Dahlquist:Yeast Cold Shock

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Comparator Expression Datasets

Environmental Stress Response

• Gasch et al. 2000
• Causton et al. 2001

Cold or Near-freezing

Sahara et al. 2002

• Pub med reference = 12379644
• Full Sahara Paper Here
• Full dataset here
  • Strain: YPH500 (MATα, ura3-52, lys2-801, ade2-101, trp1-Δ63, his3-Δ200, leu2-Δ1)
  • Media: YPD
  • Experimental Conditions
    • t0 is A600 = 2.0, 30°C, shaking 100 rpm
    • shift to 10°C, shaking 100 rpm, t15, t30, t120 (2 h), t240 (4 h), t480 (8 h)
  • Replicates: 2 independent replicates averaged
  • Reference sample: t0
  • Methods: 15 μg total RNA directly labeled, no dye-swap control except for t0-t0 self-hybe, cDNA microrray

Schade et al. 2004

• Pub med reference = 15483057
• Full Schade Article Here
• Cold Shock Map GenMAPP
• Partial dataset here; have complete dataset from author
  • Strains: BY4743 (Mata/Matα, wild type), BSY25 (BY4743, homozygous Δmsn2::kanMX ΔMSN4::kanMX met15)
  • Media: YPD
  • Experimental conditions
    • t0 is A600 = 0.6, 30°C, shaking 170 rpm, shift to 10°C, shaking 170 rpm, t10, t30, t120 (2 h)
    • t0 is A600 = 0.4, 30°C, shaking 170 rpm, shift to 10°C, shaking 170 rpm, t720 (12 h)
    • t0 is A600 = 0.1, 30°C, shaking 170 rpm, shift to 10°C, shaking 170 rpm, t3600 (60 h)
  • Replicates: t0 (2 rep), t10 (3 rep), t30 (3 rep), t120 (2 rep), t720 (2 rep), t3600 (3 rep)
  • Reference sample: not stated in paper, assumed to be t0, so the t0 arrays were self-self hybe?
  • Methods: 3 μg mRNA directly labeled, dye swap performed, "genomic" microarray, obtained from University Health Network (so likely cDNA)

Kandror et al. 2004

• Full Kandror Article; dataset not available
  • Strains: "wild type", specific strain not stated
  • Media: YPGal
  • Experimental conditions
    • "mRNA samples from yeast growing at 30°C or 0°C for 24 hours were analyzed by whole-genome microarray hybridization"
    • Replicates: 2 independent replicates averaged
    • That's all the information provided in paper.

Murata et al. 2006

• Full Murata Article Found Here
• Murata et al. 2006; Some data available here
  • Strain: S288c (MATα SUC2 mal mel gal2 CUP1)
  • Media: YPD
  • Experimental conditions
    • t0 is A660 = 0.5, 25°C, shaking 120-130 rpm, shift to 4°C, shaking 120-130 rpm, t360 (6 h), t720 (12 h), t1440 (24 h), t2880 (48 h)
    • Replicates: 5 independent cultures
    • Reference sample: A660 = 1.0 (25°C?)
  • Methods: 1-2 μg mRNA directly labeled, cDNA microarray, no dye swap

Tai et al. 2007

• Tai et al. 2007
• Pub med reference = 17928405
• Strain: CEN.PK113-7D (MATa)
  • Media: defined synthetic medium limited by carbon or nitrogen with all other growth requirements in excess
  • Experimental conditions
    • dilution rate of 0.03 h^-1, stirrer 600 rpm
    • Carbon-limiting at 12°C or 30°C; nitrogen limited at 12°C or 30°C; all were anaerobic; steady-state growth
    • Replicates: 3 independent replicates for each condition
    • Reference sample: none because Affymetrix chips
  • Methods: Affymetrix methods

Beltran et al. 2006

• Beltran et al. (2006); dataset here
• Full Beltran Article
• Strain: QA23
• Media: YEPD

Pizarro et al. 2008

• Pizarro et al. 2008; Supplemental Data
• Pub med reference = 15368892
• Strains: CEN.PK113-7D and EC1118
• Media: nitrogen-limited, anaerobic chemostat cultures.
• Experimental Conditions
  • dilution rate of 0.05 h^-1; stirrer 300 rpm.
  • cultures for each strain were grown at both 15°C and 30°C in 2-liter chemostats.
  • pH was held at a constant of 5.0
  • Replicates: 3 independent chemostat steady state replicates for each culture.
  • Reference: none because of Affymetrix chips
• Methods: Affymetrix Methods

