In silico assessment of lignin biosynthesis genes in Arabidopsis thaliana and Zea mays

Background and Aim: Lignin is the second most prominent terrestrial biopolymer after cellulose, accounting for almost ۳۰ percentage of the organic carbon content in the biosphere. Lignin as an important phenylalnine-derived metabolite is crucial for structural integrity of the cell wall, strength and stiffness of the stem. In addition, lignin biosynthesis not only play a pivotal role in responsive to protect plants against pathogens as well as various types of abiotic stresses, such as water deficit, low temperatures, light, mineral deficiency, and UV-B radiation, but they are also pivotal mediators of the plant interactions with different organisms. The study of lignin biosynthesis and its function will have a significant impact on industrial, agricultural production and other human activities. Therefore, in this study we tried to compare the involved genes in lignin biosynthesis pathway of Arabidopsis thaliana (as dicotyledonous) and Zea mays (monocotyledonous) through analyses of existing data by some bioinformatics tools to reveal new aspects on regulatory mechanisms of these genes.Methods: The involved genes identification for the lignin biosynthesis pathway in Arabidopsis and Zea mays were accomplished using the Plantcyc, thus, ۴۷ and ۴۱ genes were retrieved. Prediction of biochemical traits were done by ProtParam tool of Expasy database. The full length of amino acid sequence of all predicted proteins were used to align using ClustalX. The phylogenetic tree was constructed using neighbor-joining method of clustal omega.Results: Molecular weight (MW) of proteins in A. thaliana varied between ۱۵.۷۸– ۷۴.۵۸ kDa while in Zea mays, they ranged between ۱۲.۷۶– ۶۳.۴۳ kDa. Most of the proteins had the isoelectric point (pI) around Acidic pH in Arabidopsis thaliana and Zea mays. Besides, the obtained results using ProtParam tool revealed that lignin biosynthesis proteins of A. thaliana were more stable than Zea mays. It seems that lignin biosynthesis proteins of Arabidopsis are more hydrophilic that can affect in their solubility. According to the phylogenetic analysis, lignin biosynthesis genes were separated into four main groups. Interestingly, all the proteins with the common motifs were placed in group number two.Conclusion: An attempt has been made to furnish further information about the genes which are engaging in lignin biosynthesis pathway that will be useful for more dissection.

Keywords:

Protein stability , bioinformatics , cell wall , environmental stresses , phylogenic study