title: Computational protein design enables a novel one-carbon assimilation pathway.
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.
authors.affiliation: Department of Chemistry, Department of Biochemistry and Molecular Medicine, and Genome Center, University of California, Davis, CA 95616; Department of Biochemistry and the Institute for Protein Design, Biomolecular Structure and Design Program.
authors.forename: Justin B
authors.initials: JB
authors.lastname: Siegel
authors.affiliation: Department of Chemical Engineering.
authors.forename: Amanda Lee
authors.initials: AL
authors.lastname: Smith
authors.affiliation: Department of Chemical and Biomolecular Engineering and Joint BioEnergy Institute, Emeryville, CA 94608;
authors.forename: Sean
authors.initials: S
authors.lastname: Poust
authors.affiliation: Department of Biochemistry and the Institute for Protein Design.
authors.forename: Adam J
authors.initials: AJ
authors.lastname: Wargacki
authors.affiliation: Department of Plant Sciences, Weizmann Institute of Sciences, Rehovot 76100, Israel;
authors.forename: Arren
authors.initials: A
authors.lastname: Bar-Even
authors.affiliation: Department of Biochemistry and the Institute for Protein Design.
authors.forename: Catherine
authors.initials: C
authors.lastname: Louw
authors.affiliation: Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98109;
authors.forename: Betty W
authors.initials: BW
authors.lastname: Shen
authors.affiliation: Department of Biochemistry and the Institute for Protein Design, Department of Chemical and Biomolecular Engineering and Joint BioEnergy Institute, Emeryville, CA 94608;
authors.forename: Christopher B
authors.initials: CB
authors.lastname: Eiben
authors.affiliation: Joint BioEnergy Institute, Emeryville, CA 94608; Biomass Science and Conversion Technology, Sandia National Laboratories, Livermore, CA 94550;
authors.forename: Huu M
authors.initials: HM
authors.lastname: Tran
authors.affiliation: Department of Plant Sciences, Weizmann Institute of Sciences, Rehovot 76100, Israel;
authors.forename: Elad
authors.initials: E
authors.lastname: Noor
authors.affiliation: Department of Biochemistry and the Institute for Protein Design.
authors.forename: Jasmine L
authors.initials: JL
authors.lastname: Gallaher
authors.affiliation: Department of Biochemistry and the Institute for Protein Design, Graduate Program in Molecular and Cellular Biology.
authors.forename: Jacob
authors.initials: J
authors.lastname: Bale
authors.affiliation: Department of Biochemistry and the Institute for Protein Design, Department of Energy, Joint Genome Institute, Lawrence National Berkeley Laboratory, Walnut Creek, CA 94598; Howard Hughes Medical Institute.
authors.forename: Yasuo
authors.initials: Y
authors.lastname: Yoshikuni
authors.affiliation: Department of Biochemistry and the Institute for Protein Design, Department of Chemistry, and.
authors.forename: Michael H
authors.initials: MH
authors.lastname: Gelb
authors.affiliation: Department of Chemical and Biomolecular Engineering and Joint BioEnergy Institute, Emeryville, CA 94608; QB3 Institute, University of California, Berkeley, CA 94270; Synthetic Biology Engineering Research Center, Emeryville, CA 94608; and Physical Bioscience Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94270.
authors.forename: Jay D
authors.initials: JD
authors.lastname: Keasling
authors.affiliation: Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98109;
authors.forename: Barry L
authors.initials: BL
authors.lastname: Stoddard
authors.affiliation: Department of Chemical Engineering, Department of Microbiology, University of Washington, Seattle, WA 98195; lidstrom@u.washington.edu dabaker@uw.edu.
authors.forename: Mary E
authors.initials: ME
authors.lastname: Lidstrom
authors.affiliation: Department of Biochemistry and the Institute for Protein Design, Biomolecular Structure and Design Program, Howard Hughes Medical Institute, lidstrom@u.washington.edu dabaker@uw.edu.
authors.forename: David
authors.initials: D
authors.lastname: Baker
mesh_terms: D018533:Biomass; D053898:Biosynthetic Pathways; D002244:Carbon / Q000737:chemistry*; D057486:Carbon Cycle; D002384:Catalysis; D003001:Cloning, Molecular; D004926:Escherichia coli / Q000201:enzymology; D005557:Formaldehyde / Q000737:chemistry; D005561:Formates / Q000737:chemistry; D009682:Magnetic Resonance Spectroscopy; D016133:Polymerase Chain Reaction; D015202:Protein Engineering / Q000379:methods*; D011506:Proteins / Q000737:chemistry*; D012984:Software; D013816:Thermodynamics
chemical_list: D005561:Formates; D011506:Proteins; C030544:formic acid; D005557:Formaldehyde; D002244:Carbon
keywords: carbon fixation; computational protein design; pathway engineering