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Evolution-inspired engineering of anthracycline methyltransferases.

Pedro Dinis1, Heli Tirkkonen1, Benjamin Nji Wandi1

  • 1Department of Life Technologies, University of Turku, BioCity, Tykistökatu 6, FIN-20014 Turku, Finland.

PNAS Nexus
|March 6, 2023
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Summary

Soil bacteria evolve diverse anticancer compounds by modifying biosynthetic enzymes. This study engineered enzymes to gain new functions, revealing how subtle changes drive natural product evolution.

Keywords:
Enzyme evolutionStreptomycesnatural productpolyketideprotein engineering

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Area of Science:

  • Microbiology
  • Biochemistry
  • Synthetic Biology

Background:

  • Streptomyces bacteria produce numerous anthracycline anticancer agents from conserved genes.
  • Enzyme evolution, particularly in methyltransferases, drives the diversity of these natural products.
  • Previous studies identified methyltransferases catalyzing 4-O-methylation, 10-decarboxylation, or 10-hydroxylation with varying specificities.

Purpose of the Study:

  • To investigate the influence of specific protein regions on the catalytic activities of S-adenosyl-l-methionine-dependent methyltransferase-like proteins.
  • To understand the factors governing hydroxylation, methylation, and substrate selection in these enzymes.
  • To engineer novel catalytic activities and expand the repertoire of microbial natural product biosynthesis.

Main Methods:

  • Engineering chimeric enzymes by combining sequences from four distinct methyltransferase subfamilies.
  • Utilizing structural studies to analyze enzyme function and substrate interactions.
  • Characterizing the catalytic activities of engineered enzymes, including methylation, decarboxylation, and hydroxylation.

Main Results:

  • Identified key protein regions influencing gain-of-hydroxylation, loss-of-methylation, and substrate specificity.
  • Engineered enzymes exhibited novel 9,10-elimination activity.
  • Demonstrated 4-O-methylation and 10-decarboxylation of unnatural substrates by engineered enzymes.
  • Provided insights into the structural basis for altered catalytic functions.

Conclusions:

  • Subtle modifications in biosynthetic enzymes can significantly expand the diversity of microbial natural products.
  • Enzyme engineering provides a powerful approach to understand and manipulate natural product biosynthesis.
  • This work offers a model for the evolution of novel functionalities in enzyme superfamilies.