Difference between revisions of "Part:BBa K4016019"

 
 
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<partinfo>BBa_K4016019 short</partinfo>
 
<partinfo>BBa_K4016019 short</partinfo>
  
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This composite part is designed to generate GFP degradation with [[Part:BBa_K4016020]] (GFPnano - Pix D) through Pix E-Pix D interaction, GFPnano’s targeting function and Trim21 based ubiquitin-proteasome degradation system.
  
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===Usage and Biology===
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==Usage and Biology==
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Protein-protein interactions are powerful tools for manipulating biological processes, and opto-genetically - mediated induction of protein interactions has high spatial resolution without the need for exogenous cofactors. In this case, the dimer ”Pix D- Pix E” is introduced in our project in order to reach such function.
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The two protein, Pix D and Pix E, can associate in the dark into large multi-subunit complexes that dissociate into dimers of Pix D and monomers of Pix E within seconds upon blue light stimulation. [1]~[5] Fusing Pix D/Pix E fragment to the Trim21 and its targeting module, we can realize the Trim21-induced degradation on it’s target protein in the dark, and the Pix D-Pix E dissociation on blue light can induced the dissociation of Trim21 and its targeting module, so as to stop the degradation.
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In our project, our composite part BBa_K4016019 is interacting with [[Part:BBa_K4016020]] (GFPnano - Pix D ), to specifically recognize and degrade GFP in the dark and stop the degradation in the light. If this can work, we can make an “OFF switch” in a system mediated by blue light.
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<html>
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<figure class="figure">
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<img src="https://static.igem.org/mediawiki/parts/6/61/T--NUDT_CHINA--Part_SchematicFigure_19-20_.png" class="figure-img img-fluid rounded"  height="350px">
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</figure>
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</html>
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Figure1. Schematic figure of BBa_K4016019 and BBa_K4016020
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*Here is the mechanism of the system:
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In the dark environment:
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1.HA-Trim21-PixE connect with PixD-GFPnano through PixE-PixD interaction and forms a complex
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2.GFPnano specifically recognize eGFP
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3.eGFP is degraded by ubiquitin-proteasome system recruited by Trim21
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In the blue light:
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1. PixD-PixE dissociate
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2. The degradation of eGFP stop because of the lack of trim21.
 +
 
 +
 
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==Characterization==
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This part is validated through 3 ways: enzyme cutting, PCR and sequencing.
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===PCR===
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The PCR is performed with Green Taq Mix by Vazyme.
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F-Prime: 5’-CTAGCGTTTAAACTTAAGCTTGCCACCATGGAGGTTCAACTGGAGGAGTCTG-3’
 +
 
 +
R-Prime: 5’- TGGATATCTGCAGAATTCTTACACGTTCACGCCGCCGTCGAT-3’
 +
 
 +
The PCR protocol is selected based on the Users Manuel. The Electrophoresis was performed on a 1% Agarose gel.
 +
 
 +
 
 +
===Enzyme Digestion===
 +
After the assembly the plasmid was transferred into the Competent E. coli DH5α). After culturing overnight in LB,we minipreped the plasmid for cutting. The cutting procedure was performed with Hind III EcoR I restriction endonuclease bought.
 +
The plasmid was cutted in a 20μL system at 37 ℃ for 2 hours. The Electrophoresis was performed on a 1％ Agarose glu.
 +
 
 +
===Sequecing===
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The plasmid was sequenced correct.
  
 
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<span class='h3bb'>Sequence and Features</span>
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===Sequence and Features===
 
<partinfo>BBa_K4016019 SequenceAndFeatures</partinfo>
 
<partinfo>BBa_K4016019 SequenceAndFeatures</partinfo>
  
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<partinfo>BBa_K4016019 parameters</partinfo>
 
<partinfo>BBa_K4016019 parameters</partinfo>
 
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===Result===
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===Reference===
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[1] Dine E, Gil AA, Uribe G, Brangwynne CP, Toettcher JE. Protein Phase Separation Provides Long-Term Memory of Transient Spatial Stimuli. Cell Syst. 2018 Jun 27;6(6):655-663.e5. doi: 10.1016/j.cels.2018.05.002. Epub 2018 May 30. PMID: 29859829; PMCID: PMC6023
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[2] Yuan H, Bauer CE. PixE promotes dark oligomerization of the BLUF photoreceptor PixD. Proc Natl Acad Sci U S A. 2008 Aug 19;105(33):11715-9. doi: 10.1073/pnas.0802149105. Epub 2008 Aug 11. PMID: 18695243; PMCID: PMC2575306.
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[3] Masuda S, Hasegawa K, Ishii A, Ono TA. Light-induced structural changes in a putative blue-light receptor with a novel FAD binding fold sensor of blue-light using FAD (BLUF); Slr1694 of synechocystis sp. PCC6803. Biochemistry. 2004 May 11;43(18):5304-13. d
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[4] Okajima K, Yoshihara S, Fukushima Y, Geng X, Katayama M, Higashi S, Watanabe M, Sato S, Tabata S, Shibata Y, Itoh S, Ikeuchi M. Biochemical and functional characterization of BLUF-type flavin-binding proteins of two species of cyanobacteria. J Biochem. 200
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[5] Sugimoto Y, Masuda S. In vivo localization and oligomerization of PixD and PixE for controlling phototaxis in the cyanobacterium Synechocystis sp. PCC 6803. J Gen Appl Microbiol. 2021 Jun 3;67(2):54-58. doi: 10.2323/jgam.2020.06.001. Epub 2020 Dec 21. PMID

Latest revision as of 16:48, 21 October 2021


HA-Trim21-PixE

This composite part is designed to generate GFP degradation with Part:BBa_K4016020 (GFPnano - Pix D) through Pix E-Pix D interaction, GFPnano’s targeting function and Trim21 based ubiquitin-proteasome degradation system.


