Difference between revisions of "Part:BBa K4414034"
 
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<partinfo>BBa_K4414034 short</partinfo>
 
<partinfo>BBa_K4414034 short</partinfo>
  
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This composite part consists of an N-terminal tetR(BBa_K4414009) domain and a C-terminal NR3C1 LBD(BBa_K4414000) domain without GS linker. It is designed to sense glucocorticoids and activates the transcription of the reporter gene.
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This composite part consists of an N-terminal tetR([[Part:BBa_K4414009]]) domain and a C-terminal GR LBD([[Part:BBa_K4414000]]) domain without GS linker. It is designed to sense glucocorticoids and activates the transcription of the reporter gene.
  
  
 
==Usage and Biology==
 
==Usage and Biology==
  
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As a glucocorticoid sensor, this part is designed to enter the nucleus upon glucocorticoid stimulation and bind to the TCE promoter to activate downstream transcription. This part consists of a tetR DNA binding domain, which binds to the TCE promoter (BBa_K4016011) consisting of seven direct 19-bp tet operator sequence (tetO) repeats. The NR3C1 LBD domain on the C terminal is the ligand�binding domain of the glucocorticoid receptor(GR). This LBD domain can translocate the fusion protein into the nucleus upon glucocorticoid stimulation. It also has a transactivating domain 2 (τ2) and an activation function domain 2 (AF2) which activates downstream gene expression.[1]
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As a glucocorticoid sensor, this part is designed to enter the nucleus upon glucocorticoid stimulation and bind to the TCE promoter to activate downstream transcription. This part consists of a tetR DNA binding domain, which binds to the TCE promoter ([[Part:BBa_K4016011]]) consisting of seven direct 19-bp tet operator sequence (tetO) repeats. The GR LBD domain on the C terminal is the ligand binding domain of the glucocorticoid receptor(GR). This LBD domain can translocate the fusion protein into the nucleus upon glucocorticoid stimulation. It also has a transactivating domain 2 (τ2) and an activation function domain 2 (AF2) which activates downstream gene expression(Weikum et al., 2017).
  
 
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<figure class="figure">
 
<figure class="figure">
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<img src="https://static.igem.org/mediawiki/parts/1/17/T--NUDT_CHINA--Part_PixD-PixE_Schematic.png" class="figure-img img-fluid rounded"  height="250px">
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<img src="https://static.igem.wiki/teams/4414/wiki/34-1.png" class="figure-img img-fluid rounded"  height="350px">
  
 
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Figure1. Schematic figure of PixE-PixD interaction under blue light stimulation
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Figure1. Schematic figure of BBa_K4414034 and ([[Part:BBa_K4414041]])
  
  
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==Characterization==
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===Sequence and Features===
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This part was measured through 3 ways:PCR, enzyme digestion, sequencing.
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<partinfo>BBa_K4414034 SequenceAndFeatures</partinfo>
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===PCR===
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The PCR is performed with Green Taq.
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F-Prime：5’GGAGGATCTGGTGGTatgagcaattcagttttgtcc 3’
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R-Prime：5’TGGATATCTGCAGAATTCTTAtcaggagttggttttattggtg 3’
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The PCR protocol is selected based on the Users Manuel.  The Electrophoresis was performed on a 1％ Agarose glu.
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===Enzyme digestion test===
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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.
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The plasmid was cutted in a 20μL system at 37 ℃ for 2 hours. The Electrophoresis was performed on a 1％ Agarose gel.
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<span class='h3bb'>Sequence and Features</span>
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<partinfo>BBa_K4016000 SequenceAndFeatures</partinfo>
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<!-- Uncomment this to enable Functional Parameter display  
 
<!-- Uncomment this to enable Functional Parameter display  
 
===Functional Parameters===
 
===Functional Parameters===
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<partinfo>BBa_K4016000 parameters</partinfo>
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<partinfo>BBa_K4414034 parameters</partinfo>
 
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==Experimental Validation==
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==Functional Test==
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We constructed tetR-PixE PixD-Vp64 and TCE-SEAP to test the expression of this part.
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To test the ability of this part to respond to glucocorticoids, HEK-293T cells were co-transfected with plasmids encoding both BBa_K4414034 and TCE-SEAP([[Part:BBa_K4414041]]).
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VP64 is a transcriptional activator. When fused to another protein domain that can bind near the promoter of a gene, VP64 acts as a strong transcriptional activator.
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TetR can recognize and combine with TCE then inhibit its downstream transcription. The interaction of PixD and PixE would restrain the TCE’s inhibition and start the transcription of SEAP.
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===Method===
 
===Method===
 
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Cells were treated with 100 nM Glucocorticoids 6 h post-transfection. Cells without glucocorticoid treatment were used as control. Culture medium was collected at 24 h post glucocorticoids treatment. SEAP activity was measured according to a published protocol (Shao, Qiu, & Xie, 2021).
  
