Hobbs, E. E. M. | bioRxiv Science

bioRxiv2026

Carbohydrate active enzymes in Pectobacteriaceae: coevolving enzyme sets and host adaptation

Many phytopathogenic bacteria have evolved large, diverse arsenals of Carbohydrate Active enZymes (CAZymes) that liberate simple sugars, and thus nutrition and energy, from the complex lignocellulosic matrices of their plant hosts. The CAZyme arsenals of these phytopathogens are expected to be influenced by and adapted to the cell wall composition of their plant hosts. The solutions these organisms have reached for the problem of degrading plant material may help us understand their host ranges and present a rich source of novel CAZymes for exploitation in industrial bioprocessing. Here we catalogue and analyse CAZyme complements (CAZomes) of publicly-available Enterobacterial phytopathogen genomes, including those of the economically significant and widely-studied Pectobacterium and Dickeya genera. These comprise a broad diversity of CAZymes, providing insight into host adaptation and a resource for bio-prospection of industrially-relevant enzymes. We find evidence supporting coevolution of sets of CAZymes specific to bacterial genus and species and, notably, CAZymes associated with pathogen preference for either woody or soft plant tissue, suggesting adaptation of CAZomes to host plant cell wall composition.

bioinformatics↗

bioRxiv2022

cazy_webscraper: local compilation and interrogation of comprehensive CAZyme datasets

Carbohydrate Active enZymes (CAZymes) are pivotal in biological processes including energy metabolism, cell structure maintenance, signalling and pathogen recognition. Bioinformatic prediction and mining of CAZymes improves our understanding of these activities, and enables discovery of candidates of interest for industrial biotechnology, particularly the processing of organic waste for biofuel production. CAZy (www.cazy.org) is a high-quality, manually-curated and authoritative database of CAZymes that is often the starting point for these analyses. Automated querying, and integration of CAZy data with other public datasets would constitute a powerful resource for mining and exploring CAZyme diversity. However, CAZy does not itself provide methods to automate queries, or integrate annotation data from other sources (except by following hyperlinks) to support further analysis. To overcome these limitations we developed cazy_webscraper, a command-line tool that retrieves data from CAZy and other online resources to build a local, shareable, and reproducible database that augments and extends the authoritative CAZy database. cazy_webscrapers integration of curated CAZyme annotations with their corresponding protein sequences, up to date taxonomy assignments, and protein structure data facilitates automated large-scale and targeted bioinformatic CAZyme family analysis and candidate screening. This tool has found widespread uptake in the community, with over 20,000 downloads. We demonstrate the use and application of cazy_webscraper to: (i) augment, update and correct CAZy database accessions; (ii) explore taxonomic distribution of CAZymes recorded in CAZy, identifying underrepresented taxa and unusual CAZy class distributions; and (iii) investigate three CAZymes having potential biotechnological application for degradation of biomass, but lacking a representative structure in the PDB database. We describe in general how cazy_webscraper facilitates functional, structural and evolutionary studies to aid identification of candidate enzymes for further characterisation, and specifically note that CAZy provides supporting evidence for recent expansion of the Auxiliary Activities (AA) CAZy family in eukaryotes, consistent with functions potentially specific to eukaryotic lifestyles. Supplementary informationcazy_webscraper source code is available at https://github.com/HobnobMancer/cazy_webscraper, and online documentation is provided at https://cazywebscraper.readthedocs.io.

bioinformatics↗