Radiation and Functional Specialization of the Family-3 Glycoside Hydrolases

Abstract

A phylogenetic analysis of the glycoside hydrolases of family 3 (GH3s) was conducted in order to infer particular trends in its evolution: functional specialization, gene transfer events, gene duplications and paralogous evolution, and gene deletions. The phylogenetic analysis of GH3s revealed six clusters, i.e., A, B, C, D, E, and F that could fit the definition of 3 sub-families, i.e., AB, AB′ and AB′′. While the sub-families AB′ and AB′′ contain a single cluster, F and E, respectively, the AB sub-family is sub-divided into four clusters. Global analysis of the GH3 phylogenetic tree suggests a primary burst of amplification of the GH3s that might have led to these sub-families. Specializations, gene transfers, and gene duplications among each of these sub-families and phylogenetic clusters might then have occurred and have been inferred. The fine comparison of the enzyme properties and phylogenetic relationships of GH3s allowed to detect common functional groups that belong to the same cluster (D, E or F), or sub-cluster (A1, A2 or B2). The prokaryotic and eukaryotic β-xylosidases and β-glucosidases belong to the AB and AB′ sub-families, and the N-acetylglucosaminidases are in sub-family AB′′ (in cluster E). In some instances (B1, B2, C1, C2, and C3), the lack of data and/or the high heterogeneity of the hydrolytic properties did not allow to infer a particular link between an enzyme functional group and a phylogenetic cluster, suggesting the emergence of some highly specialized GH3s.

Characterization of an Unusual Cold-Active β-Glucosidase Belonging to Family 3 of the Glycoside Hydrolases from the Psychrophilic Isolate Paenibacillus sp. Strain C7

“…This K m is 10-fold lower than that of the only cluster F enzyme with published kinetic analyses, SalB from A. irakense (50 M, PNPGlu) (15). Enzymes in the subcluster C3, distant from cluster F (10), are the only other GHF 3 enzymes with K m values in this low range. One of these is from Thermotoga maritima with a K m of 3.9 M on PNPGlu (16).…”

“…The need for biochemical and physiological studies of microbial glycoside hydrolases is highlighted by the prevalence of open reading frames (ORFs) homologous to genes encoding GHF 1 and GHF 3 enzymes in a majority of analyzed bacterial genomes (10). Although the original interest in ␤-glucosidases focused on their participation in degrading the plant polymers cellulose and xylan (14), the importance of the interaction of ␤-glucosidases with plant-produced compounds goes beyond catabolic degradation and includes plant-phytopathogen interactions (6,29,32).…”

Structural and Kinetic Analysis of Bacillus subtilis N-Acetylglucosaminidase Reveals a Unique Asp-His Dyad Mechanism

“…A detailed understanding of the mechanism of these enzymes is a prerequisite for the design of potent selective inhibitors that may serve as novel therapeutic agents. The identification of evolutionary and structural rela- , and His 222 ) that are highly conserved among ␤-N-acetyl-glucosaminidases of family 3 (54), are almost identical to the native, unliganded (A) and liganded structure (B). Putative hydrogen bonds between protein and ligands, identified by using the criteria of proper geometry and a distance cut off of 3.2 Å are indicated.…”

Biochemical Analysis of a β- d -Xylosidase and a Bifunctional Xylanase-Ferulic Acid Esterase from a Xylanolytic Gene Cluster in Prevotella ruminicola 23

“…a GH family 3 clusters are assigned based on phylogenetic relationships inferred by Cornoyer and Faure (12). b Functional domains were assigned utilizing the Pfam online server (24).…”