13C-constrained metabolic flux balancing analysis of Pichia pastoris grown on different carbon sources

S. Santos, Paula Jouhten, Hannu Maaheimo, J. Albiol, P. Ferrer

Research output: Chapter in Book/Report/Conference proceedingConference abstract in proceedingsScientific

Abstract

13C-constrained flux balancing analysis based on NMR data [1] has been applied as a method for the estimation of intracellular carbon fluxes of Pichia pastoris cells. In this approach, the underdetermined system of metabolite balances deduced from stoichiometric relations and measured extracellular rates is complemented with 13C constraints from metabolic flux ratio analysis [2, 3]. Steady state fluxes in central carbon metabolism of the methylotrophic yeast grown in chemostat cultures were estimated by 13C-constrained flux balancing method in different 13C-labeled carbon source experiments. In particular, cells were grown aerobically in chemostat cultures fed at two dilution rates (0.05 h 1, 0.16 h 1) with glucose, glycerol or varying mixtures of glycerol and methanol as carbon sources. In previous studies [4, 5], the metabolic pathways associated with the TCA cycle intermediates of P. pastoris were characterised in terms of metabolic flux ratios based on the 13C labelling pattern of proteinogenic amino acids using 13C-NMR measurements. Based on this data, analysis of metabolic flux responses to environmental modifications (carbon source and growth rate) has now been performed by 13C-constrained flux balancing analysis. A metabolic network has been reconstructed from literature data and summarized in a stoichiometric model including up to 54 internal metabolic reactions distributed into mitochondrial, cytoplasmic and biomass generation reactions, which include up to 55 metabolites. The underdetermined linear equation system was solved using flux partitioning ratios as additional constraints to obtain the global net flux solution. Overall, calculations show that the co-assimilation of methanol has a clear impact on the distribution of metabolic fluxes through the pentose phosphate pathway (PPP) and TCA cycle, as well as the distribution of methanol carbon into assimilatory and dissimilatory (direct oxidation to CO2) pathways. Also, such impact is clearly dependant on the specific growth rate of the cells. This study brings new insights on the P. pastoris' methanol metabolism complex regulation in the presence of a second carbon source, revealing important implications for biotechnological applications.
Original languageEnglish
Title of host publicationInternational Specialised Symposium on Yeasts ISSY25
Subtitle of host publicationSystems Biology of Yeasts - from Models to Applications
Place of PublicationEspoo
PublisherVTT Technical Research Centre of Finland
Pages118-119
ISBN (Electronic)951-38-6308-5
ISBN (Print)951-38-6307-7
Publication statusPublished - 2006
EventInternational Specialised Symposium on Yeasts, ISSY 25 - Espoo, Finland
Duration: 18 Jun 200621 Jun 2006

Publication series

SeriesVTT Symposium
Number242
ISSN0357-9387

Conference

ConferenceInternational Specialised Symposium on Yeasts, ISSY 25
Abbreviated titleISSY 25
CountryFinland
CityEspoo
Period18/06/0621/06/06

Fingerprint

methanol
carbon
chemostat
nuclear magnetic resonance
metabolite
metabolism
carbon flux
yeast
analysis
glucose
dilution
partitioning
amino acid
phosphate
oxidation
biomass
experiment
rate
distribution
method

