Table 1.
Distribution of putative genes involved in starch degradation in 85 fungal genomes.
Figure 1.
Evolutionary branches of the GH13 amylolytic enzymes from 85 fungi and their structure features.
A. The inner circle was the phylogenetic tree of the GH13 amylolytic enzymes from 85 fungal genomes and the root was put at the mid-point of the longest span across the tree. The tree was inferred by FastTree from the alignments of GH13 amylolytic enzymes constructed by HMMER packages against the profile hidden Markov model of PF00128 and edited on iTOL. The bootstrap values at the inner nodes are displayed by the color that the related edges are marked in red with the values less than 800 in 1000 replicates and otherwise maintain in dark. The outer is the taxon represented as species abbreviation (shown in Table? 1) followed by the serial number, which is covered by different colors to show its taxonomic group as the legend indicated. Each taxon links the branch with a dotted line. Distribution of putative starch-binding domains is indicated by the scattered solid circles outside the corresponding taxon. B. Primary and secondary structure features of four clades. The consensus logos of four clades were generated by Jalview from matched residues in their alignments against the profile hidden Markov model of PF00128. In the logo, the total stack height represented the information content of amino acids at that position. The relative height of each amino acid in the stack was proportional to its frequency at the position and amino acids were sorted so the most common one was on top of the stack. Secondary structures of four consensus sequences were automatically predicted by Jpred Server embedded in Jalview that helices were marked as red tubes and sheets as dark green arrows.
Figure 2.
Evolutionary branches of the GH15 family from 85 fungi and their structure features.
A. Phylogenetic tree of the GH15 family and B. Primary and secondary structure features of the two clades. For details see legend of Figure 1.
Figure 3.
Evolutionary branches of the GH31 α-glucosidases from 85 fungi and their structure features.
A. Phylogenetic tree of GH31 α-glucosidases and B. Primary and secondary structure features of the four clades. For details see legend of Figure 1.
Figure 4.
Sequence alignments of putative proteins from CBM family 20.
Multiple alignments of putative proteins were performed by aligning them to the profile hidden Markov model of PF00686 with HMMER package. Residues assigned to match states were reserved for the profile analysis and their consensus logo and numbering were generated by Jalview. Protein sequence ID is represented as species abbreviation followed by serial number and domain position.
Figure 5.
Sequence alignments of putative proteins from CBM families 21, 25 and 48.
A, B and C correspond to the alignments of CBM21, 25 and 48 adjusted against the profile hidden Markov models of PF03370, PF03423 and PF02922 respectively.
Figure 6.
Possible evolutionary scenarios for amylolytic enzyme evolution in fungi.
A. Evolutionary scenarios for the GH13 enzymes. A few α-amylases identified as heterologous α-amylases might be transferred from animals and Actinomycetes. Eukaryotic, bacterial and fungal α-amylases correspond to subfamilies GH13_1 and GH13_5, respectively. GH13 α-glucosidases seem evolved from ancestral α-amylase. B. Evolutionary scenarios for the GH15 enzymes. The function of novel GH15 branch is currently unknown. C. Evolutionary scenarios for the GH31 enzymes. The enzymes in the group of temporarily named bacterial α-glucosidase are phylogenetically close to their bacterial counterparts. They may constitute a new clade of GH31 α-glucosidases in fungi.