Genomic Science Program
U.S. Department of Energy | Office of Science | Biological and Environmental Research Program

Evolutionary Flexibility and Rigidity in the Bacterial Methylerythritol Phosphate Pathway

Authors:

Bailey Marshall1,2* (bamarshall2@wisc.edu), Kaustubh Amritkar3, Michael Wolfe1,2, Betül Kaçar3, Robert Landick1,2,3, Timothy J. Dohohue3

Institutions:

1Department of Biochemistry, University of Wisconsin–Madison; 2DOE Great Lakes Bioenergy Research Center, University of Wisconsin–Madison; 3Department of Bacteriology, University of Wisconsin–Madison

Goals

Identify potential alternative routes in bacterial methylerythritol phosphate (MEP) metabolic pathway, which is the pathway used to generate high-value terpenoid products.

Abstract

Terpenoids are a diverse class of compounds with wide-ranging uses such as industrial solvents, fragrances, and more. Industrial production of most terpenoids relies on nonrenewable feedstocks making alternative production methods desirable. Fermentation of engineered microbes using renewable feedstocks like lignocellulose is an attractive strategy for large-scale production of key terpenoids because it has the potential to be sustainable and relatively inexpensive. To achieve large-scale production of terpenoids, there are widespread efforts to engineer the metabolic pathway that generates terpenoids. All terpenoids are made from the final products of the methyl erythritol phosphate (MEP) pathway, which is composed of seven enzymatic steps. Efforts in engineering the MEP pathway have identified some of these enzymes as having unfavorable characteristics, so researchers are interested in identifying alternative enzymatic routes, which may have evolved that are functionally redundant to the canonical MEP pathway. The team used comparative genomics to search for alternative enzymes to the canonical MEP enzymes and found that enzymes early in the pathway likely evolved alternatives as supported by literature. In contrast, researchers found enzymes late in the pathway appear to have no alternatives in the database of 4,400 genomes in this study. Early pathway flexibility suggests that researchers may be able to identify the genes responsible for an incomplete canonical pathway and implement these alternatives enzymes in metabolic engineering should they have more favorable qualities. For the late pathway steps, if alternative enzymes have evolved at all, they are rare or their host organisms have not been sequenced. The ever-growing repository of sequenced bacterial genomes has great potential to provide metabolic engineers with alternative metabolic pathway solutions. The finding that late MEP pathway enzymes are evolutionarily indispensable informs both metabolic engineering efforts and the understanding of the evolution of terpenoid biosynthesis pathways.

Funding Information

This material is based upon work supported by the Great Lakes Bioenergy Research Center, DOE Office of Science, BER program under award no. DE-SC0018409.