Team:HKUST/Composite Parts
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Composite Parts | ShellBi
TCS Basal
TCS Basal Antisense
Engineered EnvZ&OmpR
eGFP antisense_PompF
mRFP1 antisense_PompC
TCS Scaffold
Scaffold gene kit
ShellBi
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Composite Parts
Detailed Explanations of Our Parts
BBa_K4061070- TCS basal
Parts - BBa_K4061070
Two Component System basal sequence or TCS basal for short, consists of 2 different promoters attached to 2 different reporter genes. Originally, the two component system is a system found in E.coli that responds to differences in osmolarity conditions inside the cell. PompC responds to a high intracellular osmolarity, while PompF responds to a low intracellular osmolarity. We attach an eGFP reporter gene to the OmpC promoter and mRFP1 reporter gene to the OmpF promoter. This system suits the purpose of our project since our biosensor detects toxins that block the porin protein of the cells which in turn cause a difference in intracellular osmolarities.
BBa_K4061075- TCS basal_antisenses
Parts - BBa_K4061075
Our project this year is aiming to make a prokaryotic biosensor that detects paralytic shellfish toxins which directly affect the intracellular cell osmolarity. Thus, we need a distinct readout of the different fluorescent proteins to account for a trustworthy biosensor. Furthermore, the OmpC promoter is a leaky promoter resulting in an unwanted green fluorescence expression. To make the biosensor more sensitive, we decided to incorporate an antisense strand that can reduce the expression of the opposite color at a transcriptional level.
We put eGFP antisense under an OmpF promoter such that at low concentration, the expression of eGFP will be repressed. On the other hand, we also attach an mRFP1 antisense under an OmpC promoter so that at high concentration, the mRFP1 expression will be suppressed.
BBa_K4061080- Engineered EnvZ and OmpR*
Parts - BBa_K4061080
EnvZ and OmpR are the heart of the two component systems. The EnvZ is a histidine kinase that will phosphorylate OmpR such that it can act as a transcription factor for the OmpF and OmpC genes. The EnvZ is engineered with an SH3 ligand and SH3 domain. While the OmpR is engineered with a leucine zipper. Under low osmolarity, the EnvZ’s SH3 domain will bind to the SH3 ligand thus inhibiting its own kinase activity.
The engineered EnvZ and OmpR need to be complemented with the scaffold to cater for their interactions. We employ the scaffold system in our project to increase the interaction of EnvZ and OmpR that will increase the rate of OmpR phosphorylation by EnvZ. Eventually, our biosensor will have a more rapid response to the intracellular osmolarity.
BBa_K4061090- Characterisation construct for eGFP antisense_PompF
Parts - BBa_K4061090
As aforementioned, we added the antisense system to our circuit in order to have a more specific reading for our biosensor. To test whether or not the antisense is reducing the expression of the opposite color significantly, we designed a constitutively expressed eGFP and antisense eGFP under the OmpF promoter. We also cloned the constitutively expressed eGFP as the reference for this experiment. Besides determining the significance of the antisense fragment, this assay can also tell us about the activity of the OmpF promoter. Since it is activated under low osmolarity conditions, we should expect a greater eGFP repression. Refer to our Experiments page for more details.
Experiments page
BBa_K4061095- Characterisation construct for mRFP1 antisense_PompC
Parts - BBa_K4061095
We designed an mRFP1 antisense with the same rationale as designing the eGFP antisense. That is, to reduce the mRFP1 expression under high intracellular osmolarity. To test the significance of the mRFP1 antisense and the OmpC promoter in which the antisense is controlled, we designed a circuit comprising a constitutively expressed mRFP1 and the mRFP1 antisense under the OmpC promoter. Since the OmpC promoter is active under a high intracellular osmolarity, we should witness a stronger mRFP1 repression under high osmolarity due to the higher expression of the antisense strand. Refer to our Experiments page for more details.
Experiments page
BBa_K4061100- TCS Scaffold*
Parts - BBa_K4061100
TCS scaffold is an expansion of the TCS basal. The TCS scaffold is basically a TCS basal with a scaffold sequence coded under the OmpC promoter. This scaffold is an integral component to the engineered EnvZ and engineered OmpR.
As aforementioned, in high intracellular osmolarity conditions, the OmpC gene will be expressed. Since we attach a scaffold sequence under OmpC, the scaffold will be expressed when the intracellular osmolarity is high. When the scaffold is present inside the cell, the leucine zipper adapter of the scaffold will bind to the engineered OmpR. Subsequently, the SH3 ligand on the scaffold will bind to the SH3 domain on the EnvZ, replacing the SH3 ligand of EnvZ due to a higher binding affinity.
All in all, the presence of the scaffold, engineered EnvZ, and engineered OmpR contribute to increase the sensitivity of our biosensor such that it performs more rapidly with a higher sensitivity.
BBa_K4061200- Scaffold gene kit*
Parts - BBa_K4061200
This is a device prepared for future teams that seek to enhance protein-protein interactions. In this device, we have compiled parts for the modular domains- SH3 binding domain and the Leucine Zipper domain. Teams must use these modular protein sequences along with their protein CDS (without stop codon) and express these two interacting engineered proteins under a promoter of interest. Here, they are shown to be constitutively expressed. A scaffold protein is required for fortifying the interaction. This scaffold could be expressed under any desired promoter. In this kit, it is regulated by an inducible promoter- induced by IPTG addition.
* These parts are yet to be characterised, wet lab efforts in progress