For best experience please turn on javascript and use a modern browser!
NL

dr. G.J. (Gertien) Smits

Faculty of Science
Swammerdam Institute for Life Sciences
Photographer: onbekend

Visiting address
  • Science Park 904
  • Room number: C3.262
Postal address
  • Postbus 94232
    1090 GE Amsterdam
Contact details
  • Who are we

    Stress response and adaptation in fungi.

    I have always been fascinated by the fact that life on earth, based on nearly identical sets of chemical reactions for all organisms, can function in such diverse environments.

    The general topic of our research are the responses to environmental changes in fungi. There are direct effects of the change on yeast physiology and cellular makeup, and there is an adaptive response which, ideally, helps the organism resume growth under the changed conditions. We ask what the effect of the change is on biology, and how the adaptie response affects cellular functioning. 

    Of particular interest are environmental conditions encountered by the fungi (yeasts and filamentous fungi) in food, in industrial production conditions, and in disease. As many of these conditions also affect central intracellular or metabolic parameters such as energy or intracellular pH, these have had our particular attention.

    Current projects

    Intracellular pH

    For a long time, it was thought that it was crucial for cells to maintian a constant, neutral pHi. This is because almost all the molecules in cells are either acids or bases, and therefore their charge and interaction properties would change with changing pH. We have found, using the pH sensitive GFP rationmetric pHluorin, that pH in yeast is far from constant, and that changes in pH function as a signal to control cellular growth, transcription, and signal transduction. We are currently investigating how pH interacts with the central pathways for nutrient signalling, Ras-PKA and TOR, and how this effects growth, stress tolerance and survival.

  • News
    Laura's paper was accepted in Aging Cell! She shows how carbon source abundance activates PKA even after the carbon has been depleted. This activity leads to a reduction of cytoplasmic pH, which is detrimental for survival in non-dividing cells. Congratulations!
    12/10/2017 Our paper on water was published in Nature Communications!
    12/06/2017 Tobias'paper was published in PLoS Genetics
  • Data

    Additional data for Orij et al., Genome Biology 2012

    Manuscript
    Orij R, Urbanus M, Vizeacoumar F, Giaever G, Boone C, Nislow C, Brul S, and Smits GJ . 2012 . Genome-wide analysis of intracellular pH reveals quantitative control of cell division rate by pHc in Saccharomyces cerevisiae . Genome Biol. 13 :R80

    Additional file 1 : All mutants with deviating pHc at various pHex, and during respiratory growth. Mutants with aberrant pHc under the standard condition (glucose, pH 5.0) were subjected to growth in pH 3.0, 7.5, as well as 2% ethanol/2% glycerol pH 5.0. Mutants were pre-grown overnight under standard conditions except for the 2% ethanol/2% glycerol experiment, in which case mutants were pre-grown in 2% ethanol/2% glycerol because of the long adaptation time to nonfermentable carbon source conditions. Cells were re-inoculated in described conditions and grown for 4 hours prior to measurements. Mutants were measured at least six timesat pH 5.0and at least three times in all other conditions. Mutants with significantly low pHc in any condition are indicated in orange, while mutants with significantly high pHc are indicated in blue.
    Additional file 2 : pHc analysis of 432 slow growing mutants. All strains were grown in standard conditions (2% glucose, pHex of 5.0) and fluorescence was registered in three to six biological replicates, and are presented as average and 95% confidence interval. pHc was compared to wild-type (WT) controls in the same replicate, to determine a Z-value. Significance of the pHc difference with WT was determined using a two-tailed t-test assuming equal variance with a P-value < 0.05. ND refers to mutants for which fewer than three replicates were successfully measured. Significantly low pHc values are shown in orange, significantly high pHc values in blue.
    Additional file 3 : Classification of mutants. Mutants are classified as having a growth rate-pHc relationship similar to wild type (WT; no significant deviation from the predicted growth rate based on pHc-growth rate relationship of the parent strain, low growth rate/pHc (significant positive deviation from the parent fit), or high growth rate/pHc (significant negative deviation from the parent fit), and are categorized according to functional classification.
    Additional file 4 : Figures S1 to S4. See Additional file 5 for further data pertaining to Figure S3.
    Additional file 5 : Data belonging to the hierarchical cluster plot in Figure S3 in Additional file 4. Mutants are listed in the order in which they appear in the cluster plot, for all three clusters. Mutant growth profiles were fitted to the parent strain pHc-growth rate relationship, and at each time point the Z-value of the digression from the fit was determined compared to the average and variance of 96 parent strain growth curves at the same time point. Time courses during the growth phase (t = 4 h to t = 9 h) of these Z-values were usedtostatistically categorize the mutants as wild type (WT; 92/173 mutants; 96 parent strain profiles also fall in this category), significantly (corrected P-value <0.01) slow growing (62/173 mutants), or significantly fast growing (19/173 mutants) with respect to pHc.

