CreA-mediated repression of gene expression occurs at low monosaccharide levels during fungal plant biomass conversion in a time and substrate dependent manner

Mao Peng,Claire Khosravi,Ronnie J.M Lubbers,Roland S Kun,Maria Victoria Aguilar Pontes,Evy Battaglia,Cindy Chen,Sacha Dalhuijsen,Paul Daly,Anna Lipzen,Vivian Ng,Juying Yan,Mei Wang,Jaap Visser,Igor V Grigoriev,Miia R Mäkelä,Ronald P De Vries

doi:10.1016/j.tcsw.2021.100050

Abstract

Carbon catabolite repression enables fungi to utilize the most favourable carbon source in the environment, and is mediated by a key regulator, CreA, in most fungi. CreA-mediated regulation has mainly been studied at high monosaccharide concentrations, an uncommon situation in most natural biotopes. In nature, many fungi rely on plant biomass as their major carbon source by producing enzymes to degrade plant cell wall polysaccharides into metabolizable sugars. To determine the role of CreA when fungi grow in more natural conditions and in particular with respect to degradation and conversion of plant cell walls, we compared transcriptomes of a creA deletion and reference strain of the ascomycete Aspergillus niger during growth on sugar beet pulp and wheat bran. Transcriptomics, extracellular sugar concentrations and growth profiling of A. niger on a variety of carbon sources, revealed that also under conditions with low concentrations of free monosaccharides, CreA has a major effect on gene expression in a strong time and substrate composition dependent manner. In addition, we compared the CreA regulon from five fungi during their growth on crude plant biomass or cellulose. It showed that CreA commonly regulated genes related to carbon metabolism, sugar transport and plant cell wall degrading enzymes across different species. We therefore conclude that CreA has a crucial role for fungi also in adapting to low sugar concentrations as occurring in their natural biotopes, which is supported by the presence of CreA orthologs in nearly all fungi.

Highlights

In nature, many filamentous fungi use plant biomass as their main carbon source
Through systematic comparison of the reference and creA deletion strain, we demonstrated that CreA significantly affects many important aspects of plant biomass conversion, including production of carbohydrate active enzymes (CAZymes), sugar transport and sugar catabolism, at significantly lower free sugar levels than previously re ported
Filamentous fungi are commonly considered to rarely experience a high free sugar concentration in their natural biotopes that could induce catabolic repression (CCR), as mainly polymeric carbon sources are present and they need to compete with other microorganisms for the available sugars

Summary

Introduction

Many filamentous fungi use plant biomass as their main carbon source They produce extensive sets of extracellular enzymes to be able to penetrate and degrade the polymeric components of plant cell walls into metabolizable sugars and other mono- and oligomers. This ability is controlled at the transcriptional level by a diverse set of tran scription factors (TFs) regulating the specificity and efficiency of fungal lignocellulose conversion (Benocci et al, 2017). There is little conservation with respect to the presence of transcriptional activators involved in plant biomass conversion across the fungal kingdom, sug gesting a highly diverse approach to the activation of this process. Fig. S1), which implies a highly important role for this regulator, irre spective of fungal lifestyle or biotope

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Conclusion