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.Electronic supplementary materialThe online version of this article (doi:10.1007/s11274-015-1979-y) contains supplementary material, which is available to authorized users.

Rethinking the starch digestion hypothesis for AMY1 copy number variation in humans

“…In addition to this initial gene duplication, some species have experienced further CN increase in both salivary ( AMY1 ) and pancreatic ( AMY2 ) α‐amylase genes. The α‐amylase enzyme exists across the broad taxonomic domains Archaea, Bacteria and Eukarya (Yan & Wu, ) but its expression in saliva has only been recognized in a few mammalian species, with varying levels of expression and diets (see Boehlke et al, ; Chauncey, Henriques, & Tanzer, ; de Sousa‐Pereira et al, ; Junqueira, Toledo, & Doine, ; Young & Schneyer, ). However, to our knowledge, the association of salivary amylase activity with AMY1 CN has only been assessed in humans (Carpenter, Mitchell, & Armour, ; Mandel, Peyrot Des Gachons, Plank, Alarcon, & Breslin, ; Perry et al, ; Tan et al, ; Viljakainen et al, ).…”

Biochemical Characterization of the Amylase Activity from the New Haloarchaeal Strain Haloarcula sp. HS Isolated in the Odiel Marshlands

“…Alpha-amylases are a large family of endo-glycosyl hydrolases that cleave the internal α,1-4 glycosidic bonds between the glucose units in polysaccharides, such as amylose and amylopectin. They are common in all kingdoms of life and their general properties, three-dimensional structures, and mechanisms of action are extensively reviewed [ 40 , 41 , 42 , 43 ].…”

“…The physicochemical parameters of the new alpha-amylases, with low isoelectric point and negative net charge ( Table 3 ) also meet the usual characteristic of haloarchaeal enzymes, as reported by other authors. Yan and Wu [ 43 ] analyzed the sequences of 88 α-amylases from archaea and observed that amylases from haloarchaea have a highly negatively charged surface, and a higher percentage of acidic residues as a mechanism of adaptation to high salinity. Other authors describe similar features for H. hispanica , which has an extracellular amylase with an isoelectric point of 4.2 and a low level of aromatic and hydrophobic residues [ 27 ].…”

Evaluation of commercial α‐amylase enzyme‐linked immunosorbent assay (ELISA) test kits for wheat

“…α‐Amylase is one of the most widespread enzymes in nature. Although all isoforms share a commonality of catalytic function, an enormous range in primary and secondary structures exists (Yan & Wu, ). As such, we consider it highly serendipitous that the AMY2 kit appears to be detecting increased α‐amylase levels associated with PHS and LMA.…”