Difference between revisions of "Part:BBa K5267041"

(→‎Usage and Biology)
 
(11 intermediate revisions by 2 users not shown)
Line 11: Line 11:
 
<br>Base Pairs: 1082bp  
 
<br>Base Pairs: 1082bp  
 
<br>Origin: Homo sapiens  
 
<br>Origin: Homo sapiens  
−
<br>Properties:As a reporter to show whether melatonin is accepted or not
+
<br>Properties:Enables sensing and characterizing the status (such as activation/inhibition) of the cAMP/PKA/CREB pathway
 
==Usage and Biology==
 
==Usage and Biology==
 
<p>'''G-protein-coupled receptors (GPCRs) '''represent the largest and most diverse group of membrane receptors in eukaryotes. G proteins are specialized proteins that can bind the nucleotides guanosine triphosphate (GTP) and guanosine diphosphate (GDP). When a ligand binds to a GPCR, it induces a conformational change in the receptor, which subsequently activates the associated G protein. The active form of the G protein is released from the receptor and dissociates into its subunits. These subunits then activate specific effectors, leading to the release of second messengers that are recognized by protein kinases, triggering a signaling cascade that results in various cellular events.[1] </p>
 
<p>'''G-protein-coupled receptors (GPCRs) '''represent the largest and most diverse group of membrane receptors in eukaryotes. G proteins are specialized proteins that can bind the nucleotides guanosine triphosphate (GTP) and guanosine diphosphate (GDP). When a ligand binds to a GPCR, it induces a conformational change in the receptor, which subsequently activates the associated G protein. The active form of the G protein is released from the receptor and dissociates into its subunits. These subunits then activate specific effectors, leading to the release of second messengers that are recognized by protein kinases, triggering a signaling cascade that results in various cellular events.[1] </p>
Line 18: Line 18:
 
<p>To achieve the function described above, we present this composite that can directly sense and accurately characterize the status of the cAMP/PKA/CREB pathway in mammalian cells.</p>
 
<p>To achieve the function described above, we present this composite that can directly sense and accurately characterize the status of the cAMP/PKA/CREB pathway in mammalian cells.</p>
 
<p>'''This composite part consisting of:'''</p>
 
<p>'''This composite part consisting of:'''</p>
−
<p>1. P_5xCRE (Part: BBa_K5267005): A synthetic promoter that assess the activation status of the cAMP/PKA/CREB signaling pathways, with 5 tandem repeats of CRE serving as a binding site for phosphorylated CREB.</p>
+
<p>'''1. P_5xCRE ([https://parts.igem.org/Part:BBa_K5267005 Part:BBa K5267005])''': A synthetic promoter that assess the activation status of the cAMP/PKA/CREB signaling pathways, with 5 tandem repeats of CRE serving as a binding site for phosphorylated CREB.</p>
−
<p>2. IgK (Part: BBa_K3117006): A signal sequence directing the protein into the secretory pathway.</p>
+
<p>'''2. IgK ([https://parts.igem.org/Part: BBa_K3117006])''': A signal sequence directing the protein into the secretory pathway.</p>
−
<p>3. Nluc (Part: BBa_K2728003): An engineered luminescent reporter that detects cAMP concentration. When expressed, it results in blue fluorescence, indicating the activation status of the cAMP/PKA/CREB pathway.</p>
+
<p>'''3. Nluc ([https://parts.igem.org/Part: BBa_K2728003])''': An engineered luminescent reporter that detects cAMP concentration. When expressed, it results in blue fluorescence, indicating the activation status of the cAMP/PKA/CREB pathway.</p>
−
<p>4. bGH_polyA (Part: BBa_K1313006): Functions as a terminator, ensuring proper cessation of gene expression.</p>
+
<p>'''4. bGH_polyA ([https://parts.igem.org/Part: BBa_K1313006])''': Functions as a terminator, ensuring proper cessation of gene expression.</p>
−
<p>By incorporating this composite part into mammalian cell chassis, such as the HEK293 cell line, we can build a cAMP/PKA/CREB pathway characterization platform that effectively senses and monitors the activation of the pathway, providing detectable reporter signals. This synthetic gene circuit can be a valuable tool for studying signaling pathways and can be applied in various biotechnological and therapeutic research areas.</p>
+
 
