Experimental and computational analysis of physiological regulation at transcriptome, proteome and metabolome level
Consortium leader: Research professor MERJA PENTTILÄ
VTT Biotechnology
Other project leaders of the consortium:
Hannu Maaheimo, NMR laboratory, VTT Biotechnology
Matej Oresic, VTT Biotechnology
Juho Rousu, Department of Computer Science, University of Helsinki
Esko Ukkonen, Department of Computer Science, University of Helsinki
Liisa Holm, professor, Institute of Biotechnology, University of Helsinki
Juha Kokkonen, VTT Processes
Doctoral students of the consortium:
Laura Salusjärvi
Paula Jouhten
Juha Kokkonen
Ari Rantanen
Katja Saarela
Esa Pitkänen
Matti Kankainen
Ashwin Sivakumar
Tuomas Hätinen
Key words: systems biology, yeast physiology, transcriptome, proteome, metabolite profiling, metabolic fluxes
Project desciption and main results:
The project develops and applies advanced experimental and computational tools to address regulation of cell physiology at all levels, at transcriptome, proteome, metabolite and metabolic flux level. The project aims for understanding of physiological regulation at these different levels and the interdependencies of the regulatory mechanisms. Dominant triggers of physiological responses are sought for in dynamic experiments. The work is done with the yeast Saccharomyces cerevisiae that provides several advantages in systems biology approach. The project aims to understand in particular redox and energy (e.g. carbon starvation) regulation, that are the major determinants of the metabolic fate of cells. The project carried out at the Institute of Biotechnology focuses on unravelling the influence of promoter architecture on regulatory programmes. These programmes are hard-coded in the combinatorial patterns of transcription factor binding sites. Transcriptional regulatory networks have been systematically mapped in yeast. Bioinformatics analyses will be used to complement the map and identify functional modules. The transcriptional regulation of the xylose/glucose systems will be modelled in quantitative detail. The ultimate goal is to generalize from insights gained from a few well-understood systems to the global organization of regulatory programmes in yeast and other organisms.
Publications: