Dahlquist:Yeast Cold Shock

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(Sahara et al. 2002: added paper link AH)
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==== Schade et al. 2004 ====
==== Schade et al. 2004 ====
-
<biblio>
+
* Pub med reference = 15483057
-
Paper2 pmid=15483057 </biblio>
+
* [http://www.molbiolcell.org/cgi/content/full/15/12/5492 Full Schade Article Here]
* [[media: Shade paper gene map.zip | Cold Shock Map GenMAPP]]
* [[media: Shade paper gene map.zip | Cold Shock Map GenMAPP]]
* [http://cbr-rbc.nrc-cnrc.gc.ca/genetics/cold/ Partial dataset here]; have complete dataset from author
* [http://cbr-rbc.nrc-cnrc.gc.ca/genetics/cold/ Partial dataset here]; have complete dataset from author
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==== Kandror et al. 2004 ====
==== Kandror et al. 2004 ====
-
* '''Kandror et al. 2004'''; dataset not available
+
* [http://www.sciencedirect.com/science/article/pii/S1097276504001480 Full Kandror Article]; dataset not available
** Strains: "wild type", specific strain not stated
** Strains: "wild type", specific strain not stated
** Media: YPGal
** Media: YPGal
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==== Murata et al. 2006 ====
==== Murata et al. 2006 ====
-
 
+
*[http://www.springerlink.com/content/u6038j7256t3013u/fulltext.html  Full Murata Article Found Here]
* '''Murata et al. 2006'''; Some data available [http://kasumi.nibh.jp/~iwahashi/yeast_DNA_Microarray_analysis.htm here]
* '''Murata et al. 2006'''; Some data available [http://kasumi.nibh.jp/~iwahashi/yeast_DNA_Microarray_analysis.htm here]
** Strain:  S288c (''MATα SUC2 mal mel gal2 CUP1'')
** Strain:  S288c (''MATα SUC2 mal mel gal2 CUP1'')
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*** Reference sample: A660 = 1.0 (25°C?)
*** Reference sample: A660 = 1.0 (25°C?)
** Methods: 1-2 μg mRNA directly labeled, cDNA microarray, no dye swap
** Methods: 1-2 μg mRNA directly labeled, cDNA microarray, no dye swap
 +
 +
==== Tai et al. 2007 ====
 +
* [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE6190 '''Tai et al. 2007''']
* [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE6190 '''Tai et al. 2007''']
-
<biblio>
+
* Pub med reference = 17928405
-
Paper1 pmid=17928405
+
-
</biblio>
+
* Strain: CEN.PK113-7D (MATa)
* Strain: CEN.PK113-7D (MATa)
** Media: defined synthetic medium limited by carbon or nitrogen with all other growth requirements in excess
** Media: defined synthetic medium limited by carbon or nitrogen with all other growth requirements in excess
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* Beltran et al. (2006); [http://biopuce.insa-toulouse.fr/jmflab/winegenomics/ dataset here]
* Beltran et al. (2006); [http://biopuce.insa-toulouse.fr/jmflab/winegenomics/ dataset here]
 +
* [http://onlinelibrary.wiley.com/doi/10.1111/j.1567-1364.2006.00106.x/full  Full Beltran Article]
 +
* Strain: QA23
 +
* Media: YEPD
==== Pizarro et al. 2008 ====
==== Pizarro et al. 2008 ====
* [http://aem.asm.org/cgi/content/abstract/74/20/6358 Pizarro et al. 2008]; [http://aem.asm.org/cgi/content/full/74/20/6358/DC1 Supplemental Data]
* [http://aem.asm.org/cgi/content/abstract/74/20/6358 Pizarro et al. 2008]; [http://aem.asm.org/cgi/content/full/74/20/6358/DC1 Supplemental Data]
-
 
+
*Pub med reference = 15368892
-
<biblio>
+
*Strains: CEN.PK113-7D and EC1118
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#Paper1 pmid=15368892
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*Media: nitrogen-limited, anaerobic chemostat cultures.
-
</biblio>
+
*Experimental Conditions
 +
** dilution rate of 0.05 h<sup>-1</sup>; 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 et al. 2003 ====
-
<biblio>
+
*[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2447359/pdf/CFG-04-366.pdf  Becerra Article Link]
-
#Paper1 pmid=18629074
+
*Pub med reference = 18629074
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</biblio>
+
*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 ===
=== Regulatory Networks ===
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** [http://www.nature.com/msb/journal/v5/n1/full/msb200952.html Genomic analysis reveals a tight link between transcription factor dynamics and regulatory network architecture];  
** [http://www.nature.com/msb/journal/v5/n1/full/msb200952.html Genomic analysis reveals a tight link between transcription factor dynamics and regulatory network architecture];  
** [http://www.nature.com/msb/journal/v5/n1/suppinfo/msb200952_S1.html Supplemental Data]
** [http://www.nature.com/msb/journal/v5/n1/suppinfo/msb200952_S1.html Supplemental Data]
-
* Zhu et al. 2009
+
* [http://genome.cshlp.org/content/19/4/556.long  Zhu et al. 2009]
-
<biblio>
+
* Pub med reference = 19158363
-
#Paper1 pmid=19158363</biblio>
+
=== Other ===
=== Other ===
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== Ribosome Biogenesis Pathway ==
== Ribosome Biogenesis Pathway ==
-
 
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*[http://www.sciencedirect.com/science/article/pii/S0955067402003368 Fatica 2002]
-
<biblio>
+
**Pub med reference = 12067653
-
#Paper1 pmid=12067653
+
*[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2749941/?tool=pubmed Zhihua 2009]
-
#Paper2 pmid=19806183
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**Pub med reference = 19806183
-
#Paper3 pmid=16544271
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*[http://onlinelibrary.wiley.com/doi/10.1002/yea.1353/full Wade 2006]
-
</biblio>
+
**Pub med reference = 16544271
-
 
+
* [[Media:Sc_RibosomeBiogenesis3.zip | Zip file containing Sc_RibosomeBiogenesis.mapp]]
* [[Media:Sc_RibosomeBiogenesis3.zip | Zip file containing Sc_RibosomeBiogenesis.mapp]]
== Genetic Screens ==
== Genetic Screens ==
 +
*[http://onlinelibrary.wiley.com/doi/10.1111/j.1567-1364.2006.00162.x/full Akira 2006]
 +
**Pub med reference = 16989656
 +
*[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2248370/  Fumiyoshi 2008]
 +
**Pub med reference = 18245339
-
<biblio>
+
== Nitrogen Utilization ==
-
#Paper1 pmid=16989656
+
*Magasanik B and Kaiser CA (2002) Nitrogen regulation in Saccharomyces cerevisiae. Gene 290(1-2):1-18
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#Paper2 pmid=18245339
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**This paper outlines the function of GLN3 in the cell in response to poor nitrogen sources [http://www.sciencedirect.com/science/article/pii/S0378111902005589]
-
</biblio>
+
*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 [http://mcb.asm.org/cgi/reprint/22/4/1246]
 +
*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 [http://www.jbc.org/content/279/18/19294.full]
 +
*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 [http://www.jbc.org/content/277/40/37559.full]
 +
*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 [http://www.jbc.org/content/276/34/32136.full]
 +
*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[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1899933/?tool=pubmed]

Current revision

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Contents

Comparator Expression Datasets

Environmental Stress Response

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

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

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.
  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.

Ribosome Biogenesis Pathway

Genetic Screens

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]
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