAMPs helps to explain their high in vivo efficacy despite unfavourable pharmacokinetics.
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Affiliation(s)
- Luzia Holfeld
- Institute of Bioanalytical Chemistry, Faculty of Chemistry and Mineralogy, Universität Leipzig, Deutscher Platz 5, Leipzig, Germany.,Center for Biotechnology and Biomedicine, Universität Leipzig, Deutscher Platz 5, Leipzig, Germany
| | - Daniel Knappe
- Institute of Bioanalytical Chemistry, Faculty of Chemistry and Mineralogy, Universität Leipzig, Deutscher Platz 5, Leipzig, Germany.,Center for Biotechnology and Biomedicine, Universität Leipzig, Deutscher Platz 5, Leipzig, Germany
| | - Ralf Hoffmann
- Institute of Bioanalytical Chemistry, Faculty of Chemistry and Mineralogy, Universität Leipzig, Deutscher Platz 5, Leipzig, Germany.,Center for Biotechnology and Biomedicine, Universität Leipzig, Deutscher Platz 5, Leipzig, Germany
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75
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Weaver J, Mohammad F, Buskirk AR, Storz G. Identifying Small Proteins by Ribosome Profiling with Stalled Initiation Complexes. mBio 2019; 10:e02819-18. [PMID: 30837344 PMCID: PMC6401488 DOI: 10.1128/mbio.02819-18] [Citation(s) in RCA: 108] [Impact Index Per Article: 21.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2018] [Accepted: 01/24/2019] [Indexed: 11/20/2022] Open
Abstract
Small proteins consisting of 50 or fewer amino acids have been identified as regulators of larger proteins in bacteria and eukaryotes. Despite the importance of these molecules, the total number of small proteins remains unknown because conventional annotation pipelines usually exclude small open reading frames (smORFs). We previously identified several dozen small proteins in the model organism Escherichia coli using theoretical bioinformatic approaches based on sequence conservation and matches to canonical ribosome binding sites. Here, we present an empirical approach for discovering new proteins, taking advantage of recent advances in ribosome profiling in which antibiotics are used to trap newly initiated 70S ribosomes at start codons. This approach led to the identification of many novel initiation sites in intergenic regions in E. coli We tagged 41 smORFs on the chromosome and detected protein synthesis for all but three. Not only are the corresponding genes intergenic but they are also found antisense to other genes, in operons, and overlapping other open reading frames (ORFs), some impacting the translation of larger downstream genes. These results demonstrate the utility of this method for identifying new genes, regardless of their genomic context.IMPORTANCE Proteins comprised of 50 or fewer amino acids have been shown to interact with and modulate the functions of larger proteins in a range of organisms. Despite the possible importance of small proteins, the true prevalence and capabilities of these regulators remain unknown as the small size of the proteins places serious limitations on their identification, purification, and characterization. Here, we present a ribosome profiling approach with stalled initiation complexes that led to the identification of 38 new small proteins.
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Affiliation(s)
- Jeremy Weaver
- Division of Molecular and Cellular Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, Maryland, USA
| | - Fuad Mohammad
- Department of Molecular Biology and Genetics, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
| | - Allen R Buskirk
- Department of Molecular Biology and Genetics, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
| | - Gisela Storz
- Division of Molecular and Cellular Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, Maryland, USA
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76
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Ho PL, Ong HK, Teo J, Ow DSW, Chao SH. HEXIM1 Peptide Exhibits Antimicrobial Activity Against Antibiotic Resistant Bacteria Through Guidance of Cell Penetrating Peptide. Front Microbiol 2019; 10:203. [PMID: 30800117 PMCID: PMC6376162 DOI: 10.3389/fmicb.2019.00203] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2018] [Accepted: 01/24/2019] [Indexed: 12/16/2022] Open
Abstract
The emergence of antibiotic resistant bacteria is one of the biggest threats to human health worldwide. In 2017, World Health Organization listed the world’s most dangerous antibiotic-resistant bacteria or “superbugs,” such as carbapenem-resistant Pseudomonas aeruginosa and Escherichia coli, indicating the highest priority needs for new antibiotics. The possibility that such infectious diseases may soon be untreatable, due to decreased antibiotic efficacy, creates an urgent need for novel and alternative antimicrobials. Antimicrobial peptides are naturally occurring small molecules found in the innate immunity of mammals, plants and bacteria, and are potentially therapeutic candidates against drug-resistant bacteria. In this study, we examine the antimicrobial activities of the cytotoxic peptides derived from the basic region (BR) of the human hexamethylene bisacetamide-inducible protein 1 (HEXIM1). We found that, when fused with a cell penetrating peptide, the HEXIM1 BR peptide and its derivative, BR-RRR12, exhibited inhibitory activities against selected “superbugs.” Negligible effects on the viability of human keratinocyte cell line were observed when the bactericidal dosages of HEXIM1 BR peptides were used. Different killing kinetics were observed between the membrane permeabilizing antimicrobial peptides and HEXIM1 BR peptides, suggesting that a different antimicrobial mechanism might be utilized by the HEXIM1 BR peptides. Using an in vitro translation system based on E. coli lysates, we found that HEXIM1 BR peptides blocked bacterial translation. Taken together, we identify the HEXIM1 BR peptide as a novel antimicrobial peptide with potent inhibitory activity against antibiotic-resistant “superbugs.”
