A multi-level study of recombinant Pichia pastoris in different oxygen conditions

K. Baumann, M. Carnicer, M. Dragosits, A. B. Graf, J. Stadlmann, Paula Jouhten, Hannu Maaheimo, B. Gasser, J. Albiol, D. Mattanovich, P. Ferrer (Corresponding Author)

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Abstract

Background: Yeasts are attractive expression platforms for many recombinant proteins, and there is evidence for an important interrelation between the protein secretion machinery and environmental stresses. While adaptive responses to such stresses are extensively studied in Saccharomyces cerevisiae, little is known about their impact on the physiology of Pichia pastoris. We have recently reported a beneficial effect of hypoxia on recombinant Fab secretion in P. pastoris chemostat cultivations. As a consequence, a systems biology approach was used to comprehensively identify cellular adaptations to low oxygen availability and the additional burden of protein production. Gene expression profiling was combined with proteomic analyses and the 13C isotope labelling based experimental determination of metabolic fluxes in the central carbon metabolism.

Results: The physiological adaptation of P. pastoris to hypoxia showed distinct traits in relation to the model yeast S. cerevisiae. There was a positive correlation between the transcriptomic, proteomic and metabolic fluxes adaptation of P. pastoris core metabolism to hypoxia, yielding clear evidence of a strong transcriptional regulation component of key pathways such as glycolysis, pentose phosphate pathway and TCA cycle. In addition, the adaptation to reduced oxygen revealed important changes in lipid metabolism, stress responses, as well as protein folding and trafficking.

Conclusions: This systems level study helped to understand the physiological adaptations of cellular mechanisms to low oxygen availability in a recombinant P. pastoris strain. Remarkably, the integration of data from three different levels allowed for the identification of differences in the regulation of the core metabolism between P. pastoris and S. cerevisiae. Detailed comparative analysis of the transcriptomic data also led to new insights into the gene expression profiles of several cellular processes that are not only susceptible to low oxygen concentrations, but might also contribute to enhanced protein secretion.
Original languageEnglish
JournalBMC Systems Biology
Volume4
Issue number141
DOIs
Publication statusPublished - 2010
MoE publication typeA1 Journal article-refereed

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Pichia
Yeast
Oxygen
Hypoxia
Secretion
Physiological Adaptation
Saccharomyces cerevisiae
Saccharomyces Cerevisiae
Metabolism
Protein
Proteomics
Proteins
Gene expression
Yeasts
Isotope Labeling
Pathway
Pentose Phosphate Pathway
Availability
Lipid Metabolism
Systems Biology

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Baumann, K., Carnicer, M., Dragosits, M., Graf, A. B., Stadlmann, J., Jouhten, P., ... Ferrer, P. (2010). A multi-level study of recombinant Pichia pastoris in different oxygen conditions. BMC Systems Biology, 4(141). https://doi.org/10.1186/1752-0509-4-141
Baumann, K. ; Carnicer, M. ; Dragosits, M. ; Graf, A. B. ; Stadlmann, J. ; Jouhten, Paula ; Maaheimo, Hannu ; Gasser, B. ; Albiol, J. ; Mattanovich, D. ; Ferrer, P. / A multi-level study of recombinant Pichia pastoris in different oxygen conditions. In: BMC Systems Biology. 2010 ; Vol. 4, No. 141.
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Baumann, K, Carnicer, M, Dragosits, M, Graf, AB, Stadlmann, J, Jouhten, P, Maaheimo, H, Gasser, B, Albiol, J, Mattanovich, D & Ferrer, P 2010, 'A multi-level study of recombinant Pichia pastoris in different oxygen conditions', BMC Systems Biology, vol. 4, no. 141. https://doi.org/10.1186/1752-0509-4-141

A multi-level study of recombinant Pichia pastoris in different oxygen conditions. / Baumann, K.; Carnicer, M.; Dragosits, M.; Graf, A. B.; Stadlmann, J.; Jouhten, Paula; Maaheimo, Hannu; Gasser, B.; Albiol, J.; Mattanovich, D.; Ferrer, P. (Corresponding Author).

