Phylogenomic Relationships between Amylolytic Enzymes from 85 Strains of Fungi

Wanping Chen,Fusheng Chen,Ting Xie,Yanchun Shao,Michael Freitag

doi:10.1371/journal.pone.0049679

Wanping Chen, Fusheng Chen + Show 3 more

Open Access

https://doi.org/10.1371/journal.pone.0049679

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Journal: PloS one	Publication Date: Nov 15, 2012
Citations: 29	License type: CC BY 4.0

Affiliation: Huazhong Agricultural University

Abstract

Fungal amylolytic enzymes, including α-amylase, gluocoamylase and α-glucosidase, have been extensively exploited in diverse industrial applications such as high fructose syrup production, paper making, food processing and ethanol production. In this paper, amylolytic genes of 85 strains of fungi from the phyla Ascomycota, Basidiomycota, Chytridiomycota and Zygomycota were annotated on the genomic scale according to the classification of glycoside hydrolase (GH) from the Carbohydrate-Active enZymes (CAZy) Database. Comparisons of gene abundance in the fungi suggested that the repertoire of amylolytic genes adapted to their respective lifestyles. Amylolytic enzymes in family GH13 were divided into four distinct clades identified as heterologous α- amylases, eukaryotic α-amylases, bacterial and fungal α-amylases and GH13 α-glucosidases. Family GH15 had two branches, one for gluocoamylases, and the other with currently unknown function. GH31 α-glucosidases showed diverse branches consisting of neutral α-glucosidases, lysosomal acid α-glucosidases and a new clade phylogenetically related to the bacterial counterparts. Distribution of starch-binding domains in above fungal amylolytic enzymes was related to the enzyme source and phylogeny. Finally, likely scenarios for the evolution of amylolytic enzymes in fungi based on phylogenetic analyses were proposed. Our results provide new insights into evolutionary relationships among subgroups of fungal amylolytic enzymes and fungal evolutionary adaptation to ecological conditions.

Highlights

Starch is the major carbohydrate storage product of green plants as a result of photosynthesis and makes up an important part of carbon and energy sources widely consumed among animals, plants and microorganisms [1,2,3]
Fungi utilize polysaccharide substrates through a complement of hydrolytic enzymes secreted into the environmental niches to digest large organic molecules into smaller molecules that may be absorbed as nutrients
Putative starch-binding domains of CBM20, CBM21, CBM25 and CBM48 are concentrated in phylogenetically related amylolytic enzymes from filamentous fungi, especially in Ascomycota

Summary

Introduction

Starch is the major carbohydrate storage product of green plants as a result of photosynthesis and makes up an important part of carbon and energy sources widely consumed among animals, plants and microorganisms [1,2,3]. The amylolytic genes from the family GH13, including a-amylases and aglucosidases (GH13), were not positively identified in some species, and seem to be non-essential in fungi compared to glucoamylases and a-glucosidases (GH31). The phylogeny of GH13 including a-amylases and a-glucosidases was analysed among the tested fungi and members of the GH13 family were divided into four clades for studying their protein features (Figure 1). These enzymes were divided into four major clades on the basis of sequence comparisons (Figure 3). Homology searches revealed that these enzymes were phylogenetically related to their bacterial counterparts Their catalytic domains showed non-specific hits to current identified groups in NCBI’s Conserved Domain. It implies that acquisition of starch-binding domains may occur in certain phylogenetic groups [36]

Conclusions

Findings

Materials and Methods