SACCHARIS: An automated pipeline to streamline discovery of carbohydrate active enzyme activities within polyspecific families and de novo sequence datasets

Improved feed utilization, repurposing of agricultural residues; and sustainable production of energy, fuels, and bioproducts are escalating priorities for Canada. To address these issues, next-generation approaches will help stimulate discovery-based science and innovation. In this regard, ‘carbohydrate active enzymes’ (i.e. CAZymes) are protein catalysts that modify carbohydrates. CAZymes fulfill essential and diverse roles in nature ranging from synthesizing polysaccharides that fortify the cell walls of plants to releasing simple sugars from complex polysaccharides during animal digestion. Importantly, CAZymes can be harnessed for diverse applications in agriculture and represent sustainable, green technologies for the conversion of biomass into useful products.

Discovering new enzymes that will improve the efficiency of a catalytic process (i.e. generate a product faster) or catalyse a new reaction are challenging feats. This challenge is compounded by the abundance of genetic information that has been sequenced and the rate at which it is accumulating. Currently, databases are stocked full of putative protein sequences, genomes, and metagenomes. In particular, cataloging ‘microbiomes’ (i.e. entire collection of genes with a community) and reporting the changes that result under host or diet induced change are not common practices. Sorting through this deep pool of genetic information to determine what unknown functions are present or determine what changes in community structure mean for animal performance still remains a difficult and relatively slow task. Indeed, assigning function to sequence has created a bottle neck in the CAZyme discovery pipeline. New approaches that help streamline this process will likely lead to breakthrough discoveries, applications for the microbiome, and innovations for Canadian agriculture.

As part of the AAFC Clean tech network, Dr. Abbott and colleagues at the Lethbridge Research and Development Centre have been trying to ‘widen the bottleneck’ for CAZyme discovery. His team has developed a new bioinformatic pipeline called ‘SACCHARIS’ (Sequence Analysis and Clustering of CarboHydrate Active enzymes for Rapid Informed prediction of Specificity), derived from the Greek word ‘sákkʰaris’ or ‘sugar’. SACCHARIS identifies proteins predicted to encode CAZymes with new activities from sequence datasets. This tool can be used to explore genomes and even metagenomes for CAZyme discovery. Additionally, SACCHARIS can also generate CAZome fingerprints for predicting the signature metabolic potential of two or more organisms. Although only recently published, the pipeline has already led to successful patent protection of two unique enzyme activities and discovered several protein functions that have not been described previously. Currently, efforts to harness SACCHARIS for other research priorities in AAFC, such as engineering the cell walls of biorefinery crops, programming gut microbiomes, or illuminating the roles of CAZymes in crop diseases. In 2018, members of the SACCHARIS team will be visiting several AAFC centres across Canada to train interested researchers and develop new potential applications for the bioinformatic pipeline.