    Additional data for Zakrzewska et al., MBoC 2011

    Manuscript
    Zakrzewska A, van Eikenhorst G , Burggraaff JEC ,  Vis DJ, Hoefsloot H, Delneri D, Oliver SG, Brul S, Smits GJ. 2011.   Genome-wide analysis of yeast stress survival and tolerance acquisition to analyze the central trade-off between growth rate and cellular robustness. Mol. Biol. Cell,  22 :4435-4446
    Log transformations of viability percentages without and with growth rate correction.
    All direct log transformed viability values of normal and heat pretreated samples are listed in "log transformed viability". All growth rate corrected log transformed viabilities are listed in "viability after growth rate cor". The non-pretreated viabiliy was corrected for growth rate at 30oC, the pretreated viability for growth rate at 38oC, and the acquired tolerance for the change in growth rate.

    Primary data
    Each microarray dataset (separated for UPtag sense, UPtag antisense, DOWNtag sense and DOWNtag antisense) was background subtracted. Fractional intensities after 24 hours of growth (FI24) foreach tag werecorrected for the growth rate of the mutant to which it belongs, leading to the FI0. These values were normalized for the used for DNA isolation.
    In the table these normalized FI0 values were used to calculate viability based on each tag independently. For instance,for mutant yal004w the strain abundance after severe oxidative stress (oxi 30oC) was determined using duplicate measurement of both sense and antisense UPtags, relative to the abundance of the strain in the growing culture). For each strain outlier values (p <0.0001) were removed. These individual ratios were averaged and multiplied by the population survival (in the case of severe oxidative stress in non-pretreated cultures 13%) to determine the survival of each individual strain (in the case of yal004w 9.9%).

    Supplemental data for Zakrzewska et al, 2010

    Supplemental data accompanying  Zakrzewska et al., OMICS , 14 :350-360

  • Publications

    2019

    • Dolz-Edo, L., van der Deen, M., Brul, S., & Smits, G. J. (2019). Caloric restriction controls stationary phase survival through Protein Kinase A (PKA) and cytosolic pH. Aging Cell, e12921. https://doi.org/10.1111/acel.12921
    • Ensing, B., Tiwari, A., Tros, M., Hunger, J., Domingos, S. R., Perez, C., ... Woutersen, S. (2019). On the origin of the extremely different solubilities of polyethers in water. Nature Communications, 10. https://doi.org/10.1038/s41467-019-10783-z

    2017

    2013

    • Ullah, A., Chandrasekaran, G., Brul, S., & Smits, G. J. (2013). Yeast adaptation to weak acids prevents futile energy expenditure. Frontiers in Microbiology, 4, 142. https://doi.org/10.3389/fmicb.2013.00142 [details]
    • Ullah, A., Lopes, M. I., Brul, S., & Smits, G. J. (2013). Intracellular pH homeostasis in Candida glabrata in infection-associated conditions. Microbiology - SGM, 159(4), 803-813. https://doi.org/10.1099/mic.0.063610-0 [details]
    • Walther, T., Mtimet, N., Alkim, C., Vax, A., Loret, M. O., Ullah, A., ... François, J. M. (2013). Metabolic phenotypes of Saccharomyces cerevisiae mutants with altered trehalose-6-phosphate dynamics. Biochemical Journal, 454(2), 227-237. https://doi.org/10.1042/BJ20130587 [details]

    2012

    • Ayer, A., Fellermeier, S., Fife, C., Li, S. S., Smits, G., Meyer, A. J., ... Perrone, G. G. (2012). A genome-wide screen in yeast identifies specific oxidative stress genes required for the maintenance of sub-cellular redox homeostasis. PLoS ONE, 7(9), e44278. https://doi.org/10.1371/journal.pone.0044278 [details]
    • Hasdemir, D., Smits, G. J., Westerhuis, J. A., & Smilde, A. K. (2012). Topology of transcriptional regulatory networks: testing and improving. PLoS ONE, 7(7), [e40082]. [details]
    • Orij, R., Urbanus, M. L., Vizeacoumar, F. J., Giaever, G., Boone, C., Nislow, C., ... Smits, G. J. (2012). Genome-wide analysis of intracellular pH reveals quantitative control of cell division rate by pHc in Saccharomyces cerevisiae. Genome Biol, 13(9), [R80]. https://doi.org/10.1186/gb-2012-13-9-r80 [details]
    • Postmus, J., Aardema, R., de Koning, L. J., de Koster, C. G., Brul, S., & Smits, G. J. (2012). Isoenzyme expression changes in response to high temperature determine the metabolic regulation of increased glycolytic flux in yeast. FEMS Yeast Research, 12, 571-581. https://doi.org/10.1111/j.1567-1364.2012.00807.x [details]
    • Ullah, A., Orij, R., Brul, S., & Smits, G. J. (2012). Quantitative analysis of the modes of growth inhibition by weak organic acids in Saccharomyces cerevisiae. Applied and Environmental Microbiology, 78(23), 8377-8387. https://doi.org/10.1128/AEM.02126-12 [details]

