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=Article=
 
=Article=
 
Sahara, T., Goda, T., & Ohgiya, S. (2002). [http://www.jbc.org/content/277/51/50015.long Comprehensive expression analysis of time-dependent genetic responses in yeast cells to low temperature]. Journal of Biological Chemistry, 277(51), 50015-50021.
 
Sahara, T., Goda, T., & Ohgiya, S. (2002). [http://www.jbc.org/content/277/51/50015.long Comprehensive expression analysis of time-dependent genetic responses in yeast cells to low temperature]. Journal of Biological Chemistry, 277(51), 50015-50021.
 +
=Presentation=
 +
[[Media:Cold_Shock_Yeast_Genome_Response.pdf|Journal Club Presentation 2]]
 +
 +
=Flow Chart=
 +
[[Image:Sahara_T_et_al_article_flowchart_CW.png]]
 
=Outline=
 
=Outline=
 +
==Experiment design and procedures==
 +
*Purchased cDNA microarray of ''Saccharomyces cervisiae'' from DNA Chip Research Inc.
 +
*Used ''S. cervisiae''YPH500
 +
*Grew yeast cells aerobically in YPD medium at 30 degrees celsius and shaken at 100rpm.
 +
*YPD is made up of:
 +
**1% yeast extract
 +
**2% peptone
 +
**2% glucose
 +
*Yeast cells were grown to "mid-log phase" where they were still maturing, but not fully reproducing
 +
*50mL of culture was taken and centrifuged to collect the cells and be used as a time 0 reference for the rest of the experiment
 +
*The time 0 reference cells were stored at -80 degrees celsius
 +
*The rest of culture was used for the experimental samples and was cold shocked at 10 degrees celsius
 +
*Samples were collected at various times: 0.25, 0.5, 2, 4, and 8h
 +
*Acidic phenol method and RNeasy Mini Kit were used to prepare the RNA
 +
*The RNA was used to prepare fluorophore-labeled cDNA probes
 +
*These probes marked the cells for array hybridization
 +
*The microarrays were scanned with a laser microscope and were analyzed
 +
*Repeated process twice
 +
*Averaged the expression ratios of the separate experiments for final data
 +
==Results & discussion==
 +
*Analyzed the microarray of cDNAs of 5,803 genes in yeast genome
 +
*There was a diauxic shift in cells that experienced cold shock
 +
**Down-shift of some diauxic shift-inducible genes in late phase of cold shock
 +
*Low temperature affects expression of ~25% of the yeast genes
 +
*Number of up-regulated genes increased from 41 at 0.25h to 536 at 8h
 +
*Number of down-regulated genes also increased from 4 at 0.25h to 488 at 8h
 +
*Gene expression changes significantly in both ways (up & down-regulation) to adapt cells to colder environment, similar to reactions to other stresses, like heat, salinity, hydrogen peroxide, and osmotic stresses
 +
*Table 1 shows the number of genes that significantly changed expression (2-fold or more), up-regulating or down-regulating
 +
===Clustering analysis===
 +
*Clustering of genes (genes that were close together) were analyzed in the ways they responded
 +
*Genes separated into 5 different clusters (Fig. 1):
 +
**1A: Unclassified proteins
 +
**1B: Amino acid biosynthesis and metabolism
 +
**1C: RNA Polymerase I & RNA processing
 +
**1D: Ribosomal proteins
 +
**1E: Not labeled
 +
*Shows cooperative regulation
 +
**1C: up-regulated in early phase (0-0.5h), then down-regulated in late phase (4-8h)
 +
**1D & 1E: up-regulated in mid-late phase (2h & 4-8h)
 +
===Transcription related genes===
 +
*Looked at clusters of genes relating to RNA polymerase I & RNA processing
 +
**All up-regulated in early phase
 +
*Cooperative regulation of genes involved in transcription (Fig. 2)
 +
*2 clusters of these genes:
 +
**Down-regulating (2A, 2B, & 2D)
 +
***2A (RNA polymerase I & RNA processing) & 2B (rRNA processing) up-regulated in early phase, then down regulated in late phase
 +
***2D: mRNA transcription
 +
**Up-regulating (2C)
 +
***2C: mRNA transcription
 +
***High up-regulating in mid phase
 +
*Up-regulated genes that had to do with basic transcriptional functions, like genes encoding for regulatory proteins for amino acid production
 +
*Down-regulated genes were not essential for basic life, like genes encoding heat shock transcription factor or a transcription factor for drug resistant genes
 +
*Factors essential to transcription & processing of rRNAs were up-regulated
 +
*Genes for synthesis and transcription regulation of mRNAs had mix responses
 +
===Ribosomal protein related genes===
 +
*Genes separated into four clusters (Fig. 3):
 +
**3A & 3B: cytosolic ribosome
 +
**3C: translational control factors
 +
**3D: tRNA syntheatases
 +
*3A up-regulated in early-mid phase, then down-regulated in late phase
 +
*3B up-regulated in early-mid phase, and slightly down-regulated in the late phase
 +
*3C continuously up-regulated starting in the early phase
 +
*3D overall down-regulated
 +
*Genes encoding ribosomal proteins = most of up-regulated genes at 2h
 +
*Almost all up-regulating ribosomal proteins had similar expressions, showing cooperative regulation
 +
*Low temperature impairs translational ability
