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Genome-wide transcriptional response of Trichoderma reesei to lignocellulose using RNA sequencing and comparison with Aspergillus niger.

Ries L, Pullan ST, Delmas S, Malla S, Blythe MJ, Archer DB - BMC Genomics (2013)

Bottom Line: This suggests a conserved strategy towards lignocellulose degradation in both saprobic fungi.This study provides a basis for further analysis and characterisation of genes shown to be highly induced in the presence of a lignocellulosic substrate.The data will help to elucidate the mechanism of solid substrate recognition and subsequent degradation by T. reesei and provide information which could prove useful for efficient production of second generation biofuels.

View Article: PubMed Central - HTML - PubMed

Affiliation: School of Biology, University of Nottingham, Nottingham NG7 2RD, UK.

ABSTRACT

Background: A major part of second generation biofuel production is the enzymatic saccharification of lignocellulosic biomass into fermentable sugars. Many fungi produce enzymes that can saccarify lignocellulose and cocktails from several fungi, including well-studied species such as Trichoderma reesei and Aspergillus niger, are available commercially for this process. Such commercially-available enzyme cocktails are not necessarily representative of the array of enzymes used by the fungi themselves when faced with a complex lignocellulosic material. The global induction of genes in response to exposure of T. reesei to wheat straw was explored using RNA-seq and compared to published RNA-seq data and model of how A. niger senses and responds to wheat straw.

Results: In T. reesei, levels of transcript that encode known and predicted cell-wall degrading enzymes were very high after 24h exposure to straw (approximately 13% of the total mRNA) but were less than recorded in A. niger (approximately 19% of the total mRNA). Closer analysis revealed that enzymes from the same glycoside hydrolase families but different carbohydrate esterase and polysaccharide lyase families were up-regulated in both organisms. Accessory proteins which have been hypothesised to possibly have a role in enhancing carbohydrate deconstruction in A. niger were also uncovered in T. reesei and categories of enzymes induced were in general similar to those in A. niger. Similarly to A. niger, antisense transcripts are present in T. reesei and their expression is regulated by the growth condition.

Conclusions: T. reesei uses a similar array of enzymes, for the deconstruction of a solid lignocellulosic substrate, to A. niger. This suggests a conserved strategy towards lignocellulose degradation in both saprobic fungi. This study provides a basis for further analysis and characterisation of genes shown to be highly induced in the presence of a lignocellulosic substrate. The data will help to elucidate the mechanism of solid substrate recognition and subsequent degradation by T. reesei and provide information which could prove useful for efficient production of second generation biofuels.

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Related in: MedlinePlus

CAZy gene expression. Comparison of the percentage of RNA transcripts corresponding to glycoside hydrolases, carbohydrate esterases and polysaccharide lyases in T. reesei and A. niger when grown for 48 h in glucose, transferred into straw-based media for 24 h and with the addition of glucose to straw-incubated cultures for 5 h. Error bars represent standard deviations of the percentage of RNA transcripts corresponding to GHs, CEs and PLs for all replicates.
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Figure 1: CAZy gene expression. Comparison of the percentage of RNA transcripts corresponding to glycoside hydrolases, carbohydrate esterases and polysaccharide lyases in T. reesei and A. niger when grown for 48 h in glucose, transferred into straw-based media for 24 h and with the addition of glucose to straw-incubated cultures for 5 h. Error bars represent standard deviations of the percentage of RNA transcripts corresponding to GHs, CEs and PLs for all replicates.

Mentions: After 48 h growth in glucose, CAZy gene mRNA represented 1.14% of total RNA in T. reesei (c.f. 3% in A. niger, Figure 1), with proteins from GH families 16, 18 and 72 (glucanases, chitinases and glucanosyltransferases) representing approximately half (45%) of the total CAZy mRNA (Figure 2). Thus in T. reesei, low levels of mRNA from genes encoding enzymes involved in the degradation of complex carbohydrates, including hemicellulose and chitin, are present when the fungus is cultivated in glucose-based medium. In this medium many of these enzymes are likely to be involved in cell wall remodelling during hyphal extension as high growth rates are achieved in the presence of glucose in T. reesei[33]. In contrast, in A. niger, transcripts from the glucoamylase glaA gene accounted for over 65% of total CAZy mRNA in glucose medium [3]. Induction of this gene in the presence of glucose and glucose-containing polysaccharides such as such starch has previously been described [34].


