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Steric complementarity directs sequence promiscuous leader binding in RiPP biosynthesis.

Jonathan R Chekan1, Chayanid Ongpipattanakul1, Satish K Nair2,3,4

  • 1Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801.

Proceedings of the National Academy of Sciences of the United States of America
|November 14, 2019
PubMed
Summary

Enzymes that create ribosomally synthesized and posttranslationally modified peptide (RiPP) natural products bind leader peptides using hydrophobic interactions. A conserved motif allows sequence-divergent binding, enabling engineering of novel RiPP products.

Keywords:
RiPPsbiochemistrybiosynthesis

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Area of Science:

  • Biochemistry
  • Natural Product Synthesis
  • Molecular Biology

Background:

  • Ribosomally synthesized and posttranslationally modified peptide (RiPP) natural products are diverse.
  • RiPP biosynthesis involves enzymes recognizing leader sequences on precursor peptides.
  • Leader sequences are thought to be highly specific for enzyme binding.

Purpose of the Study:

  • To investigate the binding mechanism of lasso peptide biosynthetic enzymes to their leader peptides.
  • To determine the sequence specificity requirements for leader peptide recognition.
  • To explore the potential for engineering RiPP biosynthesis.

Main Methods:

  • Biochemical assays to measure binding affinity.
  • Structural biology techniques to elucidate enzyme-leader peptide interactions.
  • Analysis of conserved motifs in leader peptides across different RiPP classes.

Main Results:

  • Lasso peptide enzyme binding is driven by minimal hydrophobic interactions, not strict sequence specificity.
  • A conserved hydrophobic motif enables a single binding domain to engage diverse leader peptides.
  • This motif confers low micromolar binding affinity to noncognate peptides.

Conclusions:

  • Leader peptide binding in RiPPs, specifically lasso peptides, relies on a simple, conserved hydrophobic motif.
  • This motif's portability suggests broader applicability across RiPP classes.
  • The findings facilitate the engineering of semisynthetic hybrid RiPPs.