 +
*When genes related to ribosomal proteins and rRNA processing don't work, there is cold sensitivity
 +
*Yeast up-regulates genes encoding ribosomal proteins, so compensates for less efficient/productive translation to overcome cold sensitivity
 +
===Cell rescue, defense, death, and aging genes===
 +
*Genes separated into four clusters (Fig.. 4):
 +
**4A: not labeled
 +
**4B & 4C: stress response - high up-regulation in mid-late phase
 +
**4D: stress response and chaperone - high down-regulation in mid-late phase
 +
*Heat shock protein genes (HSPs) were down-regulated in low temperatures, except HSP12 and HSP26
 +
*This may mean HSP12 and HSP26 have different transcription regulation than other HSPs
 +
*Graumann, et al., 1996 did similar experiment with Bacillus subtilis and found peptidyl prolyl cis/trans isomerases were induced in low temperatures, so protein folding genes were up-regulated
 +
===Metabolism and energy production genes===
 +
*8 clusters (Fig. 5):
 +
**5A: nucleotide metabolism - up-regulated early-mid phase, then down-regulated
 +
**5B & 5E: not annotated
 +
**5C & 5D: C-compound and carbohydrate metabolism - up-regulated
 +
**5F & 5H: amino acid metabolism - down-regulated
 +
**5G: C-compound and carbohydrate utilization - down-regulated
 +
*Clusters show a lot of cooperative regulation between glycogen and trehalose biosynthesis genes
 +
**glycogen and trehalose both reserve carbohydrates
 +
*Genes involved in glycogen production up-regulated in mid-late phases
 +
*Curious that glycogen degradation gene (GPH1) was also up-regulated
 +
*Tests in heat shock found even when glycogen levels were low, yeast still recylced/degraded it
 +
*Trehalose may help protect cellular membrane, which may help to keep yeast cells intact at low temperatures
 +
===Signal transduction genes===
 +
*Clusters (Fig. 6):
 +
**6A - down-regulated
 +
**6B - little up-regulation in early phase, then down-regulation
 +
**6C - little down-regulation in early phase, then up-regulation in late phase
 +
*Clusters were not defined in the article
 +
*20% of signal transduction genes changed expression significantly
 +
*Particularly genes related to cAMP-PKA pathway were up-regulated
 +
**increased signaling
 +
*Increase in PKA signaling known to be response to stresses and controlled by Msn2p/4p transcription factors
 +
*cAMP-PKA pathway involved in:
 +
**metabolism control
 +
**stress resistance
 +
**cell proliferation
 +
*Many Msn2p/4p genes up-regulated (50% of them), which had roles in:
 +
**glycogen synthesis
 +
**trehalose synthesis
 +
**stress resistance
 +
*Heat shock gene promoters are suppressed by Msn2p/4p
 +
*Cooperative regulation in genes of Msn2p/4p and cAMP-PKA pathway that are related to stress response and biosynthesis of glycogen and trehalose
 +
*cAMP-PKA pathway may have effect on yeast gene expression after cold shock
 +
==Conclusion==
 +
*Clustering analysis shows different responses in three phases:
 +
**Early phase (0-2h) - transcription (RNA polymerase I & rRNA processing) related genes up-regulated
 +
**Middle phase (2-4h) - ribosomal protein related genes up-regulated
 +
**Late phase (4-8h) - stress response genes up-regulated
 +
*This shows adaptation to environment (low temperature) involves three sequential events (the three phases)
 +
*RNA polymerase I & rRNA processing genes respond first by up-regulating because help transcription and translation, which become less efficient when exposed to low temperature
 +
*Ribosomal protein genes up-regulated in middle phase to further assist in maintaining translational ability
 +
*Maintaining translation is priority to yeast in cold shock because they need to make proteins to help maintain integrity and basic functions of cells
 +
*Stress response induced genes follow in up-regulation, so next step in yeast cells is to adapt and gain tolerance to low temperature
 +
=Terms=
 +
#Nucleolin: a protein associated with nucleolar in growing eukaryotic cells (NCBI, 2017).
 +
#Hypoxia: low levels of oxygen in body tissues (Hine & Martin, 2015).
 +
#Ubiquitin: a protein that marks which proteins are going to be broken down (Hine & Martin, 2015).
 +
#"Mid-log" or "lag" phase: bacterial cells are maturing, but they have not yet reached their maximum reproduction rate (Hine & Martin, 2015).
 +
#Diauxic shift: the switch of a microorganism from using one type of sugar to using another (King, et al., 2014).
 +
#Cytosolic: contents of the fluid in the cytoplasm of a cell (King, et al., 2014).
 +
#Peptidyl prolyl cis/trans isomerases: Enzymes that changes conformation of prolyl bonds to cis or trans, chaning the tertiary structure of a protein (Lackie, 2013).
 +
#cAMP-PKA pathway: the activation of PKA by cAMP (Lackie, 2013).
 +
#GTPase: enzymes that hydrolyze GTP (Lackie, 2013).
 +
#Phosphatase: an enzyme that helps remove a phosphate group from an organic compound (Hine & Martin, 2015).
 