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Affiliation(s)
- Pooi Leng Ho
- Microbial Cells, Bioprocessing Technology Institute, Agency for Science, Technology and Research, Singapore, Singapore
| | - Han Kee Ong
- Expression Engineering Groups, Bioprocessing Technology Institute, Agency for Science, Technology and Research, Singapore, Singapore
| | - Jeanette Teo
- Department of Laboratory Medicine, National University Hospital, Singapore, Singapore
| | - Dave Siak-Wei Ow
- Microbial Cells, Bioprocessing Technology Institute, Agency for Science, Technology and Research, Singapore, Singapore
| | - Sheng-Hao Chao
- Expression Engineering Groups, Bioprocessing Technology Institute, Agency for Science, Technology and Research, Singapore, Singapore.,Department of Microbiology and Immunology, National University of Singapore, Singapore, Singapore
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77
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Mardirossian M, Sola R, Degasperi M, Scocchi M. Search for Shorter Portions of the Proline‐Rich Antimicrobial Peptide Fragment Bac5(1–25) That Retain Antimicrobial Activity by Blocking Protein Synthesis. ChemMedChem 2019; 14:343-348. [DOI: 10.1002/cmdc.201800734] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Revised: 01/03/2019] [Indexed: 12/18/2022]
Affiliation(s)
- Mario Mardirossian
- Department of Life SciencesUniversity of Trieste Via Licio Giorgieri 5 34127 Trieste Italy
| | - Riccardo Sola
- Department of Life SciencesUniversity of Trieste Via Licio Giorgieri 5 34127 Trieste Italy
| | - Margherita Degasperi
- Department of Life SciencesUniversity of Trieste Via Licio Giorgieri 5 34127 Trieste Italy
| | - Marco Scocchi
- Department of Life SciencesUniversity of Trieste Via Licio Giorgieri 5 34127 Trieste Italy
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78
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Charon J, Manteca A, Innis CA. Using the Bacterial Ribosome as a Discovery Platform for Peptide-Based Antibiotics. Biochemistry 2019; 58:75-84. [PMID: 30372045 PMCID: PMC7615898 DOI: 10.1021/acs.biochem.8b00927] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
The threat of bacteria resistant to multiple antibiotics poses a major public health problem requiring immediate and coordinated action worldwide. While infectious pathogens have become increasingly resistant to commercially available drugs, antibiotic discovery programs in major pharmaceutical companies have produced no new antibiotic scaffolds in 40 years. As a result, new strategies must be sought to obtain a steady supply of novel scaffolds capable of countering the spread of resistance. The bacterial ribosome is a major target for antimicrobials and is inhibited by more than half of the antibiotics used today. Recent studies showing that the ribosome is a target for several classes of ribosomally synthesized antimicrobial peptides point to ribosome-targeting peptides as a promising source of antibiotic scaffolds. In this Perspective, we revisit the current paradigm of antibiotic discovery by proposing that the bacterial ribosome can be used both as a target and as a tool for the production and selection of peptide-based antimicrobials. Turning the ribosome into a high-throughput platform for the directed evolution of peptide-based antibiotics could be achieved in different ways. One possibility would be to use a combination of state-of-the-art microfluidics and genetic reprogramming techniques, which we will review briefly. If it is successful, this strategy has the potential to produce new classes of antibiotics for treating multi-drug-resistant pathogens.
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Affiliation(s)
- Justine Charon
- Institut Européen de Chimie et Biologie, Univ. Bordeaux, Institut National de la Santé et de la Recherche Médicale (U1212) and Centre National de la Recherche Scientifique (UMR 5320), Pessac 33607, France
| | - Aitor Manteca
- Institut Européen de Chimie et Biologie, Univ. Bordeaux, Institut National de la Santé et de la Recherche Médicale (U1212) and Centre National de la Recherche Scientifique (UMR 5320), Pessac 33607, France
| | - C. Axel Innis
- Institut Européen de Chimie et Biologie, Univ. Bordeaux, Institut National de la Santé et de la Recherche Médicale (U1212) and Centre National de la Recherche Scientifique (UMR 5320), Pessac 33607, France
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79
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Odilorhabdins, Antibacterial Agents that Cause Miscoding by Binding at a New Ribosomal Site. Mol Cell 2019; 70:83-94.e7. [PMID: 29625040 DOI: 10.1016/j.molcel.2018.03.001] [Citation(s) in RCA: 73] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2017] [Revised: 02/01/2018] [Accepted: 02/28/2018] [Indexed: 12/31/2022]
Abstract
Growing resistance of pathogenic bacteria and shortage of antibiotic discovery platforms challenge the use of antibiotics in the clinic. This threat calls for exploration of unconventional sources of antibiotics and identification of inhibitors able to eradicate resistant bacteria. Here we describe a different class of antibiotics, odilorhabdins (ODLs), produced by the enzymes of the non-ribosomal peptide synthetase gene cluster of the nematode-symbiotic bacterium Xenorhabdus nematophila. ODLs show activity against Gram-positive and Gram-negative pathogens, including carbapenem-resistant Enterobacteriaceae, and can eradicate infections in animal models. We demonstrate that the bactericidal ODLs interfere with protein synthesis. Genetic and structural analyses reveal that ODLs bind to the small ribosomal subunit at a site not exploited by current antibiotics. ODLs induce miscoding and promote hungry codon readthrough, amino acid misincorporation, and premature stop codon bypass. We propose that ODLs' miscoding activity reflects their ability to increase the affinity of non-cognate aminoacyl-tRNAs to the ribosome.
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80
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Jeon H, Le MT, Ahn B, Cho HS, Le VCQ, Yum J, Hong K, Kim JH, Song H, Park C. Copy number variation of PR-39 cathelicidin, and identification of PR-35, a natural variant of PR-39 with reduced mammalian cytotoxicity. Gene 2019; 692:88-93. [PMID: 30641213 DOI: 10.1016/j.gene.2018.12.065] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2018] [Revised: 12/12/2018] [Accepted: 12/30/2018] [Indexed: 01/10/2023]
Abstract
Proline-arginine-rich (PR)-39 is neutrophil antimicrobial peptide that has potent antimicrobial activity against a broad spectrum of microorganisms, including bacteria, fungi, and some enveloped viruses as a part of the innate immune system. We analyzed the nucleotide sequence variations of PR-39 exon 4, which is the mature peptide region responsible for antimicrobial activity, from 48 pigs of six breeds using sequence-based typing. The analysis identified four alleles including allele PR-35 with a 12-bp deletion near the N-terminus. Interestingly, 16.7% of individuals showed the presence of three alleles per individual, but only in the Berkshire and Duroc breeds. We further analyzed the genetic diversity of PR-39 for the entire genomic region of the gene from PR-39 exon 1 to the 3' untranslated region for different alleles by PCR amplification and cloning. The antimicrobial activity of chemically synthesized PR-35 was similar to that of PR-39, but the level of mammalian cell cytotoxicity was lower than the wild type. Better knowledge of the genetic diversity of PR-39 among different individuals and breeds may contribute to improved immune defense of pigs. PR-35, as a natural antimicrobial peptide variant, could be an interesting candidate for the development of peptide antibiotics.
