Thrust 1: New Biocatalysts for Pathway Engineering

CBiRC has assembled a world-class team of scientists that are well known for their work on fatty acid/ polyketide metabolism and metabolic engineering. The team is focused on the enzymes involved in Claisen condensation-based carbon-chain extension and chain termination with the aim of directing the process of fatty acid assembly in microbes.

The enzymes and proteins of interest include:

  • 3-ketoacyl-ACP Synthase
  • Acetoacetyl-CoA
  • Acetyl-CoA/Propionyl-CoA Synthetase
  • Acyl-CoA Carboxylases
  • Methylketone Synthase
  • Thioesterases
  • Biocatalysts of the Acetyl-CoA Condensation
  • Fatty Acid Elongase
  • Biotin

Participating faculty/research staff:

  1. Joseph P. Noel, (Thrust Leader), Jack H. Skirball Center for Chemical Biology & Proteomics, Salk Institute for Biological Studies
  2. Basil J. Nikolau (Thrust Co-Leader), Biochemistry, Biophysics & Molecular Biology, Iowa State University
  3. Adam Barb, Biochemistry, Biophysics & Molecular Biology, Iowa State University
  4. Alexis Campbell, Biochemistry, Biophysics & Molecular Biology, Iowa State University
  5. Eran Pichersky, Molecular, Cellular & Developmental Biology, University of Michigan
  6. Eve S. Wurtele,  Genetics, Development & Cell Biology, Iowa State University
  7. Marna Yandeau-Nelson, Genetics, Development & Cell Biology, Iowa State University

Overview of technologies:

CBiRC will develop technologies for generating a series of biologically derived chemicals that will represent a new precursor landscape for producing commodity molecules or final chemical products. This landscape will be established via a new paradigm in combinatorial metabolism based on biocatalysts identified and characterized by Thrust 1 of CBiRC. These biocatalysts will be accessed from a wide variety of organisms that harbor different polyketide/fatty acid biosynthetic pathways. These metabolic processes offer flexible biochemical conversions that can reiteratively generate a homologous series of alkyl-chains, which carry different chemical functionalities at specific positions of the molecules. Theoretically, these metabolic processes can generate alkyl-chains that range from 3- to 18-carbon atoms; however, the initial focus will be on molecules that are of up to 6-carbon atoms. It is important to note that the focus of the work is not the synthesis of complex polyketides, but using the biocatalytic machinery of the polyketide/fatty acid pathways to produce smaller molecules.

Thrust 1 projects:

Project Lead Project Title Project Goals
Basil Nikolau, Iowa State University 3-ketoacyl-ACP Synthase: Characterization of Novel Biocatalysts (3-ketoacyl Synthases) for Diversifying FAS/PKS Metabolic Pathways The goal of this project is to identify and characterize novel biocatalysts from plant and microbial polyketide synthase (PKS) systems, for the purpose of diversifying the fatty acid synthase (FAS) systems of E. coli and the yeast Saccharomyces cerevisiae.
Basil Nikolau, Iowa State University Acyl-CoA Carboxylases: Biocatalysts for Diversifying Precursor Pools for FAS/PKS Systems The goal of this project is to develop acyl-CoA carboxylases that can activate diverse acyl- CoA molecules to produce novel substrates for 3-ketoacyl-ACP synthases.
Basil Nikolau, Iowa State University Thioesterases: Characterization of Novel Biocatalysts (Thioesterases) for Diversifying FAS/PKS Metabolic Pathways The goal of this project is to identify and characterize novel biocatalysts from plant and microbial polyketide synthase systems for the purpose of diversifying the termination products of fatty acid synthase systems of E. coli and the yeast Saccharomyces cerevisiae.
Eve Wurtele and Marna Yandeau-Nelson, Iowa State University Bioinformatics-informed Molecular Genetic Optimization of the Acetyl-CoA-malonyl-CoA Metabolic Nexus in Yeast This project will identify genetic elements (both regulatory and biocatalytic) that can be bioengineered to enhance the fatty acid productivity of S. cerevisiae, which is a biological system with an established set of genetic and molecular tools.
Joe Noel, Salk Institute Claisen Condensation Enzymes Derived from Specialized Metabolism (aka Pyrone and Pogostone Synthases for Diversifying FAS/PKS Metabolic Pathways) The goals of this project include:  Biochemical and structural characterization and engineering of type III PKS (T3PKS) mutant gene libraries for altered product and substrate specificities; isolation and characterization of genes for PKSs and acyl transferases from the plant Pogostemon cablin that catalyze the formation of pogostone, and their expression in microbial systems for large scale production of final product; and selection of pyrone-specific prenyltransferases (PTases) for isoprenoid-based diversification of pyrone scaffold.