| Part Name | Registry ID | Part Type | Organism | Function and Description |
|---|---|---|---|---|
| T7 promoter | BBa_K4611014 | Promotor | T7 bacteriophage | T7 promoter, which comes from T7 bacteriophage, is a strong promoter with specific response to T7 RNA Polymerase to initiate T7 phage gene transcription. T7 RNA polymerase is highly promoter-specific and can specifically transcribe DNA or DNA replicas located downstream of T7 promoter in T7 phage. T7 RNA polymerase can selectively activate the transcription of T7 phage promoter, and its synthesis rate of mRNA is about 5 times faster than that of RNA polymerase from E.coli. |
| lac operator | BBa_K3286004 | Regulatory | E. coli | lac operator of the lac operon from E. coli. |
| Terminator (T7 RNAP specific, T_Phi) | BBa_B0016 | Terminator | T7 bacteriophage | The T7 late terminator, located between genes 10 and 11 on the T7 genome, is structurally similar to the rho-independent terminators of E. coli in that it contains a G+C-rich region of dyad symmetry followed by a template deoxyadenosine tract, but it inefficiently terminates T7 RNA polymerase either in vitro or in vivo. T7 RNA polymerase fails to terminate at Te, a rho-independent terminator for the bacterial RNA polymerase that is also present in the T7 genome. ([1]) |
| RBS2 | BBa_J61107 | RBS | pSB1A2 | This promoter is a medium-strength promoter derived from pSB1A2. |
| pelB | BBa_J32015 | Tag | E. coli | The pelB leader sequence is a sequence of amino acids which when attached to a protein, directs the protein to the periplasmic membrane of E. coli, where the sequence is removed by pelB peptidase. It is used to direct coat protein-antigen fusions to the cell surface. |
| TAT | BBa_K1202006 | Coding | HIV-1 | Trans Activator of Transcription (TAT) peptide is a special signal peptide that directs the attached proteins into eukaryotic cells in the extracellular matrix. The proteins conduct this kind of activity called "cell penetrating peptides" (CPP). This allows the transportation of desired proteins into the cells. The efficiency of the part can be manipulated by adding additional sequences such as HA2. |
| GFP | BBa_E0040 | Reporter | Aequeorea victoria | The green fluorescent protein (GFP) is a protein that exhibits green fluorescence when exposed to light in the blue to ultraviolet range. ([2]) |
| PhoB Promotor | BBa_K116401 | Regulatory | E.coli | Promoter of phoB in E.coli, an external phosphate regulated promoter that can be activated when encountering phosphate limitation. |
| MazF | BBa_K1096002 | Coding | E.coli | MazF is toxin protein in MazE-MazF, toxin-antitoxin module. It is function as mRNA endonuclease |
| TrpE | BBa_K3875009 | Coding | Escherichia coli str. K-12 substr. MG1655 | anthranilate synthase subunit TrpE |
| TrpC | BBa_K3875002 | Coding | Escherichia coli str. K-12 substr. MG1655 | fused indole-3-glycerol phosphate synthase/phosphoribosylanthranilate isomerase |
| TrpB | BBa_K187029 | Coding | Escherichia coli str. K-12 substr. MG1655 | tryptophan synthase subunit beta |
| TrpA | BBa_K804002 | Coding | Escherichia coli str. K-12 substr. MG1655 | tryptophan synthase subunit alpha |
On this page, we carefully present pathways that include brand new modules conceived by our team. The layout is thoughtfully structured to accurately convey the functions these parts fulfill within the distinct modules of our project. For a richer perspective on our contributions and to explore the nuances of our parts, we encourage perusing the relevant part pages in the iGEM Parts Registry.
You can click here to learn more about the reasons we chose these components.
