Abstract
BackgroundThe capacity of fungi, such as Aspergillus niger, to degrade lignocellulose is harnessed in biotechnology to generate biofuels and high-value compounds from renewable feedstocks. Most feedstocks are currently pretreated to increase enzymatic digestibility: improving our understanding of the transcriptomic responses of fungi to pretreated lignocellulosic substrates could help to improve the mix of activities and reduce the production costs of commercial lignocellulose saccharifying cocktails.ResultsWe investigated the responses of A. niger to untreated, ionic liquid and hydrothermally pretreated wheat straw over a 5-day time course using RNA-seq and targeted proteomics. The ionic liquid pretreatment altered the cellulose crystallinity while retaining more of the hemicellulosic sugars than the hydrothermal pretreatment. Ionic liquid pretreatment of straw led to a dynamic induction and repression of genes, which was correlated with the higher levels of pentose sugars saccharified from the ionic liquid-pretreated straw. Hydrothermal pretreatment of straw led to reduced levels of transcripts of genes encoding carbohydrate-active enzymes as well as the derived proteins and enzyme activities. Both pretreatments abolished the expression of a large set of genes encoding pectinolytic enzymes. These reduced levels could be explained by the removal of parts of the lignocellulose by the hydrothermal pretreatment. The time course also facilitated identification of temporally limited gene induction patterns.ConclusionsThe presented transcriptomic and biochemical datasets demonstrate that pretreatments caused modifications of the lignocellulose, to both specific structural features as well as the organisation of the overall lignocellulosic structure, that determined A. niger transcript levels. The experimental setup allowed reliable detection of substrate-specific gene expression patterns as well as hitherto non-expressed genes. Our data suggest beneficial effects of using untreated and IL-pretreated straw, but not HT-pretreated straw, as feedstock for CAZyme production.
Highlights
The capacity of fungi, such as Aspergillus niger, to degrade lignocellulose is harnessed in biotechnology to generate biofuels and high-value compounds from renewable feedstocks
After HT pretreatment, the amount of hemicellulose and pectin components was reduced compared to the untreated (KMS) and ionic liquid (IL)-pretreated straw (ILS), as shown by a reduction of at least tenfold in the amount of arabinose and galactose, and sixfold in the amount of xylose, as quantified in the acid hydrolysates of the straw (Fig. 1a)
The cumulative changes in straw due to pretreatment resulted in an enrichment in lignin content in the remaining solids of HTpretreated straw (HTS) (290 mg g−1) compared to knife-milled wheat straw (KMS) (234 mg g−1), whereas the lignin content was depleted in the remaining solids of ILS (180 mg g−1) (Fig. 1a)
Summary
The capacity of fungi, such as Aspergillus niger, to degrade lignocellulose is harnessed in biotechnology to generate biofuels and high-value compounds from renewable feedstocks. Most feedstocks are currently pretreated to increase enzymatic digestibility: improving our understanding of the transcriptomic responses of fungi to pretreated lignocellulosic substrates could help to improve the mix of activities and reduce the production costs of commercial lignocellulose saccharifying cocktails. One barrier to cost-efficient production of biofuels is the inefficient saccharification step, which requires excessive amounts of costly enzymes produced by industry using fungi [3]. As part of an approach to improve efficiency, lignocellulosic substrates are routinely pretreated to render the lignocellulose more amenable to saccharification by enzymes [4]. Production of more efficient and cheaper enzyme mixtures would be aided by improved knowledge gained from studying the responses of nature’s lignocellulose-degrading fungi to pretreated lignocellulosic feedstocks. Pretreatments consist of a physical and/or chemical process that has the aim of opening up the structure of the lignocellulose to improve the efficiency of saccharification [5]. In our study we pretreated wheat straw, which is a major agricultural waste residue with potential for use to produce bioethanol [8]
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