Difference between revisions of "YMR090W"

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|valign="top" nowrap bgcolor="{{SGDblue}}"| '''Systematic name''' || [http://db.yeastgenome.org/cgi-bin/locus.pl?dbid=S000004696 YMR090W]  
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|valign="top" nowrap bgcolor="{{SGDblue}}"| '''Systematic name''' || [http://www.yeastgenome.org/cgi-bin/locus.pl?dbid=S000004696 YMR090W]  
 
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|valign="top" nowrap bgcolor="{{SGDblue}}"| '''Gene name'''        ||'' ''
 
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|valign="top" nowrap bgcolor="{{SGDblue}}"| '''Coordinates'''
 
|valign="top" nowrap bgcolor="{{SGDblue}}"| '''Coordinates'''
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|nowrap| Chr XIII:449244..449927
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|nowrap| Chr XIII:449245..449928
 
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|valign="top" nowrap bgcolor="{{SGDblue}}"| '''Primary SGDID'''          || S000004696
 
|valign="top" nowrap bgcolor="{{SGDblue}}"| '''Primary SGDID'''          || S000004696
 
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'''Description of YMR090W:''' Putative protein of unknown function with similarity to DTDP-glucose 4,6-dehydratases; GFP-fusion protein localizes to the cytoplasm; up-regulated in response to the fungicide mancozeb; not essential for viability<ref name='S000128935'>Santos PM, et al. (2009) Insights into yeast adaptive response to the agricultural fungicide mancozeb: a toxicoproteomics approach. Proteomics 9(3):657-70 {{SGDpaper|S000128935}} PMID 19137554</ref><ref name='S000074185'>Huh WK, et al. (2003) Global analysis of protein localization in budding yeast. Nature 425(6959):686-91 {{SGDpaper|S000074185}} PMID 14562095</ref><ref name='S000071347'>Giaever G, et al. (2002) Functional profiling of the Saccharomyces cerevisiae genome. Nature 418(6896):387-91
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'''Description of YMR090W:''' Putative protein of unknown function with similarity to DTDP-glucose 4,6-dehydratases; GFP-fusion protein localizes to the cytoplasm; up-regulated in response to the fungicide mancozeb; not essential for viability<ref name='S000071347'>Giaever G, et al. (2002) Functional profiling of the Saccharomyces cerevisiae genome. Nature 418(6896):387-91 {{SGDpaper|S000071347}} PMID 12140549</ref><ref name='S000074185'>Huh WK, et al. (2003) Global analysis of protein localization in budding yeast. Nature 425(6959):686-91 {{SGDpaper|S000074185}} PMID 14562095</ref><ref name='S000128935'>Santos PM, et al. (2009) Insights into yeast adaptive response to the agricultural fungicide mancozeb: a toxicoproteomics approach. Proteomics 9(3):657-70
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  {{SGDpaper|S000071347}} PMID 12140549</ref>
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  {{SGDpaper|S000128935}} PMID 19137554</ref>
 
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__TOC__
 
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==Community Commentary==
 
==Community Commentary==
 
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===[[UW-Stout/Sensitivity To Nitrogen Starvation]]===
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[[File: YMRO90W_growth plate.JPG|thumb|Growth of YMRO90W on synthetic defined media (SDC).]]
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[[File: YMRO90W_starvation plate.JPG|thumb|Growth of YMRO90W on omission media that lacks nitrogen.]]
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Knocking out the YMRO90W seems to have no effect on growth after incubating for 5 days on the Nitrogen omitted media.
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===[[UW-Stout/Ultraviolet Light|Ultraviolet Sensitivity]]===
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[[File:YMR090W uv light.jpg|300 px]]
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[[File:BY4735(wild) uv light.jpg|300 px]]
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YPL068C is more sensitive than YMR090W given that there is less colonizes present when under the same stress.
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=== DNA and RNA Details ===
 
=== DNA and RNA Details ===
 
[[Category:Topic:DNA and RNA Details]]
 
