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

Author

Listed:
  • Dmitrii Y. Travin

    (Skolkovo Institute of Science and Technology
    Russian Academy of Science)

  • Zoe L. Watson

    (University of California)

  • Mikhail Metelev

    (Skolkovo Institute of Science and Technology
    Russian Academy of Science
    Uppsala University)

  • Fred R. Ward

    (University of California)

  • Ilya A. Osterman

    (Skolkovo Institute of Science and Technology
    Lomonosov Moscow State University)

  • Irina M. Khven

    (Lomonosov Moscow State University
    Lomonosov Moscow State University)

  • Nelli F. Khabibullina

    (University of Illinois at Chicago
    National Medical Research Center for Phthisiopulmology & Infectious Diseases)

  • Marina Serebryakova

    (Lomonosov Moscow State University)

  • Peter Mergaert

    (University Paris-Saclay)

  • Yury S. Polikanov

    (University of Illinois at Chicago
    University of Illinois at Chicago)

  • Jamie H. D. Cate

    (University of California
    University of California)

  • Konstantin Severinov

    (Skolkovo Institute of Science and Technology
    Russian Academy of Science
    The State University of New Jersey)

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.

Suggested Citation

  • 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. , 2019. "Structure of ribosome-bound azole-modified peptide phazolicin rationalizes its species-specific mode of bacterial translation inhibition," Nature Communications, Nature, vol. 10(1), pages 1-11, December.
    • Handle: RePEc:nat:natcom:v:10:y:2019:i:1:d:10.1038_s41467-019-12589-5
    DOI: 10.1038/s41467-019-12589-5
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