Klebsazolicin inhibits 70S ribosome by obstructing the peptide exit tunnel
Abstract
Whereas screening of the small-molecule metabolites produced by most cultivatable microorganisms often results in the rediscovery of known compounds, genome-mining programs allow researchers to harness much greater chemical diversity, and result in the discovery of new molecular scaffolds. Here we report the genome-guided identification of a new antibiotic, klebsazolicin (KLB), from Klebsiella pneumoniae that inhibits the growth of sensitive cells by targeting ribosomes. A ribosomally synthesized post-translationally modified peptide (RiPP), KLB is characterized by the presence of a unique N-terminal amidine ring that is essential for its activity. Biochemical in vitro studies indicate that KLB inhibits ribosomes by interfering with translation elongation. Structural analysis of the ribosome–KLB complex showed that the compound binds in the peptide exit tunnel overlapping with the binding sites of macrolides or streptogramin-B. KLB adopts a compact conformation and largely obstructs the tunnel. Engineered KLB fragments were observed to retain in vitro activity, and thus have the potential to serve as a starting point for the development of new bioactive compounds.
- Publication Date:
- Research Org.:
- Argonne National Lab. (ANL), Argonne, IL (United States). Advanced Photon Source (APS)
- Sponsoring Org.:
- NIHFOREIGNSTATE OF ILLINOIS
- OSTI Identifier:
- 1409111
- Resource Type:
- Journal Article
- Journal Name:
- Nature Chemical Biology
- Additional Journal Information:
- Journal Volume: 13; Journal Issue: 10; Journal ID: ISSN 1552-4450
- Publisher:
- Nature Publishing Group
- Country of Publication:
- United States
- Language:
- ENGLISH
- Subject:
- 59 BASIC BIOLOGICAL SCIENCES
Citation Formats
Metelev, Mikhail, Osterman, Ilya A., Ghilarov, Dmitry, Khabibullina, Nelli F., Yakimov, Alexander, Shabalin, Konstantin, Utkina, Irina, Travin, Dmitry Y., Komarova, Ekaterina S., Serebryakova, Marina, Artamonova, Tatyana, Khodorkovskii, Mikhail, Konevega, Andrey L., Sergiev, Petr V., Severinov, Konstantin, and Polikanov, Yury S. Klebsazolicin inhibits 70S ribosome by obstructing the peptide exit tunnel. United States: N. p., 2017.
Web. doi:10.1038/nchembio.2462.
Metelev, Mikhail, Osterman, Ilya A., Ghilarov, Dmitry, Khabibullina, Nelli F., Yakimov, Alexander, Shabalin, Konstantin, Utkina, Irina, Travin, Dmitry Y., Komarova, Ekaterina S., Serebryakova, Marina, Artamonova, Tatyana, Khodorkovskii, Mikhail, Konevega, Andrey L., Sergiev, Petr V., Severinov, Konstantin, & Polikanov, Yury S. Klebsazolicin inhibits 70S ribosome by obstructing the peptide exit tunnel. United States. https://doi.org/10.1038/nchembio.2462
Metelev, Mikhail, Osterman, Ilya A., Ghilarov, Dmitry, Khabibullina, Nelli F., Yakimov, Alexander, Shabalin, Konstantin, Utkina, Irina, Travin, Dmitry Y., Komarova, Ekaterina S., Serebryakova, Marina, Artamonova, Tatyana, Khodorkovskii, Mikhail, Konevega, Andrey L., Sergiev, Petr V., Severinov, Konstantin, and Polikanov, Yury S. Mon .
"Klebsazolicin inhibits 70S ribosome by obstructing the peptide exit tunnel". United States. https://doi.org/10.1038/nchembio.2462.
