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.
Highlights
Fucose is a hexose deoxy sugar with a relatively low abundance in the biosphere
To analyze the evolution of FUCs, we searched the UniProt database using the FUCs from humans (UniProt ID: P04066), Arabidopsis (Q8GW72), Dictyostelium discoideum (P10901), and Bacteroides thetaiotaomicron (Q9WYE2) as query sequences, which have been experimentally characterized
6208 sequences were collected (Supplementary Sheet) and FUC homologs were found to be widespread in metazoans, plant, fungi, and bacteria; in addition, a few homologs were found in archaea
Summary
Fucose is a hexose deoxy sugar with a relatively low abundance in the biosphere. Fucoses are usually attached to oligosaccharides, oligolipids, and other glycoconjugates by α-1,3 linkages to glucose (Glc), α-1,2 linkages to galactose (Gal), or 1,3/4/6 linkages to N-acetylglucosamine (GlcNAc) (Becker and Lowe, 2003). α-L-fucosidase (FUC) (EC 3.2.1.51) is a group of glycoside hydrolase (EC 3.2.1) that catalyzes the reaction to remove the Non-reducing terminal L-fucose; recently, an FUC from the bacterium Elizabethkingia meningoseptica was found to have catalytic activity against the substrates with core α-1,3-fucosylation (Moreti et al, 2013; Li et al, 2018). Α-L-fucosidase (FUC) (EC 3.2.1.51) is a group of glycoside hydrolase (EC 3.2.1) that catalyzes the reaction to remove the Non-reducing terminal L-fucose; recently, an FUC from the bacterium Elizabethkingia meningoseptica was found to have catalytic activity against the substrates with core α-1,3-fucosylation (Moreti et al, 2013; Li et al, 2018). GH29 FUCs are well-studied because of the biological importance of L-fucose and the fucosylated conjugates in several critical biological processes such as the immune response, early embryogenesis and development, signal transduction, adhesion of pathogens, apoptosis, and extravasation of leukocytes (Intra et al, 2007). Fucose and FUC play important roles in gamete interactions in bull, ascidians, and molluscs (Matsumoto et al, 2002). FUC and/or L-Fucose may have function in sperm-egg interaction in amphibians and mammals (Venditti et al, 2007)
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