A metabolic pathway for catabolizing levulinic acid in bacteria

Nat Microbiol. 2017 Dec;2(12):1624-1634. doi: 10.1038/s41564-017-0028-z. Epub 2017 Sep 25.


Microorganisms can catabolize a wide range of organic compounds and therefore have the potential to perform many industrially relevant bioconversions. One barrier to realizing the potential of biorefining strategies lies in our incomplete knowledge of metabolic pathways, including those that can be used to assimilate naturally abundant or easily generated feedstocks. For instance, levulinic acid (LA) is a carbon source that is readily obtainable as a dehydration product of lignocellulosic biomass and can serve as the sole carbon source for some bacteria. Yet, the genetics and structure of LA catabolism have remained unknown. Here, we report the identification and characterization of a seven-gene operon that enables LA catabolism in Pseudomonas putida KT2440. When the pathway was reconstituted with purified proteins, we observed the formation of four acyl-CoA intermediates, including a unique 4-phosphovaleryl-CoA and the previously observed 3-hydroxyvaleryl-CoA product. Using adaptive evolution, we obtained a mutant of Escherichia coli LS5218 with functional deletions of fadE and atoC that was capable of robust growth on LA when it expressed the five enzymes from the P. putida operon. This discovery will enable more efficient use of biomass hydrolysates and metabolic engineering to develop bioconversions using LA as a feedstock.

MeSH terms

  • Bacteria / enzymology*
  • Bacteria / genetics*
  • Bacteria / metabolism
  • Bacterial Proteins / genetics
  • Base Sequence
  • Biomass
  • CRISPR-Cas Systems / genetics
  • Carbon / metabolism
  • DNA Transposable Elements
  • Escherichia coli / genetics
  • Escherichia coli / growth & development
  • Escherichia coli / metabolism
  • Gene Expression Regulation, Bacterial
  • Gene Knockdown Techniques
  • Genes, Bacterial / genetics*
  • Levulinic Acids / chemistry
  • Levulinic Acids / metabolism*
  • Metabolic Engineering
  • Metabolic Networks and Pathways / genetics*
  • Operon / genetics
  • Propionates / metabolism
  • Pseudomonas putida / enzymology
  • Pseudomonas putida / genetics
  • Pseudomonas putida / metabolism


  • Bacterial Proteins
  • DNA Transposable Elements
  • Levulinic Acids
  • Propionates
  • Carbon