Functional and Phylogenetic Diversity of BSH and PVA Enzymes

Abstract

Bile salt hydrolase (BSH) and penicillin V acylase (PVA) are related enzymes that are classified as choloylglycine hydrolases (CGH). BSH enzymes have attracted significant interest for their ability to modulate the composition of the bile acid pool, alter bile acid signaling events mediated by the host bile acid receptors FXR and TGR5 and influence cholesterol homeostasis in the host, while PVA enzymes have been widely utilised in an industrial capacity in the production of semi-synthetic antibiotics. The similarities between BSH and PVA enzymes suggest common evolution of these enzymes and shared mechanisms for substrate binding and catalysis. Here, we compare BSH and PVA through analysis of the distribution, phylogeny and biochemistry of these microbial enzymes. The development of new annotation approaches based upon functional enzyme analyses and the potential implications of BSH enzymes for host health are discussed.

Keywords: FXR; TGR5; bile acid; bile salt hydrolase; cholesterol; microbiome; penicillin V acylase.

Figure 1

The 2-dimensional chemical structure of glycocholic acid (GCA) (PubChem identifier: 10140) and phenoxymethylpenicillin (Pen V) (PubChem identifier: 6869). The amide bonds hydrolysed by either bile salt hydrolase (BSH) or penicillin V acylase (PVA) are annotated by the green arrow.

Figure 2

Microbial metabolism of bile acids. Primary bile acids (BAs) are conjugated to an amino acid, either glycine (indicated by “G”) or taurine (indicated by “T”), in the liver to form conjugated bile acids, such as taurocholic acid (TCA) and glycochenodeoxycholic acid (GCDCA). In the intestinal tract, numerous gut bacteria exhibit bile salt hydrolase enzymatic activity capable of cleaving the amide bond of conjugated bile acids resulting in unconjugated primary bile acids and freed glycine or taurine. Certain gut bacteria may act upon these unconjugated primary bile acids through further enzymatic activity, such as 7α-dehydroxylation, to form secondary bile acids, such as deoxycholic acid (DCA) and lithocholic acid (LCA).

Figure 3

Molecular phylogenetic analysis of several members of the Ntn-hydrolase superfamily. Five clusters emerge correlating with substrate specificity: AHL acylase-like proteins are divided between two distinct clusters, AHL acylase group A and AHL acylase group B. The PGA group consists of penicillin G acylase proteins. The closely related bile salt hydrolase and penicillin V acylase proteins are grouped within the CGH group. A novel Amidase group was identified composed of an AHL acylase-like protein from Acinetobacter sp. Ooi24. Proteins that exhibit both AHL acylase and penicillin acylase activities are indicated by asterisks. The evolutionary history was inferred using the neighbour-joining (NJ) method within the 3DM and MEGA X packages. From [40].

Figure 4

(a) The 3D structure of Clostridium perfringens CpBSH following the hydrolysis of glycocholic acid (GCA) with the products glycine bound in the active site (siteL) and cholate bound in the binding site (siteA) (both products are shown in stick representation and labelled). (b) The geometrical arrangement of the six major catalytic residues in the active site of CpBSH. (c) The superimposition of the four loops of the substrate binding site (loop1-loop4) from Bifidobacterium longum BlBSH (red), CpBSH (magenta), Bacteroides thetaiotaomicron BtBSH (yellow), Lyinibacillus sphaericus BspPVA (blue) and Bacillus subtilis BsuPVA (green). The active site nucleophilic residue Cys is shown and labelled. From [10].