=Acknowledgments=
 
=Acknowledgments=
 +
#I met with Dina outside of class, and we worked on our presentation together.
 +
 +
While I worked with the people noted above, this individual journal entry was completed by me and not copied from another source. [[User:Cwong34|Cwong34]] ([[User talk:Cwong34|talk]]) 17:28, 20 November 2017 (PST)
 +
 
=References=
 
=References=
 +
#Graumann, P., Schröder, K., Schmid, R., & Marahiel, M.A. (1996). Cold shock stress-induced proteins in Bacillus subtilis. ''Journal of Bacteriology'', 178(15), 4611-4619. doi: 10.1128/jb.178.15.4611-4619.1996
 +
#Hine, R. & Martin, E. (Eds.). (2015). ''A Dictionary of Biology''. In ''Oxford Reference''. Retrieved from http://www.oxfordreference.com/view/10.1093/acref/9780198714378.001.0001/acref-9780198714378
 +
#King, R.C., Mulligan, P.K., & Stansfield, W.D. (Eds.). (2014). ''A Dictionary of Genetics''. In ''Oxford Reference''. Retrieved from http://www.oxfordreference.com/view/10.1093/acref/9780199766444.001.0001/acref-9780199766444
 +
#Lackie, J.L. (2013). ''The Dictionary of Cell and Molecular Biology''. In ''Science Direct''. Retrieved from http://www.sciencedirect.com/science/book/9780123849311
 
#LMU BioDB 2017. (2017). Week 12. Retrieved November 14, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_12
 
#LMU BioDB 2017. (2017). Week 12. Retrieved November 14, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_12
 +
#NCBI. (2017). Nucleolin. Retrieved November 20, 2017, from http://www.uniprot.org/uniprot/P19338
 
#Sahara, T., Goda, T., & Ohgiya, S. (2002). Comprehensive expression analysis of time-dependent genetic responses in yeast cells to low temperature. Journal of Biological Chemistry, 277(51), 50015-50021.
 
