Difference between revisions of "Part:BBa K3600002"

(→‎Usage and Biology)
(→‎Usage and Biology)
 
(22 intermediate revisions by 2 users not shown)
Line 3: Line 3:
 
<partinfo>BBa_K3600002 short</partinfo>
 
<partinfo>BBa_K3600002 short</partinfo>
  
−
This part contains the promoter of the gene YCF1 from S. Cerevisiae.
+
YCF1 promoter part plasmid was made in order to create a part plasmid which contains the YCF1 promoter and is compatible with the Yeast Toolkit. To create a promoter part plasmid compatible with the yeast toolkit, at first, we designed a gBlock consisting of the 500bp promoter region, that was retrieved from the yeast genome database, and two linking sequences which were added to the ends of the promoter.These linking sequences contained a BsaI and a BsmBI cutting site each to make Golden Gate assembly possible.Then, the gBlock was inserted into the part plasmid entry vector (pYTK001) through a BsmBI assembly.
 +
 
  
 
===Usage and Biology===
 
===Usage and Biology===
−
* activator: Yap1p
+
The YCF1 gene encodes the Yeast cadmium factor 1 <html><a href="#Bhuiyan2011"><sup>1</sup></a></html> and is required for yeast cells to better resist exposure to cadmium <html><a href="#Li1996"><sup>2</sup></a></html>. The YCF1 promoter is regulated by the transcription factor Yap1p. The binding site for Yap1p, in the promoter YCF1, is TTACTAA <html><a href="#Kuge1994"><sup>4</sup></a></html>. Using the yeast toolkit for modular assembly, the YCF1 promoter plasmid was used as a part of type II .
−
*YCF1 gene encodes encodes a 1,515-amino acid ATP-binding cassette (ABC) protein (ref)
+
−
*The promoter YCF1 has been chosen in order to express fluorescent protein [ref] when the S.cervisiae is exposed to toxic effects in particular the toxic effect of cadmium(ref).
+
−
*The binding site for Yap1p, in the promoter YCF1, is TTACTAA.<html><a href="#Kuge1994"><sup>1</sup></a></html>
+
−
 
+
−
*The yeast toolkit for modular assembly <html><a href="#Lee2015"><sup>2</sup></a></html> was used to assemble transcriptional units. This promoter was used as a part of type II.
+
−
 
+
  
  
Line 30: Line 25:
  
 
===References===
 
===References===
−
<HTML><a name=Kuge1994 style="color:black">
+
 
−
[1]  
+
<HTML><a name=Bhuiyan2011 style="color:black">
 +
[1] Bhuiyan, M. S. U. et al. Overexpression of a yeast cadmium factor 1 (YCF1) enhances heavy metal tolerance and accumulation in Brassica juncea. Plant Cell Tiss Organ Cult 105, 85–91 (2011).
 +
</a></html>
 +
 
 +
 
 +
<HTML><a name=Li1996 style="color:black">
 +
[2] Li, Z.-S., Szczypka, M., Lu, Y.-P., Thiele, D. J. & Rea, P. A. The Yeast Cadmium Factor Protein (YCF1) Is a Vacuolar Glutathione S-Conjugate Pump. J. Biol. Chem. 271, 6509–6517 (1996).
 
</a></html>
 
</a></html>
  
 
<HTML><a name=Lee2015 style="color:black">
 
<HTML><a name=Lee2015 style="color:black">
−
[2] Lee, M. E., DeLoache, W. C., Cervantes, B. & Dueber, J. E. A Highly Characterized Yeast Toolkit for Modular, Multipart Assembly. ACS Synth. Biol. 4, 975–986 (2015).
+
[3] Lee, M. E., DeLoache, W. C., Cervantes, B. & Dueber, J. E. A Highly Characterized Yeast Toolkit for Modular, Multipart Assembly. ACS Synth. Biol. 4, 975–986 (2015).
 +
</a></html>
 +
 
 +
<HTML><a name=Kuge1994 style="color:black">
 +
[4] Kuge, S. & Jones, N. YAP1 dependent activation of TRX2 is essential for the response of Saccharomyces cerevisiae to oxidative stress by hydroperoxides. The EMBO Journal 13, 655–664 (1994).
 
