title: Analysis on evolutionary relationship of amylases from archaea, bacteria and eukaryota.
abstract: Amylase is one of the earliest characterized enzymes and has many applications in clinical and industrial settings. In biotechnological industries, the amylase activity is enhanced through modifying amylase structure and through cloning and expressing targeted amylases in different species. It is important to understand how engineered amylases can survive from generation to generation. This study used phylogenetic and statistical approaches to explore general patterns of amylases evolution, including 3118 α-amylases and 280 β-amylases from archaea, eukaryota and bacteria with fully documented taxonomic lineage. First, the phylogenetic tree was created to analyze the evolution of amylases with focus on individual amylases used in biofuel industry. Second, the average pairwise p-distance was computed for each kingdom, phylum, class, order, family and genus, and its diversity implies multi-time and multi-clan evolution. Finally, the variance was further partitioned into inter-clan variance and intra-clan variance for each taxonomic group, and they represent horizontal and vertical gene transfer. Theoretically, the results show a full picture on the evolution of amylases in manners of vertical and horizontal gene transfer, and multi-time and multi-clan evolution as well. Practically, this study provides the information on the surviving chance of desired amylase in a given taxonomic group, which may potentially enhance the successful rate of cloning and expression of amylase gene in different species.
authors.affiliation: State Key Laboratory of Non-food Biomass Enzyme Technology, National Engineering Research Center for Non-food Biorefinery, Guangxi Biomass Industrialization Engineering Institute, Guangxi Key Laboratory of Biorefinery, Guangxi Academy of Sciences, 98 Daling Road, Nanning, 530007, Guangxi, China.
authors.forename: Shaomin
authors.initials: S
authors.lastname: Yan
authors.affiliation: State Key Laboratory of Non-food Biomass Enzyme Technology, National Engineering Research Center for Non-food Biorefinery, Guangxi Biomass Industrialization Engineering Institute, Guangxi Key Laboratory of Biorefinery, Guangxi Academy of Sciences, 98 Daling Road, Nanning, 530007, Guangxi, China. hongguanglishibahao@yahoo.com.
authors.forename: Guang
authors.initials: G
authors.lastname: Wu
mesh_terms: D000595:Amino Acid Sequence; D000681:Amylases / Q000145:classification / Q000235:genetics* / Q000378:metabolism; D001105:Archaea / Q000201:enzymology* / Q000235:genetics; D001419:Bacteria / Q000201:enzymology* / Q000235:genetics; D003627:Data Interpretation, Statistical; D056890:Eukaryota / Q000201:enzymology* / Q000235:genetics; D019143:Evolution, Molecular; D022761:Gene Transfer, Horizontal; D005818:Genetic Engineering; D014644:Genetic Variation; D008969:Molecular Sequence Data; D010802:Phylogeny; D016415:Sequence Alignment
chemical_list: D000681:Amylases
keywords: Amylase; Engineering; Evolution; Phylogenetics; Statistics