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Affiliation(s)
- Hyoim Jeon
- Department of Stem Cell and Regenerative Biotechnology, Konkuk University, Seoul 05029, Republic of Korea
| | - Minh Thong Le
- Department of Stem Cell and Regenerative Biotechnology, Konkuk University, Seoul 05029, Republic of Korea
| | - Byeongyong Ahn
- Department of Stem Cell and Regenerative Biotechnology, Konkuk University, Seoul 05029, Republic of Korea
| | - Hye-Sun Cho
- Department of Stem Cell and Regenerative Biotechnology, Konkuk University, Seoul 05029, Republic of Korea
| | - Van Chanh Quy Le
- Department of Stem Cell and Regenerative Biotechnology, Konkuk University, Seoul 05029, Republic of Korea
| | - Joori Yum
- Department of Stem Cell and Regenerative Biotechnology, Konkuk University, Seoul 05029, Republic of Korea
| | - Kwonho Hong
- Department of Stem Cell and Regenerative Biotechnology, Konkuk University, Seoul 05029, Republic of Korea
| | - Jin-Hoi Kim
- Department of Stem Cell and Regenerative Biotechnology, Konkuk University, Seoul 05029, Republic of Korea
| | - Hyuk Song
- Department of Stem Cell and Regenerative Biotechnology, Konkuk University, Seoul 05029, Republic of Korea
| | - Chankyu Park
- Department of Stem Cell and Regenerative Biotechnology, Konkuk University, Seoul 05029, Republic of Korea.
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81
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Intracellular Antimicrobial Peptides Targeting the Protein Synthesis Machinery. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1117:73-89. [PMID: 30980354 DOI: 10.1007/978-981-13-3588-4_6] [Citation(s) in RCA: 57] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
While antimicrobial peptides (AMPs) are well-known for their disruptive effects on bacterial membranes, the mechanism of many intracellular AMPs is still being elucidated. In the recent years, it has been demonstrated that the subclass of proline-rich AMPs (PrAMPs) can pass through the bacterial membrane and kill bacteria by inhibiting protein synthesis. PrAMPs are a product of the innate immune system and are secreted in response to bacterial infection. So far PrAMPs have been identified in many arthropods, such as beetles, wasps, and flies, as well as some mammals, such as sheep, cows, and goats. PrAMPs show high potency against Gram-negative bacteria, while exhibiting low toxicity in eukaryotes, suggesting that they may represent a promising avenue for the development of future antimicrobial agents to combat the increase of multidrug-resistant bacterial pathogens. Structural and biochemical data have revealed the PrAMP binding sites on the ribosome as well as insight into their mechanisms of action. While the binding site of all so far investigated PrAMPs is situated within nascent polypeptide exit tunnel, the mechanism of action is distinct between class I and II PrAMPs. Specifically, class I PrAMPs, such as Bac7, Onc112, pyrrhocoricin, and metalnikowin, block the delivery of aa-tRNA by EF-Tu to the ribosomal A-site, whereas the class II PrAMPs, such as apidaecin 1b and Api137, act during translation termination and inhibit protein synthesis by trapping of release factors on the 70S ribosome following hydrolysis of the nascent polypeptide chain.
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82
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Lai PK, Geldart K, Ritter S, Kaznessis YN, Hackel BJ. Systematic Mutagenesis of Oncocin Reveals Enhanced Activity and Insights into the Mechanisms of Antimicrobial Activity. MOLECULAR SYSTEMS DESIGN & ENGINEERING 2018; 3:930-941. [PMID: 31105969 PMCID: PMC6519479 DOI: 10.1039/c8me00051d] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Oncocin is a proline-rich antimicrobial peptide that inhibits protein synthesis by binding to the bacterial ribosome. In this work, the antimicrobial activity of oncocin was improved by systematic peptide mutagenesis and activity evaluation. We found that a pair of cationic substitutions (P4K and L7K/R) improves the activity by 2-4 fold (p<0.05) against multiple Gram-negative bacteria. An in vitro transcription / translation assay indicated that the increased activity was not because of stronger ribosome binding. Rather a cellular internalization assay revealed a higher internalization rate for the optimized analogs thereby suggesting a mechanism to increase potency. In addition, we found that the optimized peptides' benefit is dependent upon nutrient-depleted media conditions. The molecular design and characterization strategies have broad potential for development of antimicrobial peptides.
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Affiliation(s)
- Pin-Kuang Lai
- Department of Chemical Engineering and Materials Science, University of Minnesota - Twin Cities, Minneapolis, MN 55455, USA
| | - Kathryn Geldart
- Department of Chemical Engineering and Materials Science, University of Minnesota - Twin Cities, Minneapolis, MN 55455, USA
| | - Seth Ritter
- Department of Chemical Engineering and Materials Science, University of Minnesota - Twin Cities, Minneapolis, MN 55455, USA
| | - Yiannis N Kaznessis
- Department of Chemical Engineering and Materials Science, University of Minnesota - Twin Cities, Minneapolis, MN 55455, USA
| | - Benjamin J Hackel
- Department of Chemical Engineering and Materials Science, University of Minnesota - Twin Cities, Minneapolis, MN 55455, USA
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83
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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
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84
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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.
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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
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85
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Fragments of the Nonlytic Proline-Rich Antimicrobial Peptide Bac5 Kill Escherichia coli Cells by Inhibiting Protein Synthesis. Antimicrob Agents Chemother 2018; 62:AAC.00534-18. [PMID: 29844040 DOI: 10.1128/aac.00534-18] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2018] [Accepted: 05/19/2018] [Indexed: 11/20/2022] Open
Abstract
Unlike most antimicrobial peptides (AMPs), the main mode of action of the subclass of proline-rich antimicrobial peptides (PrAMPs) is not based on disruption of the bacterial membrane. Instead, PrAMPs exploit the inner membrane transporters SbmA and YjiL/MdtM to pass through the bacterial membrane and enter the cytosol of specific Gram-negative bacteria, where they exert an inhibitory effect on protein synthesis. Despite sharing a high proline and arginine content with other characterized PrAMPs, the PrAMP Bac5 has a low sequence identity with them. Here we investigated the mode of action of three N-terminal Bac5 fragments, Bac5(1-15), Bac5(1-25), and Bac5(1-31). We show that Bac5(1-25) and Bac5(1-31) retained excellent antimicrobial activity toward Escherichia coli and low toxicity toward eukaryotic cells, whereas Bac5(1-15) was inactive. Bac5(1-25) and Bac5(1-31) inhibited bacterial protein synthesis in vitro and in vivo Competition assays suggested that the binding site of Bac5 is within the ribosomal tunnel, where it prevents the transition from the initiation to the elongation phase of translation, as reported for other PrAMPs, such as the bovine PrAMP Bac7. Surprisingly, unlike Bac7, Bac5(1-25) exhibited species-specific inhibition, being an excellent inhibitor of protein synthesis on E. coli ribosomes but a poor inhibitor on Thermus thermophilus ribosomes. This indicates that while Bac5 most likely has an overlapping binding site with Bac7, the mode of interaction is distinct, suggesting that Bac5 fragments may be interesting alternative lead compounds for the development of new antimicrobial agents.
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86
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Kumar A, Kuhn LT, Balbach J. A Cu 2+ complex induces the aggregation of human papillomavirus oncoprotein E6 and stabilizes p53. FEBS J 2018; 285:3013-3025. [PMID: 29931810 DOI: 10.1111/febs.14591] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Revised: 05/14/2018] [Accepted: 06/20/2018] [Indexed: 12/13/2022]
Abstract
Papillomavirus oncoprotein E6 is a critical factor in the modulation of cervical cancer in humans. At the molecular level, formation of the E6-E6AP-p53 ternary complex, which directs p53's degradation, is the key instigator of cancer transforming properties. Herein, a Cu2+ anthracenyl-terpyridine complex is described which specifically induces the aggregation of E6 in vitro and in cultured cells. For a hijacking mechanism, both E6 and E6AP are required for p53 ubiquitination and degradation. The Cu2+ complex interacts with E6 at the E6AP and p53 binding sites. We show that E6 function is suppressed by aggregation, rendering it incapable of hijacking p53 and thus increasing its cellular level. Therapeutic treatments of cervical cancer are currently unavailable to infected individuals. We anticipate that this Cu2+ complex might open up a new therapeutic avenue for the design and development of new chemical entities for the diagnosis and treatment of HPV-induced cancers.
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Affiliation(s)
- Amit Kumar
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, University of Leeds, UK.,Institute of Physics, Biophysics, Martin-Luther-University Halle-Wittenberg, Germany.,Institute of Technical Biochemistry e.V., Martin-Luther-University Halle-Wittenberg, Germany
| | - Lars T Kuhn
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, University of Leeds, UK
| | - Jochen Balbach
- Institute of Physics, Biophysics, Martin-Luther-University Halle-Wittenberg, Germany.,Institute of Technical Biochemistry e.V., Martin-Luther-University Halle-Wittenberg, Germany
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87
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Moravej H, Moravej Z, Yazdanparast M, Heiat M, Mirhosseini A, Moosazadeh Moghaddam M, Mirnejad R. Antimicrobial Peptides: Features, Action, and Their Resistance Mechanisms in Bacteria. Microb Drug Resist 2018; 24:747-767. [PMID: 29957118 DOI: 10.1089/mdr.2017.0392] [Citation(s) in RCA: 170] [Impact Index Per Article: 28.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
In recent years, because of increased resistance to conventional antimicrobials, many researchers have started to study the synthesis of new antibiotics to control the disease-causing effects of infectious pathogens. Antimicrobial peptides (AMPs) are among the newest antibiotics; these peptides are integral compounds in all kinds of organisms and play a significant role in microbial ecology, and critically contribute to the innate immunity of organisms by destroying invading microorganisms. Moreover, AMPs may encourage cells to produce chemokines, stimulate angiogenesis, accelerate wound healing, and influence programmed cell death in multicellular organisms. Bacteria differ in their inherent susceptibility and resistance mechanisms to these peptides when responding to the antimicrobial effects of AMPs. Generally, the development of AMP resistance mechanisms is driven by direct competition between bacterial species, and host and pathogen interactions. Several studies have shown diverse mechanisms of bacterial resistance to AMPs, for example, some bacteria produce proteases and trapping proteins; some modify cell surface charge, change membrane fluidity, and activate efflux pumps; and some species make use of biofilms and exopolymers, and develop sensing systems by selective gene expression. A closer understanding of bacterial resistance mechanisms may help in developing novel therapeutic approaches for the treatment of infections caused by pathogenic organisms that are successful in developing extensive resistance to AMPs. Based on these observations, this review discusses the properties of AMPs, their targeting mechanisms, and bacterial resistance mechanisms against AMPs.
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Affiliation(s)
- Hoda Moravej
- 1 Molecular Biology Research Center, Systems Biology and Poisoning Institute, Baqiyatallah University of Medical Sciences , Tehran, Iran
| | - Zahra Moravej
- 2 Department of Hepatitis and AIDS, Pasteur Institute of Iran , Tehran, Iran
| | - Maryam Yazdanparast
- 3 Department of Pharmacology, Experimental Medicine Research Center, School of Medicine, Tehran University of Medical Sciences , Tehran, Iran
| | - Mohammad Heiat
- 4 Applied Biotechnology Research Center, Baqiyatallah University of Medical Sciences , Tehran, Iran
| | - Ali Mirhosseini
- 5 Applied Microbiology Research Center, Systems Biology and Poisoning Institute, Baqiyatallah University of Medical Sciences , Tehran, Iran
| | | | - Reza Mirnejad
- 1 Molecular Biology Research Center, Systems Biology and Poisoning Institute, Baqiyatallah University of Medical Sciences , Tehran, Iran
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88
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Mardirossian M, Pérébaskine N, Benincasa M, Gambato S, Hofmann S, Huter P, Müller C, Hilpert K, Innis CA, Tossi A, Wilson DN. The Dolphin Proline-Rich Antimicrobial Peptide Tur1A Inhibits Protein Synthesis by Targeting the Bacterial Ribosome. Cell Chem Biol 2018; 25:530-539.e7. [PMID: 29526712 PMCID: PMC6219704 DOI: 10.1016/j.chembiol.2018.02.004] [Citation(s) in RCA: 80] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2017] [Revised: 01/08/2018] [Accepted: 02/05/2018] [Indexed: 12/22/2022]
Abstract
Proline-rich antimicrobial peptides (PrAMPs) internalize into susceptible bacteria using specific transporters and interfere with protein synthesis and folding. To date, mammalian PrAMPs have so far been identified only in artiodactyls. Since cetaceans are co-phyletic with artiodactyls, we mined the genome of the bottlenose dolphin Tursiops truncatus, leading to the identification of two PrAMPs, Tur1A and Tur1B. Tur1A, which is orthologous to the bovine PrAMP Bac7, is internalized into Escherichia coli, without damaging the membranes, using the inner membrane transporters SbmA and YjiL/MdM. Furthermore, like Bac7, Tur1A also inhibits bacterial protein synthesis by binding to the ribosome and blocking the transition from the initiation to the elongation phase. By contrast, Tur1B is a poor inhibitor of protein synthesis and may utilize another mechanism of action. An X-ray structure of Tur1A bound within the ribosomal exit tunnel provides a basis to develop these peptides as novel antimicrobial agents.
