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Re-routing of sugar catabolism provides a better insight into fungal flexibility in using plant biomass-derived monomers as substrates

ABSTRACT: The filamentous ascomycete Aspergillus niger has received increasing interest as a cell factory, being able to efficiently degrade plant cell wall polysaccharides as well as having an extensive metabolism to convert the released monosaccharides into value added compounds. The pentoses D-xylose and L-arabinose are the most abundant monosaccharides in plant biomass after D-glucose, being major constituents of xylan, pectin and xyloglucan. In this study, the influence of selected pentose catabolic pathway (PCP) deletion strains on growth on plant biomass and re-routing of sugar catabolism was addressed to gain a better understanding of the flexibility of this fungus in using plant biomass-derived monomers. The transcriptome, metabolome and proteome response of three PCP mutant strains, ΔlarAΔxyrAΔxyrB, ΔladAΔxdhAΔsdhA and ΔxkiA, grown on wheat bran (WB) and sugar beet pulp (SBP), was evaluated. Our results showed that despite the absolute impact of these PCP mutations on pure pentose sugars, they are not as critical for growth of A. niger on more complex biomass substrates, such as WB and SBP. However, significant phenotypic variation was observed between the two biomass substrates, but also between the different PCP mutants. This shows that the high sugar heterogeneity of these substrates in combination with the high complexity and adaptability of the fungal sugar metabolism allow for activation of alternative strategies to support growth.

ORGANISM(S): Aspergillus niger

PROVIDER: GSE162901 | GEO | 2021/03/08

REPOSITORIES: GEO

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Project description:Enzymatic degradation of plant biomass requires the coordinated action of various enzymes. In this study, the production of reducing sugars from pectic substrates and sugar beet pulp (SBP) was investigated and compared using commercial enzyme preparations, including M2, pectinase (E1) from Aspergillus niger, Viscozyme® L (V-L) and L-40. V-L, a cellulolytic enzyme mix produced by Aspergillus sp. was further evaluated as the most robust enzyme cocktail with the strongest SBP degradation ability in terms of dynamic release of monosaccharides, methanol, and acetate from substrate SBP. Glucose, the building block of cellulose, was the first product to reach its maximum concentration within 2.5 hours. In contrast, the major monosaccharides in pectin, including arabinose and galacturonic acid, were continuously released from the residue until reaching a peak of 2,092 mg L-1 and 7,069 mg L-1 after 19 hours of fermentation. Label-free proteomics analysis (MS/MS) of V-L revealed 151 individual proteins. Of these, 137 proteins were annotated as containing a carbohydrate-active enzymes (CAZyme) module. Notably, of the 50 most abundant proteins, which accounted for over 90% of the protein amount in V-L, ca. 40% were predicted to be involved in pectin degradation (belonging mainly to CAZyme families GH28, CE8, CE16, PL1 and PL3). To reveal the role of individual putative key enzymes of pectic substrate decomposition, two galacturonases (PglA and PglB), which are core of pectin-degrading enzymes of the GH28 family, were heterologously expressed in Pichia pastoris strain GB10 and further characterized. PglA and PglB demonstrated maximum activity at 57 °C and 67 °C, respectively. Both enzymes exhibited endo-cleavage patterns towards polygalacturonic acid (PGA) and released oligosaccharides with different degrees of polymerization (DP). In conclusion, our study identified two pectin-cleaving enzymes present in major amounts in a highly efficient SBP-saccharifying enzyme mix and characterized some of their properties. Further studies along this line may facilitate the understanding of SBP degradation and may help to design improved artificial enzyme mixtures with a lower complexity than V-L for future application in biotechnology.

Project description:Genomic analysis of the model lignocellulosic biomass degrading bacteria C. phytofermentans indicates that it can degrade, transport, and utilize a wide-range of carbohydrates as possible growth substrates. Previous experiments characterized the expression of the degradation and transport machinery using custom whole genome oligonucleotide microarrays. The results indicate that C. phytofermentans utilizes ATP-binding cassette (ABC) transporters for carbohydrate uptake and does not use the sole phosphoenolpyruvate-phosphotransferase system (PTS) for any of the tested substrates. While some ABC transporters are specific for a single carbohydrate, the expression profiles indicate that others may be capable of transporting multiple substrates. Distinct sets of Carbohydrate Active Enzymes (CAZy) genes were also up-regulated on specific substrates indicative of C. phytofermentans ability to selectively degrade plant biomass. We also identified a highly expressed cluster of genes which includes seven extracellular glycoside hydrolases and two ABC transporters with unknown specificity. These results lead to the hypothesis that when grown on plant biomass, C. phytofermentans is capable of degrading and transporting all major carbohydrate components of the plant cell. To test this, C. phytofermentans was grown on cornstover and switchgrass. Results from this expression data and HPLC analysis indicates that C. phytofermentans is utilizing multiple substrates. with multiple sugar ABC transporter clusters and glycoside hydrolases being expressed. Interestingly all of the transporters were initially identified on disaccharides or oligio-saccharides, and none of the transporters identified as monosaccharide specific transporters were expressed. This could be an indication that C. phytofermentans prefers to transport oligiosacchrides over monosaccharides. The results presented here corroborate the genomic data which indicates the breath of the carbohydrate degradation, transport, and utilization machinery of C. phytofermentans. C. phytofermentans was cultured anaerobically on switchgrass and corn stover to determine specific expression patterns. The data in this series consists three independent RNA preparations from replicate cultures.

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Re-routing of sugar catabolism provides a better insight into fungal flexibility in using plant biomass-derived monomers as substrates

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