 
<figure class="figure">
 
<figure class="figure">
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<img src="https://static.igem.org/mediawiki/parts/6/65/T--NUDT_CHINA--Part_Validation_SEAP_PixE-PixD.png
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<img src="https://static.igem.wiki/teams/4414/wiki/34-2.png
 
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1. Cell transfection and stimulation:
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Figure2.Schematic representation of the experimental process of validation for BBa_K4414034 and ([[Part:BBa_K4414041]]).
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(a) Seed approximately 5×104 cells into 24-well cell culture plates.
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(b) Culture for 16 h before transfection.
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(c) Total plasmid mixes of 500 ng per well are mixed thoroughly in serum-free DMEM before a polyethylenimine (PEI) solution (1 mg/mL) is added into the plasmid mixture in a ratio of 1:3 (plasmid weight/PEI weight).
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(d) The plasmid–PEI mixture is vortexed and incubated at room temperature for 15 min. The mixture is then added into the cells and incubated for at least 6 h.
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(e) Cells are then changed into fresh medium and applied with 5mA blue light(dark/blue 2/28S) for before sampling and analysis assay.
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2. SEAP assay in vitro.
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(a) Sample 200μL culture medium from each well, heat inactivate at 65℃ for 30 min.
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(b) During the heat inactivation procedure, warm up 2×SEAP buffer (100μL/well) at 37℃.
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(c) Add 1/5 buffer volume of pNPP (20μL/well) substrate into the 2×buffer to prepare the “Detection Mixture.”
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(d) Add 80μL heated medium into the 96-well plate, add 120μL Detection Mixture.
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(e) Measure absorption at 405 nm, 30 s per read for 10 reads.
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(f) Calculate enzymatic activity.
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===Result===
 
===Result===
 
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Results showed similar increased SEAP expression in glucocorticoid-treated cells compared to the non-treated control (1.29 folds)(Figure 3).
 
<figure class="figure">
 
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<img src="https://2021.igem.org/wiki/images/d/d6/T--NUDT_CHINA--Part_Result_00-01_.png
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<img src="https://static.igem.wiki/teams/4414/wiki/34-3.png
 
" class="figure-img img-fluid rounded"  height="350px">
 
" class="figure-img img-fluid rounded"  height="350px">
  
 
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Figure3. Glucocorticoid-stimulated transcriptional activation of SEAP mediated by BBa_K4414034.
 
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Figure 2 Result of SEAP test. The SEAP activity was calculated at 24h and 48h after transfection.
 
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The cells showed a nearly 40% decrease in SEAP activity after 24h blue light exposure, compared with the group exposed to dark. And after 48h, the SEAP activity in blue light group was reduce to 0. This can validate PixD and PixE’s interaction.
 
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===Reference===
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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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1. Weikum, E. R., Knuesel, M. T., Ortlund, E. A., & Yamamoto, K. R. (2017). Glucocorticoid receptor control of transcription: precision and plasticity via allostery. Nat Rev Mol Cell Biol, 18(3), 159-174. doi:10.1038/nrm.2016.152
  
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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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2. Shao, J., Qiu, X., & Xie, M. (2021). Engineering Mammalian Cells to Control Glucose Homeostasis. Methods Mol Biol, 2312, 35-57. doi:10.1007/978-1-0716-1441-9_3

Latest revision as of 09:13, 13 October 2022


TetR-LBD

This composite part consists of an N-terminal tetR(Part:BBa_K4414009) domain and a C-terminal GR LBD(Part:BBa_K4414000) domain without GS linker. It is designed to sense glucocorticoids and activates the transcription of the reporter gene.


Usage and Biology

As a glucocorticoid sensor, this part is designed to enter the nucleus upon glucocorticoid stimulation and bind to the TCE promoter to activate downstream transcription. This part consists of a tetR DNA binding domain, which binds to the TCE promoter (Part:BBa_K4016011) consisting of seven direct 19-bp tet operator sequence (tetO) repeats. The GR LBD domain on the C terminal is the ligand binding domain of the glucocorticoid receptor(GR). This LBD domain can translocate the fusion protein into the nucleus upon glucocorticoid stimulation. It also has a transactivating domain 2 (τ2) and an activation function domain 2 (AF2) which activates downstream gene expression(Weikum et al., 2017).

Figure1. Schematic figure of BBa_K4414034 and (Part:BBa_K4414041)


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
    COMPATIBLE WITH RFC[25]
  • 1000
    COMPATIBLE WITH RFC[1000]



Functional Test

To test the ability of this part to respond to glucocorticoids, HEK-293T cells were co-transfected with plasmids encoding both BBa_K4414034 and TCE-SEAP(Part:BBa_K4414041).

Method

Cells were treated with 100 nM Glucocorticoids 6 h post-transfection. Cells without glucocorticoid treatment were used as control. Culture medium was collected at 24 h post glucocorticoids treatment. SEAP activity was measured according to a published protocol (Shao, Qiu, & Xie, 2021).

Figure2.Schematic representation of the experimental process of validation for BBa_K4414034 and (Part:BBa_K4414041).

Result

Results showed similar increased SEAP expression in glucocorticoid-treated cells compared to the non-treated control (1.29 folds)(Figure 3).

Figure3. Glucocorticoid-stimulated transcriptional activation of SEAP mediated by BBa_K4414034.


Reference

1. Weikum, E. R., Knuesel, M. T., Ortlund, E. A., & Yamamoto, K. R. (2017). Glucocorticoid receptor control of transcription: precision and plasticity via allostery. Nat Rev Mol Cell Biol, 18(3), 159-174. doi:10.1038/nrm.2016.152

2. Shao, J., Qiu, X., & Xie, M. (2021). Engineering Mammalian Cells to Control Glucose Homeostasis. Methods Mol Biol, 2312, 35-57. doi:10.1007/978-1-0716-1441-9_3