Systematic review of publicly available non-Dikarya fungal proteomes for understanding their plant biomass-degrading and bioremediation potentials

Abstract

In the last two decades, studies on plant biomass-degrading fungi have remarkably increased to understand and reveal the underlying molecular mechanisms responsible for their life cycle and wood-decaying abilities. Most of the plant biomass-degrading fungi reported till date belong to basidiomycota or ascomycota phyla. Thus, very few studies were conducted on fungi belonging to other divisions. Recent sequencing studies have revealed complete genomic sequences of various fungi. Our present study is focused on understanding the plant biomass-degrading potentials, by retrieving genome-wide annotations of 56 published fungi belonging to Glomeromycota, Mucoromycota, Zoopagomycota, Blastocladiomycota, Chytridiomycota, Neocallimastigomycota, Microsporidia and Cryptomycota from JGI-Myco-Cosm repository. We have compared and analyzed the proteomic annotations, especially CAZy, KOG, KEGG and SM clusters by separating the proteomic annotations into lignin-, cellulose-, hemicellulose-, pectin-degrading enzymes and also highlighted the KEGG, KOG molecular mechanisms responsible for the metabolism of carbohydrates (lignocellulolytic pathways of fungi), complex organic pollutants, xenobiotic compounds, biosynthesis of secondary metabolites. However, we strongly agree that studying genome-wide distributions of fungal CAZyme does not completely corresponds to its biomass-degrading ability. Thus, our present study can be used as preliminary materials for selecting ideal fungal candidate for the degradation and conversion of plant biomass components, especially carbohydrates to bioethanol and other commercially valuable products. which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made.

Hallmarks of Basidiomycete Soft- and White-Rot in Wood-Decay -Omics Data of Two Armillaria Species

“…A significant portion (35–50%) of upregulated genes were annotated as CBM67s in the CAZy database [ 44 ]. CBM67 are l -rhamnose binding modules, which are reported to be involved in pectin degradation [ 17 , 74 ]. Apart from CBM67, there were a number of other pectinolytic enzymes (e.g., GH78, PL4) associated with these GBDPs, which were upregulated in the two species ( Supplementary Table S6 ).…”

“…There was one downstream multicopper oxidase gene with increased abundance in the mycelium only of A. cepistipes and not in A. ostoyae . The iron permease system along with iron reductases and MCOs is specifically seen upregulated in brown-rot wood decay [ 56 , 67 , 74 , 76 , 77 , 78 ].…”

Phylogenomics of a new fungal phylum reveals multiple waves of reductive evolution across Holomycota

“…All ortholog counts were transformed into a presence/absence matrix (encoded as 0/1) and analysed with the R script 136 Chytridiomycota. We then screened for canonical cellulose, hemicellulose, pectin and chitin degrading enzymes identified in Fungi from previous studies 13,141,142 . The identified hits were (which was not certified by peer review) is the author/funder.…”

CAZymes-based ranking of fungi (CBRF): an interactive web database for identifying fungi with extrinsic plant biomass degrading abilities

“…Similarly, CAZy groups and classes encoding for laccase, p-diphenol oxygen oxidoreductase, ferroxidase, laccase-like multicopper oxidase, lignin peroxidase, manganese peroxidase, versatile peroxidase, peroxidase, aryl-alcohol oxidase, alcohol oxidase, pyranose oxidase, cellobiose dehydrogenase, GMC-oxidoreductases, vanillyl alcohol oxidase, alcohol oxidase, glyoxal oxidase, galactose oxidase, 1,4-benzoquinone reductase, Iron reductase, pyrroloquinoline quinone-dependent oxidoreductase, feruloyl esterase, cinnamoyl esterase, 4-O-methyl-glucuronoyl methylesterase and aryl esterase, carboxyl esterase were listed as lignin depolymerizing enzyme (Fig. 2) (Kameshwar and Qin 2019). The pectindepolymerizing enzymes contained CAZy groups and classes encoding for polygalacturonase, exo-polygalacturonase, exo-poly-galacturonosidase, rhamnogalacturonase, rhamnogalacturonan α-1,2-galacturonohydrolase, α-l-rhamnosidase, exo-polygalacturonase, rhamnogalacturonan α-l-rhamnohydrolase, α-l-arabinofuranosidase, exo-α-l-1,5-arabinanase, β-galactosidase, pectate lyase, exo-pectate lyase, pectin Lyase, rhamnogalacturonan endolyase, rhamnogalacturonan exolyase, oligogalacturonate lyase, pectin methylesterase, pectin acetylesterase, rhamnogalacturonan acetylesterase, pectin acetylesterase, acetylesterase, pectin binding modules, galactan binding modules, l-rhamnose binding modules, arabinogalactan binding modules, respectively (Fig.…”

“…Finally, the CAZy groups and classes encoding for α-amylases, LPMO, α-glucosidase, starch phosphorylase, starch binding modules and endo-inulinase, exo-inulinase, inulin lyase and inulin binding module were listed for the starch and inulin depolymerizing enzymes, respectively (Fig. 2) (Kameshwar and Qin 2019).…”