Klebsazolicin inhibits 70S ribosome by obstructing the peptide exit tunnel

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.

doi:10.1038/nchembio.2462

Title: Klebsazolicin inhibits 70S ribosome by obstructing the peptide exit tunnel

Journal Article · Mon Aug 28 00:00:00 EDT 2017 · Nature Chemical Biology

DOI:https://doi.org/10.1038/nchembio.2462· OSTI ID:1409111

; 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;

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.

Cite

Export

Save

Research Organization:: Argonne National Laboratory (ANL), Argonne, IL (United States). Advanced Photon Source (APS)

Sponsoring Organization:: NIHFOREIGNSTATE OF ILLINOIS

OSTI ID:: 1409111

Journal Information:: Nature Chemical Biology, Vol. 13, Issue 10; ISSN 1552-4450

Publisher:: Nature Publishing Group

Country of Publication:: United States

Language:: ENGLISH

References (42)

Sequence selectivity of macrolide-induced translational attenuation Davis, A. R.; Gohara, D. W.; Yap, M. -N. F. Proceedings of the National Academy of Sciences, Vol. 111, Issue 43 https://doi.org/10.1073/pnas.1410356111	journal	October 2014
Characterization of Peptide Chain Length and Constituency Requirements for YejABEF-Mediated Uptake of Microcin C Analogues Vondenhoff, G. H. M.; Blanchaert, B.; Geboers, S. Journal of Bacteriology, Vol. 193, Issue 14 https://doi.org/10.1128/JB.00172-11	journal	May 2011
YcaO domains use ATP to activate amide backbones during peptide cyclodehydrations Dunbar, Kyle L.; Melby, Joel O.; Mitchell, Douglas A. Nature Chemical Biology, Vol. 8, Issue 6 https://doi.org/10.1038/nchembio.944	journal	April 2012
The genomic landscape of ribosomal peptides containing thiazole and oxazole heterocycles Cox, Courtney L.; Doroghazi, James R.; Mitchell, Douglas A. BMC Genomics, Vol. 16, Issue 1 https://doi.org/10.1186/s12864-015-2008-0	journal	October 2015
Insect-Derived Proline-Rich Antimicrobial Peptides Kill Bacteria by Inhibiting Bacterial Protein Translation at the 70 S Ribosome Krizsan, Andor; Volke, Daniela; Weinert, Stefanie Angewandte Chemie International Edition, Vol. 53, Issue 45 https://doi.org/10.1002/anie.201407145	journal	September 2014
Antibiotic resistance—the need for global solutions Laxminarayan, Ramanan; Duse, Adriano; Wattal, Chand The Lancet Infectious Diseases, Vol. 13, Issue 12 https://doi.org/10.1016/S1473-3099(13)70318-9	journal	December 2013
Synthetic Biotechnology to Study and Engineer Ribosomal Bottromycin Biosynthesis Huo, Liujie; Rachid, Shwan; Stadler, Marc Chemistry & Biology, Vol. 19, Issue 10 https://doi.org/10.1016/j.chembiol.2012.08.013	journal	October 2012
Revisiting the structures of several antibiotics bound to the bacterial ribosome Bulkley, D.; Innis, C. A.; Blaha, G. Proceedings of the National Academy of Sciences, Vol. 107, Issue 40 https://doi.org/10.1073/pnas.1008685107	journal	September 2010
Small molecules from the human microbiota Donia, M. S.; Fischbach, M. A. Science, Vol. 349, Issue 6246 https://doi.org/10.1126/science.1254766	journal	July 2015
Prospects for new antibiotics: a molecule-centered perspective Walsh, Christopher T.; Wencewicz, Timothy A. The Journal of Antibiotics, Vol. 67, Issue 1 https://doi.org/10.1038/ja.2013.49	journal	June 2013
Discovery of a new ATP-binding motif involved in peptidic azoline biosynthesis Dunbar, Kyle L.; Chekan, Jonathan R.; Cox, Courtney L. Nature Chemical Biology, Vol. 10, Issue 10 https://doi.org/10.1038/nchembio.1608	journal	August 2014
Binding Site of Macrolide Antibiotics on the Ribosome: New Resistance Mutation Identifies a Specific Interaction of Ketolides with rRNA Garza-Ramos, G.; Xiong, L.; Zhong, P. Journal of Bacteriology, Vol. 183, Issue 23 https://doi.org/10.1128/JB.183.23.6898-6907.2001	journal	December 2001
Functional Characterization of SbmA, a Bacterial Inner Membrane Transporter Required for Importing the Antimicrobial Peptide Bac7(1-35) Runti, G.; Lopez Ruiz, M. d. C.; Stoilova, T. Journal of Bacteriology, Vol. 195, Issue 23 https://doi.org/10.1128/JB.00818-13	journal	September 2013
