Comprehensive genome-wide analysis reveals different classes of enigmatic old yellow enzyme in fungi

Abstract

In this study, we systematically identify Old Yellow Enzymes (OYEs) from a diverse range of economically important fungi representing different ecology and lifestyle. Using active site residues and sequence alignments, we present a classification for these proteins into three distinct classes including a novel class (Class III) and assign names to sequences. Our in-depth phylogenetic analysis suggests a complex history of lineage-specific expansion and contraction for the OYE gene family in fungi. Comparative analyses reveal remarkable diversity in the number and classes of OYE among fungi. Quantitative real-time PCR (qRT-PCR) of Ascochyta rabiei OYEs indicates differential expression of OYE genes during oxidative stress and plant infection. This study shows relationship of OYE with fungal ecology and lifestyle, and provides a foundation for future functional analysis and characterization of OYE gene family.

Old Yellow Enzyme-Catalysed Asymmetric Hydrogenation: Linking Family Roots with Improved Catalysis

“…However, the fungal OYEs originate from different families such as Saccharomycotina [61,62], and Pezizomycotina [63,64]. Fewer studies have been performed on OYEs originating from plants.…”

“…In 2016, Nizam and co-workers performed a comprehensive study of 424 putative OYEs from 60 fungal species and indicated a novel group among fungal OYEs [63]. However, none of these enzymes has been characterised thus far.…”

Characterization of the Novel Ene Reductase Ppo-Er1 from Paenibacillus Polymyxa

“…To account for these differences in sequence and the resulting structural features, the old yellow enzyme family can be further divided into five subclasses [15]. While enzyme members of the subclass I, also termed "classical" old yellow enzymes, and class II, introduced by Scrutton's group in 2010 and dubbed "thermophilic-like" [23], have been well explored [7,14], the recently described class III-V are less well investigated [15,24].…”

Enzyme-substrate matching in biocatalysis: in silico studies to predict substrate preference of ten putative ene-reductases from Mucor circinelloides MUT44

“…A recent fungal OYE classification by Nizam and collaborators [10,12] clearly showed that this class of enzymes is divided in 3 distinct groups according to the structural peculiarity (e.g. core of the active site, accessory residues, loop regions): class I, class II and class III.…”

“…Among the organisms where these enzymes have been described, fungi have been shown to possess a different number of OYEs homologs in their genomes [10].…”