Transcriptional analysis of Trichoderma reesei bioprocesses with the novel TRAC method

Jari Rautio, Kari Kataja, Reetta Satokari, Merja Penttilä, Hans Söderlund, Markku Saloheimo

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

Abstract

Moving of biological research to postgenomic era with a growing number of
organisms including filamentous fungi has increased the interest in functional
genomics, and the need for fast and reliable transcriptional profiling methods is
thus growing. We have developed a rapid method for transcriptional profiling of
microbial cultivations based on a novel technique called TRAC "transcriptional
profiling with the aid of affinity capture". This method allows fast gene
expression analysis for sets of mRNAs by solution hybridisation with a pool of
target-specific oligonucleotide probes of distinct sizes that are identified and
quantified by capillary electrophoresis. The assay procedure has been semiautomated for simultaneous treatment of 96 samples using magnetic bead
particle processor. To further enhance the robustness of the method it was set
up to work with crude cell lysates. TRAC has been shown to produce results
highly consistent with mRNA quantification by Northern hybridisation.
Computational methods have been applied for design of target-specific
oligonucleotide probes and to assign them into minimal number of pools. The
whole assay procedure can be performed in three hours, implying its usefulness
in bioprocess monitoring and control. The developed TRAC method application has been used for monitoring the levels of a set of mRNAs in the filamentous fungus Trichoderma reesei in fermentation conditions. Chosen gene markers for bioprocess monitoring are involved in various cellular pathways including unfolded protein response, protection against various stress conditions, oxygen and nutrient limitation responses, protein synthesis and growth. Data collected from different types of fermentations, batch, fed-batch and continuous cultures, shows the potential of the method for use in optimisation of production processes and provides novel information about regulation of various genes during different phases cultivations. We have also used TRAC successfully for assessment of steady states in chemostat cultures.
Original languageEnglish
Title of host publication8th European Conference on Fungal Genetics
EditorsIrina S. Druzhinina, Alexey G. Kopchisnkiy, Christian P. Kubicek
PublisherVienna University of Technology
ChapterVII Cell-Factories and Biotechnology
Pages251
Publication statusPublished - 2006
Event8th European Conference on Fungal Genetics - Vienna, Austria
Duration: 8 Apr 200611 Apr 2006

Conference

Conference8th European Conference on Fungal Genetics
CountryAustria
CityVienna
Period8/04/0611/04/06

Fingerprint

Trichoderma
Messenger RNA
Fermentation
Fungi
Unfolded Protein Response
Batch Cell Culture Techniques
Oligonucleotide Probes
Capillary Electrophoresis
Genes
Oxygen
Food

Cite this

Rautio, J., Kataja, K., Satokari, R., Penttilä, M., Söderlund, H., & Saloheimo, M. (2006). Transcriptional analysis of Trichoderma reesei bioprocesses with the novel TRAC method. In I. S. Druzhinina, A. G. Kopchisnkiy, & C. P. Kubicek (Eds.), 8th European Conference on Fungal Genetics (pp. 251). [VIIo-2] Vienna University of Technology.
Rautio, Jari ; Kataja, Kari ; Satokari, Reetta ; Penttilä, Merja ; Söderlund, Hans ; Saloheimo, Markku. / Transcriptional analysis of Trichoderma reesei bioprocesses with the novel TRAC method. 8th European Conference on Fungal Genetics. editor / Irina S. Druzhinina ; Alexey G. Kopchisnkiy ; Christian P. Kubicek. Vienna University of Technology, 2006. pp. 251
@inbook{d11a8c9bbd7d4e2981f67d6645158752,
title = "Transcriptional analysis of Trichoderma reesei bioprocesses with the novel TRAC method",
abstract = "Moving of biological research to postgenomic era with a growing number oforganisms including filamentous fungi has increased the interest in functionalgenomics, and the need for fast and reliable transcriptional profiling methods isthus growing. We have developed a rapid method for transcriptional profiling ofmicrobial cultivations based on a novel technique called TRAC {"}transcriptionalprofiling with the aid of affinity capture{"}. This method allows fast geneexpression analysis for sets of mRNAs by solution hybridisation with a pool oftarget-specific oligonucleotide probes of distinct sizes that are identified andquantified by capillary electrophoresis. The assay procedure has been semiautomated for simultaneous treatment of 96 samples using magnetic beadparticle processor. To further enhance the robustness of the method it was setup to work with crude cell lysates. TRAC has been shown to produce resultshighly consistent with mRNA quantification by Northern hybridisation.Computational methods have been applied for design of target-specificoligonucleotide probes and to assign them into minimal number of pools. Thewhole assay procedure can be performed in three hours, implying its usefulnessin bioprocess monitoring and control. The developed TRAC method application has been used for monitoring the levels of a set of mRNAs in the filamentous fungus Trichoderma reesei in fermentation conditions. Chosen gene markers for bioprocess monitoring are involved in various cellular pathways including unfolded protein response, protection against various stress conditions, oxygen and nutrient limitation responses, protein synthesis and growth. Data collected from different types of fermentations, batch, fed-batch and continuous cultures, shows the potential of the method for use in optimisation of production processes and provides novel information about regulation of various genes during different phases cultivations. We have also used TRAC successfully for assessment of steady states in chemostat cultures.",
author = "Jari Rautio and Kari Kataja and Reetta Satokari and Merja Penttil{\"a} and Hans S{\"o}derlund and Markku Saloheimo",
note = "CA2: TK402",
year = "2006",
language = "English",
pages = "251",
editor = "Druzhinina, {Irina S.} and Kopchisnkiy, {Alexey G.} and Kubicek, {Christian P.}",
booktitle = "8th European Conference on Fungal Genetics",
publisher = "Vienna University of Technology",
address = "Austria",

}

Rautio, J, Kataja, K, Satokari, R, Penttilä, M, Söderlund, H & Saloheimo, M 2006, Transcriptional analysis of Trichoderma reesei bioprocesses with the novel TRAC method. in IS Druzhinina, AG Kopchisnkiy & CP Kubicek (eds), 8th European Conference on Fungal Genetics., VIIo-2, Vienna University of Technology, pp. 251, 8th European Conference on Fungal Genetics, Vienna, Austria, 8/04/06.

