Computational protein design enables a novel one-carbon assimilation pathway

Justin Siegel, Amanda Lee Smith, Sean Poust, Adam J. Wargacki, Arren Bar-Even, Catherine Louw, Betty W. Shen, Christopher B. Eiben, Huu M. Tran, Elad Noor, Jasmine L. Gallaher, Jacob Bale, Yasuo Yoshikuni, Michael H. Gelb, Jay D. Keasling, Barry L. Stoddard, Mary E. Lidstrom, David Baker

Research output: Contribution to journalArticle

119 Scopus citations

Abstract

We describe a computationally designed enzyme, formolase (FLS), which catalyzes the carboligation of three one-carbon formaldehyde molecules into one three-carbon dihydroxyacetone molecule. The existence of FLS enables the design of a new carbon fixation pathway, the formolase pathway, consisting of a small number of thermodynamically favorable chemical transformations that convert formate into a three-carbon sugar in central metabolism. The formolase pathway is predicted to use carbon more efficiently and with less backward flux than any naturally occurring one-carbon assimilation pathway. When supplemented with enzymes carrying out the other steps in the pathway, FLS converts formate into dihydroxyacetone phosphate and other central metabolites in vitro. These results demonstrate how modern protein engineering and design tools can facilitate the construction of a completely new biosynthetic pathway.

Original languageEnglish (US)
Pages (from-to)3704-3709
Number of pages6
JournalProceedings of the National Academy of Sciences of the United States of America
Volume112
Issue number12
DOIs
StatePublished - Mar 24 2015

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Keywords

  • Carbon fixation
  • Computational protein design
  • Pathway engineering

ASJC Scopus subject areas

  • General

Cite this

Siegel, J., Smith, A. L., Poust, S., Wargacki, A. J., Bar-Even, A., Louw, C., Shen, B. W., Eiben, C. B., Tran, H. M., Noor, E., Gallaher, J. L., Bale, J., Yoshikuni, Y., Gelb, M. H., Keasling, J. D., Stoddard, B. L., Lidstrom, M. E., & Baker, D. (2015). Computational protein design enables a novel one-carbon assimilation pathway. Proceedings of the National Academy of Sciences of the United States of America, 112(12), 3704-3709. https://doi.org/10.1073/pnas.1500545112