Formedium’s YNB used in Systems Level Analysis of the Yeast Osmo-Stat

Formedium’s YNB has been used in Systems Level Analysis of the Yeast Osmo-Stat. Soheil Rastgon, Carl-Fredrik Tiger, Mikael Andersson, Roja Babazadeh, Nick Welkenhuysen, Edda Klipp, Stefan Hohmann, Jorg Schaber.

Published on 12th August 2016.

The following is a snippet from the report:

Experimental methods

Yeast strains, media, plasmids and sampling.

Wild type cells in the W303 strain background and W303 cells transformed with the relevant plasmids. Cells were grown in Yeast Nitrogen Base medium (1x Difco™ YNB base, 1x Formedium™ Complete Supplement Mixture, 5.0 g/L ammonium sulfate, 20 g/L glucose) to exponential phase. Plasmids used were YEplac195 and YEplac195-fps1∆1 for experiments with constitutively open Fps122. For all sampling cells were grown to mid-log phase in YNB medium. After addition of stress agent to cultures samples were taken at indicated time points with zero samples taken before addition of stressor. For hyper-osmotic stress sorbitol was added to the medium to a final concentration of 0.8 M or 1.0 M sorbitol depending on the experiment, for initial model validation 0.4 M NaCl was also used for hyper-osmotic stress. For the calcofluor treatment 0.11 μM (100 μg/mL) was added to the medium.

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Reference:
http://www.nature.com/articles/srep30950

  1. 1.

    Schaber, J. et al. Biophysical properties of Saccharomyces cerevisiae and their relationship with HOG pathway activation. Eur Biophys J 39, 1547–1556, doi: 10.1007/s00249-010-0612-0 (2010).

  2. 2.

    Schaber, J. & Klipp, E. Short-term volume and turgor regulation in yeast. Essays Biochem 45, 147–159, doi: 10.1042/BSE0450147 (2008).

  3. 3.

    Klipp, E., Nordlander, B., Kruger, R., Gennemark, P. & Hohmann, S. Integrative model of the response of yeast to osmotic shock. Nat Biotechnol 23, 975–982, doi: 10.1038/nbt1114 (2005).

  4. 4.

    Hohmann, S. Osmotic stress signaling and osmoadaptation in yeasts. Microbiol Mol Biol Rev 66, 300–372 (2002).

  5. 5.

    Levin, D. E. Regulation of cell wall biogenesis in Saccharomyces cerevisiae: the cell wall integrity signaling pathway. Genetics 189, 1145–1175, doi: 10.1534/genetics.111.128264 (2011).

  6. 6.

    Petelenz-Kurdziel, E. et al. Quantitative Analysis of Glycerol Accumulation, Glycolysis and Growth under Hyper Osmotic Stress. PLoS computational biology 9, e1003084 (2013).

  7. 7.

    Beese, S. E., Negishi, T. & Levin, D. E. Identification of positive regulators of the yeast fps1 glycerol channel. PLoS Genet 5, e1000738, doi: 10.1371/journal.pgen.1000738 (2009).

  8. 8.

    Lee, J. et al. MAPK Hog1 closes the S. cerevisiae glycerol channel Fps1 by phosphorylating and displacing its positive regulators. Genes Dev 27, 2590–2601, doi: 10.1101/gad.229310.113 (2013).

  9. 9.

    Hersen, P., McClean, M. N., Mahadevan, L. & Ramanathan, S. Signal processing by the HOG MAP kinase pathway. Proceedings of the National Academy of Sciences 105, 7165–7170 (2008).

  10. 10.

    Mettetal, J. T., Muzzey, D., Gomez-Uribe, C. & van Oudenaarden, A. The frequency dependence of osmo-adaptation in Saccharomyces cerevisiae. Science 319, 482–484, doi: 10.1126/science.1151582 (2008).

  11. 11.

    Muzzey, D., Gomez-Uribe, C. A., Mettetal, J. T. & van Oudenaarden, A. A systems-level analysis of perfect adaptation in yeast osmoregulation. Cell 138, 160–171, doi: 10.1016/j.cell.2009.04.047 (2009).

  12. 12.

    Zi, Z., Liebermeister, W. & Klipp, E. A quantitative study of the Hog1 MAPK response to fluctuating osmotic stress in Saccharomyces cerevisiae. PLoS One 5, e9522, doi: 10.1371/journal.pone.0009522 (2010).

  13. 13.

    Schaber, J., Baltanas, R., Bush, A., Klipp, E. & Colman-Lerner, A. Modelling reveals novel roles of two parallel signalling pathways and homeostatic feedbacks in yeast. Mol Syst Biol 8, 622, doi: 10.1038/msb.2012.53 (2012).

  14. 14.

    Rodriguez-Pena, J. M., Garcia, R., Nombela, C. & Arroyo, J. The high-osmolarity glycerol (HOG) and cell wall integrity (CWI) signalling pathways interplay: a yeast dialogue between MAPK routes. Yeast 27, 495–502, doi: 10.1002/yea.1792 (2010).

  15. 15.

    Baltanas, R. et al. Pheromone-induced morphogenesis improves osmoadaptation capacity by activating the HOG MAPK pathway. Sci Signal 6, ra26, doi: 10.1126/scisignal.2003312 (2013).

