Phylogenetic, Sequence Analysis and Structural Studies of Maturase K Proteins from Mangroves

Abstract

Background: Mangroves are of great significance to numerous people living along tropical shorelines. Mangroves are a rich source of various components having medicinal values. Recently, biodiversity and conservation of mangroves have been globally recognized as one of the critical issue. Objective: It is necessary to study proteins isolated from different mangroves in detail at molecular level along with their taxonomical relationship. The goal of the present study is to use bioinformatics tools to understand evolutionary significance by constructing phylogenetic tree in order to address relationship between true, minor and associate mangroves. Methods: Maturase K (matK) protein sequences of various mangroves were retrieved from NCBI and used for multiple sequence alignment and phylogenetic analysis. Bioinformatics tools were used to understand evolutionary significance by constructing phylogenetic tree. Three-dimensional structures of matK proteins from mangrove species were constructed by homology modeling. Results: Our study indicates that matK proteins are conserved in all groups of mangroves. The residues like histidine and lysine observed in place of glutamine might play a crucial role to provide proper three-dimensional fold to matK proteins. Three-dimensional models of matK obtained from different mangroves showed structural homology to each other. The homology model of matK contains predominantly helices, sheets and loops. Analysis of taxonomical relationship of mangroves through phylogenetic, sequence alignment and structural studies may provide valuable alternative to explore biological role of mangrove plants. Conclusion: Thus, this study suggests that matK proteins could be a good candidate for plant systematics and DNA barcoding studies of mangrove species. Keywords: Mangroves, maturase K, sequence alignment, phylogeny, homology modeling.