Systems biology of yeast

Genome-wide analysis of pentose metabolism in Saccharomyces cerevisiae

Laura Salusjärvi, Juha-Pekka Pitkänen, Heini Koivistoinen, Laura Ruohonen, Merja Penttilä

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

Abstract

We are interested in broadening the substrate utilisation range of the yeast Saccharomyces cerevisiae and in connection to this to study nutritional responses and signalling at a global level. S. cerevisiae does not naturally utilise pentose sugars unlike most other fungi, and recombinant S. cerevisiae strains have been constructed that contain the xylose utilisation pathway from other yeasts. The xylose reductase enzyme (XR) prefers NADPH as a cofactor while the next step in the pathway xylitol dehydrogenase (XDH), NAD+. This is believed to create a redox cofactor imbalance in the cells and limit xylose fermentation. Other suggested rate-limiting steps in xylose utilisation and the use of xylose as a fermentative carbon source include xylose uptake and limitations in the pentose phosphate pathway (PPP) reactions. In order to understand redox and nutrient regulation in general, and the physiology of xylose utilising S. cerevisiae, we carried out chemostat cultures on xylose as a carbon source, and compared those with glucose cultures. Transcriptional profiling and proteomics were carried out. The results are in good agreement. In addition to the expected responses in cellular redox metabolism and PPP, also new responses towards xylose as a carbon source were discovered such as the up-regulation of pathways for alternative carbon source utilisation and responses for nutritional control and starvation. The physiology of the recombinant yeast appears to be neither fully repressed (fermentative) nor derepressed (gluconeogenic).
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
Pages149
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

NameVTT Symposium
PublisherVTT
Number242
ISSN (Print)0357-9387
ISSN (Electronic)1455-0873

Conference

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

Fingerprint

pentoses
xylose
Saccharomyces cerevisiae
yeasts
Biological Sciences
metabolism
genome
carbon
physiology
phosphates
xylitol
NAD (coenzyme)
NADP (coenzyme)
proteomics
starvation
fermentation
sugars
uptake mechanisms
glucose
fungi

Cite this

Salusjärvi, L., Pitkänen, J-P., Koivistoinen, H., Ruohonen, L., & Penttilä, M. (2006). Systems biology of yeast: Genome-wide analysis of pentose metabolism in Saccharomyces cerevisiae. In International Specialised Symposium on Yeasts ISSY25: Systems Biology of Yeasts - from Models to Applications (pp. 149). [P93] Espoo: VTT Technical Research Centre of Finland. VTT Symposium, No. 242
Salusjärvi, Laura ; Pitkänen, Juha-Pekka ; Koivistoinen, Heini ; Ruohonen, Laura ; Penttilä, Merja. / Systems biology of yeast : Genome-wide analysis of pentose metabolism in Saccharomyces cerevisiae. International Specialised Symposium on Yeasts ISSY25: Systems Biology of Yeasts - from Models to Applications. Espoo : VTT Technical Research Centre of Finland, 2006. pp. 149 (VTT Symposium; No. 242).
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Salusjärvi, L, Pitkänen, J-P, Koivistoinen, H, Ruohonen, L & Penttilä, M 2006, Systems biology of yeast: Genome-wide analysis of pentose metabolism in Saccharomyces cerevisiae. in International Specialised Symposium on Yeasts ISSY25: Systems Biology of Yeasts - from Models to Applications., P93, VTT Technical Research Centre of Finland, Espoo, VTT Symposium, no. 242, pp. 149, International Specialised Symposium on Yeasts, ISSY 25 , Espoo, Finland, 18/06/06.

Systems biology of yeast : Genome-wide analysis of pentose metabolism in Saccharomyces cerevisiae. / Salusjärvi, Laura; Pitkänen, Juha-Pekka; Koivistoinen, Heini; Ruohonen, Laura; Penttilä, Merja.

