Ecology and Evolution
2100 København Ø
Cells respond to environmental changes through physiological adaptation at the short term level and adaptive evolution at the long term level.
Our research is focused on physiological adaptation and adaptive evolution of the eukaryotic cell to nutrient availability. For this the yeast, S. cerevisiae is used as model to study:
- Adaptation of yeast to nitrogen limitation
- Molecular mechanisms for yeast biofilm development
- Development of drug resistance
- Extrachromosomal DNA elements
Methods applied to investigate adaptations are sequencing and DNA array based global studies of the transcriptome and genome; metabolic engineering; Confocal Laser Scanning Microscopy as well as classical methods in fermentation, biochemistry, molecular biology and genetics.
Adaptation of yeast to nitrogen limitation – role of transporters: Nitrogen is central in the regulation of S. cerevisiae life cycle, regulating mating, morphology and biofilm. We find that S. cerevisiae adapt to nitrogen limitation by transcriptional modulation of nitrogen transporters. Prolonged exposure to nitrogen limitation leads to evolution of cells with altered 1) copy number 2) Km and 3) regulation of the nitrogen transporters. We study the transcriptional regulation of nitrogen transporter and their influence on biofilm.
Molecular mechanisms for yeast biofilm development: We have discovered that nitrogen limitation leads to evolution of biofilm forming yeast, suggesting that constraints on the physiological system influence the possible outcome of adaptive evolution. Yeast biofilms adversely influence the health of an increasing number of individuals with infections affecting cancer and AIDS patients. We study the molecular mechanisms and physiological factors regulating biofilm development with Confocal Laser Scanning Microscopy (CLSM) and contemporary system biology methods. Funding: FTP grant 10-084027-.
Drug resistance in yeast biofilm: A remarkable feature of yeast biofilms is their ability to tolerate many unrelated antifugal agents. Central goals in treatment of yeast infections are therefore 1) to understand the molecular basis for drug tolerance in biofilms and 2) to develop novel efficient antifungal agents that can prevent or eradicate biofilms. We pursue these goals in collaboration with industrial partners and partners at DTU. Funding: FTP grant 10-084027-.
Extrachromosomal DNA elements (also known as double minutes) are found in tumor cells where they carry amplified oncogenes or genes involved in drug resistance. We have discovery double minute like elements in S. cerevisiae that confer selective advantage under nutrient limitation through the amplification of nutrient transporter genes. We use S. cerevisiae to study the molecular mechanisms for formation and maintenance of extrachromosomal elements and plan to investigate genetic and chemical approaches to inhibit their formation in the eukaryotic cell.
1. Gresham, D.,Usaite, R., Germann, S.M., Lisby, M., Botstein, D. and B. Regenberg, B. (2010) Adaptation to Diverse Nitrogen Limited Environments by Deletion or Extrachromosomal Circularization of the GAP1 Locus. P.N.A.S. 107, 18551-18556.
2. Usaite, R., Ochmann, D., Grotkjær, T., Yvonnet, V., Boles, E. and Regenberg, B. (2011) Biofilm, invasive and pseudohyphal growth evolve in Saccharomyces cerevisiae under N-limitation via the cAMP-PKA pathway and amino-acid transporter genes. Mol. Microbiol. Resubmitted with recommended changes.
3. M.W. Nielsen, M.W., Sternberg, C., Molin, S. and Regenberg, B. (2011) Pseudomonas aeruginosa and Saccharomyces cerevisiae Biofilm in Flow Cells. J. Vis. Exp., in press.
4. Haagensen J.A.J., Regenberg, B. and Sternberg, C. (2010) Advanced microscopy of microbial cells in High Resolution Microbial Single Cell Analytics, Springer DE.
5. De Jong, W.A., Bro, C., Østergaard, S., Regenberg, B., Olsson, L. and Nielsen, J. (2008) The roles of galactitol, galactose-1-phosphate, and phosphoglucomutase in galactose-induced toxicity in Saccharomyces cerevisiae. Biotechnol Bioeng. 101, 317-326.
6. Regenberg, B., Grotkjær, T., Winther, O., Fausbøll, A., Bro, C., Åkesson, M., Brunak, S., Hansen, L.K. and Nielsen, J. (2006) Growth-rate regulated genes have profound impact on interpretation of transcriptome profiling in Saccharomyces cerevisiae. Genome Biol. 7, R107.
7. Usaite, R., Grotkjær, T., Patil, K.R., Nielsen, J. and Regenberg, B. (2006) Global transcriptional and physiological response of Saccharomyces cerevisiae to ammonium, L-alanine, or L-glutamine Limitation. Appl. Environ. Microbiol. 72, 6194-6203-.
8. Eckert-Boule, N., Larsson, K., Wu, B., Poulsen, P., Regenberg, B., Nielsen, J. and Kielland-Brandt M.C. (2006) Deletion of RTS1, encoding a regulatory subunit of Protein Phosphatase 2A, results in constitutive amino acid signaling via increased Stp1p processing. Eukaryot. Cell. 5, 174-179.