@article{osti_1409111,
title = {Klebsazolicin inhibits 70S ribosome by obstructing the peptide exit tunnel},
author = {Metelev, Mikhail and Osterman, Ilya A. and Ghilarov, Dmitry and Khabibullina, Nelli F. and Yakimov, Alexander and Shabalin, Konstantin and Utkina, Irina and Travin, Dmitry Y. and Komarova, Ekaterina S. and Serebryakova, Marina and Artamonova, Tatyana and Khodorkovskii, Mikhail and Konevega, Andrey L. and Sergiev, Petr V. and Severinov, Konstantin and Polikanov, Yury S.},
abstractNote = {Whereas screening of the small-molecule metabolites produced by most cultivatable microorganisms often results in the rediscovery of known compounds, genome-mining programs allow researchers to harness much greater chemical diversity, and result in the discovery of new molecular scaffolds. Here we report the genome-guided identification of a new antibiotic, klebsazolicin (KLB), from Klebsiella pneumoniae that inhibits the growth of sensitive cells by targeting ribosomes. A ribosomally synthesized post-translationally modified peptide (RiPP), KLB is characterized by the presence of a unique N-terminal amidine ring that is essential for its activity. Biochemical in vitro studies indicate that KLB inhibits ribosomes by interfering with translation elongation. Structural analysis of the ribosome–KLB complex showed that the compound binds in the peptide exit tunnel overlapping with the binding sites of macrolides or streptogramin-B. KLB adopts a compact conformation and largely obstructs the tunnel. Engineered KLB fragments were observed to retain in vitro activity, and thus have the potential to serve as a starting point for the development of new bioactive compounds.},
doi = {10.1038/nchembio.2462},
url = {https://www.osti.gov/biblio/1409111},
journal = {Nature Chemical Biology},
issn = {1552-4450},
number = 10,
volume = 13,
place = {United States},
year = {2017},
month = {8}
}
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Works referenced in this record:
Sequence selectivity of macrolide-induced translational attenuation
journal, October 2014
- Davis, A. R.; Gohara, D. W.; Yap, M. -N. F.
- Proceedings of the National Academy of Sciences, Vol. 111, Issue 43
Characterization of Peptide Chain Length and Constituency Requirements for YejABEF-Mediated Uptake of Microcin C Analogues
journal, May 2011
- Vondenhoff, G. H. M.; Blanchaert, B.; Geboers, S.
- Journal of Bacteriology, Vol. 193, Issue 14
YcaO domains use ATP to activate amide backbones during peptide cyclodehydrations
journal, April 2012
- Dunbar, Kyle L.; Melby, Joel O.; Mitchell, Douglas A.
- Nature Chemical Biology, Vol. 8, Issue 6
The genomic landscape of ribosomal peptides containing thiazole and oxazole heterocycles
journal, October 2015
- Cox, Courtney L.; Doroghazi, James R.; Mitchell, Douglas A.
- BMC Genomics, Vol. 16, Issue 1
Insect-Derived Proline-Rich Antimicrobial Peptides Kill Bacteria by Inhibiting Bacterial Protein Translation at the 70 S Ribosome
journal, September 2014
- Krizsan, Andor; Volke, Daniela; Weinert, Stefanie
- Angewandte Chemie International Edition, Vol. 53, Issue 45
Antibiotic resistance—the need for global solutions
journal, December 2013
- Laxminarayan, Ramanan; Duse, Adriano; Wattal, Chand
- The Lancet Infectious Diseases, Vol. 13, Issue 12
Synthetic Biotechnology to Study and Engineer Ribosomal Bottromycin Biosynthesis
journal, October 2012
- Huo, Liujie; Rachid, Shwan; Stadler, Marc
- Chemistry & Biology, Vol. 19, Issue 10
Revisiting the structures of several antibiotics bound to the bacterial ribosome
journal, September 2010
- Bulkley, D.; Innis, C. A.; Blaha, G.
- Proceedings of the National Academy of Sciences, Vol. 107, Issue 40
Small molecules from the human microbiota
journal, July 2015
- Donia, M. S.; Fischbach, M. A.
- Science, Vol. 349, Issue 6246
Discovery of a new ATP-binding motif involved in peptidic azoline biosynthesis
journal, August 2014
- Dunbar, Kyle L.; Chekan, Jonathan R.; Cox, Courtney L.
