Expression of Aspergillus niger CAZymes is determined by compositional changes in wheat straw generated by hydrothermal or ionic liquid pretreatments

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.Electronic supplementary materialThe online version of this article (doi:10.1186/s13068-017-0700-9) contains supplementary material, which is available to authorized users.

Colonies of the fungus Aspergillus niger are highly differentiated to adapt to local carbon source variation

“…This however does not mean that no movement of nutrients occurred in our experimental setup. The part of the colony growing on d ‐glucose also showed higher transcript levels of plant biomass degrading CAZymes than expected from a culture where only d ‐glucose was present even if that d ‐glucose had been mostly consumed (Daly et al ., ) and extracellular CAZymes were identified in the compartments where d ‐glucose was the substrate. However, we cannot rule out contribution of a low level of sugars that appear to diffuse into an adjacent compartment (Supporting Information Fig.…”

Succession of physiological stages hallmarks the transcriptomic response of fungusAspergillus nigerto lignocellulose

“…Miscanthus (cv. Giganteus) was ground to pass an 0.5 mm sieve as described previously (31). The ionic liquid (IL) pretreatment was performed using 1-ethyl-3-methylimidazolium acetate ([C2mim][OAc]) for 2 h at 160 ºC and hydrothermal treatment was performed at 200 ºC for 2 h, as described in detail previously for wheat straw (31).…”

“…We investigated the transcriptional landscape of niger to untreated and pretreated Miscanthus to elucidate the effect of feedstock and pretreatment on gene expression, and to identify the system-level fungal responses to cultivation. We analysed the data together with that of cultivations on untreated and pretreated wheat straw from our previous study (31), where the broader physiological responses beyond CAZymes had not yet been analysed. This resulted in a data matrix of 47 conditions of A. niger cultured with a particular (preor untreated) substrate (Fig 1).…”

“…However, even small differences in composition and structure of plant cell walls can significantly affect their digestibility (20,26). As ascomycetes have been described to strongly respond to differences in polysaccharides used as carbon source (27)(28)(29) and also exhibit partially conserved (substrate independent) responses to complex lignocellulose (30)(31)(32)(33), here we investigated the effect of both hydrothermal and ionic liquid pretreated biomass as well as untreated feedstocks on the system-level response of A. niger.…”

“…Subsequent degradation of lignocellulose components can be expected to reflect the evolved fungal biochemical capacity (27,43). Fungal production of CAZymes and signalling responses to different sources of complex carbohydrates have been documented extensively, often capturing a snapshot of events at one or a selected few moments, such as when the CAZyme expression was peaking, in the cultivation time (28)(29)(30)(31)(32)(33)(34)(43)(44)(45)(46). Knowledge on the wider, and potentially time-staged, physiological responses and degradative strategies of A. niger is however still very limited.…”