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Affiliation(s)
- Mario Mardirossian
- Gene Center, Department for Biochemistry and Center for Integrated Protein Sciences, Munich (CiPSM), University of Munich, 81377 Munich, Germany
| | - Natacha Pérébaskine
- ARNA Laboratory, University of Bordeaux, Inserm U1212, CNRS UMR 5320, IECB, 33607 Pessac, France
| | - Monica Benincasa
- Antimicrobial Peptides Laboratory, Department of Life Sciences, University of Trieste, 34127 Trieste, Italy
| | - Stefano Gambato
- Antimicrobial Peptides Laboratory, Department of Life Sciences, University of Trieste, 34127 Trieste, Italy
| | - Sven Hofmann
- Institute of Infection and Immunity, St George's, University of London, SW17 0RE London, UK
| | - Paul Huter
- Gene Center, Department for Biochemistry and Center for Integrated Protein Sciences, Munich (CiPSM), University of Munich, 81377 Munich, Germany; Institute for Biochemistry and Molecular Biology, University of Hamburg, Martin-Luther-King-Platz 6, 20146 Hamburg, Germany
| | - Claudia Müller
- Gene Center, Department for Biochemistry and Center for Integrated Protein Sciences, Munich (CiPSM), University of Munich, 81377 Munich, Germany; Institute for Biochemistry and Molecular Biology, University of Hamburg, Martin-Luther-King-Platz 6, 20146 Hamburg, Germany
| | - Kai Hilpert
- Institute of Infection and Immunity, St George's, University of London, SW17 0RE London, UK
| | - C Axel Innis
- ARNA Laboratory, University of Bordeaux, Inserm U1212, CNRS UMR 5320, IECB, 33607 Pessac, France
| | - Alessandro Tossi
- Antimicrobial Peptides Laboratory, Department of Life Sciences, University of Trieste, 34127 Trieste, Italy
| | - Daniel N Wilson
- Gene Center, Department for Biochemistry and Center for Integrated Protein Sciences, Munich (CiPSM), University of Munich, 81377 Munich, Germany; Institute for Biochemistry and Molecular Biology, University of Hamburg, Martin-Luther-King-Platz 6, 20146 Hamburg, Germany.
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89
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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: 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.
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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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90
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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: 170] [Impact Index Per Article: 28.3] [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.
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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;
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91
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Zhu S, Sani M, Separovic F. Interaction of cationic antimicrobial peptides from Australian frogs with lipid membranes. Pept Sci (Hoboken) 2018. [DOI: 10.1002/pep2.24061] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Shiying Zhu
- School of ChemistryBio21 Institute, University of MelbourneMelbourne VIC3010 Australia
| | - Marc‐Antoine Sani
- School of ChemistryBio21 Institute, University of MelbourneMelbourne VIC3010 Australia
| | - Frances Separovic
- School of ChemistryBio21 Institute, University of MelbourneMelbourne VIC3010 Australia
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92
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Huter P, Arenz S, Bock LV, Graf M, Frister JO, Heuer A, Peil L, Starosta AL, Wohlgemuth I, Peske F, Nováček J, Berninghausen O, Grubmüller H, Tenson T, Beckmann R, Rodnina MV, Vaiana AC, Wilson DN. Structural Basis for Polyproline-Mediated Ribosome Stalling and Rescue by the Translation Elongation Factor EF-P. Mol Cell 2017; 68:515-527.e6. [PMID: 29100052 DOI: 10.1016/j.molcel.2017.10.014] [Citation(s) in RCA: 95] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Revised: 09/29/2017] [Accepted: 10/11/2017] [Indexed: 12/15/2022]
Abstract
Ribosomes synthesizing proteins containing consecutive proline residues become stalled and require rescue via the action of uniquely modified translation elongation factors, EF-P in bacteria, or archaeal/eukaryotic a/eIF5A. To date, no structures exist of EF-P or eIF5A in complex with translating ribosomes stalled at polyproline stretches, and thus structural insight into how EF-P/eIF5A rescue these arrested ribosomes has been lacking. Here we present cryo-EM structures of ribosomes stalled on proline stretches, without and with modified EF-P. The structures suggest that the favored conformation of the polyproline-containing nascent chain is incompatible with the peptide exit tunnel of the ribosome and leads to destabilization of the peptidyl-tRNA. Binding of EF-P stabilizes the P-site tRNA, particularly via interactions between its modification and the CCA end, thereby enforcing an alternative conformation of the polyproline-containing nascent chain, which allows a favorable substrate geometry for peptide bond formation.
