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Transcription factors regulating expression of AQY1 and screens for germination mutants Cecilia Geijer Dept. of Cell and Molecular Biology Göteborg University March 5 2007 Life cycle of budding yeast S. cerevisiae 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. 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. 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 Putative transcription factor binding sites for the AQY1 promoter Consensus sites identified: • Msn2/4 • Gcr1 • Fkh1/2 • Mcm1 • War1 • Ash1 • Nrg1 • Mot3 • Xbp1 • Tec1 No sporulation-specific transcription factor hits! www.yeastract.com Workpackage 1 Deliverable 9 AQY1prom-lacZ fusion construct Reporter gene lacZ system AQY1prom lacZ Yeast lacZ reporter plasmid to search for transcription factors regulating expression of AQY1 • X-gal overlay assay • β-galactosidase activity assay ONPG Workpackage 1 Deliverable 9 X-gal overlay assay BY4741 KO collection used to search for transcription factors wild type tec1Δ mot3Δ war1Δ X-gal overlay assay works to identify transcription factors regulating the AQY1 expression in vegetative cells fkh2Δ_1 fkh2Δ_2 Preliminary data: fkh2Δ strain seem to have lower expression of AQY1 than wild type Workpackage 1 Deliverable 9 Sporulation plates with X-gal overlay assay SK1a/α ε1278ba/α Spores treated with chloroform and overlayed with agarose X-gal are not turning blue – this assay probably not suitable for spores. Workpackage 1 Deliverable 9 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 βgalactosidase 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 Germination – search for mutants What gene products are essential for the germination process in Saccharomyces cerevisiae? Involvement of actin and polarisome in morphological change during spore germination of Saccharomyces cerevisiae Workpackage 2 Deliverable 14 Keiko Kono, Rino Matsunaga, Aiko Hirata, Genjiro Suzuki, Mitsuhiro Abe, Yoshikazu Ohya YEAST 2005 Workpackage 4 Deliverable 23 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 Germination mutants – heterozygous diploids 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 Workpackage 2 Deliverable 14 Workpackage 4 Deliverable 23 Germination mutants – heterozygous diploids 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 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 Synthetic Genetic Array (SGA) Analysis Will find: Sporulation mutants, aneuploid strains, true germination mutants (?) Will not find: Essential genes Workpackage 2 Deliverable 14 Workpackage 4 Deliverable 23 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 Control Mechanisms of Dormancy and Germination of The Baker’s Yeast S. cerevisiae Spore Ivan Pirkov Dept. Of Cell and Molecular Biology Göteborg University 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 Microarray on Germinating Yeast Spores (WP2) The experimental outline • Diploid cells were sporulated in 1% KAc solution • The spores were left resting at 4C 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 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 Percent of spores that have germinated after 24 hrs sensing of S. cerevisiae Y55 spores Herman and Rine (1997),Glucose EMBO J, 16:6171-6181 100 90 80 70 60 50 40 30 20 10 0 1000 100 10 1 mM Glucose 0,1 0,01 0,001 Spore Germination • RNA synthesis increases within minutes upon addition of glucose and nutrients Brengues et al (2002), JBC, 277:40505-40512 Microarray on Germinating Yeast Spores (WP2) Number of genes significantly up/down-regulated (2-fold) relative to resting spores experiment) (2% Glucose 300 No. of genes up/down 200 100 0 0 4 8 16 32 48 100 200 300 400 Time samples [min] 64 96 128 Up regulated Down regulated Microarray on Germinating Yeast Spores (WP2) Clustering of significantly up/down-regulated genes (2-fold) relative resting spores experiment) 1 9 0 8 7 6 5 4 3 2 1 (2%Glucose Microarray on Germinating Yeast Spores (WP2) Clustering result (GO Annotations) of significantly up/down-regulated (2-fold) relative to resting spores (2%Glucose experiment) 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) 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 transport (4) electron • Biosynthesis of Glycogen and Trehalose (4) (10) Microarray on Germinating Yeast Spores (WP2) Commitment-step synchrony of S. cerevisiae Y55 No. of genes significantly up/down-regulated (2-fold) relative resting spores spores in YPD experiment) (YPD No. of genes up/down 600 400 200 0 0 200 400 600 800 Percent of spores commited for germination 100 90 80 70 60 50 4 8 16 32 48 64 96 128 40 30 20 10 0 0 15 30 45 60 75 90 105 120 135 150 165 180 195 Time samples [min] Time [min] Up regulated Down regulated Microarray on Germinating Yeast Spores (WP2) Clustering of significantly up/down-regulated genes (2-fold) relative resting spores (YPD experiment) 9 8 7 6 5 4 3 2 1 Microarray on Germinating Yeast Spores (WP2) Clustering result (GO Annotations) of significantly up/down-regulated (2-fold) relative resting spores (YPD experiment) Groups of up-regulated genes (Cluster: 3, 4, 6, 7 and 9) Groups of down-regulated genes (Cluster: 1, 2, 5 and 8) • Ribosome biogenesis (3) (4) (7) • Stress response (1) (2) •Transcription and Translation (3) (4) (6) (7) • Meiosis (1) • Nucleotide metabolism (3) • Pheromone response – mating type determination (4) • Glycolysis and gluconeogenesis (1) (2) • Fatty acid oxidation and transport (2) • TCA-cycle (2) • Glucose transport and signaling (6) •Peroxisome and vacuole (2) • Protein folding and stabilization (8) • Glyoxylate cycle (2) •Ion transport (6) (9) • 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) Microarray on Germinating Yeast Spores (WP2) • Potential problems – Different mRNA to total RNA ratios between reference and time-samples – Global shifts in mRNA population during germination 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) CMB - Cell and Molecular Biology - Group Stefan Hohmann Avi Ericsson, 2007 Total number of up/down regulated genes in the YPD experiment CMB - Cell and Molecular Biology - Group Stefan Hohmann 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 Avi Ericsson, 2007 Control experiment schematically Resting spores Time point X CMB - Cell and Molecular Biology - Group Stefan Hohmann Time point Y Avi Ericsson, 2007 CMB - Cell and Molecular Biology - Group Stefan Hohmann Avi Ericsson, 2007 CMB - Cell and Molecular Biology - Group Stefan Hohmann 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 Avi Ericsson, 2007 Acknowledgements to The Hohmann lab Microarray on Germinating Yeast Spores (WP2) Test – mRNA to total RNA ratios Total RNA from sample X 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 Total RNA from sample X Oligo dT + Random primers, Label with Cy5 Only oligo dT, Label with Cy5 Cy5 labeled cDNA from only mRNA How to solve these problems? Suggestions? Cy 5 labeled cDNA from total RNA Cy5 signal in cDNA from mRNA (M) and total RNA (T) 0M 48M 128M 0T 48T 0x 5x 25x Ratio mRNA vs. total RNA 0min 48min 128min ?? ?? ?? 128T