Open Access Research article

Monitoring of transcriptional regulation in Pichia pastoris under protein production conditions

Brigitte Gasser1, Michael Maurer12, Jari Rautio3, Michael Sauer12, Anamitra Bhattacharyya4, Markku Saloheimo3, Merja Penttilä3 and Diethard Mattanovich12*

Author Affiliations

1 University of Natural Resources and Applied Life Sciences Vienna, Department of Biotechnology, Institute of Applied Microbiology, Muthgasse 18, A-1190 Vienna, Austria

2 School of Bioengineering, University of Applied Sciences FH Campus Wien, Muthgasse 18, A-1190 Vienna, Austria

3 VTT Technical Research Centre of Finland, P.O. Box 1000, 02044 VTT, Espoo, Finland

4 Integrated Genomics, Inc., 2201 W. Campbell Park Drive, Suite 15, 606012-3547 Chicago, IL, USA

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BMC Genomics 2007, 8:179  doi:10.1186/1471-2164-8-179

Published: 19 June 2007



It has become evident that host cells react to recombinant protein production with a variety of metabolic and intrinsic stresses such as the unfolded protein response (UPR) pathway. Additionally, environmental conditions such as growth temperature may have a strong impact on cell physiology and specific productivity. However, there is little information about the molecular reactions of the host cells on a genomic level, especially in context to recombinant protein secretion. For the first time, we monitored transcriptional regulation of a subset of marker genes in the common production host Pichia pastoris to gain insights into the general physiological status of the cells under protein production conditions, with the main focus on secretion stress related genes.


Overexpression of the UPR activating transcription factor Hac1p was employed to identify UPR target genes in P. pastoris and the responses were compared to those known for Saccharomyces cerevisiae. Most of the folding/secretion related genes showed similar regulation patterns in both yeasts, whereas genes associated with the general stress response were differentially regulated. Secretion of an antibody Fab fragment led to induction of UPR target genes in P. pastoris, however not to the same magnitude as Hac1p overproduction. Overexpression of S. cerevisiae protein disulfide isomerase (PDI1) enhances Fab secretion rates 1.9 fold, but did not relief UPR stress. Reduction of cultivation temperature from 25°C to 20°C led to a 1.4-fold increase of specific product secretion rate in chemostat cultivations, although the transcriptional levels of the product genes (Fab light and heavy chain) were significantly reduced at the lower temperature. A subset of folding related genes appeared to be down-regulated at the reduced temperature, whereas transcription of components of the ER associated degradation and the secretory transport was enhanced.


Monitoring of genomic regulation of marker genes with the transcriptional profiling method TRAC in P. pastoris revealed similarities and discrepancies of the responses compared to S. cerevisiae. Thus our results emphasize the importance to analyse the individual hosts under real production conditions instead of drawing conclusions from model organisms. Cultivation temperature has a significant influence on specific productivity that cannot be related just to thermodynamic effects, but strongly impacts the regulation of specific genes.