Usage and Biology

Protein-protein interactions are powerful tools for manipulating biological processes, and opto-genetically - mediated induction of protein interactions has high spatial resolution without the need for exogenous cofactors. In this case, the dimer ”Pix D- Pix E” is introduced in our project in order to reach such function.

The two protein, Pix D and Pix E, can associate in the dark into large multi-subunit complexes that dissociate into dimers of Pix D and monomers of Pix E within seconds upon blue light stimulation. [1]~[5] Fusing Pix D/Pix E fragment to the Trim21 and its targeting module, we can realize the Trim21-induced degradation on it’s target protein in the dark, and the Pix D-Pix E dissociation on blue light can induced the dissociation of Trim21 and its targeting module, so as to stop the degradation.

In our project, our composite part BBa_K4016019 is interacting with Part:BBa_K4016020 (GFPnano - Pix D ), to specifically recognize and degrade GFP in the dark and stop the degradation in the light. If this can work, we can make an “OFF switch” in a system mediated by blue light.

Figure1. Schematic figure of BBa_K4016019 and BBa_K4016020

  • Here is the mechanism of the system:

In the dark environment:

1.HA-Trim21-PixE connect with PixD-GFPnano through PixE-PixD interaction and forms a complex

2.GFPnano specifically recognize eGFP

3.eGFP is degraded by ubiquitin-proteasome system recruited by Trim21

In the blue light:

1. PixD-PixE dissociate

2. The degradation of eGFP stop because of the lack of trim21.


Characterization

This part is validated through 3 ways: enzyme cutting, PCR and sequencing.

PCR

The PCR is performed with Green Taq Mix by Vazyme.

F-Prime: 5’-CTAGCGTTTAAACTTAAGCTTGCCACCATGGAGGTTCAACTGGAGGAGTCTG-3’

R-Prime: 5’- TGGATATCTGCAGAATTCTTACACGTTCACGCCGCCGTCGAT-3’

The PCR protocol is selected based on the Users Manuel. The Electrophoresis was performed on a 1% Agarose gel.


Enzyme Digestion

After the assembly the plasmid was transferred into the Competent E. coli DH5α). After culturing overnight in LB,we minipreped the plasmid for cutting. The cutting procedure was performed with Hind III EcoR I restriction endonuclease bought. The plasmid was cutted in a 20μL system at 37 ℃ for 2 hours. The Electrophoresis was performed on a 1％ Agarose glu.

Sequecing

The plasmid was sequenced correct.

Sequence and Features


Assembly Compatibility:
  • 10
    INCOMPATIBLE WITH RFC[10]
    Unknown
  • 12
    INCOMPATIBLE WITH RFC[12]
    Unknown
  • 21
    INCOMPATIBLE WITH RFC[21]
    Unknown
  • 23
    COMPATIBLE WITH RFC[23]
  • 25
    INCOMPATIBLE WITH RFC[25]
    Unknown
  • 1000
    INCOMPATIBLE WITH RFC[1000]
    Illegal BsaI site found at 1251




Result

Reference

[1] Dine E, Gil AA, Uribe G, Brangwynne CP, Toettcher JE. Protein Phase Separation Provides Long-Term Memory of Transient Spatial Stimuli. Cell Syst. 2018 Jun 27;6(6):655-663.e5. doi: 10.1016/j.cels.2018.05.002. Epub 2018 May 30. PMID: 29859829; PMCID: PMC6023

[2] Yuan H, Bauer CE. PixE promotes dark oligomerization of the BLUF photoreceptor PixD. Proc Natl Acad Sci U S A. 2008 Aug 19;105(33):11715-9. doi: 10.1073/pnas.0802149105. Epub 2008 Aug 11. PMID: 18695243; PMCID: PMC2575306.

[3] Masuda S, Hasegawa K, Ishii A, Ono TA. Light-induced structural changes in a putative blue-light receptor with a novel FAD binding fold sensor of blue-light using FAD (BLUF); Slr1694 of synechocystis sp. PCC6803. Biochemistry. 2004 May 11;43(18):5304-13. d

[4] Okajima K, Yoshihara S, Fukushima Y, Geng X, Katayama M, Higashi S, Watanabe M, Sato S, Tabata S, Shibata Y, Itoh S, Ikeuchi M. Biochemical and functional characterization of BLUF-type flavin-binding proteins of two species of cyanobacteria. J Biochem. 200

[5] Sugimoto Y, Masuda S. In vivo localization and oligomerization of PixD and PixE for controlling phototaxis in the cyanobacterium Synechocystis sp. PCC 6803. J Gen Appl Microbiol. 2021 Jun 3;67(2):54-58. doi: 10.2323/jgam.2020.06.001. Epub 2020 Dec 21. PMID