International Specialised Symposium on Yeasts ISSY25: Systems Biology of Yeasts - from Models to Applications. Espoo : VTT Technical Research Centre of Finland, 2006. p. 149 P93 (VTT Symposium; No. 242).

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

TY - CHAP

T1 - Systems biology of yeast

T2 - Genome-wide analysis of pentose metabolism in Saccharomyces cerevisiae

AU - Salusjärvi, Laura

AU - Pitkänen, Juha-Pekka

AU - Koivistoinen, Heini

AU - Ruohonen, Laura

AU - Penttilä, Merja

PY - 2006

Y1 - 2006

N2 - We are interested in broadening the substrate utilisation range of the yeast Saccharomyces cerevisiae and in connection to this to study nutritional responses and signalling at a global level. S. cerevisiae does not naturally utilise pentose sugars unlike most other fungi, and recombinant S. cerevisiae strains have been constructed that contain the xylose utilisation pathway from other yeasts. The xylose reductase enzyme (XR) prefers NADPH as a cofactor while the next step in the pathway xylitol dehydrogenase (XDH), NAD+. This is believed to create a redox cofactor imbalance in the cells and limit xylose fermentation. Other suggested rate-limiting steps in xylose utilisation and the use of xylose as a fermentative carbon source include xylose uptake and limitations in the pentose phosphate pathway (PPP) reactions. In order to understand redox and nutrient regulation in general, and the physiology of xylose utilising S. cerevisiae, we carried out chemostat cultures on xylose as a carbon source, and compared those with glucose cultures. Transcriptional profiling and proteomics were carried out. The results are in good agreement. In addition to the expected responses in cellular redox metabolism and PPP, also new responses towards xylose as a carbon source were discovered such as the up-regulation of pathways for alternative carbon source utilisation and responses for nutritional control and starvation. The physiology of the recombinant yeast appears to be neither fully repressed (fermentative) nor derepressed (gluconeogenic).

AB - We are interested in broadening the substrate utilisation range of the yeast Saccharomyces cerevisiae and in connection to this to study nutritional responses and signalling at a global level. S. cerevisiae does not naturally utilise pentose sugars unlike most other fungi, and recombinant S. cerevisiae strains have been constructed that contain the xylose utilisation pathway from other yeasts. The xylose reductase enzyme (XR) prefers NADPH as a cofactor while the next step in the pathway xylitol dehydrogenase (XDH), NAD+. This is believed to create a redox cofactor imbalance in the cells and limit xylose fermentation. Other suggested rate-limiting steps in xylose utilisation and the use of xylose as a fermentative carbon source include xylose uptake and limitations in the pentose phosphate pathway (PPP) reactions. In order to understand redox and nutrient regulation in general, and the physiology of xylose utilising S. cerevisiae, we carried out chemostat cultures on xylose as a carbon source, and compared those with glucose cultures. Transcriptional profiling and proteomics were carried out. The results are in good agreement. In addition to the expected responses in cellular redox metabolism and PPP, also new responses towards xylose as a carbon source were discovered such as the up-regulation of pathways for alternative carbon source utilisation and responses for nutritional control and starvation. The physiology of the recombinant yeast appears to be neither fully repressed (fermentative) nor derepressed (gluconeogenic).

M3 - Conference abstract in proceedings

SN - 951-38-6307-7

T3 - VTT Symposium

SP - 149

BT - International Specialised Symposium on Yeasts ISSY25

PB - VTT Technical Research Centre of Finland

CY - Espoo

ER -

Salusjärvi L, Pitkänen J-P, Koivistoinen H, Ruohonen L, Penttilä M. Systems biology of yeast: Genome-wide analysis of pentose metabolism in Saccharomyces cerevisiae. In International Specialised Symposium on Yeasts ISSY25: Systems Biology of Yeasts - from Models to Applications. Espoo: VTT Technical Research Centre of Finland. 2006. p. 149. P93. (VTT Symposium; No. 242).