[[Category:Topic:DNA and RNA Details]]
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===[[UW-Stout/Growth_Curve|Growth Curve]]===
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[[File:ymr090w_growth.png]]
  
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In a BY4735 background, knocking out YMR090W seems to have a moderate effect on growth rate in log-phase.  In this assay, the BY4735 strain's doubling time was 124 minutes, while the YMR090W knock-out strain's doubling time was 208 minutes.
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===[[UW-Stout/G-418 | G-418 Stress]]===
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[[File:image002.png]]
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In the BY4735 background, knocking out YMR090W seems to have a little effect on the growth rate. In the knock-out experiment, the BY4735 strain's doubling time was 149 minutes, whereas the YMR090W knock-out strain's doubling time was 242 minutes. The calibration experiment, the BY4735 strain's doubling time was 64 minutes, whereas the YMR090W knock-out strain's doubling time was 95 minutes.
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===Methanol Sensitivity===
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The wild type had a doubling time of 170 min, the YMR090w had a doubling time of 225 min. The doubling time increased for both after we added the methanol which means that this strain is sensitive.
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[https://wiki.yeastgenome.org/index.php/UW-Stout/Methanol]
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[[File:YMR090W_Methanol_sensitivity.png]]
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===Heat Shock===
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[[File:YMR090w Heat Shock.PNG]]
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Heat shock had no change on the doubling time, but the starting amount of yeast cells less. The heat seemed to kill off the cells, the longer they were in the hot water bath.
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===Stressing with Hydroxyurea===
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[[UW-Stout/Hydroxyurea|Hydroxyurea Protocol]]
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-The wild type strain had only a small difference in doubling time when stressed with Hydroxyurea;YMR090W showed about a 30 minute difference in doubling time compared to the wild type strain, indicating that this gene most likely plays a role in DNA replication.
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[[file:HU_YMR090W.png|left]]
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===Fermentation===
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Fermentation protocol link [https://wiki.yeastgenome.org/index.php/UW-Stout/Fermentation]
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- There appears to be no major difference in fermentation rate. The lower final ethanol percentage could be a result of evaporation. If this experiment were to be carried out again then it should be done in an air tight container.
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[[File:Fer YMR090W.PNG]]
  
 
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J Biol Chem 278(5):3265-74</ref>
 
J Biol Chem 278(5):3265-74</ref>
 
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===Caffeine Sensitivity===
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[[File:YMR090W.png|YMR090W VS BY4735]]
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Caffeine protocol [[UW-Stout/Caffeine]], the graphs look as if the genes reacted very similarly.
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----
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===Stressing with pH===
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pH stress protocol link [https://wiki.yeastgenome.org/index.php/UW-Stout/pH]
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When I looked at the data this graph shows I see that the yeast strain YMR090W has more of a linear pathway developed than does the wild type does. And So, therefore the yeast strain YMR090C is more resilient than the wild type is.
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[[File:pH-YMR090W.PNG]]
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===Cold Shock Sensitivity===
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[[File:YMR090WBB.png]]
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Protocol: [https://wiki.yeastgenome.org/index.php/UW-Stout/Cold_Shock Cold Shock]
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YMR090W is neither more or less sensitive to the cold than the wild type strain. This is shown because the doubling times change the same amount before and after the cold shock in both the wild type strain and YMR090W.
  
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Latest revision as of 18:56, 9 May 2019

Share your knowledge...Edit this entry!

Systematic name YMR090W
Gene name
Aliases
Feature type ORF, Uncharacterized
Coordinates Chr XIII:449245..449928
Primary SGDID S000004696


Description of YMR090W: Putative protein of unknown function with similarity to DTDP-glucose 4,6-dehydratases; GFP-fusion protein localizes to the cytoplasm; up-regulated in response to the fungicide mancozeb; not essential for viability[1][2][3]




Community Commentary

About Community Commentary. Please share your knowledge!

UW-Stout/Sensitivity To Nitrogen Starvation

Growth of YMRO90W on synthetic defined media (SDC).
Growth of YMRO90W on omission media that lacks nitrogen.

