Parts
Utilized and Characterized Existing Parts
| Gene Name | Part name | Description | Utilization and Characterization |
|---|---|---|---|
| CueR | BBa_K1758320 | cueR is a merR like regulator, which stimulates the transcription of copAP, a P-type ATPase pump (Outten et al. 2000). | We have adopted this part as a transcriptional regulatory factor for copper ions (Cu). |
| pCoA | BBa_K190017 | BBa_K190017 is a Promoter sequence with a recognition site for the CueR transcription-regulating protein | We utilize this part as a promoter responsive to copper ions to initiate the expression of downstream reporter genes. Furthermore, we have demonstrated with this example that endogenous promoters from Escherichia coli can function independently within E. coli without the need for additional expression of their corresponding transcriptional regulatory proteins; they can directly use the proteins already present in the genome. |
New Basic Parts
| Gene Name | Part name | Description | Utilize and Characteration | |
|---|---|---|---|---|
| pSQU-03 | BBa_K5459003 | basic | Predicted promoter from the E.coli genome | BBa_K5459003 - BBa_K5459007 are predicted endogenous promoters of Escherichia coli, identified through methods like RNA sequencing. The specific prediction methods can be found in the article: doi/10.1128/jb.02096-14. We screened 88 promoters from this article and used high-throughput screening to verify how these promoters, through the CueR protein, affect copper ion response in our dual plasmid system. This process generates a dataset that indirectly measures the activity of these promoters. Using this dataset, we applied machine learning to extract the relationship between sequence and promoter strength. |
| pSQU-04 | BBa_K5459004 | basic | Predicted promoter from the E.coli genome | BBa_K5459003 - BBa_K5459007 are predicted endogenous promoters of Escherichia coli, identified through methods like RNA sequencing. The specific prediction methods can be found in the article: doi/10.1128/jb.02096-14. We screened 88 promoters from this article and used high-throughput screening to verify how these promoters, through the CueR protein, affect copper ion response in our dual plasmid system. This process generates a dataset that indirectly measures the activity of these promoters. Using this dataset, we applied machine learning to extract the relationship between sequence and promoter strength. |
| pSQU-05 | BBa_K5459005 | basic | Predicted promoter from the E.coli genome | BBa_K5459003 - BBa_K5459007 are predicted endogenous promoters of Escherichia coli, identified through methods like RNA sequencing. The specific prediction methods can be found in the article: doi/10.1128/jb.02096-14. We screened 88 promoters from this article and used high-throughput screening to verify how these promoters, through the CueR protein, affect copper ion response in our dual plasmid system. This process generates a dataset that indirectly measures the activity of these promoters. Using this dataset, we applied machine learning to extract the relationship between sequence and promoter strength. |
| pSQU-06 | BBa_K5459006 | basic | Predicted promoter from the E.coli genome | BBa_K5459003 - BBa_K5459007 are predicted endogenous promoters of Escherichia coli, identified through methods like RNA sequencing. The specific prediction methods can be found in the article: doi/10.1128/jb.02096-14. We screened 88 promoters from this article and used high-throughput screening to verify how these promoters, through the CueR protein, affect copper ion response in our dual plasmid system. This process generates a dataset that indirectly measures the activity of these promoters. Using this dataset, we applied machine learning to extract the relationship between sequence and promoter strength. |
| pSQU-07 | BBa_K5459007 | basic | Predicted promoter from the E.coli genome | BBa_K5459003 - BBa_K5459007 are predicted endogenous promoters of Escherichia coli, identified through methods like RNA sequencing. The specific prediction methods can be found in the article: doi/10.1128/jb.02096-14. We screened 88 promoters from this article and used high-throughput screening to verify how these promoters, through the CueR protein, affect copper ion response in our dual plasmid system. This process generates a dataset that indirectly measures the activity of these promoters. Using this dataset, we applied machine learning to extract the relationship between sequence and promoter strength. |
New Composite Parts
| Description | Part name | Function |
|---|---|---|
| pSQU-01 | BBa_K5459001 | CueR family proteins are key metal regulatory proteins in Escherichia coli that specifically sense monovalent copper ions (Cu⁺) in the internal and external cellular environment. CueR belongs to the MerR family of transcriptional regulators and plays a crucial role in regulating copper ion homeostasis and resistance to copper toxicity. When copper ion concentrations rise, CueR binds to copper ions with high affinity. Once copper ions enter the cell, CueR rapidly binds to them, triggering a conformational change in the CueR protein. When used in conjunction with BBa_K5459002, it can detect copper ion concentrations. |
| pSQU-02 | 🏆 BBa_K5459002 | BBa_K190017 is a Promoter sequence with recognition site for the CueR transcription regulating protein. When copper levels in the cell rise CueR activates transcription mVenusNB is BBa_K864100 codes for the bright yellow fluorescent protein SYFP2 We utilize this part as a promoter responsive to copper ions to initiate the expression of downstream reporter genes. Furthermore, we have demonstrated with this example that endogenous promoters from Escherichia coli can function independently within E. coli without the need for additional expression of their corresponding transcriptional regulatory proteins; they can directly use the proteins already present in the genome. |
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