<html>
 
<html>
 
<figure class="figure">
 
<figure class="figure">
 
<div style="width=100%; height=auto; text-align: center">
 
<div style="width=100%; height=auto; text-align: center">
−
<img src="https://static.igem.wiki/teams/5267/mao-parts/pathway1.png"  height="100px">
+
<img src="https://static.igem.wiki/teams/5267/i-m-zhangrenjie/017.png"  height="100px">
 
</div>
 
</div>
 
</figure>
 
</figure>
Line 33: Line 32:
  
 
==Special design==
 
==Special design==
−
This basic part is an important element for testing whether the downstream pathway of melatonin responds successfully. At present, the commonly used method to study the signaling pathway is to clone the response element of the transcription factor corresponding to the signaling pathway into the luciferase reporter gene vector, that is, pCRE-luc .[3] However, the expression effect of a single responder is weak，so multiple tandem repeats of the same responder element are usually inserted upstream of the reporter gene (the 5 '-UTR region) to enhance the activation of the signaling pathway. By searching through literature, we constructed the 4xCRE-Pmin sequence，It contains a 5′ minimal promoter incorporating 4 multimerized palin-dromic CREs with the sequence 5′-AGCC[TGACGTCC]GAG-3′. (CRE denoted in brackets)，with the exception of a single nucleotide substitution (C for A) within the CRE[4]，which may strengthen gene expression downstream.  
+
The composite part P_5xCRE->IgK->Nluc->bGH_polyA ([https://parts.igem.org/Part:BBa_K5267041 Part:BBa K5267041]) is essential for evaluating the responsiveness of the melatonin signaling pathway. Standard approaches for studying signaling pathways typically involve cloning the response element of the relevant transcription factor into a luciferase reporter gene vector, such as pCRE-luc.[3] Due to the limited transcriptional impact of a single response element, we incorporated multiple tandem copies of the element near the reporter gene's genomic location. This amplification enhanced the initiation efficacy of the signaling cascade. Therefore, we constructed the P<sub>min</sub>_5xCRE sequence, which includes a 5′ minimal promoter incorporating 5 tandem repeats of CREs.[4] (Figure 2)
−
+
<html>
 +
<figure class="figure">
 +
<div style="width=100%; height=auto; text-align: center">
 +
<img src="https://static.igem.wiki/teams/5267/mao-parts/gaoqing.png"  height="300px">
 +
</div>
 +
</figure>
 +
</html>
 +
'''Figure 2. Schematic of cAMP-CREB Signaling Transduction. When melatonin binds to the MT1, it activates adenylate cyclase (AC), which in turn regulates the level of the second messenger cAMP. The increase in cAMP activates protein kinase A (PKA), which amplifies the signal. PKA then catalyzes the phosphorylation of CREB in the nucleus, thereby binding to the P_4xCRE/P_5xCRE/P_6xCRE and initiate the transcription of Nluc '''
 +
 
