Comparative analysis of fungal genomes reveals different plant cell wall degrading capacity in fungi

Abstract

BackgroundFungi produce a variety of carbohydrate activity enzymes (CAZymes) for the degradation of plant polysaccharide materials to facilitate infection and/or gain nutrition. Identifying and comparing CAZymes from fungi with different nutritional modes or infection mechanisms may provide information for better understanding of their life styles and infection models. To date, over hundreds of fungal genomes are publicly available. However, a systematic comparative analysis of fungal CAZymes across the entire fungal kingdom has not been reported.ResultsIn this study, we systemically identified glycoside hydrolases (GHs), polysaccharide lyases (PLs), carbohydrate esterases (CEs), and glycosyltransferases (GTs) as well as carbohydrate-binding modules (CBMs) in the predicted proteomes of 103 representative fungi from Ascomycota, Basidiomycota, Chytridiomycota, and Zygomycota. Comparative analysis of these CAZymes that play major roles in plant polysaccharide degradation revealed that fungi exhibit tremendous diversity in the number and variety of CAZymes. Among them, some families of GHs and CEs are the most prevalent CAZymes that are distributed in all of the fungi analyzed. Importantly, cellulases of some GH families are present in fungi that are not known to have cellulose-degrading ability. In addition, our results also showed that in general, plant pathogenic fungi have the highest number of CAZymes. Biotrophic fungi tend to have fewer CAZymes than necrotrophic and hemibiotrophic fungi. Pathogens of dicots often contain more pectinases than fungi infecting monocots. Interestingly, besides yeasts, many saprophytic fungi that are highly active in degrading plant biomass contain fewer CAZymes than plant pathogenic fungi. Furthermore, analysis of the gene expression profile of the wheat scab fungus Fusarium graminearum revealed that most of the CAZyme genes related to cell wall degradation were up-regulated during plant infection. Phylogenetic analysis also revealed a complex history of lineage-specific expansions and attritions for the PL1 family.ConclusionsOur study provides insights into the variety and expansion of fungal CAZyme classes and revealed the relationship of CAZyme size and diversity with their nutritional strategy and host specificity.

Microbial regulation of the soil carbon cycle: evidence from gene–enzyme relationships

“…significant (Po0.05) direct control of microbial structure on AG and CB activity. This is not surprising as AG and CB are involved in degradation of labile forms of C and the gene(s) encoding the production of AG and CB are present in a number of soil microbial groups (Trivedi et al, 2013;Zhao et al, 2013). The activity of all four studied enzymes was directly and significantly regulated by the abundance of genes encoding the respective enzymes (Figure 3).…”

“…There is a difference in the number of genes involved in the degradation of various C sources among different microbial groups and in many instances the genes involved in the degradation of moderately labile and recalcitrant forms of C are phylogenetically conserved (Trivedi et al, 2013;Zhao et al, 2013). The production of NAG and XYL was significantly linked to δ-Proteobacteria, Actinobacteria and Acidobacteria in bacteria and Eurotiomycetes (subphylum Pezizomycotina) and Leotiomycetes (very closely related to subphylum Pezizomycotina) in fungi (Figures 3a2 and c2).…”

“…The production of NAG and XYL was significantly linked to δ-Proteobacteria, Actinobacteria and Acidobacteria in bacteria and Eurotiomycetes (subphylum Pezizomycotina) and Leotiomycetes (very closely related to subphylum Pezizomycotina) in fungi (Figures 3a2 and c2). Genomic analysis of these groups has shown that they have a higher potential to produce these enzymes as compared with other groups within bacteria and fungi (Karlsson and Stenlid, 2008;Trivedi et al, 2013;Zhao et al, 2013). SEM showed that bacterial phyla Acidobacteria, Deltaproteobacteria and Actinobacteria are important predictors of activity of enzymes CB, XYL and NAG.…”

Lignocellulolytic Capability of Endophytic Phyllosticta sp.

“…[27], Fusarium sp. [28], In this study, we examined the production of ligninolytic enzymes on seven previously characterized lignocellulosic agro-industrial residues by four Phyllosticta sp. : the pathogenic P. citrimaxima and three strains of the non-pathogenic endophyte P. capitalensis.…”

Cloning and characterization of an endo--1,4-xylanase gene from Colletotrichum lindemuthianum and phylogenetic analysis of similar genes from phytopathogenic fungus

“…Comparison of these genes has contributed to our understanding of their lifestyle and helped to create infection models (Zhao et al, 2013). For example, biotrophic fungi tend to have fewer CAZymes than necrotrophic and hemibiotrophic fungi.…”