Enzymes of early-diverging, zoosporic fungi

Abstract

The secretome, the complement of extracellular proteins, is a reflection of the interaction of an organism with its host or substrate, thus a determining factor for the organism's fitness and competitiveness. Hence, the secretome impacts speciation and organismal evolution. The zoosporic Chytridiomycota, Blastocladiomycota, Neocallimastigomycota, and Cryptomycota represent the earliest diverging lineages of the Fungal Kingdom. The review describes the enzyme compositions of these zoosporic fungi, underscoring the enzymes involved in biomass degradation. The review connects the lifestyle and substrate affinities of the zoosporic fungi to the secretome composition by examining both classical phenotypic investigations and molecular/genomic-based studies. The carbohydrate-active enzyme profiles of 19 genome-sequenced species are summarized. Emphasis is given to recent advances in understanding the functional role of rumen fungi, the basis for the devastating chytridiomycosis, and the structure of fungal cellulosome. The approach taken by the review enables comparison of the secretome enzyme composition of anaerobic versus aerobic early-diverging fungi and comparison of enzyme portfolio of specialized parasites, pathogens, and saprotrophs. Early-diverging fungi digest most major types of biopolymers: cellulose, hemicellulose, pectin, chitin, and keratin. It is thus to be expected that early-diverging fungi in its entirety represents a rich and diverse pool of secreted, metabolic enzymes. The review presents the methods used for enzyme discovery, the diversity of enzymes found, the status and outlook for recombinant production, and the potential for applications. Comparative studies on the composition of secretome enzymes of early-diverging fungi would contribute to unraveling the basal lineages of fungi.

Keywords: Biomass-degrading enzymes; Biotech potential; Early-diverging fungi; Functional genomics; Secretome enzyme composition; Secretome evolution; Zoosporic aerobic and anaerobic fungi.

Fig. 1

Summary of the anaerobic fungal life cycle. The stages in the life cycle where “resistant” structures (that have been reported to date) may be formed are also indicated (marked by asterisk). With courtesy of FEMS Microbiology Ecology, Volume 90, Issue 1, October 2014, Pages 1–17, 10.1111/1574-6941.12383

Fig. 2

Comparing gene structure of different copies of GH5 (EC 3.2.1.4), found in the R. rosea genome. The uppermost GH5 variant of R. rosea has one intron in the catalytic domain and no CBM. The other GH5 gene variants have a more typical fungal gene structure: a CBM1 domain and up to many (here 9) introns and additional protein domain inserts. The gene structure of the bacterial-related R. rosea GH5 has a gene structure more closely related to bacterial genes. From Lange et al. (2018), with courtesy of Fungal Biology Reviews

Fig. 3

Phylogenetic tree of fungal AA9, placing diversity of zoosporic AA9 in a fungal kingdom perspective. A maximum likelihood phylogenetic tree of CAZy-listed AA9 sequences. Triangles represent collapsed clades of similar LPMO AA9 sequences from the same phylum. To generate the tree, amino acid sequences were downloaded from GenBank (www.ncbi.nlm.nih.gov/), trimmed to the predicted catalytic domains using dbCAN (http://bcb.unl.edu/dbCAN2/), and aligned in MAFFT (www.ebi.ac.uk/Tools/msa/mafft/). This alignment was used to generate the final tree in RaxML-blackbox, available on the CIPRESS server (https://www.phylo.org/). Branch colors: green = Ascomycota; purple = Basidiomycota; red = Rhizophlyctis rosea, Rhizophlyctidiales, Chytridiomycota; orange = Caulochytrium protosteloides, Caulochytriales, Chytridiomycota (marked by single asterisk); blue = Gonapodya prolifera, Monoblepharidales, Chytridiomycota (marked by double asterisks). The tree is an updated version of the AA9 phylogenetic tree of Lange et al. (2018), with courtesy of Fungal Biology Reviews