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Affiliation(s)
- Paul Huter
- Gene Center, Department for Biochemistry and Center for integrated Protein Science Munich (CiPSM), University of Munich, Feodor-Lynenstr. 25, 81377 Munich, Germany
| | - Stefan Arenz
- Gene Center, Department for Biochemistry and Center for integrated Protein Science Munich (CiPSM), University of Munich, Feodor-Lynenstr. 25, 81377 Munich, Germany
| | - Lars V Bock
- Department of Theoretical and Computational Biophysics, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, Göttingen 37077, Germany
| | - Michael Graf
- Gene Center, Department for Biochemistry and Center for integrated Protein Science Munich (CiPSM), University of Munich, Feodor-Lynenstr. 25, 81377 Munich, Germany
| | - Jan Ole Frister
- Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Andre Heuer
- Gene Center, Department for Biochemistry and Center for integrated Protein Science Munich (CiPSM), University of Munich, Feodor-Lynenstr. 25, 81377 Munich, Germany
| | - Lauri Peil
- University of Tartu, Institute of Technology, Nooruse 1, 50411 Tartu, Estonia
| | - Agata L Starosta
- Gene Center, Department for Biochemistry and Center for integrated Protein Science Munich (CiPSM), University of Munich, Feodor-Lynenstr. 25, 81377 Munich, Germany
| | - Ingo Wohlgemuth
- Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Frank Peske
- Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Jiří Nováček
- Central European Institute of Technology (CEITEC), Masaryk University, Kamenice 5, 62500 Brno, Czech Republic
| | - Otto Berninghausen
- Gene Center, Department for Biochemistry and Center for integrated Protein Science Munich (CiPSM), University of Munich, Feodor-Lynenstr. 25, 81377 Munich, Germany
| | - Helmut Grubmüller
- Department of Theoretical and Computational Biophysics, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, Göttingen 37077, Germany
| | - Tanel Tenson
- University of Tartu, Institute of Technology, Nooruse 1, 50411 Tartu, Estonia
| | - Roland Beckmann
- Gene Center, Department for Biochemistry and Center for integrated Protein Science Munich (CiPSM), University of Munich, Feodor-Lynenstr. 25, 81377 Munich, Germany
| | - Marina V Rodnina
- Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Andrea C Vaiana
- Department of Theoretical and Computational Biophysics, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, Göttingen 37077, Germany
| | - Daniel N Wilson
- Gene Center, Department for Biochemistry and Center for integrated Protein Science Munich (CiPSM), University of Munich, Feodor-Lynenstr. 25, 81377 Munich, Germany; Institute for Biochemistry and Molecular Biology, University of Hamburg, Martin-Luther-King-Platz 6, 20146 Hamburg, Germany.
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93
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Metelev M, Osterman IA, Ghilarov D, Khabibullina NF, Yakimov A, Shabalin K, Utkina I, Travin DY, Komarova ES, Serebryakova M, Artamonova T, Khodorkovskii M, Konevega AL, Sergiev PV, Severinov K, Polikanov YS. Klebsazolicin inhibits 70S ribosome by obstructing the peptide exit tunnel. Nat Chem Biol 2017; 13:1129-1136. [PMID: 28846667 PMCID: PMC5701663 DOI: 10.1038/nchembio.2462] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2017] [Accepted: 07/19/2017] [Indexed: 12/19/2022]
Abstract
While screening of small-molecular metabolites produced by most cultivatable microorganisms often results in rediscovery of known compounds, genome-mining programs allow to harness much greater chemical diversity and result in discovery of new molecular scaffolds. Here we report genome-guided identification of a new antibiotic klebsazolicin (KLB) from Klebsiella pneumoniae that inhibits growth of sensitive cells by targeting ribosome. A member of ribosomally-synthesized post-translationally modified peptides (RiPPs), KLB is characterized by the presence of unique N-terminal amidine ring essential for its activity. Biochemical in vitro studies indicate that KLB inhibits ribosome by interfering with translation elongation. Structural analysis of the ribosome-KLB complex reveals the compound bound in the peptide exit tunnel overlapping with the binding sites of macrolides or streptogramins-B. KLB adopts compact conformation and largely obstructs the tunnel. Engineered KLB fragments retain in vitro activity and can serve as a starting point for the development of new bioactive compounds.
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Affiliation(s)
- Mikhail Metelev
- Research Center of Nanobiotechnologies, Peter the Great St.Petersburg Polytechnic University, St. Petersburg, Russia.,Institute of Antimicrobial Chemotherapy, Smolensk State Medical Academy, Smolensk, Russia.,Center for Data-Intensive Biomedicine and Biotechnology, Skolkovo Institute of Science and Technology, Moscow, Russia.,Institute of Gene Biology of the Russian Academy of Sciences, Moscow, Russia
| | - Ilya A Osterman
- Center for Data-Intensive Biomedicine and Biotechnology, Skolkovo Institute of Science and Technology, Moscow, Russia.,Department of Chemistry and A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Dmitry Ghilarov
- Center for Data-Intensive Biomedicine and Biotechnology, Skolkovo Institute of Science and Technology, Moscow, Russia.,Institute of Gene Biology of the Russian Academy of Sciences, Moscow, Russia
| | - Nelli F Khabibullina
- Department of Biological Sciences, University of Illinois at Chicago, Chicago, Illinois, USA
| | - Alexander Yakimov
- Research Center of Nanobiotechnologies, Peter the Great St.Petersburg Polytechnic University, St. Petersburg, Russia.,Petersburg Nuclear Physics Institute, NRC Kurchatov Institute, Gatchina, Russia
| | - Konstantin Shabalin
- Petersburg Nuclear Physics Institute, NRC Kurchatov Institute, Gatchina, Russia
| | - Irina Utkina
- Research Center of Nanobiotechnologies, Peter the Great St.Petersburg Polytechnic University, St. Petersburg, Russia.,Center for Data-Intensive Biomedicine and Biotechnology, Skolkovo Institute of Science and Technology, Moscow, Russia
| | - Dmitry Y Travin
- Department of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia
| | - Ekaterina S Komarova
- Center for Data-Intensive Biomedicine and Biotechnology, Skolkovo Institute of Science and Technology, Moscow, Russia.,Department of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia
| | - Marina Serebryakova
- Institute of Gene Biology of the Russian Academy of Sciences, Moscow, Russia.,Department of Chemistry and A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Tatyana Artamonova
- Research Center of Nanobiotechnologies, Peter the Great St.Petersburg Polytechnic University, St. Petersburg, Russia
| | - Mikhail Khodorkovskii
- Research Center of Nanobiotechnologies, Peter the Great St.Petersburg Polytechnic University, St. Petersburg, Russia
