Structure of ribosome-bound azole-modified peptide phazolicin rationalizes its species-specific mode of bacterial translation inhibition

Dmitrii Y. Travin, Zoe L. Watson, Mikhail Metelev, Fred R. Ward, Ilya A. Osterman, Irina M. Khven, Nelli F. Khabibullina, Marina Serebryakova, Peter Mergaert, Yury S. Polikanov (), Jamie H. D. Cate () and Konstantin Severinov ()
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Dmitrii Y. Travin: Skolkovo Institute of Science and Technology
Zoe L. Watson: University of California
Mikhail Metelev: Skolkovo Institute of Science and Technology
Fred R. Ward: University of California
Ilya A. Osterman: Skolkovo Institute of Science and Technology
Irina M. Khven: Lomonosov Moscow State University
Nelli F. Khabibullina: University of Illinois at Chicago
Marina Serebryakova: Lomonosov Moscow State University
Peter Mergaert: University Paris-Saclay
Yury S. Polikanov: University of Illinois at Chicago
Jamie H. D. Cate: University of California
Konstantin Severinov: Skolkovo Institute of Science and Technology

Nature Communications, 2019, vol. 10, issue 1, 1-11

Abstract: Abstract Ribosome-synthesized post-translationally modified peptides (RiPPs) represent a rapidly expanding class of natural products with various biological activities. Linear azol(in)e-containing peptides (LAPs) comprise a subclass of RiPPs that display outstanding diversity of mechanisms of action while sharing common structural features. Here, we report the discovery of a new LAP biosynthetic gene cluster in the genome of Rhizobium Pop5, which encodes the precursor peptide and modification machinery of phazolicin (PHZ) – an extensively modified peptide exhibiting narrow-spectrum antibacterial activity against some symbiotic bacteria of leguminous plants. The cryo-EM structure of the Escherichia coli 70S-PHZ complex reveals that the drug interacts with the 23S rRNA and uL4/uL22 proteins and obstructs ribosomal exit tunnel in a way that is distinct from other compounds. We show that the uL4 loop sequence determines the species-specificity of antibiotic action. PHZ expands the known diversity of LAPs and may be used in the future as biocontrol agent for agricultural needs.

Date: 2019
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DOI: 10.1038/s41467-019-12589-5

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