A Global Survey of Carbohydrate Esterase Families 1 and 10 in Oomycetes

Abstract

Carbohydrate-active enzymes (CAZymes) are a cornerstone in the phytopathogenicity of filamentous microbes. CAZymes are required for every step of a successful infection cycle-from penetration, to nutrient acquisition (during colonization), to exit and dispersal. Yet, CAZymes are not a unique feature of filamentous pathogens. They are found across eukaryotic genomes and including, for example, saprotrophic relatives of major pathogens. Comparative genomics and functional analyses revealed that CAZyme content is shaped by a multitude of factors, including utilized substrate, lifestyle, and host preference. Yet, family size alone says little about usage. Indeed, in a previous study, we found that genes putatively coding for the CAZyme families of carbohydrate esterase (CE)1 and CE10, while not specifically enriched in number, were suggested to have lifestyle-specific gene expression patterns. Here, we used comparative genomics and a clustering approach to understand how the repertoire of the CE1-and CE10encoding gene families is shaped across oomycete evolution. These data are combined with comparative transcriptomic analyses across homologous clusters within the gene families. We find that CE1 and CE10 have been reduced in number in biotrophic oomycetes independent of the phylogenetic relationship of the biotrophs to each other. The reduction in CE1 is different from that observed for CE10: While in CE10 specific clusters of homologous sequences show convergent reduction, CE1 reduction is caused by species-specific losses. Comparative transcriptomics revealed that some clusters of CE1 or CE10 sequences have a higher expression than others, independent of the species composition within them. Further, we find that CE1-and CE10-encoding genes are mainly induced in plant pathogens and that some homologous genes show lifestyle-specific gene expression levels during infection, with hemibiotrophs showing the highest expression levels.

Comprehensive analysis of 84 Faecalibacterium prausnitzii strains uncovers their genetic diversity, functional characteristics, and potential risks

“…The function of CEs is to participate in the metabolism of carbohydrate esters ( Armendariz-Ruiz et al., 2018 ). Genes putatively coding for the CAZyme families of carbohydrate esterases CE1 and CE10 have been suggested to have lifestyle-specific gene expression patterns ( de Vries and de Vries, 2020 ).…”

Genome-wide comparison deciphers lifestyle adaptation and glass biodeterioration property of Curvularia eragrostidis C52

“…C. eragrostidis C52 was rich of CAZymes responsible for colonization cycle, nutrient acquisition and dispersal that are shaped by utilized substrate, lifestyle, and host preference 27 . A recent study proved that the repertoire of CE1 and CE10 genes was significantly reduced in biotrophic pathogens 28 . As it stands, plant-derived Curvularia strains ( C. lunata CX-3, C. lunata W3, C. geniculata P1, C. geniculata W_3) and human-derived strains ( C. kusanoi 30M1, C. papendorfii UM 226) had an average CE10 of 16 genes.…”

Physiological and Dual Transcriptional Analysis of Microalga Graesiella emersonii–Amoeboaphelidium protococcarum Pathosystem Uncovers Conserved Defense Response and Robust Pathogenicity

“…For pathogenic fungi invading a host, carbohydrate-active enzymes (CAZymes) play important roles in penetration, colonization, exit, and dispersal during infection progress [ 30 ]. Several studies have indicated that massive CAZyme-encoding genes are activated during infection [ 31 , 32 ].…”