Identifying the targets of aminoacyl-tRNA synthetase inhibitors by primer extension inhibition Orelle, Cédric; Szal, Teresa; Klepacki, Dorota Nucleic Acids Research, Vol. 41, Issue 14 https://doi.org/10.1093/nar/gkt526	journal	June 2013
Emergence of plasmid-mediated colistin resistance mechanism MCR-1 in animals and human beings in China: a microbiological and molecular biological study Liu, Yi-Yun; Wang, Yang; Walsh, Timothy R. The Lancet Infectious Diseases, Vol. 16, Issue 2 https://doi.org/10.1016/S1473-3099(15)00424-7	journal	February 2016
A roadmap for natural product discovery based on large-scale genomics and metabolomics Doroghazi, James R.; Albright, Jessica C.; Goering, Anthony W. Nature Chemical Biology, Vol. 10, Issue 11 https://doi.org/10.1038/nchembio.1659	journal	September 2014
Platforms for antibiotic discovery Lewis, Kim Nature Reviews Drug Discovery, Vol. 12, Issue 5 https://doi.org/10.1038/nrd3975	journal	April 2013
Role of the Escherichia coli SbmA in the antimicrobial activity of proline-rich peptides Mattiuzzo, Maura; Bandiera, Antonella; Gennaro, Renato Molecular Microbiology, Vol. 66, Issue 1 https://doi.org/10.1111/j.1365-2958.2007.05903.x	journal	October 2007
The mechanism of inhibition of protein synthesis by the proline-rich peptide oncocin Roy, Raktim N.; Lomakin, Ivan B.; Gagnon, Matthieu G. Nature Structural & Molecular Biology, Vol. 22, Issue 6 https://doi.org/10.1038/nsmb.3031	journal	May 2015
Dissecting Bottromycin Biosynthesis Using Comparative Untargeted Metabolomics Crone, William J. K.; Vior, Natalia M.; Santos-Aberturas, Javier Angewandte Chemie International Edition, Vol. 55, Issue 33 https://doi.org/10.1002/anie.201604304	journal	July 2016
The Cyanobactin Heterocyclase Enzyme: A Processive Adenylase That Operates with a Defined Order of Reaction Koehnke, Jesko; Bent, Andrew F.; Zollman, David Angewandte Chemie International Edition, Vol. 52, Issue 52 https://doi.org/10.1002/anie.201306302	journal	November 2013
Discovery of a widely distributed toxin biosynthetic gene cluster Lee, S. W.; Mitchell, D. A.; Markley, A. L. Proceedings of the National Academy of Sciences, Vol. 105, Issue 15 https://doi.org/10.1073/pnas.0801338105	journal	March 2008
Structure of the mammalian antimicrobial peptide Bac7(1–16) bound within the exit tunnel of a bacterial ribosome Seefeldt, A. Carolin; Graf, Michael; Pérébaskine, Natacha Nucleic Acids Research, Vol. 44, Issue 5 https://doi.org/10.1093/nar/gkv1545	journal	January 2016
Synergy of Streptogramin Antibiotics Occurs Independently of Their Effects on Translation Noeske, Jonas; Huang, Jian; Olivier, Nelson B. Antimicrobial Agents and Chemotherapy, Vol. 58, Issue 9 https://doi.org/10.1128/AAC.03389-14	journal	June 2014
The proline-rich antimicrobial peptide Onc112 inhibits translation by blocking and destabilizing the initiation complex Seefeldt, A. Carolin; Nguyen, Fabian; Antunes, Stéphanie Nature Structural & Molecular Biology, Vol. 22, Issue 6 https://doi.org/10.1038/nsmb.3034	journal	May 2015
A Systematic Analysis of Biosynthetic Gene Clusters in the Human Microbiome Reveals a Common Family of Antibiotics Donia, Mohamed S.; Cimermancic, Peter; Schulze, Christopher J. Cell, Vol. 158, Issue 6 https://doi.org/10.1016/j.cell.2014.08.032	journal	September 2014
The Escherichia coli Yej Transporter Is Required for the Uptake of Translation Inhibitor Microcin C Novikova, M.; Metlitskaya, A.; Datsenko, K. Journal of Bacteriology, Vol. 189, Issue 22 https://doi.org/10.1128/JB.01028-07	journal	September 2007
Structures of proline-rich peptides bound to the ribosome reveal a common mechanism of protein synthesis inhibition Gagnon, Matthieu G.; Roy, Raktim N.; Lomakin, Ivan B. Nucleic Acids Research, Vol. 44, Issue 5 https://doi.org/10.1093/nar/gkw018	journal	January 2016
