Combined whole cell wall analysis and streamlined in silico carbohydrate-active enzyme discovery to improve biocatalytic conversion of agricultural crop residues

Abstract

The production of biofuels as an efficient source of renewable energy has received considerable attention due to increasing energy demands and regulatory incentives to reduce greenhouse gas emissions. Second-generation biofuel feedstocks, including agricultural crop residues generated on-farm during annual harvests, are abundant, inexpensive, and sustainable. Unlike first-generation feedstocks, which are enriched in easily fermentable carbohydrates, crop residue cell walls are highly resistant to saccharification, fermentation, and valorization. Crop residues contain recalcitrant polysaccharides, including cellulose, hemicelluloses, pectins, and lignin and lignin-carbohydrate complexes. In addition, their cell walls can vary in linkage structure and monosaccharide composition between plant sources. Characterization of total cell wall structure, including high-resolution analyses of saccharide composition, linkage, and complex structures using chromatography-based methods, nuclear magnetic resonance, -omics, and antibody glycome profiling, provides critical insight into the fine chemistry of feedstock cell walls. Furthermore, improving both the catalytic potential of microbial communities that populate biodigester reactors and the efficiency of pre-treatments used in bioethanol production may improve bioconversion rates and yields. Toward this end, knowledge and characterization of carbohydrate-active enzymes (CAZymes) involved in dynamic biomass deconstruction is pivotal. Here we overview the use of common “-omics”-based methods for the study of lignocellulose-metabolizing communities and microorganisms, as well as methods for annotation and discovery of CAZymes, and accurate prediction of CAZyme function. Emerging approaches for analysis of large datasets, including metagenome-assembled genomes, are also discussed. Using complementary glycomic and meta-omic methods to characterize agricultural residues and the microbial communities that digest them provides promising streams of research to maximize value and energy extraction from crop waste streams.

Comparative transcriptomics reveals the molecular toolkit used by an algivorous protist for cell wall perforation

“…The degradation of biomass containing recalcitrant polysaccharides is important in biofuel processing, for example, and the discovery of efficient CAZymes using ''omics''-based functional prediction in non-model organisms could help to optimize this process in the future. 41…”

Comprehensive Leaf Cell Wall Analysis Using Carbohydrate Microarrays Reveals Polysaccharide-Level Variation between Vitis Species with Differing Resistance to Downy Mildew

“…The status of pectin could also influence the porosity and integrity of the cell wall [ 38 , 39 ]. The pectin main chain with can be highly methylated will need the additional enzymes for thorough breakdown, and, therefore, decrease the availability of substrates targeted by other pathogenic cell wall-degrading enzymes (CWDEs), such as hemicellulases and cellulases [ 40 ]. Previous studies on some crops (tomato, cotton and wheat) have suggested that a high degree of esterification (DE) level of pectin is positively correlated with plant defense.…”

“…In addition to pectin, mAb BS-400-2 (recognizes callose), which did not show zero on heatmap, however, shows its association with other pectin recognizing mAbs in the PCA plot. Callose has been well documented in many studies for its roles in plant/microbial interactions; it has been found to be deposited around the infection sites to block the pathogens [ 15 , 40 ].…”

Approaches to Investigate Selective Dietary Polysaccharide Utilization by Human Gut Microbiota at a Functional Level

“…Different glycomic methods are required to study unique structural features of carbohydrates, such as linkage, monosaccharide content, or dp, and selecting the appropriate preparative and analytical method needs to be carefully considered (Tingley et al, 2021). Dietary polysaccharide analysis begins with hot water extraction from source material, followed by sequential fractionation by preparative column chromatography, solvent extraction, and ethanol precipitation.…”