Origins and Evolution of the α-L-Fucosidases: From Bacteria to Metazoans

Abstract

α-L-fucosidases (EC 3.2.1.51, FUC), belonging to the glycoside hydrolase family 29 (GH29), play important roles in several biological processes and are markers used for detecting hepatocellular carcinoma. In this study, a protein sequence similarity network (SSN) was generated and a subsequent evolutionary analysis was performed to understand the enzymes comprehensively. The SSN indicated that the proteins in the FUC family are mainly present in bacteria, fungi, metazoans, plants, as well as in archaea, but less abundantly. The sequences in bacteria were found to be more diverse than those in other taxonomic groups. The SSN and a phylogenetic tree both supported that the proteins in the FUC family can be classified into 3 subfamilies. FUCs in each subfamily are under the pressure of negative selection. The enzymes from metazoans, fungi, and plants separated into the three subfamilies and shared high similarity with the bacterial homologs. The multiple sequence alignment results indicated that the amino acid residues for binding α-L-fucosidase and catalysis are highly conserved in the 3 subfamilies; however, the evolutionary patterns were different, based on the coevolution analysis in the subfamily of metazoans and bacteria. Finally, gene duplication plays an important role for α-L-fucosidase evolution, not only in metazoans, but also in bacteria and fungi.

Keywords: bacteria; evolution; metazoa; sequence similarity network; α-L-fucosidase.

FIGURE 1

Sequence similarity network (SSN) of α-L-fucosidases from metazoans (A), fungi (B), plants (C), and bacteria (D). The sequences were retrieved from the UniProt database using BLASTP with an E-value = 10^–2. The proteins with known function from the literature were used as query sequences. The SSN of the enzymes was constructed with an E-value = 10^–60. Each node corresponds to one putative FUC. Edges are drawn with E-values < 10^–60 for BLASTP. The colors represent different phyla and the percentage of the proteins in each phylum are recorded at the bottom.

FIGURE 2

Sequence similarity network (SSN) of α-L-fucosidases across biospheres. The SSN of the putative FUCs was constructed with E-values = 10^–70 (A), 10^–75 (B), and 10^–80 (C). Each node corresponds to one putative FUC. Edges are required to have E-values less than the cutoff values. Metazoans, fungi, bacteria, and archaea proteins are displayed in purple, blue, green, and yellow, respectively. The putative FUCs from metagenomes are displayed in red.

FIGURE 3

Phylogenetic analysis of α-L-fucosidases. Molecular phylogenetic analysis of the proteins generated via the maximum likelihood method using MEGA7. The replicate percentage of the trees is shown near the branches. The accession numbers of the proteins in the UniProt database are indicated in front of the names of the species. The proteins from metazoans, fungi, bacteria, and plants are highlighted in violet, blue, green, and pink.

FIGURE 4

Multiple sequence alignment of the α-L-fucosidase homologs in the three subfamilies. Secondary structure elements (SSE) of hFUCA1 are shown at the top of the alignment. The amino acids that function as catalytic nucleophiles and the general acids/bases are blue triangles, and the residues that interact with fucose within the catalytic pocket are denoted as yellow triangles.

FIGURE 5

Conservation and coevolution of the amino acids in α-L-fucosidases represented by α-L-fucosidase from B. thetaiotaomicron (A) and human (B). (a) Coevolution of the residues analyzed via the circular network. The connectivity of the coevolving residues is shown by the circular network. The labels in the outermost circle show the amino acid code and the alignment position of hFUCA1. In the second circle, the boxes indicate conservation in the multiple sequence alignment (MSA), from blue (less conserved ones) to red (highly conserved). The proximity and cumulative MI values as histograms are indicated in the third and fourth circles. The edges that link positions in the center of the circle correspond to a MI value higher than 6.5: red lines: top 5%, black lines: 70–95%, and gray lines: < 70%. (b) The top conserved FUC residues mapped in the structure of the proteins. The residues binding fucose within the catalytic pocket were highlighted in red.