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

Mari Häkkinen (Corresponding Author), Mikko Arvas, Merja Oja, Nina Aro, Merja Penttilä, Markku Saloheimo, Tiina M. Pakula

Research output: Contribution to journalArticleScientificpeer-review

94 Citations (Scopus)

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.

Original languageEnglish
Article number134
JournalMicrobial Cell Factories
Volume11
DOIs
Publication statusPublished - 4 Oct 2012
MoE publication typeA1 Journal article-refereed

Fingerprint

Molecular Sequence Annotation
Trichoderma
Transcription
Genes
Substrates
Enzymes
Carbohydrates
Genome
Cellulose
Polysaccharide-Lyases
Fungi
Galactosidases
Glucosidases
Xylans
Chitinases
Ascomycota
Glycoside Hydrolases
Esterases
Regulator Genes
Transcriptome

Keywords

  • Bagasse
  • Biorefinery
  • Carbohydrate active enzymes
  • Cellulase
  • Gene regulation
  • Hemicellulase
  • Lignocellulose
  • Spruce
  • Transcriptional profiling
  • Transcriptome
  • Wheat

Cite this

@article{f77d08a9309a4fea869ff0b6e2f0708f,
title = "Re-annotation of the CAZy genes of Trichoderma reesei and transcription in the presence of lignocellulosic substrates",
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.",
keywords = "Bagasse, Biorefinery, Carbohydrate active enzymes, Cellulase, Gene regulation, Hemicellulase, Lignocellulose, Spruce, Transcriptional profiling, Transcriptome, Wheat",
author = "Mari H{\"a}kkinen and Mikko Arvas and Merja Oja and Nina Aro and Merja Penttil{\"a} and Markku Saloheimo and Pakula, {Tiina M.}",
year = "2012",
month = "10",
day = "4",
doi = "10.1186/1475-2859-11-134",
language = "English",
volume = "11",
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issn = "1475-2859",

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Re-annotation of the CAZy genes of Trichoderma reesei and transcription in the presence of lignocellulosic substrates. / Häkkinen, Mari (Corresponding Author); Arvas, Mikko; Oja, Merja; Aro, Nina; Penttilä, Merja; Saloheimo, Markku; Pakula, Tiina M.

In: Microbial Cell Factories, Vol. 11, 134, 04.10.2012.

Research output: Contribution to journalArticleScientificpeer-review

TY - JOUR

T1 - Re-annotation of the CAZy genes of Trichoderma reesei and transcription in the presence of lignocellulosic substrates

AU - Häkkinen, Mari

AU - Arvas, Mikko

AU - Oja, Merja

AU - Aro, Nina

AU - Penttilä, Merja

AU - Saloheimo, Markku

AU - Pakula, Tiina M.

PY - 2012/10/4

Y1 - 2012/10/4

N2 - 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.

AB - 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.

KW - Bagasse

KW - Biorefinery

KW - Carbohydrate active enzymes

KW - Cellulase

KW - Gene regulation

KW - Hemicellulase

KW - Lignocellulose

KW - Spruce

KW - Transcriptional profiling

KW - Transcriptome

KW - Wheat

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U2 - 10.1186/1475-2859-11-134

DO - 10.1186/1475-2859-11-134

M3 - Article

C2 - 23035824

AN - SCOPUS:84871398239

VL - 11

JO - Microbial Cell Factories

JF - Microbial Cell Factories

SN - 1475-2859

M1 - 134

ER -