Structure and evolution of 4-coumarate : coenzyme A ligase (4CL) gene families

The phenylpropanoid enzyme 4-coumarate:coenzyme A ligase (4CL) plays a key role in general phenylpropanoid metabolism, 4CL is related to a larger clas s of prokaryotic and eukaryotic adenylate-forming enzymes and shares severa l conserved peptide motifs with these enzymes. In order to better character ize the nature of 4CL gene families in poplar, parsley, and tobacco, we use d degenerate primers to amplify 4CL sequences from these species. In each s pecies additional, divergent 4CL genes were found. Complete cDNA clones for the two new poplar 4CL genes were obtained, allowing examination of their expression patterns and determination of the substrate utilization profile of a xylem-specific isoform. Phylogenetic analysis of these genes and gene fragments confirmed previous results showing that 4CL proteins fall into tw o evolutionarily ancient subgroups. A comparative phylogenetic analysis of enzymes in the adenylate-forming superfamily showed that 4CLs, luciferases, and acetate CoA ligases each form distinct clades within the superfamily. According to this analysis, four Arabidopsis 4CL-like genes identified from the Arabidopsis Genome Project are only distantly related to bona fide 4CL s or are more closely related to fatty acid CoA ligases, suggesting that th e three Arabidopsis 4CL genes previously characterized represent the extent of the 4CL gene family in this species.