Transcriptional monitoring of steady state and effects of anaerobic phases in chemostat cultures of the filamentous fungus Trichoderma reesei

In cultures with good steady states, the expression of the marker genes varied less than 20% on average between sequential samples for at least 5 or 6 residence times. However, in a number of T. reesei cultures continuous flow did not result in a good steady state. Perturbations to the steady state were always evident at the transcriptional level, even when they were not measurable as changes in biomass or product concentrations. Both unintentional and intentional perturbations of the steady state demonstrated that a number of genes involved in growth, protein production and secretion are sensitive markers for culture disturbances. Exposure to anaerobic conditions caused strong responses at the level of gene expression, but surprisingly the cultures could regain their previous steady state quickly, even after 3 h O2 depletion. The main effect of producing M. albomyces laccase was down-regulation of the native cellulases compared with the host strain.This study demonstrates the usefulness of transcriptional analysis by TRAC in ensuring the quality of chemostat cultures prior to costly and laborious genome-wide analysis. In addition TRAC was shown to be an efficient tool in studying gene expression dynamics in transient conditions.Systems-wide methods have become an important part of physiological research in industrial biotechnology, with the aim of improving industrially relevant production strains and processes, for example by identifying physiological reactions that limit metabolism or the production of proteins. Transcriptional profiling can be particularly useful, since it can reveal previously unknown, but relevant pathways [1].Chemostat and other continuous flow cultures are the technique of choice for producing biomass for global studies, such as transcriptomic, proteomic and metabolomic profiles, since parameters such as growth rate, dissolved oxygen and nutrient concentrations can be kept constant, providing a reproducible environment and populations of cel