#Sahara, T., Goda, T., & Ohgiya, S. (2002). Comprehensive expression analysis of time-dependent genetic responses in yeast cells to low temperature. Journal of Biological Chemistry, 277(51), 50015-50021.
  

Latest revision as of 08:05, 21 November 2017

Article

Sahara, T., Goda, T., & Ohgiya, S. (2002). Comprehensive expression analysis of time-dependent genetic responses in yeast cells to low temperature. Journal of Biological Chemistry, 277(51), 50015-50021.

Presentation

Journal Club Presentation 2

Flow Chart

Sahara T et al article flowchart CW.png

Outline

Experiment design and procedures

  • Purchased cDNA microarray of Saccharomyces cervisiae from DNA Chip Research Inc.
  • Used S. cervisiaeYPH500
  • Grew yeast cells aerobically in YPD medium at 30 degrees celsius and shaken at 100rpm.
  • YPD is made up of:
    • 1% yeast extract
    • 2% peptone
    • 2% glucose
  • Yeast cells were grown to "mid-log phase" where they were still maturing, but not fully reproducing
  • 50mL of culture was taken and centrifuged to collect the cells and be used as a time 0 reference for the rest of the experiment
  • The time 0 reference cells were stored at -80 degrees celsius
  • The rest of culture was used for the experimental samples and was cold shocked at 10 degrees celsius
  • Samples were collected at various times: 0.25, 0.5, 2, 4, and 8h
  • Acidic phenol method and RNeasy Mini Kit were used to prepare the RNA
  • The RNA was used to prepare fluorophore-labeled cDNA probes
  • These probes marked the cells for array hybridization
  • The microarrays were scanned with a laser microscope and were analyzed
  • Repeated process twice
  • Averaged the expression ratios of the separate experiments for final data

Results & discussion

  • Analyzed the microarray of cDNAs of 5,803 genes in yeast genome
  • There was a diauxic shift in cells that experienced cold shock
    • Down-shift of some diauxic shift-inducible genes in late phase of cold shock
  • Low temperature affects expression of ~25% of the yeast genes
  • Number of up-regulated genes increased from 41 at 0.25h to 536 at 8h
  • Number of down-regulated genes also increased from 4 at 0.25h to 488 at 8h
  • Gene expression changes significantly in both ways (up & down-regulation) to adapt cells to colder environment, similar to reactions to other stresses, like heat, salinity, hydrogen peroxide, and osmotic stresses
  • Table 1 shows the number of genes that significantly changed expression (2-fold or more), up-regulating or down-regulating

Clustering analysis

  • Clustering of genes (genes that were close together) were analyzed in the ways they responded
  • Genes separated into 5 different clusters (Fig. 1):
    • 1A: Unclassified proteins
    • 1B: Amino acid biosynthesis and metabolism
    • 1C: RNA Polymerase I & RNA processing
    • 1D: Ribosomal proteins
    • 1E: Not labeled
  • Shows cooperative regulation
    • 1C: up-regulated in early phase (0-0.5h), then down-regulated in late phase (4-8h)
    • 1D & 1E: up-regulated in mid-late phase (2h & 4-8h)

