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The impact of oxygen on the transcriptome of recombinant S. cerevisiae and P. pastoris - a comparative analysis.

Baumann K, Dato L, Graf AB, Frascotti G, Dragosits M, Porro D, Mattanovich D, Ferrer P, Branduardi P - BMC Genomics (2011)

Bottom Line: 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.The 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.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Chemical Engineering, Autonomous University of Barcelona, Spain.

ABSTRACT

Background: 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, 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.

Results: The 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.

Conclusions: The 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.

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Related in: MedlinePlus

GO group enrichment as determined by Fisher's exact test. Significantly enriched GO functional groups (computed with the Fisher's exact test with a p-value ≤ 0.05) are labeled in red (upregulated genes), green (downregulated genes) and orange (both up- and downregulated genes). Pairwise comparisons in S. cerevisiae (Sc) and P. pastoris (Pp) are abbreviated as in figure 1.
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Figure 2: GO group enrichment as determined by Fisher's exact test. Significantly enriched GO functional groups (computed with the Fisher's exact test with a p-value ≤ 0.05) are labeled in red (upregulated genes), green (downregulated genes) and orange (both up- and downregulated genes). Pairwise comparisons in S. cerevisiae (Sc) and P. pastoris (Pp) are abbreviated as in figure 1.

Mentions: Overrepresentation of up- and downregulated genes in gene ontology (GO) functional groups was evaluated by a Fisher's exact test (p-value ≤ 0.05). These enriched functional groups were analyzed with the fold change values of the pair wise comparisons, i.e. hypoxic vs. normoxic (HvsN), hypoxic vs. oxygen-limited (HvsL), and oxygen-limited vs. normoxic conditions (LvsN). The results are illustrated in Figure 2. While the comparison of hypoxic and normoxic conditions yielded a more extensive set of regulated genes, the number of enriched groups in the intermediate set points was generally more moderate, in particular for S. cerevisiae. While no statistically enriched GO terms were found for the P. pastoris reference strain comparing the lower oxygen conditions (HvsL), the extent of responsive GO categories for LvsN was similar to that in HvsN. These results were not only in good accordance with the PCA and direct comparison of equally regulated genes, but also with the different fermentative properties of the yeasts. Even though P. pastoris is facultative anaerobe, it has a higher propensity for respiratory growth than S. cerevisiae. This might explain a less drastic reorganization of the S. cerevisiae transcriptome after a shift to a reduced oxygen environment.


The impact of oxygen on the transcriptome of recombinant S. cerevisiae and P. pastoris - a comparative analysis.

Baumann K, Dato L, Graf AB, Frascotti G, Dragosits M, Porro D, Mattanovich D, Ferrer P, Branduardi P - BMC Genomics (2011)

GO group enrichment as determined by Fisher's exact test. Significantly enriched GO functional groups (computed with the Fisher's exact test with a p-value ≤ 0.05) are labeled in red (upregulated genes), green (downregulated genes) and orange (both up- and downregulated genes). Pairwise comparisons in S. cerevisiae (Sc) and P. pastoris (Pp) are abbreviated as in figure 1.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3116504&req=5

Figure 2: GO group enrichment as determined by Fisher's exact test. Significantly enriched GO functional groups (computed with the Fisher's exact test with a p-value ≤ 0.05) are labeled in red (upregulated genes), green (downregulated genes) and orange (both up- and downregulated genes). Pairwise comparisons in S. cerevisiae (Sc) and P. pastoris (Pp) are abbreviated as in figure 1.
Mentions: Overrepresentation of up- and downregulated genes in gene ontology (GO) functional groups was evaluated by a Fisher's exact test (p-value ≤ 0.05). These enriched functional groups were analyzed with the fold change values of the pair wise comparisons, i.e. hypoxic vs. normoxic (HvsN), hypoxic vs. oxygen-limited (HvsL), and oxygen-limited vs. normoxic conditions (LvsN). The results are illustrated in Figure 2. While the comparison of hypoxic and normoxic conditions yielded a more extensive set of regulated genes, the number of enriched groups in the intermediate set points was generally more moderate, in particular for S. cerevisiae. While no statistically enriched GO terms were found for the P. pastoris reference strain comparing the lower oxygen conditions (HvsL), the extent of responsive GO categories for LvsN was similar to that in HvsN. These results were not only in good accordance with the PCA and direct comparison of equally regulated genes, but also with the different fermentative properties of the yeasts. Even though P. pastoris is facultative anaerobe, it has a higher propensity for respiratory growth than S. cerevisiae. This might explain a less drastic reorganization of the S. cerevisiae transcriptome after a shift to a reduced oxygen environment.

Bottom Line: 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.The 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.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Chemical Engineering, Autonomous University of Barcelona, Spain.

ABSTRACT

Background: 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, 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.

Results: The 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.

Conclusions: The 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.

Show MeSH
Related in: MedlinePlus