Existing Parts
New Basic Parts
| Part Name | Part Type | Organism | Function and Description |
|---|---|---|---|
| pET-32a(+) - RBS(MCS) | RBS | pET-32a(+) | This is a high-intensity promoter derived from pET-32a(+). |
| GALA3 | Coding | - | GALA3 effectively promotes the escape of fusion proteins from endosomes into the cytoplasm in a pH-dependent manner. This peptide significantly improves the cytoplasmic distribution of fusion proteins, allowing protein drugs to enter cells through clathrin/caveolin-dependent endocytosis. ([3]) |
| hasB | Coding | Streptococcus pyogenes | HasB encodes UDP-glucose dehydrogenase, a protein with a predicted M(r) of 45.5 kDa that catalyzes the oxidation of UDP-glucose to UDP-glucuronic acid ([4]). |
| Crimson | Reporter | Synthetic construct | Red fluorescent protein is a fluorescent protein cloned from coral that is homologous to green fluorescent protein (GFP) and emits red fluorescence under ultraviolet light exposure. |
| GS-Flexible linker | Coding | - | Flexible linkers are mainly composed of Gly and Ser residues (the "GS" linker) segments. By adjusting the copy number "n," the length of the GS linker can be optimized to achieve appropriate separation of functional domains while maintaining the necessary interdomain interactions. |
| (EAAAK) - Rigid linker | Coding | - | Alpha helix-forming linkers with the sequence (EAAAK)(n) have been applied in the construction of many recombinant fusion proteins. The α-helix structure is rigidly stabilized, with hydrogen bonds within the chain and a tightly packed backbone. This is more effective than flexible linkers for separating functional domains. ([5]) |
| Target peptide | Coding | - | This is a short peptide designed through computer software modeling to specifically bind to the AQP0 protein. We use this sequence in our project for precise drug delivery targeting lens fiber cells. |
| hasA | Coding | Lachnellula hyalina | HasA gene encodes hyaluronic acid synthase (HAS), which is 419 amino acids in length. HasA gene is part of the hyaluronic acid synthesis operon in S.zooepidemicus genome by simulataneously catalyzing gluconuronic acid and acetaminoglucose transfer reaction. In vivo, the synthesis of hyaluronic acid is achieved by the alternating aggregation of monosaccharides uridine 5 '- 2 - glucose phosphate aldehyde (uridine 5' - diphosphate - GlcUA, UDP - GlcUA) and uridine 5 '- diphosphate - acetylglucosamine (uridine 5' - diphosphate - GlcNAc, UDP - GlcNAc) into HA long polysaccharide chain. |
| anti-trpC sRNA | RNA | - | By using TrpCgRNA, the CRISPR/Cas9 system can be precisely guided to knock out the trpC gene. |
| anti-HisA sRNA | RNA | - | By using anti-HisA sRNA, the CRISPR/Cas9 system can be precisely guided to knock out the trpC gene. |
| aroG | Coding | Escherichia coli str. K-12 substr. MG1655 | aroG encoding 3-deamino-D-aromatic amino acid transaminase (DAHP synthase) |
| TrpD | Coding | Escherichia coli str. K-12 substr. MG1655 | anthranilate synthase subunit TrpD |
| hisL | Coding | Escherichia coli str. K-12 substr. MG1655 | his operon leader peptide |
| hisG | Coding | Escherichia coli str. K-12 substr. MG1655 | ATP phosphoribosyltransferase |
| hisD | Coding | Escherichia coli str. K-12 substr. MG1655 | histidinal/histidinol dehydrogenase |
| hisC | Coding | Escherichia coli str. K-12 substr. MG1655 | histidinol-phosphate aminotransferase |
| hisB | Coding | Escherichia coli str. K-12 substr. MG1655 | imidazoleglycerol-phosphate dehydratase/histidinol-phosphatase |
| hisH | Coding | Escherichia coli str. K-12 substr. MG1655 | imidazole glycerol phosphate synthase subunit |
| hisA | Coding | Escherichia coli str. K-12 substr. MG1655 | 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino]imidazole-4-carboxamide isomerase |
| hisF | Coding | Escherichia coli str. K-12 substr. MG1655 | imidazole glycerol phosphate synthase subunit HisF |
| hisI | Coding | Escherichia coli str. K-12 substr. MG1655 | putative bifunctional phosphoribosyl-AMP cyclohydrolase/phosphoribosyl-ATP pyrophosphatase |
New Composite Parts
| Part Name | Part Type | Function and Description |
|---|---|---|
| pET-32a(+) - T7 promoter - lac operator - Shine-Dalgarno (RBS1) - pelB - GS-linker*1 - TAT - GS-linker*1 - Target peptide - GS-linker*5 - GALA3 - rigid-linker (EAAAK)*3 - RNF114 - BBa_J61107 (RBS2) - Crimson - T7 terminator | Device | The polycistronic gene expression system for producing recombinant RNF114 protein generates the active component of the therapeutic system, recombinant RNF114. |
