Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Transcriptional comparison of the filamentous fungus Neurospora crassa growing on three major monosaccharides D-glucose, D-xylose and L-arabinose

ABSTRACT: D-glucose, D-xylose and L-arabinose are three major monosaccharides in the plant cell wall. 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 the gene expression profiles during L-arabinose utilization in fungi at genome-wide level and a comparison of the genome-wide fungal response to these three major monosaccharides has not yet been reported. To better understand the microbial response and utilization of L-arabinose for subsequent microbial engineering for co-fermentation all three sugars, we performed transcriptome analysis of N. crassa grown on L-arabinose, compared with that on D-xylose and D-glucose. RNA was extracted from cultures of N. carassa in early growth stage growing with D-glucose, L-arabinose or D-xylose as carbon source; duplicate cultures were sampled in some conditions.

ORGANISM(S): Neurospora crassa

SUBMITTER: Jingen Li

PROVIDER: E-GEOD-51091 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Transcriptional comparison of the filamentous fungus Neurospora crassa growing on three major monosaccharides D-glucose, D-xylose and L-arabinose.

Li Jingen J Lin Liangcai L Li Huiyan H Tian Chaoguang C Ma Yanhe Y

Biotechnology for biofuels 20140228 1

<h4>Background</h4>D-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.<h4>Results</h4>Using next-g ...[more]

PMID: 24581151

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Project description:Filamentous fungi are powerful producers of hydrolytic enzymes for the deconstruction of plant cell wall polysaccharides. However, the central question of how these sugars are perceived in the context of the complex cell wall matrix remains largely elusive. To address this question in a systematic fashion we performed an extensive comparative systems analysis of how the model filamentous fungus Neurospora crassa responds to the three main cell wall polysaccharides: pectin, hemicellulose and cellulose. We found the pectic response to be largely independent of the cellulolytic one with some overlap to hemicellulose, and in its extent surprisingly high, suggesting advantages for the fungus beyond being a mere carbon source. Our approach furthermore allowed us to identify carbon source-specific adaptations, such as the induction of the unfolded protein response on cellulose, and a commonly induced set of 29 genes likely involved in carbon scouting. Moreover, by hierarchical clustering we generated a co-expression matrix useful for the discovery of new components involved in polysaccharide utilization. This is exemplified by the identification of lat-1, which we demonstrate to encode for the physiologically relevant arabinose transporter in Neurospora. The analyses presented here are an important step towards understanding fungal degradation processes of complex biomass. Our data are based on carbon source transfer experiments. For this, N. crassa pregrown in sucrose for 16 hrs was washed in media without carbon and then transferred to either pectin, orange peel powder (OPP), xylan, Avicel (cellulose), sucrose, or media without carbon (NoC) for another 4 hrs. Biological triplicates (pectin, Avicel, sucrose, NoC) or duplicates (OPP) were used to identify differentially expressed genes in WT. For xylan only a single library was prepared, which was found to correlate well with previously published microarray data (Sun et al. 2012; doi: 10.1128/EC.05327-11)

Dataset Information

Transcriptional comparison of the filamentous fungus Neurospora crassa growing on three major monosaccharides D-glucose, D-xylose and L-arabinose

Publications

Transcriptional comparison of the filamentous fungus Neurospora crassa growing on three major monosaccharides D-glucose, D-xylose and L-arabinose.

Similar Datasets

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