In: BMC Systems Biology, Vol. 4, No. 141, 2010.

Research output: Contribution to journalArticleScientificpeer-review

TY - JOUR

T1 - A multi-level study of recombinant Pichia pastoris in different oxygen conditions

AU - Baumann, K.

AU - Carnicer, M.

AU - Dragosits, M.

AU - Graf, A. B.

AU - Stadlmann, J.

AU - Jouhten, Paula

AU - Maaheimo, Hannu

AU - Gasser, B.

AU - Albiol, J.

AU - Mattanovich, D.

AU - Ferrer, P.

PY - 2010

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N2 - Background: Yeasts are attractive expression platforms for many recombinant proteins, and there is evidence for an important interrelation between the protein secretion machinery and environmental stresses. While adaptive responses to such stresses are extensively studied in Saccharomyces cerevisiae, little is known about their impact on the physiology of Pichia pastoris. We have recently reported a beneficial effect of hypoxia on recombinant Fab secretion in P. pastoris chemostat cultivations. As a consequence, a systems biology approach was used to comprehensively identify cellular adaptations to low oxygen availability and the additional burden of protein production. Gene expression profiling was combined with proteomic analyses and the 13C isotope labelling based experimental determination of metabolic fluxes in the central carbon metabolism.Results: The physiological adaptation of P. pastoris to hypoxia showed distinct traits in relation to the model yeast S. cerevisiae. There was a positive correlation between the transcriptomic, proteomic and metabolic fluxes adaptation of P. pastoris core metabolism to hypoxia, yielding clear evidence of a strong transcriptional regulation component of key pathways such as glycolysis, pentose phosphate pathway and TCA cycle. In addition, the adaptation to reduced oxygen revealed important changes in lipid metabolism, stress responses, as well as protein folding and trafficking.Conclusions: This systems level study helped to understand the physiological adaptations of cellular mechanisms to low oxygen availability in a recombinant P. pastoris strain. Remarkably, the integration of data from three different levels allowed for the identification of differences in the regulation of the core metabolism between P. pastoris and S. cerevisiae. Detailed comparative analysis of the transcriptomic data also led to new insights into the gene expression profiles of several cellular processes that are not only susceptible to low oxygen concentrations, but might also contribute to enhanced protein secretion.

AB - Background: Yeasts are attractive expression platforms for many recombinant proteins, and there is evidence for an important interrelation between the protein secretion machinery and environmental stresses. While adaptive responses to such stresses are extensively studied in Saccharomyces cerevisiae, little is known about their impact on the physiology of Pichia pastoris. We have recently reported a beneficial effect of hypoxia on recombinant Fab secretion in P. pastoris chemostat cultivations. As a consequence, a systems biology approach was used to comprehensively identify cellular adaptations to low oxygen availability and the additional burden of protein production. Gene expression profiling was combined with proteomic analyses and the 13C isotope labelling based experimental determination of metabolic fluxes in the central carbon metabolism.Results: The physiological adaptation of P. pastoris to hypoxia showed distinct traits in relation to the model yeast S. cerevisiae. There was a positive correlation between the transcriptomic, proteomic and metabolic fluxes adaptation of P. pastoris core metabolism to hypoxia, yielding clear evidence of a strong transcriptional regulation component of key pathways such as glycolysis, pentose phosphate pathway and TCA cycle. In addition, the adaptation to reduced oxygen revealed important changes in lipid metabolism, stress responses, as well as protein folding and trafficking.Conclusions: This systems level study helped to understand the physiological adaptations of cellular mechanisms to low oxygen availability in a recombinant P. pastoris strain. Remarkably, the integration of data from three different levels allowed for the identification of differences in the regulation of the core metabolism between P. pastoris and S. cerevisiae. Detailed comparative analysis of the transcriptomic data also led to new insights into the gene expression profiles of several cellular processes that are not only susceptible to low oxygen concentrations, but might also contribute to enhanced protein secretion.

U2 - 10.1186/1752-0509-4-141

DO - 10.1186/1752-0509-4-141

M3 - Article

VL - 4

JO - BMC Systems Biology

JF - BMC Systems Biology

SN - 1752-0509

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