Location: Crop Genetics and Breeding ResearchTitle: Molecular evolution of the plant ECERIFERUM1 and ECERIFERUM3 genes involved in aliphatic hydrocarbon production
Submitted to: Journal of Computational Biology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 2/25/2019
Publication Date: 6/1/2019
Citation: Wang, H., Ni, X., Harris-Shultz, K.R. 2019. Molecular evolution of the plant ECERIFERUM1 and ECERIFERUM3 genes involved in aliphatic hydrocarbon production. Journal of Computational Biology. 80:1-9.
Interpretive Summary: The plant cuticle covers the above ground organs of land plants and functions primarily to prevent water loss but also has a role in signaling, plant defense, and development. The cuticle is made up of two types of lipids: cutin and wax. The CER1 protein, a decarbonylase, from Arabidopsis converts long chain fatty acid aldehydes to alkanes, the major constituents of cuticle waxes. Since plant decarbonylase encoded by CER1 gene has only been confirmed in model plants Arabidopsis, we sought to identify and characterize CER1 homologs in the genomes of other plants species whose genomes have been fully sequenced. CER1 homologs were found in all examined plant species except the aquatic plant duckweed. Early plants that reproduce using spores had a single CER1 gene copy whereas multiple copies were found in angiosperms. Furthermore 15 protein motifs were identified in the CER1 genes and purifying selection that removes deleterious alleles was a pivotal driving force in CER1 evolution. These results identify and characterize homologs of CER1 gene involved in the production of cuticle alkane waxes through fatty acid decarbonylation. The in silico identified adecarbonylases from 56 plant species will undergo further experimental investigation.
Technical Abstract: The Arabidopsis CER1 protein is a decarbonylase that converts fatty acid metabolites into alkanes. Aliphatic hydrocarbons are the major components of waxes in the plant cuticle, a waterproof barrier against both biotic and abiotic stimuli in terrestrial plants. Plant CER1 enzymes can be used to produce alternative and sustainable hydrocarbons in eukaryotic systems. In this report, 56 plant genomes were examined to elucidate the phylogeny of the CER1 genes. We retrieved 193 putative CER1 sequences that all encode histidine-containing motifs similar to fatty acid hydroxylase and stearoyl-CoA desaturase. Among the 56 plant species, all four cryptogams have only a single copy of the CER1 gene, whereas gene duplications are common in most angiosperm plants. Protein sequences encoded by CER1 genes have evolved slowly. There was no significant loss or gain of protein motifs after ancient and recent duplications. To facilitate the understanding of the catalytic mechanisms underlying CER1 decarbonylation, the structure of Arabidopsis CER1 protein was predicted and conserved residues were profiled. The codon-based assessments of selection modes indicated that purifying selection is a pivotal driving force in CER1 evolution. The study is the first evolutionary analysis of the CER1 genes across terrestrial plants. The obtained results suggest that the primary structures of CER1 proteins were largely shaped at the ancestral stage, but gene duplication and functional divergence occurred after the emergence of angiosperm plants.