1. Transcription factors regulating expression of AQY1 and screens for germination mutants Cecilia Geijer Dept. of Cell and Molecular Biology Göteborg University March 5 2007

2. Life cycle of budding yeast S. cerevisiae

3. Sporulation in S. cerevisiae – the process Sporulation encompasses two overlapping processes: meiosis and spore formation. Cells go through meiosis which leads to the generation of four haploid nuclei Plasma membranes for four daugther cells are constructed within the mother cell cytoplasm, and these surrounds the four haploid nuclei. Spore wall synthesis occurs.

4. Aquaporins Aquaporins mediate the transport of water across biological membranes. Some also transport other substrates such as glycerol, urea and nitrogen. The genome of S cerevisiae contains four aquaporin genes.

5. Yeast aquaporin 1 (Aqy1) is involved in sporulation Northern Blot analysis of AQY1 in strain SK1. Low basal level of expression of AQY1 in vegetative cells. Upregulation of expression ~8 h after transfer to sporulation medium (1% KAc) (The Saccharomyces cerevisiae aquaporin Aqy1 is involved in sporulation, Sidoux-Walter et al, PNAS 2004) AQY1/AQY1-GFP diploids – expression in two out of four spores suggests role in later stages of sporulation Workpackage 1 Deliverable 9

6. Putative transcription factor binding sites for the AQY1 promoter www.yeastract.com Msn2/4 Fkh1/2 War1 Nrg1 Xbp1 Gcr1 Mcm1 Ash1 Mot3 Tec1 Consensus sites identified: No sporulation-specific transcription factor hits! Workpackage 1 Deliverable 9

7. AQY1prom-lacZ fusion construct Reporter gene lacZ system Yeast lacZ reporter plasmid to search for transcription factors regulating expression of AQY1 X-gal overlay assay β-galactosidase activity assay ONPG AQY1promlacZ Workpackage 1 Deliverable 9

8. X-gal overlay assay

9. BY4741 KO collection used to search for transcription factors Preliminary data: fkh2Δ strain seem to have lower expression of AQY1 than wild type wild type tec1Δ mot3Δ war1Δ fkh2Δ_1 fkh2Δ_2 X-gal overlay assay works to identify transcription factors regulating the AQY1 expression in vegetative cells Workpackage 1 Deliverable 9

10. Sporulation plates with X-gal overlay assay Spores treated with chloroform and overlayed with agarose X-gal are not turning blue – this assay probably not suitable for spores. SK1a/α ε1278ba/α Workpackage 1 Deliverable 9

11. Conclusions - transcription factor search Stationary phase cells, grown on YPD plates for 36h, express AQY1. Search for transcription factors regulating the expression of AQY1 revealed Fkh2 as a potential candidate. X-gal overlay assay is not suitable for spores, instead β- galactosidase activity assay using ONPG. Transcription factors regulating late sporulation induced genes are not yet identified. Finding regulators of AQY1 will point to transcription factors that possibly regulates other late sporulation genes as well. Workpackage 1 Deliverable 9

12. Germination – search for mutants Involvement of actin and polarisome in morphological change during spore germination of Saccharomyces cerevisiae Keiko Kono, Rino Matsunaga, Aiko Hirata, Genjiro Suzuki, Mitsuhiro Abe, Yoshikazu Ohya YEAST 2005 What gene products are essential for the germination process in Saccharomyces cerevisiae? Workpackage 2 Deliverable 14 Workpackage 4 Deliverable 23

13. Screen for Germination mutants using heterozygous mutants Heterozygous diploids – wild type and mutant mated to create diploid with one functional allele of gene of interest. Deletion of gene by insertion of KanMX cassette at gene locus. Heterozygous diploids – all cells can go through sporulation with one functional copy of the gene as diploid. Hoping to find true germination mutants avoiding sporulation mutants. Workpackage 2 Deliverable 14 Workpackage 4 Deliverable 23

14. Workpackage 2 Deliverable 14 Workpackage 4 Deliverable 23 Sporulation of heterozygous diploids with mutated genes of interest. Tetrad dissection of spores Germination on geneticin plates selecting for haploid cells carrying deletion cassette with geneticin resistance marker Germination mutants – heterozygous diploids