Human commensals producing a novel antibiotic impair pathogen colonization Zipperer, Alexander; Konnerth, Martin C.; Laux, Claudia Nature, Vol. 535, Issue 7613 https://doi.org/10.1038/nature18634	journal	July 2016
Coot model-building tools for molecular graphics Emsley, Paul; Cowtan, Kevin Acta Crystallographica Section D Biological Crystallography, Vol. 60, Issue 12, p. 2126-2132 https://doi.org/10.1107/S0907444904019158	journal	November 2004
Interaction of tRNA with 23S rRNA in the ribosomal A, P, and E sites Moazed, Danesh; Noller, Harry F. Cell, Vol. 57, Issue 4 https://doi.org/10.1016/0092-8674(89)90128-1	journal	May 1989
PHENIX: a comprehensive Python-based system for macromolecular structure solution Adams, Paul D.; Afonine, Pavel V.; Bunkóczi, Gábor Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 2, p. 213-221 https://doi.org/10.1107/S0907444909052925	journal	January 2010
The Complete Atomic Structure of the Large Ribosomal Subunit at 2.4 A Resolution Ban, N. Science, Vol. 289, Issue 5481 https://doi.org/10.1126/science.289.5481.905	journal	August 2000
YcaO-Dependent Posttranslational Amide Activation: Biosynthesis, Structure, and Function Burkhart, Brandon J.; Schwalen, Christopher J.; Mann, Greg Chemical Reviews, Vol. 117, Issue 8 https://doi.org/10.1021/acs.chemrev.6b00623	journal	March 2017
Intermediate states in the movement of transfer RNA in the ribosome Moazed, Danesh; Noller, Harry F. Nature, Vol. 342, Issue 6246 https://doi.org/10.1038/342142a0	journal	November 1989
The general mode of translation inhibition by macrolide antibiotics Kannan, Krishna; Kanabar, Pinal; Schryer, David Proceedings of the National Academy of Sciences, Vol. 111, Issue 45 https://doi.org/10.1073/pnas.1417334111	journal	October 2014
Antibacterial drug discovery in the resistance era Brown, Eric D.; Wright, Gerard D. Nature, Vol. 529, Issue 7586 https://doi.org/10.1038/nature17042	journal	January 2016
Agar and broth dilution methods to determine the minimal inhibitory concentration (MIC) of antimicrobial substances Wiegand, Irith; Hilpert, Kai; Hancock, Robert E. W. Nature Protocols, Vol. 3, Issue 2 https://doi.org/10.1038/nprot.2007.521	journal	January 2008
Structural insights into the role of rRNA modifications in protein synthesis and ribosome assembly Polikanov, Yury S.; Melnikov, Sergey V.; Söll, Dieter Nature Structural & Molecular Biology, Vol. 22, Issue 4 https://doi.org/10.1038/nsmb.2992	journal	March 2015
Selective Protein Synthesis by Ribosomes with a Drug-Obstructed Exit Tunnel Kannan, Krishna; Vázquez-Laslop, Nora; Mankin, Alexander S. Cell, Vol. 151, Issue 3 https://doi.org/10.1016/j.cell.2012.09.018	journal	October 2012
Phaser crystallographic software McCoy, Airlie J.; Grosse-Kunstleve, Ralf W.; Adams, Paul D. Journal of Applied Crystallography, Vol. 40, Issue 4 https://doi.org/10.1107/S0021889807021206	journal	July 2007
Follow the leader: the use of leader peptides to guide natural product biosynthesis Oman, Trent J.; van der Donk, Wilfred A. Nature Chemical Biology, Vol. 6, Issue 1 https://doi.org/10.1038/nchembio.286	journal	December 2009

Similar Records

The structure of ribosome-lankacidin complex reveals ribosomal sites for synergistic antibiotics

Journal Article · Mon Apr 26 00:00:00 EDT 2010 · Proc. Natl. Acad. Sci. USA · OSTI ID:1409111

Auerbach, Tamar; Mermershtain, Inbal; Davidovich, Chen; +10 more

Automated genome mining of ribosomal peptide natural products

Journal Article · Thu Jul 31 00:00:00 EDT 2014 · ACS Chemical Biology, 9(7):1545-1551 · OSTI ID:1409111

Mohimani, Hosein; Kersten, Roland; Liu, Wei; +9 more

Mechanistic Basis for Ribosomal Peptide Backbone Modifications

Journal Article · Tue Apr 16 00:00:00 EDT 2019 · ACS Central Science · OSTI ID:1409111

Dong, Shi-Hui; Liu, Andi; Mahanta, Nilkamal; +2 more

Related Subjects

59 BASIC BIOLOGICAL SCIENCES

Title: Klebsazolicin inhibits 70S ribosome by obstructing the peptide exit tunnel

Citation Formats

References (42)

Similar Records

Related Subjects