- Nature Chemical Biology, Vol. 10, Issue 10
Binding Site of Macrolide Antibiotics on the Ribosome: New Resistance Mutation Identifies a Specific Interaction of Ketolides with rRNA
journal, December 2001
- Garza-Ramos, G.; Xiong, L.; Zhong, P.
- Journal of Bacteriology, Vol. 183, Issue 23
Functional Characterization of SbmA, a Bacterial Inner Membrane Transporter Required for Importing the Antimicrobial Peptide Bac7(1-35)
journal, September 2013
- Runti, G.; Lopez Ruiz, M. d. C.; Stoilova, T.
- Journal of Bacteriology, Vol. 195, Issue 23
Identifying the targets of aminoacyl-tRNA synthetase inhibitors by primer extension inhibition
journal, June 2013
- Orelle, Cédric; Szal, Teresa; Klepacki, Dorota
- Nucleic Acids Research, Vol. 41, Issue 14
Tools for Characterizing Bacterial Protein Synthesis Inhibitors
journal, September 2013
- Orelle, Cédric; Carlson, Skylar; Kaushal, Bindiya
- Antimicrobial Agents and Chemotherapy, Vol. 57, Issue 12
Emergence of plasmid-mediated colistin resistance mechanism MCR-1 in animals and human beings in China: a microbiological and molecular biological study
journal, February 2016
- Liu, Yi-Yun; Wang, Yang; Walsh, Timothy R.
- The Lancet Infectious Diseases, Vol. 16, Issue 2
A roadmap for natural product discovery based on large-scale genomics and metabolomics
journal, September 2014
- Doroghazi, James R.; Albright, Jessica C.; Goering, Anthony W.
- Nature Chemical Biology, Vol. 10, Issue 11
Platforms for antibiotic discovery
journal, April 2013
- Lewis, Kim
- Nature Reviews Drug Discovery, Vol. 12, Issue 5
Role of the Escherichia coli SbmA in the antimicrobial activity of proline-rich peptides
journal, October 2007
- Mattiuzzo, Maura; Bandiera, Antonella; Gennaro, Renato
- Molecular Microbiology, Vol. 66, Issue 1
The mechanism of inhibition of protein synthesis by the proline-rich peptide oncocin
journal, May 2015
- Roy, Raktim N.; Lomakin, Ivan B.; Gagnon, Matthieu G.
- Nature Structural & Molecular Biology, Vol. 22, Issue 6
Dissecting Bottromycin Biosynthesis Using Comparative Untargeted Metabolomics
journal, July 2016
- Crone, William J. K.; Vior, Natalia M.; Santos-Aberturas, Javier
- Angewandte Chemie International Edition, Vol. 55, Issue 33
The Cyanobactin Heterocyclase Enzyme: A Processive Adenylase That Operates with a Defined Order of Reaction
journal, November 2013
- Koehnke, Jesko; Bent, Andrew F.; Zollman, David
- Angewandte Chemie International Edition, Vol. 52, Issue 52
Discovery of a widely distributed toxin biosynthetic gene cluster
journal, March 2008
- Lee, S. W.; Mitchell, D. A.; Markley, A. L.
- Proceedings of the National Academy of Sciences, Vol. 105, Issue 15
Synergy of Streptogramin Antibiotics Occurs Independently of Their Effects on Translation
journal, June 2014
- Noeske, Jonas; Huang, Jian; Olivier, Nelson B.
- Antimicrobial Agents and Chemotherapy, Vol. 58, Issue 9
The proline-rich antimicrobial peptide Onc112 inhibits translation by blocking and destabilizing the initiation complex
journal, May 2015
- Seefeldt, A. Carolin; Nguyen, Fabian; Antunes, Stéphanie
- Nature Structural & Molecular Biology, Vol. 22, Issue 6
A Systematic Analysis of Biosynthetic Gene Clusters in the Human Microbiome Reveals a Common Family of Antibiotics
journal, September 2014
- Donia, Mohamed S.; Cimermancic, Peter; Schulze, Christopher J.
