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
    Country/TerritoryAustria
    CityVienna
    Period8/04/0611/04/06

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