 
==Function Test==
 
==Function Test==
 
===Method===
 
===Method===
−
In order to validate the composite part P_5*CRE->IgK->Nluc->bGH_polyA([https://parts.igem.org/Part:BBa_K5267041 Part:BBa_K5267041]), which can express receptor in mammalian cells, we designed a controlled cell experiment, according to the natural gene pathway in human SCN cells that the activated MTNR1a receptors could activate several gene pathways which all lead to the activation of CREB (cAMP response element binding protein)[5], activating the expression of gene with CRE (cAMP response element) promotors.
+
<p>Forskolin, a known activator of adenylate cyclase (AC), is used to stimulate the cAMP signaling pathway2. We used forskolin as a stimulant and constructed plasmids carrying the reporter gene NanoLuc and different CRE copies (4×CRE, 5×CRE, and 6×CRE; BBa_K5267040, BBa_K5267041, BBa_K5267042), such as our composite part 5xCRE_Pmin-IgK->Nluc->bGH_polyA ([https://parts.igem.org/Part:BBa_K5267041 Part:BBa K5267041]). These plasmids were co-transfected with PCMV->MTNR1A->bGH_polyA ([https://parts.igem.org/Part:BBa_K5267047 Part:BBa K5267047]) into HEK293T cells. The cells were then stimulated with forskolin to determine whether forskolin-induced activation of the cAMP/PKA/CREB signaling pathway can be sensed and characterized by our composite part P_5xCRE -> IgK -> Nluc -> bGH_polyA.</p>
−
We prepared two dishes of HEK-293T cell lines, each with the same passage number, identical viability, and a cell count of 500,000. One dish served as the experimental group, and the other as the control group. The experimental group was co-transfected with pLeo694 plasmids, one carrying the construct PCMV -> MTNR1a -> bGH polyA([https://parts.igem.org/Part:BBa_K5267047 Part:BBa_K5267047]) and the other carrying the construct P_5xCRE-> lgK -> Nluc -> bGH polyA([https://parts.igem.org/Part:BBa_K5267041 Part:BBa_K5267041]), in a 100 ng to 50 ng ratio (the optimal transfection ratio validated by experiments). The control group was transfected only with 50 ng of the plasmid carrying the P_5xCRE-> lgK -> Nluc -> bGH polyA ([https://parts.igem.org/Part:BBa_K5267041 Part:BBa_K5267041])construct. After transfection, both groups of cells were stimulated with 1 nM melatonin, and samples were collected at 24 and 48 hours to detect Nluc expression.
+
<p>To further validate and evaluate the function of the composite part P_5xCRE -> IgK -> Nluc -> bGH polyA ([https://parts.igem.org/Part:BBa_K5267041 Part:BBa K5267041]), we co-transfected it with MTNR1A ([https://parts.igem.org/Part:BBa_K5267001 Part:BBa K5267001]) into HEK-293T cell lines. This setup aims to mimic the melatonin receptor-mediated cAMP/PKA/CREB signaling transduction pathway. The melatonin-activated MTNR1A receptors should activate CREB, thereby binding to the 5xCREs and initiating NanoLuc expression from the composite part.</p>
 +
<p>Theoretically, upon stimulation with forskolin or melatonin, the cAMP/PKA/CREB signaling pathway is triggered, ultimately leading to the phosphorylation of the endogenous transcription factor CREB and activation of the PCre, thereby regulating the expression of downstream genes.</p>
  
 
===Result===
 
===Result===
Line 44: Line 52:
 
<figure class="figure">
 
<figure class="figure">
 
<div style="width=100%; height=auto; text-align: center">
 
<div style="width=100%; height=auto; text-align: center">
−
<img src="https://static.igem.wiki/teams/5267/mao-parts/huge4xcre-f3.png"  height="300px">
+
<img src="https://static.igem.wiki/teams/5267/mao-parts/4xcre.jpg"  height="200px">
 
