Cloning and characterization of the ferulic acid catabolic genes of Sphingomonas paucimobilis SYK-6

Appl Environ Microbiol. 2002 Sep;68(9):4416-24. doi: 10.1128/aem.68.9.4416-4424.2002.

Abstract

Sphingomonas paucimobilis SYK-6 degrades ferulic acid to vanillin, and it is further metabolized through the protocatechuate 4,5-cleavage pathway. We obtained a Tn5 mutant of SYK-6, FA2, which was able to grow on vanillic acid but not on ferulic acid. A cosmid which complemented the growth deficiency of FA2 on ferulic acid was isolated. The 5.2-kb BamHI-EcoRI fragment in this cosmid conferred the transformation activity of ferulic acid to vanillin on Escherichia coli host cells. A sequencing analysis revealed the genes ferB and ferA in this fragment; these genes consist of 852- and 2,127-bp open reading frames, respectively. The deduced amino acid sequence of ferB showed 40 to 48% identity with that of the feruloyl-coenzyme A (CoA) hydratase/lyase genes of Pseudomonas and Amycolatopsis ferulic acid degraders. On the other hand, the deduced amino acid sequence of ferA showed no significant similarity to the feruloyl-CoA synthetase genes of other ferulic acid degraders. However, the deduced amino acid sequence of ferA did show 31% identity with pimeloyl-CoA synthetase of Pseudomonas mendocina 35, which has been classified as a new superfamily of acyl-CoA synthetase (ADP forming) with succinyl-CoA synthetase (L. B. Sánchez, M. Y. Galperin, and M. Müller, J. Biol. Chem. 275:5794-5803, 2000). On the basis of the enzyme activity of E. coli carrying each of these genes, ferA and ferB were shown to encode a feruloyl-CoA synthetase and feruloyl-CoA hydratase/lyase, respectively. p-coumaric acid, caffeic acid, and sinapinic acid were converted to their corresponding benzaldehyde derivatives by the cell extract containing FerA and FerB, thereby indicating their broad substrate specificities. We found a ferB homolog, ferB2, upstream of a 5-carboxyvanillic acid decarboxylase gene (ligW) involved in the degradation of 5,5'-dehydrodivanillic acid. The deduced amino acid sequence of ferB2 showed 49% identity with ferB, and its gene product showed feruloyl-CoA hydratase/lyase activity with a substrate specificity similar to that of FerB. Insertional inactivation of each fer gene in S. paucimobilis SYK-6 suggested that the ferA gene is essential and that ferB and ferB2 genes are involved in ferulic acid degradation.

MeSH terms

  • Amino Acid Sequence
  • Cloning, Molecular
  • Coenzyme A Ligases / genetics
  • Coenzyme A Ligases / isolation & purification
  • Coenzyme A Ligases / metabolism*
  • Coumaric Acids / metabolism*
  • DNA, Bacterial / analysis
  • Escherichia coli
  • Gene Expression
  • Genes, Bacterial / physiology*
  • Molecular Sequence Data
  • Mutagenesis, Insertional
  • Phylogeny
  • Recombinant Proteins / metabolism
  • Sequence Homology, Amino Acid
  • Sphingomonas / enzymology*
  • Sphingomonas / genetics
  • Sphingomonas / metabolism
  • Substrate Specificity

Substances

  • Coumaric Acids
  • DNA, Bacterial
  • Recombinant Proteins
  • ferulic acid
  • Coenzyme A Ligases
  • feruloyl-coenzyme A synthetase