15. Problem: Proteins inherited from the mother diploid are enough to allow mutants to germinate. Also true for kanMX – spores without the kanMX cassette germinates and can divide to the 50-cells stage on geneticin plates. Potential: Preliminary data indicates that rho1Δ haploids derived from heterozygous dipolids can not germinate. Rho1 - GTP-binding protein of the rho subfamily of Ras-like proteins, involved in establishment of cell polarity; regulates protein kinase C (Pkc1) and the cell wall synthesizing enzyme 1,3-beta-glucan synthase. Workpackage 2 Deliverable 14 Workpackage 4 Deliverable 23

16. Synthetic Genetic Array (SGA) Analysis MATa (-met) deletion collection carrying reporter MFA1pr-HIS3, only expressed in haploid a cells Mate with deletion collection of alpha cells (-lys) Homozygous diploids, each diploid with both alleles of one particular gene deleted. Select for diploids on selective plates containing no Metionine and no Lysine Sporulate diploids Germinate spores on selective plates containing no Histidine. Only haploid a cells with the MFA1pr-HIS3 cassette will grow on plates. Screen for germination mutants, ie empty spots on SGA plate

17. Will find: Sporulation mutants, aneuploid strains, true germination mutants (?) Will not find: Essential genes Synthetic Genetic Array (SGA) Analysis Workpackage 2 Deliverable 14 Workpackage 4 Deliverable 23

18. Conclusions – germination mutants Screening for germination mutants using heterozygous diploids is time consuming and results hard to interpret since proteins from the mother diploid take mutants through germination. Screening for germination mutants using SGA Analysis has potential, but also drawbacks – not only germination mutants will be picked up but also sporulation mutants. Which is which? Another possibility is to use mutants with temperature sensitive alleles for essential genes. Will potentially identify mutants that can germinate but not grow vegetatively. Workpackage 2 Deliverable 14 Workpackage 4 Deliverable 23

19. Control Mechanisms of Dormancy and Germination of The Baker’s Yeast S. cerevisiae Spore Ivan Pirkov Dept. Of Cell and Molecular Biology Göteborg University

20. Present Focus The baker’s yeast Saccharomyces cerevisiae produces a dormant stage, the spore The present aim of the project is to investigate how the yeast spore is reactivated from its dormant stage We are currently studying the global gene expression changes upon induction of germination using microarray analysis Expectations - To identify pathways and specific genes that are associated with spore germination

21. Microarray on Germinating Yeast Spores (WP2) The experimental outline Diploid cells were sporulated in 1% KAc solution The spores were left resting at 4  C in 0.5% TritonX-100 solution for at least 14 days Spores were then transferred to rich nutrient growth medium containing 2% glucose (YPD) OR only in 2% glucose solution Samples for total RNA extraction were taken in a logarithmic time-fashion, 0, 4, 8, 16 min… etc. up to 128 min Resting spores were used as reference sample The experiment was done in three independent replicates

22. Spore Germination Is most efficient when a readily fermentable carbon source is present – e.g. glucose, fructose, galactose –Presence of just a carbon source is sufficient for germination initiation –Metabolism of the carbon source is necessary for germination, mere presence is not enough Herman and Rine (1997), EMBO J, 16:6171-6181

23. RNA synthesis increases within minutes upon addition of glucose and nutrients Brengues et al (2002), JBC, 277:40505-40512 Spore Germination

24. Number of genes significantly up/down-regulated (  2-fold) relative to resting spores (2% Glucose experiment) 400 300 200 100 0 200 300 0481632486496128 Time samples [min] No. of genes up/down Up regulated Down regulated Microarray on Germinating Yeast Spores (WP2)

25. Clustering of significantly up/down-regulated genes (  2-fold) relative resting spores (2%Glucose experiment) 1 2 34 5 6789 1010 Microarray on Germinating Yeast Spores (WP2)

26. Clustering result (GO Annotations) of significantly up/down-regulated (  2-fold) relative to resting spores (2%Glucose experiment) Groups of down-regulated genes (Cluster: 1, 3, 4, 6 and 10) Stress response (1) Meiosis (1) Glycolysis and gluconeogenesis (3) Fatty acid oxidation (3) TCA-cycle (4) Glyoxylate cycle (4) Oxidative phosphorylation and electron transport (4) Biosynthesis of Glycogen and Trehalose (4) (10) Groups of up-regulated genes (Cluster: 2, 5, 7, 8 and 9) Amino acid biosynthesis and degradation (2) (7) (9) Ribosome biogenesis (2) (5) (7) Stress response (2) Glucose transport and signaling (3) (5) Protein folding and stabilization (8) Ion transport (2) (8) (9) Microarray on Germinating Yeast Spores (WP2)