</div>
 
</div>
 
</figure>
 
</figure>
 
</html>
 
</html>
−
'''Figure 2. CREB activation in response to cAMP signaling. (a) Schematic diagram of MT1 receptor activating the downstream cAMP pathway. (b) Melatonin stimulation applied to HEK-293T cells co-transfected with pCJ008(PCMV-MTNR1A) and pNC005(P_4xCRE-IgK-Nluc), pNC016(P_5xCRE-IgK-Nluc), pNC017(P_6xCRE-IgK-Nluc) respectively. Data are mean±SD of NanoLuc expression levels measured 24 h after melatonin stimulation (n = 3 independent experiments). (c) HEK-293T cells were co-transfected with pCJ008(PCMV-MTNR1A) and pNC005(P_4xCRE-IgK-Nluc) under various transfection ratio(100:25/100:50/100:100/100:200). Data are mean±SD of NanoLuc expression levels measured at 24 h after melatonin stimulation (n = 3 independent experiments). (d) Stable HEK-293T cells co-transfected with pCJ008(PCMV-MTNR1A) and pNC005(P_4xCRE-IgK-Nluc) stimulated with various  concentrations of melatonin(0.1nM /0.5nM /0.7nM /1nM /10nM /30nM) . Data are mean±SD of NanoLuc expression levels measured at different time points '''
+
'''Figure 3. The expression of NanoLuc in cAMP/PKA/CREB pathway-responsive cell platform stimulated by forskolin. '''<>
 +
<p>We measured the expression of NanoLuc in both forskolin-treated and untreated groups 48 hours post-stimulation. The results confirmed that the cAMP/PKA/CREB signaling pathway was activated by forskolin as expected. Platforms with different tandem repeats of CRE exhibited varying fold changes in NanoLuc expression. Notably, cells transfected with P_4xCRE -> IgK -> Nluc -> bGH polyA (Part: BBa_K5267040) showed the highest fold change (~8.62 fold) compared to the control. These results demonstrate the correct responsiveness of the cAMP signaling pathway '''(Figure 3)'''.</p>
 +
<html>
 +
<figure class="figure">
 +
<div style="width=100%; height=auto; text-align: center">
 +
<img src="https://static.igem.wiki/teams/5267/mao-parts/dantu.png"  height="200px">
 +
</div>
 +
</figure>
 +
</html>
 +
<p>'''Figure 4. Characterization of composite part P_5xCRE->IgK->Nluc->bGH_polyA. ''' Co-expression of MTNR1A and PCRE-promoter variants enables robust transcriptional activation upon melatonin stimulation. Melatonin stimulation was added to HEK-293T cells co-transfected with PCMV-MTNR1A and P_4xCRE-IgK-Nluc, P_5xCRE-IgK-Nluc, P_6xCRE-IgK-Nluc respectively.</p>
 +
 
 +
<p>Moreover, we utilized melatonin receptor-mediated activation of the cAMP/PKA/CREB pathway as a strategy to test the functionalities of the composite part P_5xCRE -> IgK -> Nluc -> bGH polyA. The results showed a significant increase in NanoLuc expression in the melatonin-stimulated group compared to the unstimulated group '''(Figure 4)''', indicating that the composite part can correctly respond to melatonin stimulation as expected. </p>
 +
 
  
 
==reference==
 
==reference==

Latest revision as of 13:31, 2 October 2024

P_5xCRE>IgK->Nluc->bGH_polyA

When melatonin binds to the MT1 receptor, the activation of adenylate cyclase (AC) is activated, regulating the level of the second messenger cAMP, while activating protein kinase to further amplify the signal. It catalyzes the phosphorylation of CREB in the nucleus and regulates the expression of downstream genes.

Sequence and Features


Assembly Compatibility:
  • 10
    COMPATIBLE WITH RFC[10]
  • 12
    COMPATIBLE WITH RFC[12]
  • 21
    INCOMPATIBLE WITH RFC[21]
    Illegal BglII site found at 103
  • 23
    COMPATIBLE WITH RFC[23]
  • 25
    INCOMPATIBLE WITH RFC[25]
    Illegal NgoMIV site found at 376
  • 1000
    COMPATIBLE WITH RFC[1000]

Profile

Name:P_5xCRE->IgK->Nluc->bGH_polyA
Base Pairs: 1082bp
Origin: Homo sapiens
Properties:Enables sensing and characterizing the status (such as activation/inhibition) of the cAMP/PKA/CREB pathway

Usage and Biology

G-protein-coupled receptors (GPCRs) represent the largest and most diverse group of membrane receptors in eukaryotes. G proteins are specialized proteins that can bind the nucleotides guanosine triphosphate (GTP) and guanosine diphosphate (GDP). When a ligand binds to a GPCR, it induces a conformational change in the receptor, which subsequently activates the associated G protein. The active form of the G protein is released from the receptor and dissociates into its subunits. These subunits then activate specific effectors, leading to the release of second messengers that are recognized by protein kinases, triggering a signaling cascade that results in various cellular events.[1]

