Limits...
Re-annotation of the CAZy genes of Trichoderma reesei and transcription in the presence of lignocellulosic substrates.

Häkkinen M, Arvas M, Oja M, Aro N, Penttilä M, Saloheimo M, Pakula TM - Microb. Cell Fact. (2012)

Bottom Line: In this study, the CAZyme content of the T. reesei genome was updated, the discrepancies between the different genome versions and published literature were removed and the annotation of many of the genes was refined.Expression analysis of the genes gave information on the enzyme activities potentially induced by the presence of the different substrates.Comparison of the expression profiles of the CAZyme genes under the different conditions identified co-regulated groups of genes, suggesting common regulatory mechanisms for the gene groups.

View Article: PubMed Central - HTML - PubMed

Affiliation: VTT Technical Research Centre of Finland, Tietotie 2, Espoo, FI-02044, VTT, Finland. mari.hakkinen@vtt.fi

ABSTRACT

Background: Trichoderma reesei is a soft rot Ascomycota fungus utilised for industrial production of secreted enzymes, especially lignocellulose degrading enzymes. About 30 carbohydrate active enzymes (CAZymes) of T. reesei have been biochemically characterised. Genome sequencing has revealed a large number of novel candidates for CAZymes, thus increasing the potential for identification of enzymes with novel activities and properties. Plenty of data exists on the carbon source dependent regulation of the characterised hydrolytic genes. However, information on the expression of the novel CAZyme genes, especially on complex biomass material, is very limited.

Results: In this study, the CAZyme gene content of the T. reesei genome was updated and the annotations of the genes refined using both computational and manual approaches. Phylogenetic analysis was done to assist the annotation and to identify functionally diversified CAZymes. The analyses identified 201 glycoside hydrolase genes, 22 carbohydrate esterase genes and five polysaccharide lyase genes. Updated or novel functional predictions were assigned to 44 genes, and the phylogenetic analysis indicated further functional diversification within enzyme families or groups of enzymes. GH3 β-glucosidases, GH27 α-galactosidases and GH18 chitinases were especially functionally diverse. The expression of the lignocellulose degrading enzyme system of T. reesei was studied by cultivating the fungus in the presence of different inducing substrates and by subjecting the cultures to transcriptional profiling. The substrates included both defined and complex lignocellulose related materials, such as pretreated bagasse, wheat straw, spruce, xylan, Avicel cellulose and sophorose. The analysis revealed co-regulated groups of CAZyme genes, such as genes induced in all the conditions studied and also genes induced preferentially by a certain set of substrates.

Conclusions: In this study, the CAZyme content of the T. reesei genome was updated, the discrepancies between the different genome versions and published literature were removed and the annotation of many of the genes was refined. Expression analysis of the genes gave information on the enzyme activities potentially induced by the presence of the different substrates. Comparison of the expression profiles of the CAZyme genes under the different conditions identified co-regulated groups of genes, suggesting common regulatory mechanisms for the gene groups.

Show MeSH

Related in: MedlinePlus

CAZy family members induced in the presence of the different lignocellulose substrates. The number of genes in each CAZy family induced in the presence of the different lignocellulose substrates: BO, ground bagasse; BS, steam exploded bagasse; BE, enzymatically hydrolysed steam exploded bagasse; XO, oat spelt xylan; XB, birch xylan; AV1, 1% Avicel cellulose; AV0.75, 0.75% Avicel cellulose; WH, steam exploded wheat straw; SP, steam exploded spruce; SO, sophorose. The intensity of the colour represents the amount of genes induced. The total number of genes in each CAZy family induced by at least one of the substrates, and the total number of the CAZy family members in T. reesei genome are shown on the right. The total number of genes induced by the substrate and the number of CAZy families the genes belong to, are shown at the bottom. LC, lignocellulose substrate.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC3526510&req=5

Figure 2: CAZy family members induced in the presence of the different lignocellulose substrates. The number of genes in each CAZy family induced in the presence of the different lignocellulose substrates: BO, ground bagasse; BS, steam exploded bagasse; BE, enzymatically hydrolysed steam exploded bagasse; XO, oat spelt xylan; XB, birch xylan; AV1, 1% Avicel cellulose; AV0.75, 0.75% Avicel cellulose; WH, steam exploded wheat straw; SP, steam exploded spruce; SO, sophorose. The intensity of the colour represents the amount of genes induced. The total number of genes in each CAZy family induced by at least one of the substrates, and the total number of the CAZy family members in T. reesei genome are shown on the right. The total number of genes induced by the substrate and the number of CAZy families the genes belong to, are shown at the bottom. LC, lignocellulose substrate.

Mentions: The majority (179 genes) of the 228 CAZyme genes (excluding GT and CE10 family genes) were induced by at least one of the substrates used (higher expression level in the induced cultures as compared to the uninduced cultures at the same time point). The largest number of genes and CAZy families induced was detected in the cultures with the hemicellulosic material, bagasse, xylans and wheat straw (68–124 genes in 39–47 CAZy families), whereas cultivation in the presence of cellulosic or cellulose derived materials, Avicel cellulose, pretreated spruce, or sophorose, resulted in a clearly smaller number of genes induced (43–58 genes in 28–36 families). The number of induced genes within each CAZy family is represented in Figure 2.