| pET-32a(+) - T7 promoter - lac operator - Shine-Dalgarno (RBS1) - pelB - rigid-linker (EAAAK)*3 - RNF114 - rigid-linker (EAAAK)*3 - GS-linker*2 - GFP - BBa_J61107 (RBS2) - Crimson - T7 terminator | Device | The gene expression system for validating pelB function uses GFP as a fusion protein reporter gene and employs a polycistronic system to simultaneously express crimson as a reporter gene for normal plasmid expression. |
| pET-32a(+) - T7 promoter - lac operator - Shine-Dalgarno (RBS1) - hasA - BBa_J61107 (RBS2) - hasB - T7 terminator | Device | The polycistronic gene expression system for producing HA generates hasA and hasB proteins that catalyze the conversion of carbon sources into HA. |
| pET-32a(+) - T7 promoter - lac operator - Shine-Dalgarno (RBS1) - TAT - rigid-linker (EAAAK)*3 - RNF114 - rigid-linker (EAAAK)*3 - GS-linker*2 - GFP - BBa_J61107 (RBS2) - Crimson - T7 terminator | Device | The gene expression system for validating TAT function uses GFP as a fusion protein reporter gene and employs a polycistronic system to simultaneously express crimson as a reporter gene for normal plasmid expression. |
| pET-32a(+) - T7 promoter - lac operator - Shine-Dalgarno (RBS1) - Target peptide - rigid-linker (EAAAK)*3 - RNF114 - rigid-linker (EAAAK)*3 - GS-linker*2 - GFP - BBa_J61107 (RBS2) - Crimson - T7 terminator | Device | The gene expression system for validating the functionality of targeting short peptides uses GFP as a fusion protein reporter gene and employs a polycistronic system to simultaneously express crimson as a reporter gene for normal plasmid expression. |
| pET-32a(+) - T7 promoter - lac operator - Shine-Dalgarno (RBS1) - GALA3 - rigid-linker (EAAAK)*3 - RNF114 - rigid-linker (EAAAK)*3 - GS-linker*2 - GFP - BBa_J61107 (RBS2) - Crimson - T7 terminator | Device | The gene expression system for validating GALA3 functionality uses GFP as a fusion protein reporter gene and employs a polycistronic system to simultaneously express crimson as a reporter gene for normal plasmid expression. |
| pET-32a(+) - T7 promoter - lac operator - Shine-Dalgarno (RBS1) - GFP - BBa_J61107 (RBS2) - Crimson - T7 terminator | Device | The gene expression system for validating polycistronic function and detecting RBS strength uses GFP and Crimson as reporter genes. |
| pET-32a(+) - T7 promoter - lac operator - Shine-Dalgarno (RBS1) - rigid-linker (EAAAK)*3 - RNF114 - rigid-linker (EAAAK)*3 - GS-linker*2 - GFP - BBa_J61107 (RBS2) - Crimson - T7 terminator | Device | As negative control. |
| pET-32a(+) - p_PhoB-mazF | Device | Suicidal pathway based on phosphate-sensitive promoter. |
| pET-32a(+) - T7 promoter - lac operator - RBS1 - aroG - BBa_J61107 (RBS2) - TrpE - BBa_J61107 (RBS3) - TrpD - BBa_J61107 (RBS4) - TrpC - BBa_J61107 (RBS5) - TrpB - BBa_J61107 (RBS6) - TrpA - T7 terminator | Device | The tryptophan biosynthetic pathway based on the trpEDCBA gene cluster in the tryptophan operon. |
| pET-32a(+) - T7 promoter - lac operator - RBS1 - HisL - BBa_J61107 (RBS2) - HisG - BBa_J61107 (RBS3) - HisD - BBa_J61107 (RBS4) - HisC - BBa_J61107 (RBS5) - HisB - BBa_J61107 (RBS6) - HisH - BBa_J61107 (RBS7) - HisA - BBa_J61107 (RBS8) - HisF - BBa_J61107 (RBS9) - HisI - T7 terminator | Device | The histidine biosynthesis pathway of HisLGDCBHAFI in the Escherichia coli genome. |
| pdCas9-trpCgRNA | Device | pdCas9-trpCgRNA plasmid is used to knock out the trpC gene, blocking the synthesis of tryptophan. |
| pdCas9-HisAgRNA | Device | pdCas9-HisAgRNA plasmid is used to knock out the HisA gene, blocking the synthesis of histidine. |
| pEVOL-pAzf | Device | The pEVOL-pAzf plasmid can generate a tRNA synthetase/tRNA pair that recognizes UAG and carries p-azidophenylalanine |
References
[1]
Jeng, S. T., Gardner, J. F., & Gumport, R. I. (1990). Transcription termination by bacteriophage T7 RNA polymerase at rho-independent terminators. Journal of Biological Chemistry, 265(7), 3823-3830.
Link
[3]
Li, C., Cao, XW., Zhao, J. et al. Effective Therapeutic Drug Delivery by GALA3, an Endosomal Escape Peptide with Reduced Hydrophobicity. J Membrane Biol 253, 139–152 (2020).
DOI: 10.1007/s00232-020-00109-2
[4]
Dougherty, B. A., & van de Rijn, I. (1993). Molecular characterization of hasB from an operon required for hyaluronic acid synthesis in group A streptococci. Demonstration of UDP-glucose dehydrogenase activity. The Journal of biological chemistry, 268(10), 7118–7124.
Link
[5]
Chen, X., Zaro, J. L., & Shen, W. C. (2013). Fusion protein linkers: property, design and functionality. Advanced drug delivery reviews, 65(10), 1357–1369.
DOI: 10.1016/j.addr.2012.09.039