Transcription related genes

  • Looked at clusters of genes relating to RNA polymerase I & RNA processing
    • All up-regulated in early phase
  • Cooperative regulation of genes involved in transcription (Fig. 2)
  • 2 clusters of these genes:
    • Down-regulating (2A, 2B, & 2D)
      • 2A (RNA polymerase I & RNA processing) & 2B (rRNA processing) up-regulated in early phase, then down regulated in late phase
      • 2D: mRNA transcription
    • Up-regulating (2C)
      • 2C: mRNA transcription
      • High up-regulating in mid phase
  • Up-regulated genes that had to do with basic transcriptional functions, like genes encoding for regulatory proteins for amino acid production
  • Down-regulated genes were not essential for basic life, like genes encoding heat shock transcription factor or a transcription factor for drug resistant genes
  • Factors essential to transcription & processing of rRNAs were up-regulated
  • Genes for synthesis and transcription regulation of mRNAs had mix responses

Ribosomal protein related genes

  • Genes separated into four clusters (Fig. 3):
    • 3A & 3B: cytosolic ribosome
    • 3C: translational control factors
    • 3D: tRNA syntheatases
  • 3A up-regulated in early-mid phase, then down-regulated in late phase
  • 3B up-regulated in early-mid phase, and slightly down-regulated in the late phase
  • 3C continuously up-regulated starting in the early phase
  • 3D overall down-regulated
  • Genes encoding ribosomal proteins = most of up-regulated genes at 2h
  • Almost all up-regulating ribosomal proteins had similar expressions, showing cooperative regulation
  • Low temperature impairs translational ability
  • When genes related to ribosomal proteins and rRNA processing don't work, there is cold sensitivity
  • Yeast up-regulates genes encoding ribosomal proteins, so compensates for less efficient/productive translation to overcome cold sensitivity

Cell rescue, defense, death, and aging genes

  • Genes separated into four clusters (Fig.. 4):
    • 4A: not labeled
    • 4B & 4C: stress response - high up-regulation in mid-late phase
    • 4D: stress response and chaperone - high down-regulation in mid-late phase
  • Heat shock protein genes (HSPs) were down-regulated in low temperatures, except HSP12 and HSP26
  • This may mean HSP12 and HSP26 have different transcription regulation than other HSPs
  • Graumann, et al., 1996 did similar experiment with Bacillus subtilis and found peptidyl prolyl cis/trans isomerases were induced in low temperatures, so protein folding genes were up-regulated

Metabolism and energy production genes

  • 8 clusters (Fig. 5):
    • 5A: nucleotide metabolism - up-regulated early-mid phase, then down-regulated
    • 5B & 5E: not annotated
    • 5C & 5D: C-compound and carbohydrate metabolism - up-regulated
    • 5F & 5H: amino acid metabolism - down-regulated
    • 5G: C-compound and carbohydrate utilization - down-regulated
  • Clusters show a lot of cooperative regulation between glycogen and trehalose biosynthesis genes
    • glycogen and trehalose both reserve carbohydrates
  • Genes involved in glycogen production up-regulated in mid-late phases
  • Curious that glycogen degradation gene (GPH1) was also up-regulated
  • Tests in heat shock found even when glycogen levels were low, yeast still recylced/degraded it
  • Trehalose may help protect cellular membrane, which may help to keep yeast cells intact at low temperatures

Signal transduction genes

  • Clusters (Fig. 6):
    • 6A - down-regulated
    • 6B - little up-regulation in early phase, then down-regulation
    • 6C - little down-regulation in early phase, then up-regulation in late phase
  • Clusters were not defined in the article
  • 20% of signal transduction genes changed expression significantly
  • Particularly genes related to cAMP-PKA pathway were up-regulated
    • increased signaling
  • Increase in PKA signaling known to be response to stresses and controlled by Msn2p/4p transcription factors
  • cAMP-PKA pathway involved in:
    • metabolism control
    • stress resistance
    • cell proliferation
  • Many Msn2p/4p genes up-regulated (50% of them), which had roles in:
    • glycogen synthesis
    • trehalose synthesis
    • stress resistance
  • Heat shock gene promoters are suppressed by Msn2p/4p
  • Cooperative regulation in genes of Msn2p/4p and cAMP-PKA pathway that are related to stress response and biosynthesis of glycogen and trehalose
  • cAMP-PKA pathway may have effect on yeast gene expression after cold shock