Genome-wide transcriptional response of Trichoderma reesei to lignocellulose using RNA sequencing and comparison with Aspergillus niger.

Ries L, Pullan ST, Delmas S, Malla S, Blythe MJ, Archer DB - BMC Genomics (2013)

CAZy gene expression. Comparison of the percentage of RNA transcripts corresponding to glycoside hydrolases, carbohydrate esterases and polysaccharide lyases in T. reesei and A. niger when grown for 48 h in glucose, transferred into straw-based media for 24 h and with the addition of glucose to straw-incubated cultures for 5 h. Error bars represent standard deviations of the percentage of RNA transcripts corresponding to GHs, CEs and PLs for all replicates.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3750697&req=5

Figure 1: CAZy gene expression. Comparison of the percentage of RNA transcripts corresponding to glycoside hydrolases, carbohydrate esterases and polysaccharide lyases in T. reesei and A. niger when grown for 48 h in glucose, transferred into straw-based media for 24 h and with the addition of glucose to straw-incubated cultures for 5 h. Error bars represent standard deviations of the percentage of RNA transcripts corresponding to GHs, CEs and PLs for all replicates.
Mentions: After 48 h growth in glucose, CAZy gene mRNA represented 1.14% of total RNA in T. reesei (c.f. 3% in A. niger, Figure 1), with proteins from GH families 16, 18 and 72 (glucanases, chitinases and glucanosyltransferases) representing approximately half (45%) of the total CAZy mRNA (Figure 2). Thus in T. reesei, low levels of mRNA from genes encoding enzymes involved in the degradation of complex carbohydrates, including hemicellulose and chitin, are present when the fungus is cultivated in glucose-based medium. In this medium many of these enzymes are likely to be involved in cell wall remodelling during hyphal extension as high growth rates are achieved in the presence of glucose in T. reesei[33]. In contrast, in A. niger, transcripts from the glucoamylase glaA gene accounted for over 65% of total CAZy mRNA in glucose medium [3]. Induction of this gene in the presence of glucose and glucose-containing polysaccharides such as such starch has previously been described [34].

Bottom Line: This suggests a conserved strategy towards lignocellulose degradation in both saprobic fungi.This study provides a basis for further analysis and characterisation of genes shown to be highly induced in the presence of a lignocellulosic substrate.The data will help to elucidate the mechanism of solid substrate recognition and subsequent degradation by T. reesei and provide information which could prove useful for efficient production of second generation biofuels.

View Article: PubMed Central - HTML - PubMed

Affiliation: School of Biology, University of Nottingham, Nottingham NG7 2RD, UK.

ABSTRACT

Background: A major part of second generation biofuel production is the enzymatic saccharification of lignocellulosic biomass into fermentable sugars. Many fungi produce enzymes that can saccarify lignocellulose and cocktails from several fungi, including well-studied species such as Trichoderma reesei and Aspergillus niger, are available commercially for this process. Such commercially-available enzyme cocktails are not necessarily representative of the array of enzymes used by the fungi themselves when faced with a complex lignocellulosic material. The global induction of genes in response to exposure of T. reesei to wheat straw was explored using RNA-seq and compared to published RNA-seq data and model of how A. niger senses and responds to wheat straw.

Results: In T. reesei, levels of transcript that encode known and predicted cell-wall degrading enzymes were very high after 24h exposure to straw (approximately 13% of the total mRNA) but were less than recorded in A. niger (approximately 19% of the total mRNA). Closer analysis revealed that enzymes from the same glycoside hydrolase families but different carbohydrate esterase and polysaccharide lyase families were up-regulated in both organisms. Accessory proteins which have been hypothesised to possibly have a role in enhancing carbohydrate deconstruction in A. niger were also uncovered in T. reesei and categories of enzymes induced were in general similar to those in A. niger. Similarly to A. niger, antisense transcripts are present in T. reesei and their expression is regulated by the growth condition.

Conclusions: T. reesei uses a similar array of enzymes, for the deconstruction of a solid lignocellulosic substrate, to A. niger. This suggests a conserved strategy towards lignocellulose degradation in both saprobic fungi. This study provides a basis for further analysis and characterisation of genes shown to be highly induced in the presence of a lignocellulosic substrate. The data will help to elucidate the mechanism of solid substrate recognition and subsequent degradation by T. reesei and provide information which could prove useful for efficient production of second generation biofuels.

Show MeSH
Related in: MedlinePlus