Transcriptional analysis of Trichoderma reesei bioprocesses with the novel TRAC method. / Rautio, Jari; Kataja, Kari; Satokari, Reetta; Penttilä, Merja; Söderlund, Hans; Saloheimo, Markku.

8th European Conference on Fungal Genetics. ed. / Irina S. Druzhinina; Alexey G. Kopchisnkiy; Christian P. Kubicek. Vienna University of Technology, 2006. p. 251 VIIo-2.

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

TY - CHAP

T1 - Transcriptional analysis of Trichoderma reesei bioprocesses with the novel TRAC method

AU - Rautio, Jari

AU - Kataja, Kari

AU - Satokari, Reetta

AU - Penttilä, Merja

AU - Söderlund, Hans

AU - Saloheimo, Markku

N1 - CA2: TK402

PY - 2006

Y1 - 2006

N2 - Moving of biological research to postgenomic era with a growing number oforganisms including filamentous fungi has increased the interest in functionalgenomics, and the need for fast and reliable transcriptional profiling methods isthus growing. We have developed a rapid method for transcriptional profiling ofmicrobial cultivations based on a novel technique called TRAC "transcriptionalprofiling with the aid of affinity capture". This method allows fast geneexpression analysis for sets of mRNAs by solution hybridisation with a pool oftarget-specific oligonucleotide probes of distinct sizes that are identified andquantified by capillary electrophoresis. The assay procedure has been semiautomated for simultaneous treatment of 96 samples using magnetic beadparticle processor. To further enhance the robustness of the method it was setup to work with crude cell lysates. TRAC has been shown to produce resultshighly consistent with mRNA quantification by Northern hybridisation.Computational methods have been applied for design of target-specificoligonucleotide probes and to assign them into minimal number of pools. Thewhole assay procedure can be performed in three hours, implying its usefulnessin bioprocess monitoring and control. The developed TRAC method application has been used for monitoring the levels of a set of mRNAs in the filamentous fungus Trichoderma reesei in fermentation conditions. Chosen gene markers for bioprocess monitoring are involved in various cellular pathways including unfolded protein response, protection against various stress conditions, oxygen and nutrient limitation responses, protein synthesis and growth. Data collected from different types of fermentations, batch, fed-batch and continuous cultures, shows the potential of the method for use in optimisation of production processes and provides novel information about regulation of various genes during different phases cultivations. We have also used TRAC successfully for assessment of steady states in chemostat cultures.

AB - Moving of biological research to postgenomic era with a growing number oforganisms including filamentous fungi has increased the interest in functionalgenomics, and the need for fast and reliable transcriptional profiling methods isthus growing. We have developed a rapid method for transcriptional profiling ofmicrobial cultivations based on a novel technique called TRAC "transcriptionalprofiling with the aid of affinity capture". This method allows fast geneexpression analysis for sets of mRNAs by solution hybridisation with a pool oftarget-specific oligonucleotide probes of distinct sizes that are identified andquantified by capillary electrophoresis. The assay procedure has been semiautomated for simultaneous treatment of 96 samples using magnetic beadparticle processor. To further enhance the robustness of the method it was setup to work with crude cell lysates. TRAC has been shown to produce resultshighly consistent with mRNA quantification by Northern hybridisation.Computational methods have been applied for design of target-specificoligonucleotide probes and to assign them into minimal number of pools. Thewhole assay procedure can be performed in three hours, implying its usefulnessin bioprocess monitoring and control. The developed TRAC method application has been used for monitoring the levels of a set of mRNAs in the filamentous fungus Trichoderma reesei in fermentation conditions. Chosen gene markers for bioprocess monitoring are involved in various cellular pathways including unfolded protein response, protection against various stress conditions, oxygen and nutrient limitation responses, protein synthesis and growth. Data collected from different types of fermentations, batch, fed-batch and continuous cultures, shows the potential of the method for use in optimisation of production processes and provides novel information about regulation of various genes during different phases cultivations. We have also used TRAC successfully for assessment of steady states in chemostat cultures.

M3 - Conference abstract in proceedings

SP - 251

BT - 8th European Conference on Fungal Genetics

A2 - Druzhinina, Irina S.

A2 - Kopchisnkiy, Alexey G.

A2 - Kubicek, Christian P.

PB - Vienna University of Technology

ER -

Rautio J, Kataja K, Satokari R, Penttilä M, Söderlund H, Saloheimo M. Transcriptional analysis of Trichoderma reesei bioprocesses with the novel TRAC method. In Druzhinina IS, Kopchisnkiy AG, Kubicek CP, editors, 8th European Conference on Fungal Genetics. Vienna University of Technology. 2006. p. 251. VIIo-2