9. Bro, C., Regenberg, B., Förster, J. and Nielsen, J. (2006) In silico aided metabolic engineering of Saccharomyces cerevisiae for improved bioethanol production. Metab. Eng. 8, 102-111.
10. Grotkjær, T., Winther, O., Regenberg, B., Nielsen, J. and Hansen, L.K., (2006) Robust multi-scale clustering of large DNA microarray datasets with the consensus algorithm. Bioinformatics. 22, 58-67.
11. Bro, C., Knudsen, S., Regenberg, B., Olsson, L. and Nielsen, J. (2005) Improvement of the galactose uptake in Saccharomyces cerevisiae through overexpression of phosphoglucomutase: An example of transcript analysis as a tool in inverse metabolic engineering. Appl. Environ. Microbiol. 71, 6465-6472-.
12. Eckert-Boulet, N., Regenberg, B. and Nielsen, J. (2005) A dual role of Grr1p the transcriptional regulation of amino acid permease genes and genes in carbon metabolism. Curr. Genet. 4, 139-149.
13. Regenberg, B., Krühne, U., Beyer, M., Pedersen, L.H., Simón, M., Thomas, O.R.T., Nielsen, J. and Ahl, T. (2004) Micro arraying with laminar flow patterning. Lab. Chip. 4, 654-657.
14. Eckert-Boulet, N., Nielsen, P.S., Friis, C., dos Santos, M.M., Nielsen, J., Kielland-Brandt, M.C. and Regenberg, B. (2004) Transcriptional profiling of extracellular amino acid sensing in Saccharomyces cerevisiae and the role of Stp1p and Stp2p. Yeast 21, 635-648.
15. Bro, C., Regenberg, B. and Nielsen, J. (2004) Genome-wide transcriptional response of a Saccharomyces cerevisiae strain with an altered redox metabolism. Biotechnol. Bioeng. 85, 269-276.
16. Bro, C., Regenberg, B., Lagniel, G., Labarre, J., Montero-Lomeli, M., and Nielsen, J. (2003). Transcriptional, proteomic, and metabolic responses to lithium in galactose-grown yeast cells. J. Biol. Chem. 278, 32141-32149.
17. Piper M.D., Daran-Lapujade, P., Bro, C., Regenberg, B., Knudsen, S., Nielsen, J., and Pronk, J.T. (2002). Reproducibility of oligonucleotide microarray transcriptome analyses. An interlaboratory comparison using chemostat cultures of Saccharomyces cerevisiae. J. Biol. Chem. 277, 37001-37008.
18. Regenberg, B., and Kielland-Brandt, M.C. (2001). Amino acid residues important for substrate specificity of the amino acid permeases Can1p and Gnp1p in Saccharomyces cerevisiae. Yeast 18, 1429-1440.
19. Regenberg, B., and Hansen, J. (2000). GAP1, a novel selection and counter-selection marker for multiple gene disruptions in Saccharomyces cerevisiae. Yeast 16, 1111-1119.
20. Regenberg, B., Düring-Olsen, L., Kielland-Brandt, M.C., and Holmberg, S. (1999). Substrate specificity and regulation of amino acid permeases in Saccharomyces cerevisiae. Curr. Genet. 36, 317-328.
21. Düring-Olsen, L., Regenberg, B., Gjermansen, C., Kielland-Brandt, M.C., and Hansen, J. (1999). Cysteine uptake in Saccharomyces cerevisiae is accomplished by the activity of multiple permeases. Curr. Genet. 35, 609-617.
22. Didion, T., Regenberg, B., Jørgensen, M.U., Kielland-Brandt M.C., and Andersen, H. (1998). The permease homologue Ssy1p controls the expression of amino acid and peptide transporter genes in Saccharomyces cerevisiae. Mol. Microbiol. 27, 643-650.
23. Regenberg, B., Holmberg, S., Düring-Olsen, L., and Kielland-Brandt, M.C. (1998). Dip5p mediates high-affinity and high-capacity transport of L-glutamate and L-aspartate in Saccharomyces cerevisiae. Curr. Genet. 33, 171-177.
24. Regenberg, B., Villalba, J.M., Lanfermeijer, F.C., and Palmgren, M.G. (1995). C-terminal deletion analysis of plant plasma membrane H+-ATPase: yeast as a model system for solute transport across the plant plasma membrane. Plant Cell 7, 1655-1666.
25. Lanfermeijer, F.C., Regenberg, B., Baunsgaard, L.,Villalba, J.M., and Palmgren, M.G. (1995). Plant and fungal plant plasma membrane H+-ATPases – how alike are they with respect to regulation? In Plant Membrane Biology (Møller, I. M. & Brodelius, P. eds.) pp. 247-264.
26. Bro, C., Regenberg, B., and Nielsen, J. (2003) Yeast Functional Genomics and Metabolic Engineering: Past, Present and Future. I: Functional Genetics of Industrial Yeasts. Han de Winde (ed).
27. US2005009135 Metabolically engineered micro-organism having improved galactose uptake.
28. WO2004048559 Metabolically engineered micro-organisms having a reduced production of undesired metabolic by-products.