Abstract

Aspergillus niger is one of the most widely used fungi to study the conversion of the lignocellulosic feedstocks into fermentable sugars. Understanding the sugar uptake system of A. niger is essential to improve the efficiency of the process of fungal plant biomass degradation. In this study, we report a comprehensive characterization of the sugar transportome of A. niger by combining phylogenetic and comparative transcriptomic analyses. We identified 86 putative sugar transporter (ST) genes based on a conserved protein domain search. All these candidates were then classified into nine subfamilies and their functional motifs and possible sugar-specificity were annotated according to phylogenetic analysis and literature mining. Furthermore, we comparatively analyzed the ST gene expression on a large set of fungal growth conditions including mono-, di- and polysaccharides, and mutants of transcriptional regulators. This revealed that transporter genes from the same phylogenetic clade displayed very diverse expression patterns and were regulated by different transcriptional factors. The genome-wide study of STs of A. niger provides new insights into the mechanisms underlying an extremely flexible metabolism and high nutritional versatility of A. niger and will facilitate further biochemical characterization and industrial applications of these candidate STs.

Highlights

  • Aspergillus niger is a filamentous ascomycete fungus, which is found in a wide range of biotopes on earth and has a long history of use for the industrial production of hydrolytic enzymes (Culleton et al, 2013) and organic acids (Andersen et al, 2011)

  • Compared to the nearly 100 sugar transporter (ST) genes predicted in the A. niger genome, only 10 transporters have been biochemically characterized in A. niger for their sugar specificity, resulting in five D-glucose transporters (Vankuyk et al, 2004; Jorgensen et al, 2007; Sloothaak et al, 2015), three D-xylose transporters (Sloothaak et al, 2016b), one D-galacturonic acid transporter (Sloothaak et al, 2014), and one L-rhamnose transporter (Sloothaak et al, 2016a)

  • The protein sequences of all predicted A. niger ST genes together with 61 literature reported STs in other fungi were used for phylogenetic analysis (Supplementary File 1)

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Summary

Introduction

Aspergillus niger is a filamentous ascomycete fungus, which is found in a wide range of biotopes on earth and has a long history of use for the industrial production of hydrolytic enzymes (Culleton et al, 2013) and organic acids (Andersen et al, 2011). It can efficiently degrade all major polysaccharide components of the plant cell wall (cellulose, hemicellulose, and pectin) by secreting a versatile set of carbohydrate active enzymes (CAZymes) (de Vries and Visser, 2001). Recent 3D structure and genetic mutation experiments have revealed that the mutation of only a limited number of key amino acids could significantly change the specificity and affinity of STs (Quistgaard et al, 2013; Madej et al, 2014; Young et al, 2014)

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