Cyclic adenosine monophosphate (cAMP) serves as a pivotal second messenger that transduces extracellular signals to intracellular effectors by modulating its concentration within the cell. Upon ligand binding to GPCRs, adenylate cyclase is activated via the Gα subunit, resulting in elevated levels of intracellular cAMP. Subsequently, cAMP interacts with the regulatory subunits of protein kinase A (PKA), leading to the dissociation of its catalytic subunits. The liberated catalytic subunits of PKA translocate to the nucleus, where they phosphorylate the transcription factor cAMP response element-binding protein (CREB). Phosphorylated CREB then binds to the coactivator CREB-binding protein (CBP), forming a complex that recognizes and binds to the cAMP response element (CRE) within the regulatory regions of target genes, thereby initiating transcriptional activation. [2]

This cAMP/PKA/CREB pathway is a well-established and common signaling pathway in mammalian cells, regulated by various importance upstream pathways such as GPCRs we describe above. Therefore, in the view of mammalian cell synthetic biology, a synthetic gene circuit that enables sensing and characterizing the status (such as activation/inhibition) of the cAMP/PKA/CREB pathway can be very useful that only provide valuable insights into their functionality and but also offer toolkits for potential biotechnological applications..

To achieve the function described above, we present this composite that can directly sense and accurately characterize the status of the cAMP/PKA/CREB pathway in mammalian cells.

This composite part consisting of:

1. P_5xCRE (Part:BBa K5267005): A synthetic promoter that assess the activation status of the cAMP/PKA/CREB signaling pathways, with 5 tandem repeats of CRE serving as a binding site for phosphorylated CREB.

2. IgK (BBa_K3117006): A signal sequence directing the protein into the secretory pathway.

3. Nluc (BBa_K2728003): An engineered luminescent reporter that detects cAMP concentration. When expressed, it results in blue fluorescence, indicating the activation status of the cAMP/PKA/CREB pathway.

4. bGH_polyA (BBa_K1313006): Functions as a terminator, ensuring proper cessation of gene expression.

Figure 1 Concrete schematic diagram of BBa_K5267041 composite part

Special design

The composite part P_5xCRE->IgK->Nluc->bGH_polyA (Part:BBa K5267041) is essential for evaluating the responsiveness of the melatonin signaling pathway. Standard approaches for studying signaling pathways typically involve cloning the response element of the relevant transcription factor into a luciferase reporter gene vector, such as pCRE-luc.[3] Due to the limited transcriptional impact of a single response element, we incorporated multiple tandem copies of the element near the reporter gene's genomic location. This amplification enhanced the initiation efficacy of the signaling cascade. Therefore, we constructed the Pmin_5xCRE sequence, which includes a 5′ minimal promoter incorporating 5 tandem repeats of CREs.[4] (Figure 2)

Figure 2. Schematic of cAMP-CREB Signaling Transduction. When melatonin binds to the MT1, it activates adenylate cyclase (AC), which in turn regulates the level of the second messenger cAMP. The increase in cAMP activates protein kinase A (PKA), which amplifies the signal. PKA then catalyzes the phosphorylation of CREB in the nucleus, thereby binding to the P_4xCRE/P_5xCRE/P_6xCRE and initiate the transcription of Nluc

Function Test

Method

Forskolin, a known activator of adenylate cyclase (AC), is used to stimulate the cAMP signaling pathway2. We used forskolin as a stimulant and constructed plasmids carrying the reporter gene NanoLuc and different CRE copies (4×CRE, 5×CRE, and 6×CRE; BBa_K5267040, BBa_K5267041, BBa_K5267042), such as our composite part 5xCRE_Pmin-IgK->Nluc->bGH_polyA (Part:BBa K5267041). These plasmids were co-transfected with PCMV->MTNR1A->bGH_polyA (Part:BBa K5267047) into HEK293T cells. The cells were then stimulated with forskolin to determine whether forskolin-induced activation of the cAMP/PKA/CREB signaling pathway can be sensed and characterized by our composite part P_5xCRE -> IgK -> Nluc -> bGH_polyA.

