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

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.