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Online Journal of Bioinformatics©
Volume 5:32-48, 2004.
Phylogenetic Clustering and Secondary structural analysis of Plant Terpenoid Synthases.
Singh IV1, Agrawal S2, Khan3 F, Mishra BN4
1,3,4 Department of Biotechnology, Institute of Engineering & Technology, Uttar Pradesh, 2 Bioinformatics Division, Indian Institute of Information Technology, Allahabad, India
Singh IV, Agrawal S, Khan F, Mishra BN Phylogenetic Clustering and Secondary structural analysis of Plant Terpenoid Synthases Onl J Bioinform., 5:32-48, 2004. The present work describes the evolutionary, secondary structural and functional relationship among 95 plant derived terpene synthases. Amino acid sequences of selected plant terpene synthases were retrieved from the NCBI data bank. Tree Top (TT) and Conserve Domain Database (CDD) programs were used for phylogenetic analysis, and domain identification and creation of phylogenetic trees, respectively. The phylogenetic tree of primary sequences revealed significant synteny in individual groups as well as groups in combinations, whereas the secondary structure analysis in terms of a helix, b extended sheets and random coils showed almost similar percentage of occurrence with varying structural arrangements in the individual classes of enzyme. Most of the members in each class of the terpenoid synthases were functionally analyzed to have common conserved domain(s). Henceforth, secondary structural and functional relatedness could be established both in terpenoid synthases as a whole as well as in individual class.
KEY WORDS: Isoprenoids, Terpenoids, Terpene synthases, Phylogenetic clustering, Secondary structure analysis.