Becerra et al. 2003

• Becerra Article Link
• Pub med reference = 18629074
• Strain: haploid strain FY73 (Matα, ura3-52, his3Δ200)
• Media: YPD with 2% glucose
• Experimental Conditions:
  • All cells grown to OD600= 0.8 at 30°C
  • Cells were divided into three groups:
    • The first group was moved from 30°C to 4°C for 180 minutes
    • The second group was moved to 45°C for 15 minutes
    • The third group was moved to 37°C for 30 minutes.
    • The third group was then divided into two:
      • The first half remained at 37°C for 15 minutes
      • The second half was moved to 45°C for 15 minutes

Regulatory Networks

• Jothi et al. 2009
  • Genomic analysis reveals a tight link between transcription factor dynamics and regulatory network architecture;
  • Supplemental Data
• Zhu et al. 2009
• Pub med reference = 19158363

Other

• Check with online compendia, Hughes and Princeton

Zinc

1. De Nicola R, Hazelwood LA, De Hulster EA, Walsh MC, Knijnenburg TA, Reinders MJ, Walker GM, Pronk JT, Daran JM, Daran-Lapujade P. (2007) Physiological and transcriptional responses of Saccharomyces cerevisiae to zinc limitation in chemostat cultures.Appl Environ Microbiol. 73(23):7680-7692.
   • Supplemental Data but not complete dataset
2. Rutherford JC, Bird AJ. (2004) Metal-responsive transcription factors that regulate iron, zinc, and copper homeostasis in eukaryotic cells. Eukaryot Cell. 3(1):1-13.
3. Rutherford JC, Chua G, Hughes T, Cardenas ME, Heitman J. (2008) A Mep2-dependent transcriptional profile links permease function to gene expression during pseudohyphal growth in Saccharomyces cerevisiae. Mol Biol Cell. 19(7):3028-3039.
4. Wu CY, Bird AJ, Chung LM, Newton MA, Winge DR, Eide DJ. (2008) Differential control of Zap1-regulated genes in response to zinc deficiency in Saccharomyces cerevisiae. BMC Genomics. 9:370.
5. Eide DJ. (2009) Homeostatic and adaptive responses to zinc deficiency in Saccharomyces cerevisiae. J Biol Chem. 284(28):18565-18569.
6. Eide DJ. (2006) Zinc transporters and the cellular trafficking of zinc. Biochim Biophys Acta. 1763(7):711-722.
7. Eide DJ, Clark S, Nair TM, Gehl M, Gribskov M, Guerinot ML, Harper JF. (2005) Characterization of the yeast ionome: a genome-wide analysis of nutrient mineral and trace element homeostasis in Saccharomyces cerevisiae. Genome Biol. 6(9):R77.
8. Eide DJ. (2003) J Nutr. Multiple regulatory mechanisms maintain zinc homeostasis in Saccharomyces cerevisiae. 133(5 Suppl 1):1532S-1535S.

• Zip file containing Sc_ZincIonHomeostasis.mapp

Ribosome Biogenesis Pathway

• Fatica 2002
  • Pub med reference = 12067653
• Zhihua 2009
  • Pub med reference = 19806183
• Wade 2006
  • Pub med reference = 16544271
• Zip file containing Sc_RibosomeBiogenesis.mapp

Genetic Screens

• Akira 2006
  • Pub med reference = 16989656
• Fumiyoshi 2008
  • Pub med reference = 18245339

Nitrogen Utilization

• Magasanik B and Kaiser CA (2002) Nitrogen regulation in Saccharomyces cerevisiae. Gene 290(1-2):1-18
  • This paper outlines the function of GLN3 in the cell in response to poor nitrogen sources [1]
• Bertram PG, et al. (2002) Convergence of TOR-nitrogen and Snf1-glucose signaling pathways onto Gln3. Mol Cell Biol 22(4):1246-52
  • Outlines the role of glucose and snf1 [2]
• Cox KH, et al. (2004) Actin cytoskeleton is required for nuclear accumulation of Gln3 in response to nitrogen limitation but not rapamycin treatment in Saccharomyces cerevisiae. J Biol Chem 279(18):19294-301
  • Outlines the nonspecific dissociation of Gln3p in the cytoplasm caused by the presence of the actin cytoskeleton [3]
• Cox KH, et al. (2002) Cytoplasmic compartmentation of Gln3 during nitrogen catabolite repression and the mechanism of its nuclear localization during carbon starvation in Saccharomyces cerevisiae. J Biol Chem 277(40):37559-66
  • Outlines the mechanism of localization for Gln3p during cellular starvation [4]
• Kulkarni AA, et al. (2001) Gln3p nuclear localization and interaction with Ure2p in Saccharomyces cerevisiae. J Biol Chem 276(34):32136-44
  • Describes Ure2p role in the regulation of the function of Gln3p [5]
• Patrice Godard (2007) Effect of 21 Different Nitrogen Sources on Global Gene Expression in the Yeast Saccharomyces cerevisiae
  • Outlines the effect of varying nitrogen sources to that of transcriptional response variation[6]