Re-annotation of the CAZy genes of Trichoderma reesei and transcription in the presence of lignocellulosic substrates.

Häkkinen M, Arvas M, Oja M, Aro N, Penttilä M, Saloheimo M, Pakula TM - Microb. Cell Fact. (2012)

CAZy family members induced in the presence of the different lignocellulose substrates. The number of genes in each CAZy family induced in the presence of the different lignocellulose substrates: BO, ground bagasse; BS, steam exploded bagasse; BE, enzymatically hydrolysed steam exploded bagasse; XO, oat spelt xylan; XB, birch xylan; AV1, 1% Avicel cellulose; AV0.75, 0.75% Avicel cellulose; WH, steam exploded wheat straw; SP, steam exploded spruce; SO, sophorose. The intensity of the colour represents the amount of genes induced. The total number of genes in each CAZy family induced by at least one of the substrates, and the total number of the CAZy family members in T. reesei genome are shown on the right. The total number of genes induced by the substrate and the number of CAZy families the genes belong to, are shown at the bottom. LC, lignocellulose substrate.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3526510&req=5

Figure 2: CAZy family members induced in the presence of the different lignocellulose substrates. The number of genes in each CAZy family induced in the presence of the different lignocellulose substrates: BO, ground bagasse; BS, steam exploded bagasse; BE, enzymatically hydrolysed steam exploded bagasse; XO, oat spelt xylan; XB, birch xylan; AV1, 1% Avicel cellulose; AV0.75, 0.75% Avicel cellulose; WH, steam exploded wheat straw; SP, steam exploded spruce; SO, sophorose. The intensity of the colour represents the amount of genes induced. The total number of genes in each CAZy family induced by at least one of the substrates, and the total number of the CAZy family members in T. reesei genome are shown on the right. The total number of genes induced by the substrate and the number of CAZy families the genes belong to, are shown at the bottom. LC, lignocellulose substrate.
Mentions: The majority (179 genes) of the 228 CAZyme genes (excluding GT and CE10 family genes) were induced by at least one of the substrates used (higher expression level in the induced cultures as compared to the uninduced cultures at the same time point). The largest number of genes and CAZy families induced was detected in the cultures with the hemicellulosic material, bagasse, xylans and wheat straw (68–124 genes in 39–47 CAZy families), whereas cultivation in the presence of cellulosic or cellulose derived materials, Avicel cellulose, pretreated spruce, or sophorose, resulted in a clearly smaller number of genes induced (43–58 genes in 28–36 families). The number of induced genes within each CAZy family is represented in Figure 2.

Bottom Line: In this study, the CAZyme content of the T. reesei genome was updated, the discrepancies between the different genome versions and published literature were removed and the annotation of many of the genes was refined.Expression analysis of the genes gave information on the enzyme activities potentially induced by the presence of the different substrates.Comparison of the expression profiles of the CAZyme genes under the different conditions identified co-regulated groups of genes, suggesting common regulatory mechanisms for the gene groups.

View Article: PubMed Central - HTML - PubMed

Affiliation: VTT Technical Research Centre of Finland, Tietotie 2, Espoo, FI-02044, VTT, Finland. mari.hakkinen@vtt.fi

ABSTRACT

Background: Trichoderma reesei is a soft rot Ascomycota fungus utilised for industrial production of secreted enzymes, especially lignocellulose degrading enzymes. About 30 carbohydrate active enzymes (CAZymes) of T. reesei have been biochemically characterised. Genome sequencing has revealed a large number of novel candidates for CAZymes, thus increasing the potential for identification of enzymes with novel activities and properties. Plenty of data exists on the carbon source dependent regulation of the characterised hydrolytic genes. However, information on the expression of the novel CAZyme genes, especially on complex biomass material, is very limited.

Results: In this study, the CAZyme gene content of the T. reesei genome was updated and the annotations of the genes refined using both computational and manual approaches. Phylogenetic analysis was done to assist the annotation and to identify functionally diversified CAZymes. The analyses identified 201 glycoside hydrolase genes, 22 carbohydrate esterase genes and five polysaccharide lyase genes. Updated or novel functional predictions were assigned to 44 genes, and the phylogenetic analysis indicated further functional diversification within enzyme families or groups of enzymes. GH3 β-glucosidases, GH27 α-galactosidases and GH18 chitinases were especially functionally diverse. The expression of the lignocellulose degrading enzyme system of T. reesei was studied by cultivating the fungus in the presence of different inducing substrates and by subjecting the cultures to transcriptional profiling. The substrates included both defined and complex lignocellulose related materials, such as pretreated bagasse, wheat straw, spruce, xylan, Avicel cellulose and sophorose. The analysis revealed co-regulated groups of CAZyme genes, such as genes induced in all the conditions studied and also genes induced preferentially by a certain set of substrates.

Conclusions: In this study, the CAZyme content of the T. reesei genome was updated, the discrepancies between the different genome versions and published literature were removed and the annotation of many of the genes was refined. Expression analysis of the genes gave information on the enzyme activities potentially induced by the presence of the different substrates. Comparison of the expression profiles of the CAZyme genes under the different conditions identified co-regulated groups of genes, suggesting common regulatory mechanisms for the gene groups.

Show MeSH
Related in: MedlinePlus