Physiological evaluation of the filamentous fungus Trichoderma reesei in production processes by marker gene expression analysis

Gene expression of secreted cellulases and recombinant Melanocarpus albomyces laccase predicted the trends in the corresponding extracellular enzyme production rates and was highest in a narrow "physiological window" in the specific growth rate (μ) range of 0.03 – 0.05 h-1. Expression of ribosomal protein mRNAs was consistent with the changes in μ. Nine starvation-related genes were found as potential markers for detection of insufficient substrate feed for maintaining optimal protein production. For two genes induced in anaerobic conditions, increasing transcript levels were measured as dissolved oxygen decreased.The data obtained by TRAC supported the usefulness of focused and intensive transcriptional analysis in monitoring of biotechnical processes providing thus tools for process optimisation purposes.Microorganisms used in various types of biotechnical processes encounter constantly changing environmental conditions, to which they adapt by changing their cellular physiology. The performance of the microorganism has a major impact on the performance of the process and as a consequence, bioprocess monitoring and control strategies based on the physiological status of the culture have become more popular [1,2]. In bioprocesses the physiological status of the culture is generally measured indirectly by analysis of extracellular variables such as enzyme activities, pH and exhaust gas concentrations. Recent developments in analytical methods allow direct evaluation of cellular physiology by analysis of intracellular variables such as proteins, RNAs or metabolites, either in focused or systems-wide manner [1,3].By combination of transcriptomic, proteomic and/or metabolic profiles with advanced bioinformatic analysis it is possible to predict from the massive amount of data biologically meaningful analytes, i.e. biomarkers which can predict certain physiological events. In biotechnical processes such biomarkers have been used e.g. for detection of osmotic and oxidativ