</a></html>
 
</a></html>

Latest revision as of 03:51, 28 October 2020


YCF1 promoter part plasmid

YCF1 promoter part plasmid was made in order to create a part plasmid which contains the YCF1 promoter and is compatible with the Yeast Toolkit. To create a promoter part plasmid compatible with the yeast toolkit, at first, we designed a gBlock consisting of the 500bp promoter region, that was retrieved from the yeast genome database, and two linking sequences which were added to the ends of the promoter.These linking sequences contained a BsaI and a BsmBI cutting site each to make Golden Gate assembly possible.Then, the gBlock was inserted into the part plasmid entry vector (pYTK001) through a BsmBI assembly.


Usage and Biology

The YCF1 gene encodes the Yeast cadmium factor 1 1 and is required for yeast cells to better resist exposure to cadmium 2. The YCF1 promoter is regulated by the transcription factor Yap1p. The binding site for Yap1p, in the promoter YCF1, is TTACTAA 4. Using the yeast toolkit for modular assembly, the YCF1 promoter plasmid was used as a part of type II .



Sequence and Features


Assembly Compatibility:
  • 10
    INCOMPATIBLE WITH RFC[10]
    Illegal EcoRI site found at 935
    Illegal EcoRI site found at 1665
    Illegal XbaI site found at 944
    Illegal XbaI site found at 1842
    Illegal SpeI site found at 2810
    Illegal PstI site found at 2819
  • 12
    INCOMPATIBLE WITH RFC[12]
    Illegal EcoRI site found at 935
    Illegal EcoRI site found at 1665
    Illegal SpeI site found at 2810
    Illegal PstI site found at 2819
    Illegal NotI site found at 923
    Illegal NotI site found at 2829
  • 21
    INCOMPATIBLE WITH RFC[21]
    Illegal suffix found in sequence at 2412
    Illegal EcoRI site found at 935
    Illegal EcoRI site found at 1665
    Illegal BglII site found at 1280
    Illegal BglII site found at 2283
  • 23
    INCOMPATIBLE WITH RFC[23]
    Illegal EcoRI site found at 935
    Illegal EcoRI site found at 1665
    Illegal XbaI site found at 944
    Illegal XbaI site found at 1842
    Illegal SpeI site found at 2810
    Illegal PstI site found at 2819
  • 25
    INCOMPATIBLE WITH RFC[25]
    Illegal EcoRI site found at 935
    Illegal EcoRI site found at 1665
    Illegal XbaI site found at 944
    Illegal XbaI site found at 1842
    Illegal SpeI site found at 2810
    Illegal PstI site found at 2819
    Illegal NgoMIV site found at 2767
  • 1000
    COMPATIBLE WITH RFC[1000]


Measurements

References

[1] Bhuiyan, M. S. U. et al. Overexpression of a yeast cadmium factor 1 (YCF1) enhances heavy metal tolerance and accumulation in Brassica juncea. Plant Cell Tiss Organ Cult 105, 85–91 (2011).


[2] Li, Z.-S., Szczypka, M., Lu, Y.-P., Thiele, D. J. & Rea, P. A. The Yeast Cadmium Factor Protein (YCF1) Is a Vacuolar Glutathione S-Conjugate Pump. J. Biol. Chem. 271, 6509–6517 (1996).

[3] Lee, M. E., DeLoache, W. C., Cervantes, B. & Dueber, J. E. A Highly Characterized Yeast Toolkit for Modular, Multipart Assembly. ACS Synth. Biol. 4, 975–986 (2015).

[4] Kuge, S. & Jones, N. YAP1 dependent activation of TRX2 is essential for the response of Saccharomyces cerevisiae to oxidative stress by hydroperoxides. The EMBO Journal 13, 655–664 (1994).