Transcriptional analysis of Trichoderma reesei cultivated in the presence of different lignocellulose substrates

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

Research output: Chapter in Book/Report/Conference proceedingConference abstract in proceedingsScientific

Abstract

Trichoderma reesei is a soft rot Ascomycete fungus able to secrete enzymes extremely efficiently. Availability of the complete genome sequence of T. reesei has made it possible to utilise genome wide methods to study protein
production by the fungus and to utilise the information obtained to develop new strains with better enzyme production qualities. In order to study the co‐expression of enzyme genes, a complete list of CAZymes of T. reesei needed to be obtained. Novel CAZymes were searched from the genome by mapping T. reesei proteome with Blast search to the protein sequences of the CAZY database. New annotation was given to several genes in order to gain more information on the possible function of novel candidate genes and to specify the annotation of previously identified genes. A phylogenetic approach was used to reveal the functional diversification of T. reesei enzyme genes within CAZY families and between the gene duplicates. Expression of the hydrolytic system of T. reesei Rut‐C30 was studied by cultivating the fungus in the presence of different lignocellulose substrates. Cultures were subjected to transcriptional profiling using oligonucleotide microarrays. Differentially expressed genes were
identified and expression profiles of genes encoding lignocellulose degrading enzymes were compared to identify co‐regulated groups of genes and genes needed for the degradation of specific substrates. Transcriptional profiling
revealed a group of genes co‐regulated on all of the substrates and genes which expression profiles were more diverse. Also some examples were found from co‐regulation of enzyme genes according to genomic localization.
Original languageEnglish
Title of host publicationAbstracts from the 11th European Conference on Fungal Genetics
PublisherNew Prairie Press
Pages237
DOIs
Publication statusPublished - 2012
Event11th European Conference on Fungal Genetics - Marburg, Germany
Duration: 30 Mar 20122 Apr 2012

Publication series

SeriesFungal Genetics Reports
Number6
Volume59
ISSN1941-4757

Conference

Conference11th European Conference on Fungal Genetics
CountryGermany
CityMarburg
Period30/03/122/04/12

Fingerprint

Trichoderma reesei
lignocellulose
genes
enzymes
fungi
genome
duplicate genes
oligonucleotides
proteome
Ascomycota
amino acid sequences

Cite this

Häkkinen, M., Arvas, M., Oja, M., Aro, N., Penttilä, M., Saloheimo, M., & Pakula, T. (2012). Transcriptional analysis of Trichoderma reesei cultivated in the presence of different lignocellulose substrates. In Abstracts from the 11th European Conference on Fungal Genetics (pp. 237). [PR8.37] New Prairie Press. Fungal Genetics Reports, No. 6, Vol.. 59 https://doi.org/10.4148/1941-4765.1014
Häkkinen, Mari ; Arvas, Mikko ; Oja, Merja ; Aro, Nina ; Penttilä, Merja ; Saloheimo, Markku ; Pakula, Tiina. / Transcriptional analysis of Trichoderma reesei cultivated in the presence of different lignocellulose substrates. Abstracts from the 11th European Conference on Fungal Genetics. New Prairie Press, 2012. pp. 237 (Fungal Genetics Reports; No. 6, Vol. 59).
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Häkkinen, M, Arvas, M, Oja, M, Aro, N, Penttilä, M, Saloheimo, M & Pakula, T 2012, Transcriptional analysis of Trichoderma reesei cultivated in the presence of different lignocellulose substrates. in Abstracts from the 11th European Conference on Fungal Genetics., PR8.37, New Prairie Press, Fungal Genetics Reports, no. 6, vol. 59, pp. 237, 11th European Conference on Fungal Genetics, Marburg, Germany, 30/03/12. https://doi.org/10.4148/1941-4765.1014

Transcriptional analysis of Trichoderma reesei cultivated in the presence of different lignocellulose substrates. / Häkkinen, Mari (Corresponding author); Arvas, Mikko; Oja, Merja; Aro, Nina; Penttilä, Merja; Saloheimo, Markku; Pakula, Tiina.

Abstracts from the 11th European Conference on Fungal Genetics. New Prairie Press, 2012. p. 237 PR8.37 (Fungal Genetics Reports; No. 6, Vol. 59).

Research output: Chapter in Book/Report/Conference proceedingConference abstract in proceedingsScientific

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AU - Häkkinen, Mari

AU - Arvas, Mikko

AU - Oja, Merja

AU - Aro, Nina

AU - Penttilä, Merja

AU - Saloheimo, Markku

AU - Pakula, Tiina

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AB - Trichoderma reesei is a soft rot Ascomycete fungus able to secrete enzymes extremely efficiently. Availability of the complete genome sequence of T. reesei has made it possible to utilise genome wide methods to study proteinproduction by the fungus and to utilise the information obtained to develop new strains with better enzyme production qualities. In order to study the co‐expression of enzyme genes, a complete list of CAZymes of T. reesei needed to be obtained. Novel CAZymes were searched from the genome by mapping T. reesei proteome with Blast search to the protein sequences of the CAZY database. New annotation was given to several genes in order to gain more information on the possible function of novel candidate genes and to specify the annotation of previously identified genes. A phylogenetic approach was used to reveal the functional diversification of T. reesei enzyme genes within CAZY families and between the gene duplicates. Expression of the hydrolytic system of T. reesei Rut‐C30 was studied by cultivating the fungus in the presence of different lignocellulose substrates. Cultures were subjected to transcriptional profiling using oligonucleotide microarrays. Differentially expressed genes wereidentified and expression profiles of genes encoding lignocellulose degrading enzymes were compared to identify co‐regulated groups of genes and genes needed for the degradation of specific substrates. Transcriptional profilingrevealed a group of genes co‐regulated on all of the substrates and genes which expression profiles were more diverse. Also some examples were found from co‐regulation of enzyme genes according to genomic localization.

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Häkkinen M, Arvas M, Oja M, Aro N, Penttilä M, Saloheimo M et al. Transcriptional analysis of Trichoderma reesei cultivated in the presence of different lignocellulose substrates. In Abstracts from the 11th European Conference on Fungal Genetics. New Prairie Press. 2012. p. 237. PR8.37. (Fungal Genetics Reports; No. 6, Vol. 59). https://doi.org/10.4148/1941-4765.1014