Identification of the Gene Responsible for Lignin-Derived Low-Molecular-Weight Compound Catabolism in Pseudomonas sp. Strain LLC-1

Genes (Basel). 2020 Nov 27;11(12):1416. doi: 10.3390/genes11121416.


Pseudomonas sp. strain LLC-1 (NBRC 111237) is capable of degrading lignin-derived low-molecular-weight compounds (LLCs). The genes responsible for the catabolism of LLCs were characterized in this study using whole-genome sequencing. Despite the close phylogenetic relationship with Pseudomonas putida, strain LLC-1 lacked the genes usually found in the P. putida genome, which included fer, encoding an enzyme for ferulic acid catabolism, and vdh encoding an NAD+-dependent aldehyde dehydrogenase specific for its catabolic intermediate, vanillin. Cloning and expression of the 8.5 kb locus adjacent to the van operon involved in vanillic acid catabolism revealed the bzf gene cluster, which is involved in benzoylformic acid catabolism. One of the structural genes identified, bzfC, expresses the enzyme (BzfC) having the ability to transform vanillin and syringaldehyde to corresponding acids, indicating that BzfC is a multifunctional enzyme that initiates oxidization of LLCs in strain LLC-1. Benzoylformic acid is a catabolic intermediate of (R,S)-mandelic acid in P. putida. Strain LLC-1 did not possess the genes for mandelic acid racemization and oxidation, suggesting that the function of benzoylformic acid catabolic enzymes is different from that in P. putida. Genome-wide characterization identified the bzf gene responsible for benzoylformate and vanillin catabolism in strain LLC-1, exhibiting a unique mode of dissimilation for biomass-derived aromatic compounds by this strain.

Keywords: Pseudomonas; benzoylformic acid; bzf gene; lignin; mandelic acid; vanillin; vanillin dehydrogenase.

Publication types

  • Comparative Study
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Aldehydes / metabolism
  • Benzaldehydes / metabolism
  • Biotransformation / genetics
  • Carboxylic Acids / metabolism
  • Escherichia coli / genetics
  • Gas Chromatography-Mass Spectrometry
  • Genes, Bacterial*
  • Glyoxylates / metabolism
  • Japan
  • Ketones / metabolism
  • Lignin / metabolism*
  • Mandelic Acids / metabolism
  • Metabolism / genetics*
  • Molecular Weight
  • Phylogeny
  • Pseudomonas / classification
  • Pseudomonas / genetics*
  • Pseudomonas / growth & development
  • Pseudomonas / metabolism
  • Pseudomonas putida / genetics
  • Ribotyping
  • Soil Microbiology
  • Species Specificity
  • Whole Genome Sequencing


  • Aldehydes
  • Benzaldehydes
  • Carboxylic Acids
  • Glyoxylates
  • Ketones
  • Mandelic Acids
  • phenylglyoxylic acid
  • Lignin
  • vanillin
  • mandelic acid