Cite this

Santos, S., Jouhten, P., Maaheimo, H., Albiol, J., & Ferrer, P. (2006). 13C-constrained metabolic flux balancing analysis of Pichia pastoris grown on different carbon sources. In International Specialised Symposium on Yeasts ISSY25: Systems Biology of Yeasts - from Models to Applications (pp. 118-119). [P63] Espoo: VTT Technical Research Centre of Finland. VTT Symposium, No. 242
Santos, S. ; Jouhten, Paula ; Maaheimo, Hannu ; Albiol, J. ; Ferrer, P. / 13C-constrained metabolic flux balancing analysis of Pichia pastoris grown on different carbon sources. International Specialised Symposium on Yeasts ISSY25: Systems Biology of Yeasts - from Models to Applications. Espoo : VTT Technical Research Centre of Finland, 2006. pp. 118-119 (VTT Symposium; No. 242).
@inbook{0e69b15a1e2e42088f05d4fb20a59eb6,
title = "13C-constrained metabolic flux balancing analysis of Pichia pastoris grown on different carbon sources",
abstract = "13C-constrained flux balancing analysis based on NMR data [1] has been applied as a method for the estimation of intracellular carbon fluxes of Pichia pastoris cells. In this approach, the underdetermined system of metabolite balances deduced from stoichiometric relations and measured extracellular rates is complemented with 13C constraints from metabolic flux ratio analysis [2, 3]. Steady state fluxes in central carbon metabolism of the methylotrophic yeast grown in chemostat cultures were estimated by 13C-constrained flux balancing method in different 13C-labeled carbon source experiments. In particular, cells were grown aerobically in chemostat cultures fed at two dilution rates (0.05 h 1, 0.16 h 1) with glucose, glycerol or varying mixtures of glycerol and methanol as carbon sources. In previous studies [4, 5], the metabolic pathways associated with the TCA cycle intermediates of P. pastoris were characterised in terms of metabolic flux ratios based on the 13C labelling pattern of proteinogenic amino acids using 13C-NMR measurements. Based on this data, analysis of metabolic flux responses to environmental modifications (carbon source and growth rate) has now been performed by 13C-constrained flux balancing analysis. A metabolic network has been reconstructed from literature data and summarized in a stoichiometric model including up to 54 internal metabolic reactions distributed into mitochondrial, cytoplasmic and biomass generation reactions, which include up to 55 metabolites. The underdetermined linear equation system was solved using flux partitioning ratios as additional constraints to obtain the global net flux solution. Overall, calculations show that the co-assimilation of methanol has a clear impact on the distribution of metabolic fluxes through the pentose phosphate pathway (PPP) and TCA cycle, as well as the distribution of methanol carbon into assimilatory and dissimilatory (direct oxidation to CO2) pathways. Also, such impact is clearly dependant on the specific growth rate of the cells. This study brings new insights on the P. pastoris' methanol metabolism complex regulation in the presence of a second carbon source, revealing important implications for biotechnological applications.",
author = "S. Santos and Paula Jouhten and Hannu Maaheimo and J. Albiol and P. Ferrer",
year = "2006",
language = "English",
isbn = "951-38-6307-7",
series = "VTT Symposium",
publisher = "VTT Technical Research Centre of Finland",
number = "242",
pages = "118--119",
booktitle = "International Specialised Symposium on Yeasts ISSY25",
address = "Finland",

}

Santos, S, Jouhten, P, Maaheimo, H, Albiol, J & Ferrer, P 2006, 13C-constrained metabolic flux balancing analysis of Pichia pastoris grown on different carbon sources. in International Specialised Symposium on Yeasts ISSY25: Systems Biology of Yeasts - from Models to Applications., P63, VTT Technical Research Centre of Finland, Espoo, VTT Symposium, no. 242, pp. 118-119, International Specialised Symposium on Yeasts, ISSY 25 , Espoo, Finland, 18/06/06.

13C-constrained metabolic flux balancing analysis of Pichia pastoris grown on different carbon sources. / Santos, S.; Jouhten, Paula; Maaheimo, Hannu; Albiol, J.; Ferrer, P.

International Specialised Symposium on Yeasts ISSY25: Systems Biology of Yeasts - from Models to Applications. Espoo : VTT Technical Research Centre of Finland, 2006. p. 118-119 P63 (VTT Symposium; No. 242).

Research output: Chapter in Book/Report/Conference proceedingConference abstract in proceedingsScientific

TY - CHAP

T1 - 13C-constrained metabolic flux balancing analysis of Pichia pastoris grown on different carbon sources

AU - Santos, S.

AU - Jouhten, Paula

AU - Maaheimo, Hannu

AU - Albiol, J.

AU - Ferrer, P.