Conclusion

  • Clustering analysis shows different responses in three phases:
    • Early phase (0-2h) - transcription (RNA polymerase I & rRNA processing) related genes up-regulated
    • Middle phase (2-4h) - ribosomal protein related genes up-regulated
    • Late phase (4-8h) - stress response genes up-regulated
  • This shows adaptation to environment (low temperature) involves three sequential events (the three phases)
  • RNA polymerase I & rRNA processing genes respond first by up-regulating because help transcription and translation, which become less efficient when exposed to low temperature
  • Ribosomal protein genes up-regulated in middle phase to further assist in maintaining translational ability
  • Maintaining translation is priority to yeast in cold shock because they need to make proteins to help maintain integrity and basic functions of cells
  • Stress response induced genes follow in up-regulation, so next step in yeast cells is to adapt and gain tolerance to low temperature

Terms

  1. Nucleolin: a protein associated with nucleolar in growing eukaryotic cells (NCBI, 2017).
  2. Hypoxia: low levels of oxygen in body tissues (Hine & Martin, 2015).
  3. Ubiquitin: a protein that marks which proteins are going to be broken down (Hine & Martin, 2015).
  4. "Mid-log" or "lag" phase: bacterial cells are maturing, but they have not yet reached their maximum reproduction rate (Hine & Martin, 2015).
  5. Diauxic shift: the switch of a microorganism from using one type of sugar to using another (King, et al., 2014).
  6. Cytosolic: contents of the fluid in the cytoplasm of a cell (King, et al., 2014).
  7. Peptidyl prolyl cis/trans isomerases: Enzymes that changes conformation of prolyl bonds to cis or trans, chaning the tertiary structure of a protein (Lackie, 2013).
  8. cAMP-PKA pathway: the activation of PKA by cAMP (Lackie, 2013).
  9. GTPase: enzymes that hydrolyze GTP (Lackie, 2013).
  10. Phosphatase: an enzyme that helps remove a phosphate group from an organic compound (Hine & Martin, 2015).

Acknowledgments

  1. I met with Dina outside of class, and we worked on our presentation together.

While I worked with the people noted above, this individual journal entry was completed by me and not copied from another source. Cwong34 (talk) 17:28, 20 November 2017 (PST)

References

  1. Graumann, P., Schröder, K., Schmid, R., & Marahiel, M.A. (1996). Cold shock stress-induced proteins in Bacillus subtilis. Journal of Bacteriology, 178(15), 4611-4619. doi: 10.1128/jb.178.15.4611-4619.1996
  2. Hine, R. & Martin, E. (Eds.). (2015). A Dictionary of Biology. In Oxford Reference. Retrieved from http://www.oxfordreference.com/view/10.1093/acref/9780198714378.001.0001/acref-9780198714378
  3. King, R.C., Mulligan, P.K., & Stansfield, W.D. (Eds.). (2014). A Dictionary of Genetics. In Oxford Reference. Retrieved from http://www.oxfordreference.com/view/10.1093/acref/9780199766444.001.0001/acref-9780199766444
  4. Lackie, J.L. (2013). The Dictionary of Cell and Molecular Biology. In Science Direct. Retrieved from http://www.sciencedirect.com/science/book/9780123849311
  5. LMU BioDB 2017. (2017). Week 12. Retrieved November 14, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_12
  6. NCBI. (2017). Nucleolin. Retrieved November 20, 2017, from http://www.uniprot.org/uniprot/P19338
  7. Sahara, T., Goda, T., & Ohgiya, S. (2002). Comprehensive expression analysis of time-dependent genetic responses in yeast cells to low temperature. Journal of Biological Chemistry, 277(51), 50015-50021.

cwong34

BIOL/CMSI 367-01: Biological Databases Fall 2017

Assignments

Journal Entries:

Shared Journals:

Group Project

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