Knocking out the YMRO90W seems to have no effect on growth after incubating for 5 days on the Nitrogen omitted media.

Ultraviolet Sensitivity

YMR090W uv light.jpg BY4735(wild) uv light.jpg

YPL068C is more sensitive than YMR090W given that there is less colonizes present when under the same stress.


DNA and RNA Details

Other DNA and RNA Details

Other Topic: expression

Specifically higher expression in nitrogen limited chemostat cultures versus nitrogen excess. [4] [5]

This gene is part of the UW-Stout Orphan Gene Project. Learn more here.

Growth Curve

ymr090w growth.png

In a BY4735 background, knocking out YMR090W seems to have a moderate effect on growth rate in log-phase. In this assay, the BY4735 strain's doubling time was 124 minutes, while the YMR090W knock-out strain's doubling time was 208 minutes.

G-418 Stress

image002.png

In the BY4735 background, knocking out YMR090W seems to have a little effect on the growth rate. In the knock-out experiment, the BY4735 strain's doubling time was 149 minutes, whereas the YMR090W knock-out strain's doubling time was 242 minutes. The calibration experiment, the BY4735 strain's doubling time was 64 minutes, whereas the YMR090W knock-out strain's doubling time was 95 minutes.

Methanol Sensitivity

The wild type had a doubling time of 170 min, the YMR090w had a doubling time of 225 min. The doubling time increased for both after we added the methanol which means that this strain is sensitive.

[1]

YMR090W Methanol sensitivity.png


Heat Shock

YMR090w Heat Shock.PNG

Heat shock had no change on the doubling time, but the starting amount of yeast cells less. The heat seemed to kill off the cells, the longer they were in the hot water bath.

Stressing with Hydroxyurea

Hydroxyurea Protocol -The wild type strain had only a small difference in doubling time when stressed with Hydroxyurea;YMR090W showed about a 30 minute difference in doubling time compared to the wild type strain, indicating that this gene most likely plays a role in DNA replication.

HU YMR090W.png

Fermentation

Fermentation protocol link [2] - There appears to be no major difference in fermentation rate. The lower final ethanol percentage could be a result of evaporation. If this experiment were to be carried out again then it should be done in an air tight container.

Fer YMR090W.PNG


Caffeine Sensitivity

YMR090W VS BY4735 Caffeine protocol UW-Stout/Caffeine, the graphs look as if the genes reacted very similarly.

Stressing with pH

pH stress protocol link [3]

When I looked at the data this graph shows I see that the yeast strain YMR090W has more of a linear pathway developed than does the wild type does. And So, therefore the yeast strain YMR090C is more resilient than the wild type is.

pH-YMR090W.PNG

Cold Shock Sensitivity

YMR090WBB.png


Protocol: Cold Shock


YMR090W is neither more or less sensitive to the cold than the wild type strain. This is shown because the doubling times change the same amount before and after the cold shock in both the wild type strain and YMR090W.

References

See Help:References on how to add references

  1. ↑ Giaever G, et al. (2002) Functional profiling of the Saccharomyces cerevisiae genome. Nature 418(6896):387-91 SGD PMID 12140549
  2. ↑ Huh WK, et al. (2003) Global analysis of protein localization in budding yeast. Nature 425(6959):686-91 SGD PMID 14562095
  3. ↑ Santos PM, et al. (2009) Insights into yeast adaptive response to the agricultural fungicide mancozeb: a toxicoproteomics approach. Proteomics 9(3):657-70 SGD PMID 19137554
  4. ↑ Boer VM, et al. (2003) The genome-wide transcriptional responses of Saccharomyces cerevisiae grown on glucose in aerobic chemostat cultures limited for carbon, nitrogen, phosphorus, or sulfur. J Biol Chem 278(5):3265-74 SGD PMID 12414795
  5. ↑ submitted by Viktor Boer on 2003-07-25

See Help:Categories on how to add the wiki page for this gene to a Category

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