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Analysis on evolutionary relationship of amylases from archaea, bacteria and eukaryota - PubMed

Analysis on evolutionary relationship of amylases from archaea, bacteria and eukaryota

Shaomin Yan et al. World J Microbiol Biotechnol. 2016 Feb.

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.

Keywords: Amylase; Engineering; Evolution; Phylogenetics; Statistics.

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Figures

Fig. 1
Fig. 1

Phylogenetic tree of 88 α-amylases from archaea. The numbers along each branch and scale bar represent the branch length, which is the number of substitutions per unit time (Tamura et al. 2013). Seven α-amylases from genus Thermococcus were marked in red and four α-amylases from genus Haloarcula were marked in green

Fig. 2
Fig. 2

Average p-distance of α-amylases for each phylum, class, order, family and genus in archaea. Blank: average p-distance is not available

Fig. 3
Fig. 3

Partitioning of p-distance into inter-clan and intra-clan variances for α-amylases from archaea along taxonomic linkage. The bifurcation is the point across taxonomic boundary. Pies show the inter-clan variance (dark color) and intra-clan variance (bright color). The green and deep green pie is an example discussed in “Results section”. Taxonomic names can be found in Supplementary Material Table S2

Fig. 4
Fig. 4

Full phylogenetic tree of 724 amylases from eukaryota. β-amylases distribute in the upper cluster marked in red bar, and only 4 β-amylases scatter among α-amylases in the bottom indicated by red line. The full phylogenetic tree in Newick format with maximum likelihood bootstrap values on all branches is available in supplementary materials

Fig. 5
Fig. 5

Average p-distance of amylases for each kingdom, phylum, class, order, family and genus in eukaryota. Blank: average p-distance is not available

Fig. 6
Fig. 6

Partitioning of p-distance into inter-clan and intra-clan variances for α-amylases from eukaryota along taxonomic linkage. The bifurcation is the point across taxonomic boundary. Pies show the inter-clan variance (dark color) and intra-clan variance (bright color). The blue and deep blue pie is an example discussed in “Results section”. Taxonomic names can be found in Supplementary Material Table S2

Fig. 7
Fig. 7

Phylogenetic tree of amylases from bacteria. Panel a is the full phylogenetic tree of 2586 amylases from bacteria, where the amylases marked in red belong to E. coli. Panel b is a detailed portion of phylogenetic tree of amylases from E. coli (red bars) and from genus Shigella (green bars). Panel c is a detailed portion of phylogenetic tree of amylases from phyla Armatimonadetes, Bacteroidetes, Firmicutes and Proteobacteria were marked in orange, black, dark green and pink bars, respectively. Panel d is a detailed portion of phylogenetic tree of amylases from E. coli (red bars) and from genus Shigella (green bars). The full phylogenetic tree in Newick format with maximum likelihood bootstrap values on all branches is available in supplementary materials

Fig. 8
Fig. 8

Average p-distance of amylases for each phylum, class, order, family and genus in bacteria. Blank: average p-distance is not available

Fig. 9
Fig. 9

Partitioning of p-distance into inter-clan and intra-clan variances for α-amylases from bacteria along taxonomic linkage. The bifurcation is the point across taxonomic boundary. Pies show the inter-clan variance (dark color) and intra-clan variance (bright color). The gray and black pie is an example discussed in “Results section”. Taxonomic names can be found in Supplementary Material Table S

Fig. 10
Fig. 10

Overall evolution of amylases from archaea, bacteria and eukaryota. Full phylogenetic tree of 3398 amylases was shown in left panel. The amylases from archaea were marked with red, of which part phylogenetic trees showed the detail distribution in the right panels. The detail distribution of two amylases from Halothermothrix orenii was shown in bottom. The amylases from archaea, bacteria and eukaryota were marked with red, black and green bars, respectively. The full phylogenetic tree in Newick format with maximum likelihood bootstrap values on all branches is available in supplementary materials

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