A pseudogene of caffeic acid-o-methyltransferase (COMT) in Acacia mangium: Comparative analysis with other COMT plant promoters

Abstract

Acacia mangium is a prominent tree species in the forest plantation industry of Southeast Asia, grown mainly to produce pulp and paper, and to a lesser extent wood chips and solid wood products. Lignin, a natural complex polymer used by plants for structural support and defence, has to be chemically removed during the production of quality paper. Delignification is very expensive and moreover, is an environmental pollutant. Understanding the complex mechanisms that underlie the regulation of lignin biosynthetic genes requires in-depth knowledge of not only the genes involved but also their regulatory elements. Using Thermal Asymmetric Interlaced PCR, a 770 bp promoter sequence with 93% identity with COMT1 gene from Acacia auriculiformis x A. mangium hybrid was isolated from A. mangium. Bioinformatics analysis revealed the presence of cis acting elements commonly found in other lignin biosynthesis genes such as TATA box, CAAT box, W box, AC-I and AC-11 elements. However, a nonsense mutation that created a premature stop codon was found on the first exon. Modelling of MYB transcription factor binding site on this newly isolated pseudogene shows it has binding sites for important transcription factors involved in lignin biosynthesis both in Arabidopsis thaliana and Eucalyptus grandis. Given the remarkable structures of its regulatory region, the possible structure of its transcript was detected using Mfold. Results show the transcript are capable of forming stem loop structures, a characteristic commonly attributed to presence of miRNA. Possible functions of pseudoAmCOMT1 were discussed.