skip to main content
OSTI.GOV title logo U.S. Department of Energy
Office of Scientific and Technical Information

Title: 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.

Authors:
ORCiD logo; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ORCiD logo
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}
}

Works referenced in this record:

Sequence selectivity of macrolide-induced translational attenuation
journal, October 2014


Characterization of Peptide Chain Length and Constituency Requirements for YejABEF-Mediated Uptake of Microcin C Analogues
journal, May 2011


YcaO domains use ATP to activate amide backbones during peptide cyclodehydrations
journal, April 2012


The genomic landscape of ribosomal peptides containing thiazole and oxazole heterocycles
journal, October 2015


Insect-Derived Proline-Rich Antimicrobial Peptides Kill Bacteria by Inhibiting Bacterial Protein Translation at the 70 S Ribosome
journal, September 2014


Antibiotic resistance—the need for global solutions
journal, December 2013


Synthetic Biotechnology to Study and Engineer Ribosomal Bottromycin Biosynthesis
journal, October 2012


Revisiting the structures of several antibiotics bound to the bacterial ribosome
journal, September 2010


Small molecules from the human microbiota
journal, July 2015


Discovery of a new ATP-binding motif involved in peptidic azoline biosynthesis
journal, August 2014


Functional Characterization of SbmA, a Bacterial Inner Membrane Transporter Required for Importing the Antimicrobial Peptide Bac7(1-35)
journal, September 2013


Identifying the targets of aminoacyl-tRNA synthetase inhibitors by primer extension inhibition
journal, June 2013


Tools for Characterizing Bacterial Protein Synthesis Inhibitors
journal, September 2013


A roadmap for natural product discovery based on large-scale genomics and metabolomics
journal, September 2014


Platforms for antibiotic discovery
journal, April 2013


Role of the Escherichia coli SbmA in the antimicrobial activity of proline-rich peptides
journal, October 2007


The mechanism of inhibition of protein synthesis by the proline-rich peptide oncocin
journal, May 2015


Dissecting Bottromycin Biosynthesis Using Comparative Untargeted Metabolomics
journal, July 2016


The Cyanobactin Heterocyclase Enzyme: A Processive Adenylase That Operates with a Defined Order of Reaction
journal, November 2013


Discovery of a widely distributed toxin biosynthetic gene cluster
journal, March 2008


Synergy of Streptogramin Antibiotics Occurs Independently of Their Effects on Translation
journal, June 2014


The proline-rich antimicrobial peptide Onc112 inhibits translation by blocking and destabilizing the initiation complex
journal, May 2015


A Systematic Analysis of Biosynthetic Gene Clusters in the Human Microbiome Reveals a Common Family of Antibiotics
journal, September 2014


The Escherichia coli Yej Transporter Is Required for the Uptake of Translation Inhibitor Microcin C
journal, September 2007


Structures of proline-rich peptides bound to the ribosome reveal a common mechanism of protein synthesis inhibition
journal, January 2016


Human commensals producing a novel antibiotic impair pathogen colonization
journal, July 2016


Coot model-building tools for molecular graphics
journal, November 2004


Interaction of tRNA with 23S rRNA in the ribosomal A, P, and E sites
journal, May 1989


PHENIX: a comprehensive Python-based system for macromolecular structure solution
journal, January 2010


YcaO-Dependent Posttranslational Amide Activation: Biosynthesis, Structure, and Function
journal, March 2017


Intermediate states in the movement of transfer RNA in the ribosome
journal, November 1989


The general mode of translation inhibition by macrolide antibiotics
journal, October 2014


Antibacterial drug discovery in the resistance era
journal, January 2016


Agar and broth dilution methods to determine the minimal inhibitory concentration (MIC) of antimicrobial substances
journal, January 2008


Structural insights into the role of rRNA modifications in protein synthesis and ribosome assembly
journal, March 2015


Selective Protein Synthesis by Ribosomes with a Drug-Obstructed Exit Tunnel
journal, October 2012


Phaser crystallographic software
journal, July 2007


Follow the leader: the use of leader peptides to guide natural product biosynthesis
journal, December 2009