Difference between revisions of "Part:BBa K2314324"
 
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<img src="https://static.igem.org/mediawiki/parts/0/01/T--OUC-China--XYL2.gif  
 
<img src="https://static.igem.org/mediawiki/parts/0/01/T--OUC-China--XYL2.gif  
  
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<html>
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<h2>Improved by <b>Jiangnan_China</b> 2021</h2>
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<p>We built a more efficient composite part <a href="https://parts.igem.org/Part:BBa_K3803016">BBa_K3803016</a> to achieve a functional improvement based on the parts <a href="https://parts.igem.org/Part:BBa_K2314913">BBa_K2314913</a> & <a href="https://parts.igem.org/Part:BBa_K2314324">BBa_K2314324</a> (Although they were uploaded as basic parts separately, they worked together as a composite part) from OUC_China in 2017 iGEM.</p>
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We express this composite part on pY15TEF1 vector and then introduced it into <i>S. cerevisiae</i> to test its function.
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<h3>Design</h3>
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<p>Xylose reductase (XR) will first transform xylose to xylitol, and xylitol dehydrogenase (XDH) can further convert xylitol to xylulose. Then, xylulose will be converted to xylulose 5-phosphate (X5P) by the native xylulose kinase (XK). Apart from the original XR and XDH genes, considering the low copy number of native XK gene in <i style="font-style: italic ">S. cerevisiae</i>, we introduced an extra XK gene to improve the xylose utilization ability.</p>
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<figure>
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<img src="https://2021.igem.org/wiki/images/8/84/T--Jiangnan_China--Xylose_Pathway.png" style="width: 100%">
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<br/><b>Fig.1</b> Xylose Utilization Pathway
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</figcaption>
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</figure>
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<br/>
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<figure>
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<img src="https://2021.igem.org/wiki/images/4/41/T--Jiangnan_China--improvement-1.png" style="width: 50%"><br/><b>Fig.2</b> The Existing &amp; Improved Parts</p>
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</figcaption>
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</figure>
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<h3>Xylose Utilization Ability: For Cell Growth</h3>
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<p>For cell growth, OUC_China achieved a final OD<sub>600</sub> around 2.35 in YNB-based xylose media. After our improvement on their parts, we could get a final OD<sub>600</sub> around 20.</p>
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<figure>
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<img src="https://2021.igem.org/wiki/images/c/c7/T--Jiangnan_China--ODduibi.png" width="100%">
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<figcaption>
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<br/><b>Fig.2</b> The OD<sub>600</sub> Value with Different Xylose Utilization Genes
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</figcaption>
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</figure>
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<h3>Xylose Utilization Ability: For Product Yield</h3>
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<p>For our own product yield, our production also improved after substituting our three-gene cassette for OUC_China's two-gene one. The improved production was very obvious after the parts improvement based on our HPLC results.</p>
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<figure>
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<img src="https://2021.igem.org/wiki/images/8/8c/T--Jiangnan_China--HPLCXYL.png" width="70%">
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<figcaption>
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<br/><b>Fig.3</b> The HPLC Results with Different Xylose Utilization Genes
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</figcaption>
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</figure>
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<p>For more information about our parts and improvement, you can see details <a href="https://2021.igem.org/Team:Jiangnan_China/Improve">here</a></p>
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<h3>Reference</h3>
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<p>[1] Construction of efficient xylose-fermenting <i style="font-style: italic">Saccharomyces cerevisiae</i> through a synthetic isozyme system of xylose reductase from <i style="font-style: italic">Scheffersomyces stipitis</i>. Bioresource Technology, Jung-Hyun Jo, Yong-Cheol Park, Yong-Su Jin, Jin-Ho Seo, Bioresource Technology, 241 (2017) 88–94.</p>
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<p>[2] Metabolic engineering of <i style="font-style: italic">Saccharomyces cerevisiae</i> for production of Shinorine, a sunscreen material, from xylose. Seong-Hee Park, Kyusung Lee, Jae Woo Jang and Ji-Sook Hahn, ACS Synthetic Biology, 2019 (8), 346−357.</p>
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</html>
 
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<!-- Add more about the biology of this part here
 
