Dahlquist:Yeast Cold Shock: Difference between revisions
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==== Sahara et al. 2002 ==== | ==== Sahara et al. 2002 ==== | ||
* Pub med reference = 12379644 | |||
* [http://www.jbc.org/content/277/51/50015.long Full Sahara Paper Here] | |||
* [http://staff.aist.go.jp/t-sahara/LowTemp.txt Full dataset here] | * [http://staff.aist.go.jp/t-sahara/LowTemp.txt Full dataset here] | ||
** Strain: YPH500 (''MATα, ura3-52, lys2-801, ade2-101, trp1-Δ63, his3-Δ200, leu2-Δ1'') | ** Strain: YPH500 (''MATα, ura3-52, lys2-801, ade2-101, trp1-Δ63, his3-Δ200, leu2-Δ1'') | ||
Line 25: | Line 25: | ||
==== Schade et al. 2004 ==== | ==== Schade et al. 2004 ==== | ||
* Pub med reference = 15483057 | |||
* [http://www.molbiolcell.org/cgi/content/full/15/12/5492 Full Schade Article Here] | |||
* [[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 | ||
** Strains: BY4743 (''Mat'''a'''/Matα'', wild type), BSY25 (BY4743, homozygous ''Δmsn2::kanMX ΔMSN4::kanMX met15'') | ** Strains: BY4743 (''Mat'''a'''/Matα'', wild type), BSY25 (BY4743, homozygous ''Δmsn2::kanMX ΔMSN4::kanMX met15'') | ||
Line 41: | Line 41: | ||
==== Kandror et al. 2004 ==== | ==== Kandror et al. 2004 ==== | ||
* | * [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 | ||
Line 50: | Line 50: | ||
==== 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'') | ||
Line 59: | Line 59: | ||
*** 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'''] | ||
* Pub med reference = 17928405 | |||
* 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 | ||
Line 75: | Line 76: | ||
* 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 | |||
< | *Strains: CEN.PK113-7D and EC1118 | ||
*Media: nitrogen-limited, anaerobic chemostat cultures. | |||
</ | *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 ==== | ||
*[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2447359/pdf/CFG-04-366.pdf 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 === | === Regulatory Networks === | ||
Line 94: | Line 114: | ||
** [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] | ||
* Pub med reference = 19158363 | |||
=== Other === | === Other === | ||
Line 103: | Line 122: | ||
== Zinc == | == Zinc == | ||
# [http://aem.asm.org/cgi/content/full/73/23/7680?view=long&pmid=17933919 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.] | |||
#* [http://aem.asm.org/cgi/content/full/73/23/7680/DC1 Supplemental Data] but not complete dataset | |||
# [http://ec.asm.org/cgi/content/full/3/1/1 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.] | |||
# [http://www.molbiolcell.org/cgi/content/full/19/7/3028 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.] | |||
# [http://www.biomedcentral.com/1471-2164/9/370 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.] | |||
# [http://www.jbc.org/content/284/28/18565.long Eide DJ. (2009) Homeostatic and adaptive responses to zinc deficiency in Saccharomyces cerevisiae. J Biol Chem. 284(28):18565-18569.] | |||
# [http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6T20-4JRV952-1&_user=945462&_coverDate=07%2F31%2F2006&_rdoc=1&_fmt=high&_orig=search&_origin=search&_sort=d&_docanchor=&view=c&_acct=C000048964&_version=1&_urlVersion=0&_userid=945462&md5=42a5a79e573746c275b91e89883ceac5&searchtype=a Eide DJ. (2006) Zinc transporters and the cellular trafficking of zinc. Biochim Biophys Acta. 1763(7):711-722.] | |||
# [http://genomebiology.com/content/6/9/R77 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.] | |||
# [http://jn.nutrition.org/cgi/pmidlookup?view=long&pmid=12730459 Eide DJ. (2003) J Nutr. Multiple regulatory mechanisms maintain zinc homeostasis in Saccharomyces cerevisiae. 133(5 Suppl 1):1532S-1535S.] | |||
<!-- | |||
<biblio> | <biblio> | ||
#Paper1 pmid=17933919 | #Paper1 pmid=17933919 | ||
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#Paper8 pmid=12730459 | #Paper8 pmid=12730459 | ||
</biblio> | </biblio> | ||
--> | |||
* [[Media:Sc_ZincIonHomeostasis_kb3.zip | Zip file containing Sc_ZincIonHomeostasis.mapp]] | * [[Media:Sc_ZincIonHomeostasis_kb3.zip | Zip file containing Sc_ZincIonHomeostasis.mapp]] | ||
== Ribosome Biogenesis Pathway == | == Ribosome Biogenesis Pathway == | ||
*[http://www.sciencedirect.com/science/article/pii/S0955067402003368 Fatica 2002] | |||
**Pub med reference = 12067653 | |||
*[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2749941/?tool=pubmed Zhihua 2009] | |||
**Pub med reference = 19806183 | |||
*[http://onlinelibrary.wiley.com/doi/10.1002/yea.1353/full Wade 2006] | |||
**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 | |||
== 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 [http://www.sciencedirect.com/science/article/pii/S0378111902005589] | |||
*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] |
Latest revision as of 16:23, 19 November 2012
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
- 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
- Zhu et al. 2009
- Pub med reference = 19158363
Other
- Check with online compendia, Hughes and Princeton
Zinc
- 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
- 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.
- 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.
- 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.
- Eide DJ. (2009) Homeostatic and adaptive responses to zinc deficiency in Saccharomyces cerevisiae. J Biol Chem. 284(28):18565-18569.
- Eide DJ. (2006) Zinc transporters and the cellular trafficking of zinc. Biochim Biophys Acta. 1763(7):711-722.
- 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.
- Eide DJ. (2003) J Nutr. Multiple regulatory mechanisms maintain zinc homeostasis in Saccharomyces cerevisiae. 133(5 Suppl 1):1532S-1535S.
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]