| | - Andrey L Konevega
- Research Center of Nanobiotechnologies, Peter the Great St.Petersburg Polytechnic University, St. Petersburg, Russia.,Petersburg Nuclear Physics Institute, NRC Kurchatov Institute, Gatchina, Russia
| | - Petr V Sergiev
- Center for Data-Intensive Biomedicine and Biotechnology, Skolkovo Institute of Science and Technology, Moscow, Russia.,Department of Chemistry and A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Konstantin Severinov
- Research Center of Nanobiotechnologies, Peter the Great St.Petersburg Polytechnic University, St. Petersburg, Russia.,Center for Data-Intensive Biomedicine and Biotechnology, Skolkovo Institute of Science and Technology, Moscow, Russia.,Institute of Gene Biology of the Russian Academy of Sciences, Moscow, Russia.,Waksman Institute for Microbiology, Rutgers, The State University of New Jersey, Piscataway, New Jersey, USA
| | - Yury S Polikanov
- Department of Biological Sciences, University of Illinois at Chicago, Chicago, Illinois, USA.,Department of Medicinal Chemistry and Pharmacognosy, University of Illinois at Chicago, Chicago, Illinois, USA
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94
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Myticalins: A Novel Multigenic Family of Linear, Cationic Antimicrobial Peptides from Marine Mussels (Mytilus spp.). Mar Drugs 2017. [DOI: 10.3390/md15080261 [doi link]] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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95
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Myticalins: A Novel Multigenic Family of Linear, Cationic Antimicrobial Peptides from Marine Mussels (Mytilus spp.). Mar Drugs 2017; 15:md15080261. [PMID: 28829401 PMCID: PMC5577615 DOI: 10.3390/md15080261] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2017] [Revised: 08/11/2017] [Accepted: 08/18/2017] [Indexed: 12/18/2022] Open
Abstract
The application of high-throughput sequencing technologies to non-model organisms has brought new opportunities for the identification of bioactive peptides from genomes and transcriptomes. From this point of view, marine invertebrates represent a potentially rich, yet largely unexplored resource for de novo discovery due to their adaptation to diverse challenging habitats. Bioinformatics analyses of available genomic and transcriptomic data allowed us to identify myticalins, a novel family of antimicrobial peptides (AMPs) from the mussel Mytilus galloprovincialis, and a similar family of AMPs from Modiolus spp., named modiocalins. Their coding sequence encompasses two conserved N-terminal (signal peptide) and C-terminal (propeptide) regions and a hypervariable central cationic region corresponding to the mature peptide. Myticalins are taxonomically restricted to Mytiloida and they can be classified into four subfamilies. These AMPs are subject to considerable interindividual sequence variability and possibly to presence/absence variation. Functional assays performed on selected members of this family indicate a remarkable tissue-specific expression (in gills) and broad spectrum of activity against both Gram-positive and Gram-negative bacteria. Overall, we present the first linear AMPs ever described in marine mussels and confirm the great potential of bioinformatics tools for the de novo discovery of bioactive peptides in non-model organisms.
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96
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Myticalins: A Novel Multigenic Family of Linear, Cationic Antimicrobial Peptides from Marine Mussels (Mytilus spp.). Mar Drugs 2017. [PMID: 28829401 DOI: 10.3390/md15080261+[doi+link]] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
The application of high-throughput sequencing technologies to non-model organisms has brought new opportunities for the identification of bioactive peptides from genomes and transcriptomes. From this point of view, marine invertebrates represent a potentially rich, yet largely unexplored resource for de novo discovery due to their adaptation to diverse challenging habitats. Bioinformatics analyses of available genomic and transcriptomic data allowed us to identify myticalins, a novel family of antimicrobial peptides (AMPs) from the mussel Mytilus galloprovincialis, and a similar family of AMPs from Modiolus spp., named modiocalins. Their coding sequence encompasses two conserved N-terminal (signal peptide) and C-terminal (propeptide) regions and a hypervariable central cationic region corresponding to the mature peptide. Myticalins are taxonomically restricted to Mytiloida and they can be classified into four subfamilies. These AMPs are subject to considerable interindividual sequence variability and possibly to presence/absence variation. Functional assays performed on selected members of this family indicate a remarkable tissue-specific expression (in gills) and broad spectrum of activity against both Gram-positive and Gram-negative bacteria. Overall, we present the first linear AMPs ever described in marine mussels and confirm the great potential of bioinformatics tools for the de novo discovery of bioactive peptides in non-model organisms.
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97
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Florin T, Maracci C, Graf M, Karki P, Klepacki D, Berninghausen O, Beckmann R, Vázquez-Laslop N, Wilson DN, Rodnina MV, Mankin AS. An antimicrobial peptide that inhibits translation by trapping release factors on the ribosome. Nat Struct Mol Biol 2017; 24:752-757. [PMID: 28741611 PMCID: PMC5589491 DOI: 10.1038/nsmb.3439] [Citation(s) in RCA: 105] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2017] [Accepted: 06/21/2017] [Indexed: 12/12/2022]
Abstract
Many antibiotics stop bacterial growth by inhibiting different steps of protein synthesis. However, no specific inhibitors of translation termination are known. Proline-rich antimicrobial peptides, a component of the antibacterial defense system of multicellular organisms, interfere with bacterial growth by inhibiting translation. Here we show that Api137, a derivative of the insect-produced antimicrobial peptide apidaecin, arrests terminating ribosomes using a unique mechanism of action. Api137 binds to the Escherichia coli ribosome and traps release factors 1 or 2 subsequent to release of the nascent polypeptide chain. A high-resolution cryo-EM structure of the ribosome complexed with release factor 1 and Api137 reveals the molecular interactions that lead to release factor trapping. Api137-mediated depletion of the cellular pool of free release factors causes the majority of ribosomes to stall at stop codons prior to polypeptide release, thereby resulting in a global shutdown of translation termination.