To further validate and evaluate the function of the composite part P_5xCRE -> IgK -> Nluc -> bGH polyA (Part:BBa K5267041), we co-transfected it with MTNR1A (Part:BBa K5267001) into HEK-293T cell lines. This setup aims to mimic the melatonin receptor-mediated cAMP/PKA/CREB signaling transduction pathway. The melatonin-activated MTNR1A receptors should activate CREB, thereby binding to the 5xCREs and initiating NanoLuc expression from the composite part.

Theoretically, upon stimulation with forskolin or melatonin, the cAMP/PKA/CREB signaling pathway is triggered, ultimately leading to the phosphorylation of the endogenous transcription factor CREB and activation of the PCre, thereby regulating the expression of downstream genes.

Result

Figure 3. The expression of NanoLuc in cAMP/PKA/CREB pathway-responsive cell platform stimulated by forskolin. <>

We measured the expression of NanoLuc in both forskolin-treated and untreated groups 48 hours post-stimulation. The results confirmed that the cAMP/PKA/CREB signaling pathway was activated by forskolin as expected. Platforms with different tandem repeats of CRE exhibited varying fold changes in NanoLuc expression. Notably, cells transfected with P_4xCRE -> IgK -> Nluc -> bGH polyA (Part: BBa_K5267040) showed the highest fold change (~8.62 fold) compared to the control. These results demonstrate the correct responsiveness of the cAMP signaling pathway (Figure 3).

Figure 4. Characterization of composite part P_5xCRE->IgK->Nluc->bGH_polyA. Co-expression of MTNR1A and PCRE-promoter variants enables robust transcriptional activation upon melatonin stimulation. Melatonin stimulation was added to HEK-293T cells co-transfected with PCMV-MTNR1A and P_4xCRE-IgK-Nluc, P_5xCRE-IgK-Nluc, P_6xCRE-IgK-Nluc respectively.

Moreover, we utilized melatonin receptor-mediated activation of the cAMP/PKA/CREB pathway as a strategy to test the functionalities of the composite part P_5xCRE -> IgK -> Nluc -> bGH polyA. The results showed a significant increase in NanoLuc expression in the melatonin-stimulated group compared to the unstimulated group (Figure 4), indicating that the composite part can correctly respond to melatonin stimulation as expected.


reference

[1] Q. Wang et al., "Structural basis of the ligand binding and signaling mechanism of melatonin receptors," Nat Commun, vol. 13, no. 1, p. 454, Jan 24 2022, doi: 10.1038/s41467-022-28111-3.

[2] A. J. Shaywitz and M. E. Greenberg, "CREB: a stimulus-induced transcription factor activated by a diverse array of extracellular signals," Annu Rev Biochem, vol. 68, pp. 821-61, 1999, doi: 10.1146/annurev.biochem.68.1.821.

[3] C. Kemmer, D. A. Fluri, U. Witschi, A. Passeraub, A. Gutzwiller, and M. Fussenegger, "A designer network coordinating bovine artificial insemination by ovulation-triggered release of implanted sperms," J Control Release, vol. 150, no. 1, pp. 23-9, Feb 28 2011, doi: 10.1016/j.jconrel.2010.11.016.

[4] O. G. Chepurny and G. G. Holz, "A novel cyclic adenosine monophosphate responsive luciferase reporter incorporating a nonpalindromic cyclic adenosine monophosphate response element provides optimal performance for use in G protein coupled receptor drug discovery efforts," J Biomol Screen, vol. 12, no. 5, pp. 740-6, Aug 2007, doi: 10.1177/1087057107301856.

[5] H. H. Okamoto, E. Cecon, O. Nureki, S. Rivara, and R. Jockers, "Melatonin receptor structure and signaling," J Pineal Res, vol. 76, no. 3, p. e12952, Apr 2024, doi: 10.1111/jpi.12952.