    2011

    • Orij, R., Brul, S., & Smits, G. J. (2011). Intracellular pH is a tightly controlled signal in yeast. Biochimica et Biophysica Acta G General Subjects, 1810(10), 933-944. https://doi.org/10.1016/j.bbagen.2011.03.011 [details]
    • Postmus, J., Tuzun, I., Bekker, M., Muller, W. H., Teixeira De Mattos, M. J., Brul, S., & Smits, G. J. (2011). Dynamic regulation of mitochondrial respiratory chain efficiency in Saccharomyces cerevisiae. Microbiology - SGM, 157(12), 3500-3511. https://doi.org/10.1099/mic.0.050039-0 [details]
    • Zakrzewska, A., van Eikenhorst, G., Burggraaff, J. E. C., Vis, D. J., Hoefsloot, H., Delneri, D., ... Smits, G. J. (2011). Genome-wide analysis of yeast stress survival and tolerance acquisition to analyze the central trade-off between growth rate and cellular robustness. Molecular Biology of the Cell, 22(22), 4435-4446. https://doi.org/10.1091/mbc.E10-08-0721 [details]
    • van Leeuwen, J. S., Orij, R., Luttik, M. A. H., Smits, G. J., Vermeulen, N. P. E., & Vos, J. C. (2011). Subunits Rip1p and Cox9p of the respiratory chain contribute to diclofenac-induced mitochondrial dysfunction. Microbiology - SGM, 157(Pt 3), 685-694. https://doi.org/10.1099/mic.0.044578-0 [details]

    2010

    • Christoffels, V. M., Smits, G. J., Kispert, A., & Moorman, A. F. M. (2010). Development of the pacemaker tissues of the heart. Circulation Research, 106(2), 240-254. https://doi.org/10.1161/CIRCRESAHA.109.205419 [details]
    • Young, B. P., Shin, J. J. H., Orij, R., Chao, J. T., Li, S. C., Guan, X. L., ... Loewen, C. J. R. (2010). Phosphatidic acid is a pH biosensor that links membrane biogenesis to metabolism. Science, 329(5995), 1085-1088. https://doi.org/10.1126/science.1191026 [details]
    • Zakrzewska, A., Boorsma, A., ter Beek, A., Hageman, J. A., Westerhuis, J. A., Hellingwerf, K. J., ... Smits, G. J. (2010). Comparative analysis of transcriptome and fitness profiles reveals general and condition-specific cellular functions involved in adaptation to environmental change in Saccharomyces cerevisiae. Omics, 14(5), 603-614. https://doi.org/10.1089/omi.2010.0049 [details]
    • van Eunen, K., Bouwman, J., Daran-Lapujade, P., Postmus, J., Canelas, A. B., Mensonides, F. I. C., ... Bakker, B. M. (2010). Measuring enzyme activities under standardized in vivo-like conditions for systems biology. The FEBS Journal, 277(3), 749-760. https://doi.org/10.1111/j.1742-4658.2009.07524.x [details]

    2009

    • Orij, R., Postmus, J., ter Beek, A., Brul, S., & Smits, G. J. (2009). In vivo measurement of cytosolic and mitochondrial pH using a pH-sensitive GFP derivative in Saccharomyces cerevisiae reveals a relation between intracellular pH and growth. Microbiology - SGM, 155(1), 268-278. https://doi.org/10.1099/mic.0.022038-0 [details]

    2008

    • Brul, S., Kallemeijn, W., & Smits, G. (2008). Functional genomics for food microbiology: Molecular mechanisms of weak organic acid preservative adaptation in yeast. Perspectives in Agriculture, Veterinary Science, Nutrition and Natural Resources, 3, 005. https://doi.org/10.1079/PAVSNNR20083005 [details]
    • Postmus, J., Canelas, A. B., Bouwman, J., Bakker, B. M., van Gulik, W., Teixeira De Mattos, M. J., ... Smits, G. J. (2008). Quantitative analysis of the high temperature-induced glycolytic flux increase in Saccharomyces cerevisiae reveals dominant metabolic regulation. The Journal of Biological Chemistry, 283(35), 23524-23532. https://doi.org/10.1074/jbc.M802908200 [details]
    • ter Beek, A., Keijser, B. J. F., Boorsma, A., Zakrzewska, A., Orij, R., Smits, G. J., & Brul, S. (2008). Transcriptome analysis of sorbic acid-stressed Bacillus subtilis reveals a nutrient limitation response and indicates plasma membrane remodeling. Journal of Bacteriology, 190(5), 1751-1761. https://doi.org/10.1128/JB.01516-07 [details]

    2015

    • ter Beek, A., Wijman, J. G. E., Zakrzewska, A., Orij, R., Smits, G. J., & Brul, S. (2015). Comparative physiological and transcriptional analysis of weak organic acid stress in Bacillus subtilis. Food Microbiology, 45(A), 71-82. https://doi.org/10.1016/j.fm.2014.02.013 [details]
    This list of publications is extracted from the UvA-Current Research Information System. Questions? Ask the library or the Pure staff of your faculty / institute. Log in to Pure to edit your publications. Log in to Personal Page Publication Selection tool to manage the visibility of your publications on this list.
  • Ancillary activities
    • No ancillary activities