<!-- Add more about the biology of this part here

Latest revision as of 06:26, 19 October 2021

Gene XYL2 encoding xylitol dehydrogenase (XDH) from Pichia stipitis

"The gene XYL2 can express xylitol dehydrogenase, Xylitol is oxidized to xylulose under the action of xylitol dehydrogenase, which relies on NAD.
The genomic XYL2 gene was isolated and the nucleotide sequence of the 1089 bp structural gene, and of adjacent non-coding regions, was determined. The XYL2 open-reading frame codes for a protein of 363 amino acids with a predicted molecular mass of 38.5 kDa. The XYL2 gene is actively expressed in S. cerevisiae transformants.
In our project, we expressed the XYL1 and XYL2 genes, which are associated with xylose metabolism in Saccharomyces cerevisiae EBY100.The whole process of xylose metabolism is as follows:
Xylose is reduced to xylulose under the action of NADPH-dependent xylose reductase (xylosereductase XR). Xylitol is then oxidized to xylulose under the action of xylitol dehydrogenase, which relies on NAD. Xylulose is then phosphorylated by xylulokinase to form 5-phosphate xylose and then into the pentose phosphate pathway, PPP. The intermediate product of PPP pathway 6-phosphate glucose and 3-phosphoric acid glycerol aldehyde through glycolysis pathway to form pyruvate. L-lactate dehydrogenase and coenzyme NADH reduced pyruvate to L-lactic acid. Saccharomyces cerevisiae is not able to use xylose as a result of the lack of enzymes that convert xylose into xylose, but can use the isomers of xylose-xylulose. In Saccharomyces cerevisiae, Xylulose is also first phosphorylated to form 5-phosphate sugar, which enters the PPP pathway and forms lactic acid by glycolysis. We have constructed engineered bacteria that can use xylose as a carbon source, which can be used as xylose and fermented xylose to produce ethanol, which is the result of our experiment.

[1]Yu, S., H. Jeppsson, and Barbel Hahnhagerdal. "Xylulose fermentation by Saccharomyces cerevisiae and xylose-fermenting yeast strains.." Applied Microbiology and Biotechnology (1995): 314-320.
[2]Kötter, Peter, and M. Ciriacy. "Xylose fermentation by Saccharomyces cerevisiae." Applied Microbiology & Biotechnology 38.6(1993):776-783.
In short, XYL2 encoding xylitol dehydrogenase (XDH) from Pichia

This is the structure of this part.


<img src="T--OUC-China--XYL2.gif


Improved by Jiangnan_China 2021

We built a more efficient composite part BBa_K3803016 to achieve a functional improvement based on the parts BBa_K2314913 & BBa_K2314324 (Although they were uploaded as basic parts separately, they worked together as a composite part) from OUC_China in 2017 iGEM.

We express this composite part on pY15TEF1 vector and then introduced it into S. cerevisiae to test its function.

Design

Xylose reductase (XR) will first transform xylose to xylitol, and xylitol dehydrogenase (XDH) can further convert xylitol to xylulose. Then, xylulose will be converted to xylulose 5-phosphate (X5P) by the native xylulose kinase (XK). Apart from the original XR and XDH genes, considering the low copy number of native XK gene in S. cerevisiae, we introduced an extra XK gene to improve the xylose utilization ability.


Fig.1 Xylose Utilization Pathway


Fig.2 The Existing & Improved Parts

Xylose Utilization Ability: For Cell Growth

For cell growth, OUC_China achieved a final OD600 around 2.35 in YNB-based xylose media. After our improvement on their parts, we could get a final OD600 around 20.


Fig.2 The OD600 Value with Different Xylose Utilization Genes

Xylose Utilization Ability: For Product Yield

For our own product yield, our production also improved after substituting our three-gene cassette for OUC_China's two-gene one. The improved production was very obvious after the parts improvement based on our HPLC results.


Fig.3 The HPLC Results with Different Xylose Utilization Genes

For more information about our parts and improvement, you can see details here

Reference

[1] Construction of efficient xylose-fermenting Saccharomyces cerevisiae through a synthetic isozyme system of xylose reductase from Scheffersomyces stipitis. Bioresource Technology, Jung-Hyun Jo, Yong-Cheol Park, Yong-Su Jin, Jin-Ho Seo, Bioresource Technology, 241 (2017) 88–94.

[2] Metabolic engineering of Saccharomyces cerevisiae for production of Shinorine, a sunscreen material, from xylose. Seong-Hee Park, Kyusung Lee, Jae Woo Jang and Ji-Sook Hahn, ACS Synthetic Biology, 2019 (8), 346−357.

"/> Sequence and Features


Assembly Compatibility:
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    COMPATIBLE WITH RFC[10]
  • 12
    COMPATIBLE WITH RFC[12]
  • 21
    COMPATIBLE WITH RFC[21]
  • 23
    COMPATIBLE WITH RFC[23]
  • 25
    INCOMPATIBLE WITH RFC[25]
    Illegal AgeI site found at 112
    Illegal AgeI site found at 688
  • 1000
    COMPATIBLE WITH RFC[1000]