27. 800 600 400 200 0 400 600 0481632486496128 Time samples [min] No. of genes up/down Up regulated Down regulated No. of genes significantly up/down-regulated (  2-fold) relative resting spores (YPD experiment) Microarray on Germinating Yeast Spores (WP2)

28. Clustering of significantly up/down-regulated genes (  2-fold) relative resting spores (YPD experiment) 165432987 Microarray on Germinating Yeast Spores (WP2)

29. Clustering result (GO Annotations) of significantly up/down-regulated (  2-fold) relative resting spores (YPD experiment) Groups of down-regulated genes (Cluster: 1, 2, 5 and 8) Stress response (1) (2) Meiosis (1) Glycolysis and gluconeogenesis (1) (2) Fatty acid oxidation and transport (2) TCA-cycle (2) Peroxisome and vacuole (2) Glyoxylate cycle (2) Oxidative phosphorylation and e - -transport (2) (8) RAS protein signal tranduction (2) (8) Metabolism of Glycogen and Trehalose (2) (8) Amino acid biosynthesis (5) Redox homeostasis (5) Groups of up-regulated genes (Cluster: 3, 4, 6, 7 and 9) Ribosome biogenesis (3) (4) (7) Transcription and Translation (3) (4) (6) (7) Nucleotide metabolism (3) Pheromone response – mating type determination (4) Glucose transport and signaling (6) Protein folding and stabilization (8) Ion transport (6) (9) Microarray on Germinating Yeast Spores (WP2)

30. Potential problems –Different mRNA to total RNA ratios between reference and time-samples –Global shifts in mRNA population during germination Microarray on Germinating Yeast Spores (WP2)

31. Future Perspectives Analyze the microarray results in more detail to look for transcriptional patterns  Publication of the results (WP2) Identifying genes that are expressed in resting spores and not in growing cells and vice versa  Done, data need to be analyzed (WP1, WP2) Work with Cecilia to construct the homozygote deletion strain and to screen for mutants that are unable to germinate (WP2) Continue with the Long-term dormancy experiment (WP1, WP2) Extract and analyze proteins from resting spores of different age (WP1) Analyze contents of resting spores  DTU (WP1)

32. Avi Ericsson, 2007 CMB - Cell and Molecular Biology - Group Stefan Hohmann

33. Avi Ericsson, 2007 Total number of up/down regulated genes in the YPD experiment CMB - Cell and Molecular Biology - Group Stefan Hohmann

34. Avi Ericsson, 2007 Control experiment Hybridize 32 and 46 min against each other Hybridize 96 and 128 min against each other And then compare the ”real” and ”expected” values of up/down regulation CMB - Cell and Molecular Biology - Group Stefan Hohmann

35. Avi Ericsson, 2007 Control experiment schematically Resting spores Time point XTime point Y CMB - Cell and Molecular Biology - Group Stefan Hohmann

36. Avi Ericsson, 2007 CMB - Cell and Molecular Biology - Group Stefan Hohmann

37. Avi Ericsson, 2007 CMB - Cell and Molecular Biology - Group Stefan Hohmann

38. Avi Ericsson, 2007 Conclusions and future work The correlation is not too bad! Which might indicate that we probably do not have a problem. To be sure - we have to measure the mRNA concentrations in our samples. When we are sure – publish! CMB - Cell and Molecular Biology - Group Stefan Hohmann

39. Acknowledgements to The Hohmann lab

40. Normalization of the data Avi will explain the normalization method No external control mRNA was used Potential problems –Different mRNA to total RNA ratios between reference and time-samples –Global shifts in mRNA population during germination How to solve these problems? Suggestions? 48T 128T 128M48M0M0T 0x 5x 25x Cy5 signal in cDNA from mRNA (M) and total RNA (T) Total RNA from sample X Only oligo dT, Label with Cy5 Oligo dT + Random primers, Label with Cy5 Cy5 labeled cDNA from only mRNA Cy 5 labeled cDNA from total RNA Test – mRNA to total RNA ratios 0min48min128min Ratio mRNA vs. total RNA ?? Microarray on Germinating Yeast Spores (WP2)