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Affiliation(s)
- Tanja Florin
- Center for Biomolecular Sciences, University of Illinois at Chicago, Chicago, Illinois, USA
| | - Cristina Maracci
- Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Michael Graf
- Gene Center, Department for Biochemistry and Center for Protein Science Munich (CiPSM), University of Munich, Munich, Germany
| | - Prajwal Karki
- Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Dorota Klepacki
- Center for Biomolecular Sciences, University of Illinois at Chicago, Chicago, Illinois, USA
| | - Otto Berninghausen
- Gene Center, Department for Biochemistry and Center for Protein Science Munich (CiPSM), University of Munich, Munich, Germany
| | - Roland Beckmann
- Gene Center, Department for Biochemistry and Center for Protein Science Munich (CiPSM), University of Munich, Munich, Germany
| | - Nora Vázquez-Laslop
- Center for Biomolecular Sciences, University of Illinois at Chicago, Chicago, Illinois, USA
| | - Daniel N Wilson
- Gene Center, Department for Biochemistry and Center for Protein Science Munich (CiPSM), University of Munich, Munich, Germany.,Institute for Biochemistry and Molecular Biology, University of Hamburg, Hamburg, Germany
| | - Marina V Rodnina
- Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Alexander S Mankin
- Center for Biomolecular Sciences, University of Illinois at Chicago, Chicago, Illinois, USA
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98
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Correlating uptake and activity of proline-rich antimicrobial peptides in Escherichia coli. Anal Bioanal Chem 2017; 409:5581-5592. [PMID: 28717895 DOI: 10.1007/s00216-017-0496-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2017] [Revised: 05/29/2017] [Accepted: 06/26/2017] [Indexed: 02/06/2023]
Abstract
Increasing death tolls accounted for by antimicrobial drug resistance demand novel antibiotic lead compounds. Among different promising candidate classes, proline-rich antimicrobial peptides (PrAMPs) are very favorable due to their intracellular mechanism, i.e., binding to the 70S ribosome and DnaK, after active uptake relying on bacterial transporters like SbmA and MdtM. Studies on peptide internalization as the first step of their complex mode of action rely typically on fluorophore or radioactive labeling and quantification using microscopy, flow cytometry, or radioactivity. Here, a liquid chromatography based assay was applied to quantify the unlabeled internalized full-length peptides and their proteolytic degradation products (metabolites) using UV absorbance and mass spectrometry. Knockout mutants lacking transporter proteins showed reduced PrAMP uptakes, explaining their reduced susceptibility against PrAMPs. Interestingly, major metabolites produced by bacterial proteases still bound to the 70S ribosome provide evidence that degradation by cytosolic proteases as a possible resistance mechanism is not very efficient. Graphical abstract The uptake of unlabeled proline-rich antimicrobial peptides (PrAMPs) is analyzed in Escherichia coli BW25113 wild-type and transporter knockout mutants ΔsbmA and BS2 (ΔsbmA yjiL::Tn10) by reversed-phase chromatography and quantified by UV detection or mass spectrometry with multi-reaction monitoring (scheme right). Internalized peptide amounts correlated to minimal inhibitory concentrations and bacterial transport activities based on the present transporter proteins (scheme left).
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Mykhailiuk PK, Kubyshkin V, Bach T, Budisa N. Peptidyl-Prolyl Model Study: How Does the Electronic Effect Influence the Amide Bond Conformation? J Org Chem 2017; 82:8831-8841. [DOI: 10.1021/acs.joc.7b00803] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Pavel K. Mykhailiuk
- Taras Shevchenko National University of Kyiv, Chemistry Department, Volodymyrska 64, 01601 Kyiv, Ukraine
- Enamine Limited, Chervonotkatska 78, 01103 Kyiv, Ukraine
| | - Vladimir Kubyshkin
- Institute
of Chemistry, Technical University of Berlin, Müller-Breslau-Strasse 10, 10623 Berlin, Germany
| | - Thorsten Bach
- Lehrstuhl
für Organische Chemie I, Technische Universität München, Lichtenbergstrasse 4, 85747 Garching, Germany
| | - Nediljko Budisa
- Institute
of Chemistry, Technical University of Berlin, Müller-Breslau-Strasse 10, 10623 Berlin, Germany
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Mishra B, Reiling S, Zarena D, Wang G. Host defense antimicrobial peptides as antibiotics: design and application strategies. Curr Opin Chem Biol 2017; 38:87-96. [PMID: 28399505 PMCID: PMC5494204 DOI: 10.1016/j.cbpa.2017.03.014] [Citation(s) in RCA: 207] [Impact Index Per Article: 29.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Revised: 03/21/2017] [Accepted: 03/22/2017] [Indexed: 12/16/2022]
Abstract
This review deals with the design and application strategies of new antibiotics based on naturally occurring antimicrobial peptides (AMPs). The initial candidate can be designed based on three-dimensional structure or selected from a library of peptides from natural or laboratory sources followed by optimization via structure-activity relationship studies. There are also advanced application strategies such as induction of AMP expression from host cells by various factors (e.g., metals, amino acids, vitamin D and sunlight), the use of engineered probiotic bacteria to deliver peptides, the design of prodrug and peptide conjugates to improve specific targeting. In addition, combined uses of newly developed AMPs with existing antimicrobial agents may provide a practical avenue for effective management of antibiotic-resistant bacteria (superbugs), including biofilms. Finally, we highlight AMPs already in use or under clinical trials.
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Affiliation(s)
- Biswajit Mishra
- Department of Pathology and Microbiology, College of Medicine, University of Nebraska Medical Center, 986495 Nebraska Medical Center, Omaha, NE 68198-6495, USA
| | - Scott Reiling
- Department of Pathology and Microbiology, College of Medicine, University of Nebraska Medical Center, 986495 Nebraska Medical Center, Omaha, NE 68198-6495, USA
| | - D Zarena
- Department of Pathology and Microbiology, College of Medicine, University of Nebraska Medical Center, 986495 Nebraska Medical Center, Omaha, NE 68198-6495, USA; Department of Physics, JNTUA College of Engineering, Anantapur 515002, India
| | - Guangshun Wang
- Department of Pathology and Microbiology, College of Medicine, University of Nebraska Medical Center, 986495 Nebraska Medical Center, Omaha, NE 68198-6495, USA.
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