Difference between revisions of "Part:BBa K4960021"
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| − | '''Figure 1. AlphaFold2 prediction of protein structure and updated schematic diagram of design ideas.''' | + | '''Figure 1. AlphaFold2 prediction of protein structure and updated schematic diagram of design ideas.''' (a). AlphaFold2 prediction of Pdp1NTD-UCP1-EGFP protein structure. The unexpected interaction between SepC and UCP1 is labeled in a red box. (b). AlphaFold2 prediction of Pdp1NTD-EGFP -UCP1 protein structure. (c). Updated schematic diagram of design ideas. In the process of designing part, we switched the original sequence of EGFP and UCP1, and carried out the same experimental treatment as a new group of experimental groups, hoping to solve the problems encountered before.<br> |
| − | (a). AlphaFold2 prediction of Pdp1NTD-UCP1-EGFP protein structure. The unexpected interaction between SepC and UCP1 is labeled in a red box. | + | |
| − | (b). AlphaFold2 prediction of Pdp1NTD-EGFP -UCP1 protein structure. | + | |
| − | (c). Updated schematic diagram of design ideas. In the process of designing part, we switched the original sequence of EGFP and UCP1, and carried out the same experimental treatment as a new group of experimental groups, hoping to solve the problems encountered before.<br> | + | |
===Sequence and Feature=== | ===Sequence and Feature=== | ||
Revision as of 12:35, 12 October 2023
Engineered Mitochondrial Uncoupler Pdp1NTD-EGFP-UCP1
enable the PVC-mediated alteration of mammalian cell energy expenditure
Profile
Name: Engineered Mitochondrial Uncoupler Pdp1NTD-EGFP-UCP1
Base Pairs: 1917 bp
Origin: Photorhabdus, Aequorea Victoria, Homo Sapiens
Properties:enable the PVC-mediated alteration of mammalian cell energy expenditure
Usage and Biology
UCP1 is a key mitochondrial uncoupling protein in mammalian cells that regulates cellular energy expenditure and thermogenesis[1]. This part demonstrates a UCP1-based synthetic mitochondrial uncoupler that is compatable to the PVC delivery system (see the Description page of iGEM23_NUDT-CHINA wiki for more information about the PVC system). In mammalian cells, this part would be translocated into mitochondria and works as a proton transporter that disconnects oxygen consumption from ATP synthesis, thereby dissipates energy in the form of heat, leading to an increase in energy expenditure and basal metabolic rate.[2]
Special Design
This part includes a Pdp1NTD domain to ensure the compatability with the PVC delivery system, an EGFP domain for visualization and improving the protein production in E.coli, and a UCP1 mitochondrial uncoupling domain to enable the functionality. In BBa_K4960022 part, we have demonstrated that the Pdp1NTD-UCP1-EGFP configuration failed to effectively localize into mitochondria, possibly due to an unintended interaction between the Pdp1NTD domain and UCP1 (as highlighted in the red box in Figure 1a). To address this issue, we used AlphaFold2 to predict some of the possible structures and found that we could resolve this problem by swapping UCP1 and EGFP (as shown in Figure 1b). Consequently, we designed this part by connecting Pdp1NTD to the N-terminus EGFP and a UCP1 to the C-terminus (as depicted in Figure 1c).
Methods To validate the function of this part, we constructed pNC088, a CMV-driven plasmid expressing this part. We transfected HEK-293T cells with pNC088 and observed the cellular localization of the fusion protein 48 hours post-transcription by widefield fluorescent microscopy and live-cell confocal imaging. We also analyzed the glucose consumption of the transfected cells by measuring the glucose levels in the culture medium. This analysis represented the level of cellular energy expenditure. We compared the results with those of the control group cells transfected with pcDNA3.1(+) vector only. Results We have also tested the compatability of this part with the PVC system using the composite part BBa_K4960031. Please refer to the functional validation of BBa_K4960031 for experimental design and detailed results.
[1] Kolonin MG, Saha PK, Chan L, Pasqualini R, Arap W. Reversal of obesity by targeted ablation of adipose tissue. Nat Med. 2004 Jun;10(6):625-32.
Figure 1. AlphaFold2 prediction of protein structure and updated schematic diagram of design ideas. (a). AlphaFold2 prediction of Pdp1NTD-UCP1-EGFP protein structure. The unexpected interaction between SepC and UCP1 is labeled in a red box. (b). AlphaFold2 prediction of Pdp1NTD-EGFP -UCP1 protein structure. (c). Updated schematic diagram of design ideas. In the process of designing part, we switched the original sequence of EGFP and UCP1, and carried out the same experimental treatment as a new group of experimental groups, hoping to solve the problems encountered before.
Sequence and Feature
Functional test
The results of both wide-field fluorescent imaging (Figure 2a) and live-cell confocal imaging (Figure 2b) indicated highly specific colocalization of Pdp1NTD-EGFP-UCP1 signal with mitochondria markers (MTS-mcherry, Figure 2c). Furthermore, cells that were transfected with pNC088 demonstrated a significantly higher glucose consumption rate when compared to cells transfected with the pcDNA3.1(+) vector (Figure 2c). This suggests that the energy consumption in these cells was significantly improved.
(a). Localization Pdp1NTD-EGFP-UCP1 in HEK-293T cells. Cells were transfected with pNC088 (PCMV-Pdp1NTD-EGFP-UCP1).
(b). Cells were co-transfected with MTS-mcherry and PNC088. Photos were taken 48 h post transfection, scale bar: 100μm for wide-field microscopy and 10 μm for confocal microscopy. Data are representative images of 3 independent experiments.
(c). Charactrization of cellular metabolism in HEK-293T cells transfected with either pNC088 or pcDNA3.1(+). Glucose concentration in the cell culture medium was measured 48 h after transfection; data shows mean±SD, n=3 independent experiments.
Compatibility with the PVC system
References
[2]Kreitz J, Friedrich MJ, Guru A, Lash B, Saito M, Macrae RK, Zhang F. Programmable protein delivery with a bacterial contractile injection system. Nature. 2023 Apr;616(7956):357-364. doi: 10.1038/s41586-023-05870-7. Epub 2023 Mar 29.