- Cell, Vol. 158, Issue 6
The Escherichia coli Yej Transporter Is Required for the Uptake of Translation Inhibitor Microcin C
journal, September 2007
- Novikova, M.; Metlitskaya, A.; Datsenko, K.
- Journal of Bacteriology, Vol. 189, Issue 22
Structures of proline-rich peptides bound to the ribosome reveal a common mechanism of protein synthesis inhibition
journal, January 2016
- Gagnon, Matthieu G.; Roy, Raktim N.; Lomakin, Ivan B.
- Nucleic Acids Research, Vol. 44, Issue 5
Human commensals producing a novel antibiotic impair pathogen colonization
journal, July 2016
- Zipperer, Alexander; Konnerth, Martin C.; Laux, Claudia
- Nature, Vol. 535, Issue 7613
Coot model-building tools for molecular graphics
journal, November 2004
- Emsley, Paul; Cowtan, Kevin
- Acta Crystallographica Section D Biological Crystallography, Vol. 60, Issue 12, p. 2126-2132
Interaction of tRNA with 23S rRNA in the ribosomal A, P, and E sites
journal, May 1989
- Moazed, Danesh; Noller, Harry F.
- Cell, Vol. 57, Issue 4
PHENIX: a comprehensive Python-based system for macromolecular structure solution
journal, January 2010
- Adams, Paul D.; Afonine, Pavel V.; Bunkóczi, Gábor
- Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 2, p. 213-221
The Complete Atomic Structure of the Large Ribosomal Subunit at 2.4 A Resolution
journal, August 2000
- Ban, N.
- Science, Vol. 289, Issue 5481
YcaO-Dependent Posttranslational Amide Activation: Biosynthesis, Structure, and Function
journal, March 2017
- Burkhart, Brandon J.; Schwalen, Christopher J.; Mann, Greg
- Chemical Reviews, Vol. 117, Issue 8
Intermediate states in the movement of transfer RNA in the ribosome
journal, November 1989
- Moazed, Danesh; Noller, Harry F.
- Nature, Vol. 342, Issue 6246
The general mode of translation inhibition by macrolide antibiotics
journal, October 2014
- Kannan, Krishna; Kanabar, Pinal; Schryer, David
- Proceedings of the National Academy of Sciences, Vol. 111, Issue 45
Antibacterial drug discovery in the resistance era
journal, January 2016
- Brown, Eric D.; Wright, Gerard D.
- Nature, Vol. 529, Issue 7586
Agar and broth dilution methods to determine the minimal inhibitory concentration (MIC) of antimicrobial substances
journal, January 2008
- Wiegand, Irith; Hilpert, Kai; Hancock, Robert E. W.
- Nature Protocols, Vol. 3, Issue 2
Structural insights into the role of rRNA modifications in protein synthesis and ribosome assembly
journal, March 2015
- Polikanov, Yury S.; Melnikov, Sergey V.; Söll, Dieter
- Nature Structural & Molecular Biology, Vol. 22, Issue 4
Ribosomally synthesized and post-translationally modified peptide natural products: overview and recommendations for a universal nomenclature
journal, January 2013
- Arnison, Paul G.; Bibb, Mervyn J.; Bierbaum, Gabriele
- Nat. Prod. Rep., Vol. 30, Issue 1
Selective Protein Synthesis by Ribosomes with a Drug-Obstructed Exit Tunnel
journal, October 2012
- Kannan, Krishna; Vázquez-Laslop, Nora; Mankin, Alexander S.
- Cell, Vol. 151, Issue 3
Phaser crystallographic software
journal, July 2007
- McCoy, Airlie J.; Grosse-Kunstleve, Ralf W.; Adams, Paul D.
- Journal of Applied Crystallography, Vol. 40, Issue 4
Follow the leader: the use of leader peptides to guide natural product biosynthesis
journal, December 2009
- Oman, Trent J.; van der Donk, Wilfred A.
- Nature Chemical Biology, Vol. 6, Issue 1