Abstract
BackgroundPichia pastoris is a well established yeast host for heterologous protein expression, however, the physiological and genetic information about this yeast remains scanty. The lack of a published genome sequence renders DNA arrays unavailable, thereby hampering more global investigations of P. pastoris from the beginning. Here, we examine the suitability of Saccharomyces cerevisiae DNA microarrays for heterologous hybridisation with P. pastoris cDNA.ResultsWe could show that it is possible to obtain new and valuable information about transcriptomic regulation in P. pastoris by probing S. cerevisiae DNA microarrays. The number of positive signals was about 66 % as compared to homologous S. cerevisiae hybridisation, and both the signal intensities and gene regulations correlated with high significance between data obtained from P. pastoris and S. cerevisiae samples. The differential gene expression patterns upon shift from glycerol to methanol as carbon source were investigated in more detail. Downregulation of TCA cycle genes and a decrease of genes related to ribonucleotide and ribosome synthesis were among the major effects identified.ConclusionsWe could successfully demonstrate that heterologous microarray hybridisations allow deep insights into the transcriptomic regulation processes of P. pastoris. The observed downregulation of TCA cycle and ribosomal synthesis genes correlates to a significantly lower specific growth rate during the methanol feed phase.
Highlights
Pichia pastoris is a well established yeast host for heterologous protein expression, the physiological and genetic information about this yeast remains scanty
Renn et al [9] compared the performance of cDNA microarrays from an African cichlid fish (Astatotilapia burtoni) for the heterologous hybridisation with cDNAs from eight different fish species, some of them closely related and others more distantly related
Qualification of heterologous hybridisation Before analysing differential gene expression data, it was our intention to verify whether the heterologous hybridisation of S. cerevisiae DNA microarrays with P. pastoris cDNA results in significant data
Summary
Pichia pastoris is a well established yeast host for heterologous protein expression, the physiological and genetic information about this yeast remains scanty. Microbial Cell Factories 2004, 3:17 http://www.microbialcellfactories.com/content/3/1/17 investigation of changes in expression patterns is not available for this yeast species To circumvent this problem, heterologous hybridisation to commercially available DNA microarrays might be conceivable. Renn et al [9] compared the performance of cDNA microarrays from an African cichlid fish (Astatotilapia burtoni) for the heterologous hybridisation with cDNAs from eight different fish species, some of them closely related (other cichlids) and others more distantly related (among them Atlantic salmon and guppy) They conclude that significant results are obtained even with distantly related species, the number of positive spots declines with the phylogenetic distance, as strikingly does the degree of measured regulation
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