Caffeic acid o-methyltransferase (COMT) is one of the important enzymes controlling lignin monomer production in plant cell wall synthesis. Analysis of the genome sequence of the new grass model Brachypodium distachyon identified four COMT gene homologs, designated as BdCOMT1, BdCOMT2, BdCOMT3, and BdCOMT4. Phylogenetic analysis suggested that they belong to the COMT gene family, whereas syntenic analysis through comparisons with rice and sorghum revealed that BdCOMT4 on Chromosome 3 is the orthologous copy of the COMT genes well characterized in other grass species. The other three COMT genes are unique to Brachypodium since orthologous copies are not found in the collinear regions of rice and sorghum genomes. Expression studies indicated that all four Brachypodium COMT genes are transcribed but with distinct patterns of tissue specificity. Full-length cDNAs were cloned in frame into the pQE-T7 expression vector for the purification of recombinant Brachypodium COMT proteins. Biochemical characterization of enzyme activity and substrate specificity showed that BdCOMT4 has significant effect on a broad range of substrates with the highest preference for caffeic acid. The other three COMTs had low or no effect on these substrates, suggesting that a diversified evolution occurred on these duplicate genes that not only impacted their pattern of expression, but also altered their biochemical properties. 1. Introduction Temperate grains like wheat and barley, along with forage grasses, contribute greatly to the human food and animal feed supply. However, the large and complex genomes in these economically important grasses present challenges for genomics studies and map-based cloning of target genes for crop improvement. Similarly, although large perennial grasses like switchgrass and Miscanthus are being developed as dedicated herbaceous energy crops, our knowledge about the biological and genetic basis of important bioenergy traits remains limited [1–4]. Brachypodium distachyon (hereafter referred as Brachypodium) is an attractive experimental system and genomics model for grass research. It has many desirable attributes (small physical stature, short generation time, easy growth requirement, etc.) and numerous freely available genomics resources (high quality genome sequence, EST collection, large-insert BAC libraries, expression/tilling microarray, T-DNA mutant population, etc.) [5]. Thus, Brachypodium can serve as a useful model system to address issues unique to grasses ranging from grain improvement to the development of superior bioenergy crops [5–7].
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