Abstract
BackgroundSaccharomyces cerevisiae and Pichia pastoris are two of the most relevant microbial eukaryotic platforms for the production of recombinant proteins. Their known genome sequences enabled several transcriptomic profiling studies under many different environmental conditions, thus mimicking not only perturbations and adaptations which occur in their natural surroundings, but also in industrial processes. Notably, the majority of such transcriptome analyses were performed using non-engineered strains.In this comparative study, the gene expression profiles of S. cerevisiae and P. pastoris, a Crabtree positive and Crabtree negative yeast, respectively, were analyzed for three different oxygenation conditions (normoxic, oxygen-limited and hypoxic) under recombinant protein producing conditions in chemostat cultivations.ResultsThe major differences in the transcriptomes of S. cerevisiae and P. pastoris were observed between hypoxic and normoxic conditions, where the availability of oxygen strongly affected ergosterol biosynthesis, central carbon metabolism and stress responses, particularly the unfolded protein response. Steady state conditions under low oxygen set-points seemed to perturb the transcriptome of S. cerevisiae to a much lesser extent than the one of P. pastoris, reflecting the major tolerance of the baker's yeast towards oxygen limitation, and a higher fermentative capacity. Further important differences were related to Fab production, which was not significantly affected by oxygen availability in S. cerevisiae, while a clear productivity increase had been previously reported for hypoxically grown P. pastoris.ConclusionsThe effect of three different levels of oxygen availability on the physiology of P. pastoris and S. cerevisiae revealed a very distinct remodelling of the transcriptional program, leading to novel insights into the different adaptive responses of Crabtree negative and positive yeasts to oxygen availability. Moreover, the application of such comparative genomic studies to recombinant hosts grown in different environments might lead to the identification of key factors for efficient protein production.
Highlights
Saccharomyces cerevisiae and Pichia pastoris are two of the most relevant microbial eukaryotic platforms for the production of recombinant proteins
While oxygen deprivation significantly increased the productivity of P. pastoris, the Fab yield in S. cerevisiae was not affected by oxygen
General overview of the transcriptional analysis We performed a global analysis of microarray data from recombinant and reference strains of S. cerevisiae and P. pastoris grown under different oxygen availability levels
Summary
Saccharomyces cerevisiae and Pichia pastoris are two of the most relevant microbial eukaryotic platforms for the production of recombinant proteins Their known genome sequences enabled several transcriptomic profiling studies under many different environmental conditions, mimicking perturbations and adaptations which occur in their natural surroundings, and in industrial processes. The recently published sequence of the Pichia pastoris genome [10,11] allowed the development of P. pastoris specific microarrays [12] and the onset of genome-wide studies in this yeast expression system, which has been gaining high industrial relevance in the recent years This advance was of special importance because the lack of host specific microarrays hindered research, and implicated a certain dependency of data interpretation on similarities to S. cerevisiae. These differences between data on P. pastoris and the established literature of S. cerevisiae point to less uniform regulatory systems in yeasts than believed until now
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