The doctoral dissertations of the former Helsinki University of Technology (TKK) and Aalto University Schools of Technology (CHEM, ELEC, ENG, SCI) published in electronic format are available in the electronic publications archive of Aalto University - Aaltodoc.
Aalto

Metabolic Modelling and 13C Flux Analysis. Application to Biotechnologically Important Yeasts and a Fungus

Paula Jouhten

Dissertation for the degree of Doctor of Science in Technology to be presented with due permission of the Faculty of Information and Natural Sciences for public examination and debate in Auditorium of Engineering Physics at Helsinki University of Technology (Espoo, Finland) on the 3rd of December, 2009, at 12 noon.

Overview in PDF format (ISBN 978-951-38-7372-1)   [966 KB]
VTT Publications 724, ISSN 1455-0849

Dissertation is also available in print (ISBN 978-951-38-7371-4)
Copyright © 2009 VTT Technical Research Centre of Finland
VTT Publications 724, ISSN 1235-0621
VTT-PUBS-724
TKK-DISS-2693

Abstract

All bioconversions in cells derive from metabolism. Microbial metabolisms contain potential for bioconversions from simple source molecules to unlimited number of biochemicals and for degradation of even detrimental compounds. Metabolic fluxes are rates of consumption and production of compounds in metabolic reactions. Fluxes emerge as an ultimate phenotype of an organism from an integrated regulatory function of the underlying networks of complex and dynamic biochemical interactions. Since the fluxes are time-dependent, they have to be inferred from other, measurable, quantities by modelling and computational analysis. 13C-labelling is crucial for quantitative analysis of fluxes through intracellular alternative pathways. Local flux ratio analysis utilises uniform 13C-labelling experiments, where the carbon source contains a fraction of uniformly 13C-labelled molecules. Carbon-carbon bonds are cleaved and formed in metabolic reactions depending on the in vivo fluxes. 13C-labelling patterns of metabolites or macromolecule components can be detected by mass spectrometry (MS) or nuclear magnetic resonance (NMR) spectroscopy. Local flux ratio analysis utilises directly the 13C-labelling data and metabolic network models to solve ratios of converging fluxes.

In this thesis the local flux ratio analysis has been extended and applied to analysis of phenotypes of biotechnologically important yeasts Saccharomyces cerevisiae and Pichia pastoris, and a fungus Trichoderma reesei. Oxygen dependence of in vivo net flux distribution of S. cerevisiae was quantified by using local flux ratios as additional constraints to the stoichiometric model of the central carbon metabolism. The distribution of fluxes in the pyruvate branching point turned out to be most responsive to different oxygen availabilities. The distribution of fluxes was observed to vary not only between the fully respiratory, respiro-fermentative and fermentative metabolic states but also between different respiro-fermentative states. The local flux ratio analysis was extended to the case of two-carbon source of glycerol and methanol co-utilisation by P. pastoris. The fraction of methanol in the carbon source did not have as profound effect on the distribution of fluxes as the growth rate. The effect of carbon catabolite repression (CCR) on fluxes of T. reesei was studied by reconstructing amino acid biosynthetic pathways and by performing local flux ratio analysis. T. reesei was observed to primarily utilise respiratory metabolism also in conditions of CCR. T. reesei metabolism was further studied and L-threo-3-deoxy-hexulosonate was identified as L-galactonate dehydratase reaction product by using NMR spectroscopy. L-galactonate dehydratase reaction is part of the fungal pathway for D-galacturonic acid catabolism.

This thesis consists of an overview and of the following 5 publications:

  1. Paula Jouhten, Eija Rintala, Anne Huuskonen, Anu Tamminen, Mervi Toivari, Marilyn Wiebe, Laura Ruohonen, Merja Penttilä, and Hannu Maaheimo. 2008. Oxygen dependence of metabolic fluxes and energy generation of Saccharomyces cerevisiae CEN.PK113-1A. BMC Systems Biology, volume 2, 60. © 2008 by authors.
  2. Aina Solà, Paula Jouhten, Hannu Maaheimo, Francesc Sánchez-Ferrando, Thomas Szyperski, and Pau Ferrer. 2007. Metabolic flux profiling of Pichia pastoris grown on glycerol/methanol mixtures in chemostat cultures at low and high dilution rates. Microbiology, volume 153, number 1, pages 281-290. © 2007 Society for General Microbiology (SGM). By permission.
  3. Paula Jouhten, Esa Pitkänen, Tiina Pakula, Markku Saloheimo, Merja Penttilä, and Hannu Maaheimo. 2009. 13C-metabolic flux ratio and novel carbon path analyses confirmed that Trichoderma reesei uses primarily the respirative pathway also on the preferred carbon source glucose. BMC Systems Biology, volume 3, 104. © 2009 by authors.
  4. Ari Rantanen, Juho Rousu, Paula Jouhten, Nicola Zamboni, Hannu Maaheimo, and Esko Ukkonen. 2008. An analytic and systematic framework for estimating metabolic flux ratios from 13C tracer experiments. BMC Bioinformatics, volume 9, 266. © 2008 by authors.
  5. Satu Kuorelahti, Paula Jouhten, Hannu Maaheimo, Merja Penttilä, and Peter Richard. 2006. L-galactonate dehydratase is part of the fungal path for D-galacturonic acid catabolism. Molecular Microbiology, volume 61, number 4, pages 1060-1068.

Keywords: metabolic modelling, metabolic flux, metabolic flux analysis, MFA, carbon-13 labelling, carbon-13 metabolic flux analysis, nuclear magnetic resonance spectroscopy

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© 2009 Helsinki University of Technology

Last update 2011-05-26