Abstract
BackgroundD-glucose, D-xylose and L-arabinose are the three major monosaccharides in plant cell walls. Complete utilization of all three sugars is still a bottleneck for second-generation cellulolytic bioethanol production, especially for L-arabinose. However, little is known about gene expression profiles during L-arabinose utilization in fungi and a comparison of the genome-wide fungal response to these three major monosaccharides has not yet been reported.ResultsUsing next-generation sequencing technology, we have analyzed the transcriptome of N. crassa grown on L-arabinose versus D-xylose, with D-glucose as the reference. We found that the gene expression profiles on L-arabinose were dramatically different from those on D-xylose. It appears that L-arabinose can rewire the fungal cell metabolic pathway widely and provoke the expression of many kinds of sugar transporters, hemicellulase genes and transcription factors. In contrast, many fewer genes, mainly related to the pentose metabolic pathway, were upregulated on D-xylose. The rewired metabolic response to L-arabinose was significantly different and wider than that under no carbon conditions, although the carbon starvation response was initiated on L-arabinose. Three novel sugar transporters were identified and characterized for their substrates here, including one glucose transporter GLT-1 (NCU01633) and two novel pentose transporters, XAT-1 (NCU01132), XYT-1 (NCU05627). One transcription factor associated with the regulation of hemicellulase genes, HCR-1 (NCU05064) was also characterized in the present study.ConclusionsWe conducted the first transcriptome analysis of Neurospora crassa grown on L-arabinose and performed a comparative analysis with cells grown on D-xylose and D-glucose, which deepens the understanding of the utilization of L-arabinose and D-xylose in filamentous fungi. The dataset generated by this research will be useful for mining target genes for D-xylose and L-arabinose utilization engineering and the novel sugar transportes identified are good targets for pentose untilization and biofuels production. Moreover, hemicellulase production by fungi could be improved by modifying the hemicellulase regulator discovered here.
Highlights
D-glucose, D-xylose and L-arabinose are the three major monosaccharides in plant cell walls
The growth of Neurospora crassa on D-glucose, D-xylose and L-arabinose To determine the utilization efficiency of D-glucose, D-xylose and L-arabinose in N. crassa, mycelia pre-cultured on D-glucose for 16 h were transferred to mixed sugar and the speed and pattern of sugar utilization were measured (See Methods and Figure 1)
The results indicate that D-xylose reductase accounts for the majority of the reductase activity on both L-arabinose and D-xylose in N. crassa, which is similar to the situation in T. reesei [25]
Summary
D-glucose, D-xylose and L-arabinose are the three major monosaccharides in plant cell walls. Little is known about gene expression profiles during L-arabinose utilization in fungi and a comparison of the genome-wide fungal response to these three major monosaccharides has not yet been reported. Compared with L-arabinose, much research has focused on both the enzymes of the D-xylose utilization pathway and the genome-wide response to D-xylose in yeast and filamentous fungi. Genome-wide analysis of the response to D-xylose has been reported in multiple fungi, such as Aspergillus niger, Neurospora crassa, Scheffersomyces stipitis and engineered Saccharomyces cerevisiae [5,6,7,8]. The sequenced genomes and transcriptome analysis open a great repository of target gene mining for xylose-fermenting yeast engineering, including D-xylose transporters. Neither growth nor xylanase activity was detected in a xyr-1 deletion strain when it was exposed to D-xylose or xylan [8]
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