Part:BBa_K4016020

GFPnano-PixD

This composite part is designed to generate GFP degradation with Part:BBa_K4016019 (HA-Trim21-PixE) through Pix E-Pix D interaction, GFPnano’s targeting function and Trim21 based ubiquitin-proteasome degradation system.

Usage and Biology

The antibody GFP-nano is designed to bind with both Trim21 and the antigen GFP to prove that the system really works. In the design we link GFP-nano with hIgG1-Fc, so that it can work as the bridge between target GFP and Trim21

Pix D and Pix E, can associate in the dark and dissociate on blue light stimulation. 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. [1]~[5]

This composite part is designed to interact with BBa_K4016019 (HA-Trim21-PixE), to test the if the Pix D/Pix E’s dissociation in light can inhabit the degradation rate of GFP by Trim21, in order to design an “OFF switch” in our project.

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 was validated through 3 ways:PCR, enzyme digestion and sequencing.

PCR

The PCR is performed with Green Taq Mix by Vazyme.

F-Prime：5’CTAGCGTTTAAACTTAAGCTTGCCACCATGgagtctgggggag 3’

R-Prime：5’TGGATATCTGCAGAATTCTTAttagaggtcgaggaaaaagttatc 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
  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 NgoMIV site found at 486
  
• 1000
  INCOMPATIBLE WITH RFC[1000]

  Illegal BsaI site found at 35
  

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