AUTHOR=Jing Fuyuan , Chen Keting , Yandeau-Nelson Marna D. , Nikolau Basil J. TITLE=Machine learning model of the catalytic efficiency and substrate specificity of acyl-ACP thioesterase variants generated from natural and in vitro directed evolution JOURNAL=Frontiers in Bioengineering and Biotechnology VOLUME=12 YEAR=2024 URL=https://www.frontiersin.org/journals/bioengineering-and-biotechnology/articles/10.3389/fbioe.2024.1379121 DOI=10.3389/fbioe.2024.1379121 ISSN=2296-4185 ABSTRACT=

Modulating the catalytic activity of acyl-ACP thioesterase (TE) is an important biotechnological target for effectively increasing flux and diversifying products of the fatty acid biosynthesis pathway. In this study, a directed evolution approach was developed to improve the fatty acid titer and fatty acid diversity produced by E. coli strains expressing variant acyl-ACP TEs. A single round of in vitro directed evolution, coupled with a high-throughput colorimetric screen, identified 26 novel acyl-ACP TE variants that convey up to a 10-fold increase in fatty acid titer, and generate altered fatty acid profiles when expressed in a bacterial host strain. These in vitro-generated variant acyl-ACP TEs, in combination with 31 previously characterized natural variants isolated from diverse phylogenetic origins, were analyzed with a random forest classifier machine learning tool. The resulting quantitative model identified 22 amino acid residues, which define important structural features that determine the catalytic efficiency and substrate specificity of acyl-ACP TE.