Analysis of Two SusE-Like Enzymes From Bacteroides thetaiotaomicron Reveals a Potential Degradative Capacity for This Protein Family.

Bacteroides thetaiotaomicron is a major constituent of the human gut microbiome and recognized as a prolific degrader of diverse and complex carbohydrates. This capacity is due to the large number of glycan-depolymerization and acquisition systems that are encoded by gene clusters known as polysaccharide utilization loci (PUL), with the starch utilization system (Sus) serving as the established model. Sharing features with the Sus are Sus-like systems, that require the presence of a specific membrane transporter and surface lipoprotein to be classified as Sus-like. Sus-like import loci are extremely varied with respect to any additional protein components encoded, that would effectively modify the functionality of the degradative and import action of each locus. Herein we have identified eight Sus-like systems in B. thetaiotaomicron that share the feature of a homologous SusE-like factor encoded immediately downstream from the transporter/lipoprotein duo susC/D. Two SusE-like proteins from these systems, BT2857 and BT3158, were characterized by X-ray crystallography and BT2857 was further analyzed by small-angle X-ray scattering. The SusE-like proteins were found to be composed of a conserved three domain architecture: a partially disordered N-terminal domain that is predicted to be proximal to the membrane and structurally homologous to an FN3-like bundle, a middle ß-sandwich domain, and a C-terminal domain homologous to family 32 carbohydrate-binding modules, that bind to galactose. Structural comparisons of SusE with SusE-like proteins suggested only a small structural divergence has occurred. However, functional analyses with BT2857 and BT3158 revealed that the SusE-like proteins exhibited galactosidase activity with para-nitrophenyl-ß-D-galactopyranoside and α-(1,4)-lactose substrates, that has not been demonstrated for SusE proteins. Using a series of domain truncations of BT2857, the predominant ß-D-galactosidase activity is suggested to be localized to the C-terminal DUF5126 domain that would be most distal from the outer membrane. The expanded functionality we have observed with these SusE-like proteins provides a plausible explanation of how Sus-like systems are adapted to target more diverse groups of carbohydrates, when compared to their Sus counterparts.

Methods for Determining Glycosyltransferase Kinetics.

Glycosyltransferases are a class of biosynthetic enzymes that transfer individual activated monosaccharide units to specific acceptors. Colorimetric assays using the detection of released products such as para-nitrophenol and coupled assays for inorganic phosphate detection allow for convenient and quantifiable kinetic characterization. These techniques may be applied to determine the enzymatic activity of glycosyltransferases by indirectly measuring the transfer of nucleotide-activated donor carbohydrate units to various cognate acceptor molecules. In addition to an overview of these methods, the protocol for quantifying the glycosyltransferase activity used for the characterization of penicillin-binding proteins (PBPs) involving the transfer of lipid II to form elongated murein chains during bacterial cell wall synthesis is described herein.

Limitations on the Persistence of Iminoxyls: Isolation of tert-Butyl 1,1-Diethylpropyl Ketiminoxyl and Related Radicals.

A series of iminoxyl radicals of the general formula R(C=NO(*))R(1), with R and R(1) usually tertiary, was synthesized in a search for radicals of increased persistence. Three new radicals were isolated as blue liquids: Et(3)C(C=NO(*))Bu-t (1), t-C(5)H(11)(C=NO(*))Bu-t (2), and (t-C(5)H(11))(2)C=NO(*) (3). Oxidation of oximes Et(3)C(C=NOH)Ph (4H), PhCH(2)CMe(2)(C=NOH)Bu-t (5H), PhCMe(2)(C=NOH)Bu-t (6H), and Me(2)CH(C=NOH)C(5)H(11)-t (7H), among others, did not lead to isolable iminoxyls. A new, convenient synthesis of symmetrical tertiary imines from tert-RCl, tert-RCN, and Na is described. Radical t-Bu(2)C=NO(*) (8) and cyclohexene readily gave the allylic substitution product, 2,2,4,4-tetramethyl-3-hexanone O-(2'-cyclohexen-1'-yl)oxime.