PY - 2006

Y1 - 2006

N2 - 13C-constrained flux balancing analysis based on NMR data [1] has been applied as a method for the estimation of intracellular carbon fluxes of Pichia pastoris cells. In this approach, the underdetermined system of metabolite balances deduced from stoichiometric relations and measured extracellular rates is complemented with 13C constraints from metabolic flux ratio analysis [2, 3]. Steady state fluxes in central carbon metabolism of the methylotrophic yeast grown in chemostat cultures were estimated by 13C-constrained flux balancing method in different 13C-labeled carbon source experiments. In particular, cells were grown aerobically in chemostat cultures fed at two dilution rates (0.05 h 1, 0.16 h 1) with glucose, glycerol or varying mixtures of glycerol and methanol as carbon sources. In previous studies [4, 5], the metabolic pathways associated with the TCA cycle intermediates of P. pastoris were characterised in terms of metabolic flux ratios based on the 13C labelling pattern of proteinogenic amino acids using 13C-NMR measurements. Based on this data, analysis of metabolic flux responses to environmental modifications (carbon source and growth rate) has now been performed by 13C-constrained flux balancing analysis. A metabolic network has been reconstructed from literature data and summarized in a stoichiometric model including up to 54 internal metabolic reactions distributed into mitochondrial, cytoplasmic and biomass generation reactions, which include up to 55 metabolites. The underdetermined linear equation system was solved using flux partitioning ratios as additional constraints to obtain the global net flux solution. Overall, calculations show that the co-assimilation of methanol has a clear impact on the distribution of metabolic fluxes through the pentose phosphate pathway (PPP) and TCA cycle, as well as the distribution of methanol carbon into assimilatory and dissimilatory (direct oxidation to CO2) pathways. Also, such impact is clearly dependant on the specific growth rate of the cells. This study brings new insights on the P. pastoris' methanol metabolism complex regulation in the presence of a second carbon source, revealing important implications for biotechnological applications.

AB - 13C-constrained flux balancing analysis based on NMR data [1] has been applied as a method for the estimation of intracellular carbon fluxes of Pichia pastoris cells. In this approach, the underdetermined system of metabolite balances deduced from stoichiometric relations and measured extracellular rates is complemented with 13C constraints from metabolic flux ratio analysis [2, 3]. Steady state fluxes in central carbon metabolism of the methylotrophic yeast grown in chemostat cultures were estimated by 13C-constrained flux balancing method in different 13C-labeled carbon source experiments. In particular, cells were grown aerobically in chemostat cultures fed at two dilution rates (0.05 h 1, 0.16 h 1) with glucose, glycerol or varying mixtures of glycerol and methanol as carbon sources. In previous studies [4, 5], the metabolic pathways associated with the TCA cycle intermediates of P. pastoris were characterised in terms of metabolic flux ratios based on the 13C labelling pattern of proteinogenic amino acids using 13C-NMR measurements. Based on this data, analysis of metabolic flux responses to environmental modifications (carbon source and growth rate) has now been performed by 13C-constrained flux balancing analysis. A metabolic network has been reconstructed from literature data and summarized in a stoichiometric model including up to 54 internal metabolic reactions distributed into mitochondrial, cytoplasmic and biomass generation reactions, which include up to 55 metabolites. The underdetermined linear equation system was solved using flux partitioning ratios as additional constraints to obtain the global net flux solution. Overall, calculations show that the co-assimilation of methanol has a clear impact on the distribution of metabolic fluxes through the pentose phosphate pathway (PPP) and TCA cycle, as well as the distribution of methanol carbon into assimilatory and dissimilatory (direct oxidation to CO2) pathways. Also, such impact is clearly dependant on the specific growth rate of the cells. This study brings new insights on the P. pastoris' methanol metabolism complex regulation in the presence of a second carbon source, revealing important implications for biotechnological applications.

M3 - Conference abstract in proceedings

SN - 951-38-6307-7

T3 - VTT Symposium

SP - 118

EP - 119

BT - International Specialised Symposium on Yeasts ISSY25

PB - VTT Technical Research Centre of Finland

CY - Espoo

ER -

Santos S, Jouhten P, Maaheimo H, Albiol J, Ferrer P. 13C-constrained metabolic flux balancing analysis of Pichia pastoris grown on different carbon sources. In International Specialised Symposium on Yeasts ISSY25: Systems Biology of Yeasts - from Models to Applications. Espoo: VTT Technical Research Centre of Finland. 2006. p. 118-119. P63. (VTT Symposium; No. 242).