ABSTRACT
Functional metagenomics is a powerful tool for both the discovery and development of biocatalysts. This study presents the high-throughput functional screening of 22 large-insert fosmid libraries containing over 300,000 clones sourced from natural and engineered ecosystems, characterization of active clones, and a demonstration of the utility of recovered genes or gene cassettes in the development of novel biocatalysts. Screening was performed in a 384-well-plate format with the fluorogenic substrate 4-methylumbelliferyl cellobioside, which releases a fluorescent molecule when cleaved by ß-glucosidases or cellulases. The resulting set of 164 active clones was subsequently interrogated for substrate preference, reaction mechanism, thermal stability, and optimal pH. The environmental DNA harbored within each active clone was sequenced, and functional annotation revealed a cornucopia of carbohydrate-degrading enzymes. Evaluation of genomic-context information revealed both synteny and polymer-targeting loci within a number of sequenced clones. The utility of these fosmids was then demonstrated by identifying clones encoding activity on an unnatural glycoside (4-methylumbelliferyl 6-azido-6-deoxy-ß-d-galactoside) and transforming one of the identified enzymes into a glycosynthase capable of forming taggable disaccharides.IMPORTANCE The generation of new biocatalysts for plant biomass degradation and glycan synthesis has typically relied on the characterization and investigation of one or a few enzymes at a time. By coupling functional metagenomic screening and high-throughput functional characterization, we can progress beyond the current scale of catalyst discovery and provide rapid annotation of catalyst function. By functionally screening environmental DNA from many diverse sources, we have generated a suite of active glycoside hydrolase-containing clones and demonstrated their reaction parameters. We then demonstrated the utility of this collection through the generation of a new catalyst for the formation of azido-modified glycans. Further interrogation of this collection of clones will expand our biocatalytic toolbox, with potential application to biomass deconstruction and synthesis of glycans.
ABSTRACT
Two isomeric aryl 2-deoxy-2-fluoro-ß-glucosides react with a ß-glucosidase at rates differing by 106-fold, despite the fact that they release the same aromatic aglycone. In contrast, the equivalent glucoside substrates react with essentially identical rate constants. Insight into the source of these surprising rate differences was obtained through a comprehensive study of the nonenzymatic (spontaneous) hydrolysis of these same substrates, wherein an approximate 105-fold difference in rates was measured, clarifying that the differences were inherent rather than being due to specific interactions with the enzyme. The possibility that an alternate nucleophilic aryl substitution mechanism was responsible for the rapid reaction of the faster substrate was excluded through 18O-labeling studies. Further exploration of the origins of these rate differences involved analysis of X-ray crystal structures as well as quantum chemical calculations, which surprisingly revealed that ground state destabilization and transition state stabilizing effects contribute almost equally to the observed reactivity differences. These studies highlight the dangers of using simple reference equilibria such as pKa values as measures of leaving group ability.
ABSTRACT
Novel fluorogenic 2-deoxy-2-fluoroglycosyl acridinone active site titrating reagents were synthesised and kinetic parameters determined for their inactivation of two retaining ß-glucosidases, a ß-galactosidase, a ß-xylosidase and several cellulases. Fluorescence-monitored active site titration using this class of reagents reliably measured active enzyme concentrations down to 3 nM.