  16. 16.

    Schaber, J., Kofahl, B., Kowald, A. & Klipp, E. A modelling approach to quantify dynamic crosstalk between the pheromone and the starvation pathway in baker’s yeast. FEBS J 273, 3520–3533, doi: 10.1111/j.1742-4658.2006.05359.x (2006).

  17. 17.

    Vaga, S. et al. Phosphoproteomic analyses reveal novel cross-modulation mechanisms between two signaling pathways in yeast. Mol Syst Biol 10, 767, doi: 10.15252/msb.20145112 (2014).

  18. 18.

    Tiger, C. F. et al. A framework for mapping, visualisation and automatic model creation of signal-transduction networks. Mol Syst Biol 8, 578, doi: 10.1038/msb.2012.12 (2012).

  19. 19.

    Bermejo, C. et al. The sequential activation of the yeast HOG and SLT2 pathways is required for cell survival to cell wall stress. Mol Biol Cell 19, 1113–1124, doi: 10.1091/mbc.E07-08-0742 (2008).

  20. 20.

    Garcia, R., Rodriguez-Pena, J. M., Bermejo, C., Nombela, C. & Arroyo, J. The high osmotic response and cell wall integrity pathways cooperate to regulate transcriptional responses to zymolyase-induced cell wall stress in Saccharomyces cerevisiae. J Biol Chem 284, 10901–10911, doi: 10.1074/jbc.M808693200 (2009).

  21. 21.

    Burnham, K. P. & Anderson, D. R. Model Selection and Multi-Model Inference: A Practical Information-Theoretic Approach. (Springer, 2010).

  22. 22.

    Tamas, M. J. et al. Fps1p controls the accumulation and release of the compatible solute glycerol in yeast osmoregulation. Mol Microbiol 31, 1087–1104 (1999).

  23. 23.

    Garcia-Rodriguez, L. J., Valle, R., Duran, A. & Roncero, C. Cell integrity signaling activation in response to hyperosmotic shock in yeast. FEBS Lett 579, 6186–6190, doi: 10.1016/j.febslet.2005.10.001 (2005).

  24. 24.

    Ketela, T., Green, R. & Bussey, H. Saccharomyces cerevisiae mid2p is a potential cell wall stress sensor and upstream activator of the PKC1-MPK1 cell integrity pathway. J Bacteriol 181, 3330–3340 (1999).

  25. 25.

    Muir, A., Roelants, F. M., Timmons, G., Leskoske, K. L. & Thorner, J. Down-regulation of TORC2-Ypk1 signaling promotes MAPK-independent survival under hyperosmotic stress. Elife 4, doi: 10.7554/eLife.09336 (2015).

  26. 26.

    Babazadeh, R., Furukawa, T., Hohmann, S. & Furukawa, K. Rewiring yeast osmostress signalling through the MAPK network reveals essential and non-essential roles of Hog1 in osmoadaptation. Sci Rep 4, 4697, doi: 10.1038/srep04697 (2014).

  27. 27.

    Schaber, J., Lapytsko, A. & Flockerzi, D. Nested autoinhibitory feedbacks alter the resistance of homeostatic adaptive biochemical networks. J R Soc Interface 11, 20130971, doi: 10.1098/rsif.2013.0971 (2014).

  28. 28.

    Macia, J. et al. Dynamic signaling in the Hog1 MAPK pathway relies on high basal signal transduction. Sci Signal 2, ra13, doi: 10.1126/scisignal.2000056 (2009).

  29. 29.

    Le Novere, N. et al. BioModels Database: a free, centralized database of curated, published, quantitative kinetic models of biochemical and cellular systems. Nucleic Acids Res 34, D689–D691, doi: 10.1093/nar/gkj092 (2006).

  30. 30.

    Eriksson, E. et al. A microfluidic device for reversible environmental changes around single cells using optical tweezers for cell selection and positioning. Lab Chip 10, 617–625, doi: 10.1039/b913587a (2010).

  31. 31.

    Babazadeh, R. et al. Osmostress-induced cell volume loss delays yeast Hog1 signaling by limiting diffusion processes and by Hog1-specific effects. PLoS One 8, e80901, doi: 10.1371/journal.pone.0080901 (2013).

  32. 32.

    Frey, S. et al. A mathematical analysis of nuclear intensity dynamics for Mig1-GFP under consideration of bleaching effects and background noise in Saccharomyces cerevisiae. Mol Biosyst 7, 215–223, doi: 10.1039/c005305h (2011).

Acknowledgements

We thank Alejandro Colman-Lerner for helpful comments on the manuscript. S.R.T. was supported by the Ministry of Education of Saxony-Anhalt (Research Centre Dynamic Systems: Biosystems Engineering (XD3639HP/0306 and CDS, MW- 21LMS 5) and the International Max Planck Research School (IMPRS) Magdeburg for Advanced Methods in Process and Systems Engineering. J.S. is supported by German Ministry for Education and Science (BMBF) (FKN 0315779 and 0316188E to JS). Work in the Hohmann and Klipp labs was supported by the European Commission, the UNICELLSYS project, No. 201142.

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