Difference between revisions of "Part:BBa K3924000"
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<partinfo>BBa_K3924000 short</partinfo> | <partinfo>BBa_K3924000 short</partinfo> | ||
| − | + | <!-- Add more about the biology of this part here> | |
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===Usage and Biology=== | ===Usage and Biology=== | ||
| − | |||
<!-- --> | <!-- --> | ||
<span class='h3bb'>Sequence and Features</span> | <span class='h3bb'>Sequence and Features</span> | ||
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==Profile== | ==Profile== | ||
Name: TFF1<br/> | Name: TFF1<br/> | ||
| − | Base Pairs: | + | Base Pairs: 183bp<br/> |
Origin: <i>Homo sapiens</i><br/> | Origin: <i>Homo sapiens</i><br/> | ||
Properties: One of human cytokine from The trefoil factor (TFF) family secreted by mucus-producing cells. <br/> | Properties: One of human cytokine from The trefoil factor (TFF) family secreted by mucus-producing cells. <br/> | ||
==Usage and Biology== | ==Usage and Biology== | ||
| − | In order to heal the intestinal tract damage, one of notable symptoms of IBD, we adopted a special therapy expressing the therapeutic proteins controllably by E.coli Nissle 1917 (EcN) in situ. The design is based on a ternary system: sensor - secretion peptide - therapeutic proteins. | + | In order to heal the intestinal tract damage, one of notable symptoms of IBD, we adopted a special therapy expressing the therapeutic proteins controllably by<i> E.coli Nissle 1917</i> (EcN) <i>in situ</i>. The design is based on a ternary system: sensor - secretion peptide - therapeutic proteins. |
| − | [[Image: General design of the treatment ternary system.png|'''Fig.1 General design of the treatment ternary system''']] | + | [[Image: T--Tsinghua--General design of the treatment ternary system.png|center|600px|thumb|'''Fig.1 General design of the treatment ternary system''']] |
| − | TFF1 is one of the candidate therapeutic proteins we screened out to treat IBD, which is the effector element in the ternary system. | + | TFF1 is one of the candidate therapeutic proteins we screened out to treat IBD, which is the effector element in the ternary system. TFFs facilitate a significant role not only in mucosal repair but also in protecting mucous epithelia from a variety of insults in the gastrointestinal tract. The potential mechanisms to treat IBD involves anti-apoptotic properties, migration and invasion, angiogenesis, and interaction with mucins. |
==Design and Construction== | ==Design and Construction== | ||
| − | According to literature research we chose 10 candidate proteins for IBD treatment. | + | According to literature research we chose 10 candidate proteins for IBD treatment. <br/> |
| − | Table 1. List of candidate therapeutic proteins< | + | <b>Table 1. List of candidate therapeutic proteins</b> |
<table border="1"> | <table border="1"> | ||
<tr> | <tr> | ||
| Line 36: | Line 34: | ||
<tr> | <tr> | ||
<td> BBa_K3924003</td> | <td> BBa_K3924003</td> | ||
| − | <td>Chromofungin(CHR | + | <td>Chromofungin(CHR)</td> |
<td>[3]</td> | <td>[3]</td> | ||
</tr> | </tr> | ||
| Line 68: | Line 66: | ||
<td>tkip</td> | <td>tkip</td> | ||
<td>[3]</td> | <td>[3]</td> | ||
| + | </tr> | ||
| + | <tr> | ||
| + | <td> BBa_K3924037</td> | ||
| + | <td>G-CSF</td> | ||
| + | <td>[8][9]</td> | ||
| + | </tr> | ||
| + | <tr> | ||
| + | <td> BBa_K3924038</td> | ||
| + | <td>GM-CSF</td> | ||
| + | <td>[8][10]</td> | ||
| + | </tr> | ||
| + | <tr> | ||
| + | <td> BBa_K3924039</td> | ||
| + | <td>Beta-defensin 4A(hBD2)</td> | ||
| + | <td>[11]</td> | ||
</tr> | </tr> | ||
</table> | </table> | ||
| − | The sequence of TFF1 is acquired from Gene database (Gene ID: 7031). The sequences were synthesized on pMV plasmids by biological companies and cloned into pEGFP & RGP-TMAR plasmids by ourselves for the following experiments. PCR technique and HiFi assembly method were frequently utilized. Eventually, we have successfully constructed the plasmids RGP-csgA-TFF1 as the best carrier of our treatment protein. The plasmids were amplified inside E. coli DH5α and imported into E. coli Nissle through electrotransformation. The protein expression of the TFF1 was tested using SDS-PAGE and western blot. | + | The sequence of TFF1 is acquired from Gene database (Gene ID: 7031). The sequences were synthesized on pMV plasmids by biological companies and cloned into pEGFP & RGP-TMAR plasmids by ourselves for the following experiments. PCR technique and HiFi assembly method were frequently utilized. Eventually, we have successfully constructed the plasmids RGP-csgA-TFF1 as the best carrier of our treatment protein. The plasmids were amplified inside E. coli DH5α and imported into E. coli Nissle through electrotransformation. The protein expression of the TFF1 was tested using SDS-PAGE and western blot. |
| + | |||
==Functional Verification== | ==Functional Verification== | ||
| − | [[Image: The scheme of the proof-of-concept for therapeutic proteins.png|'''Fig 2. The scheme of the proof-of-concept for therapeutic proteins.''']] | + | [[Image: T--Tsinghua--The scheme of the proof-of-concept for therapeutic proteins.png|center|600px|thumb|'''Fig 2. The scheme of the proof-of-concept for therapeutic proteins.''']] |
| − | All of these proteins are worth studying, but we only chose a few proteins as a proof of concept in our actual wet lab experiments because of the time limit and the high expense of gene synthesis. | + | All of these proteins are worth studying, but we only chose a few proteins as a proof of concept in our actual wet lab experiments because of the time limit and the high expense of gene synthesis. <br/> |
| − | For | + | For all candidate therapeutic proteins we did codon analysis with our own software tool.(Fig 3) |
| + | [[Image: T--Tsinghua--Codon preference confident analysis.png|center|600px|thumb|'''Fig 3. Codon preference confident analysis of all candidate therapeutic proteins(Compared with GenSmart).''']] | ||
| + | As for TFF1, the result of codon preference is shown in Fig 4. | ||
| + | [[Image: T--Tsinghua--Codon preference confident analysis of TFF1.png|center|600px|thumb|'''Fig 4. Codon preference confident analysis of TFF1.''']] | ||
==Reference== | ==Reference== | ||
| − | [1] Aamann, L., Vestergaard, E. M., & Grønbæk, H. (2014). Trefoil factors in inflammatory bowel disease. World journal of gastroenterology, 20(12), 3223–3230. | + | [1] Aamann, L., Vestergaard, E. M., & Grønbæk, H. (2014). Trefoil factors in inflammatory bowel disease. World journal of gastroenterology, 20(12), 3223–3230. <br/> |
| − | [2] Praveschotinunt, P., Duraj-Thatte, A.M., Gelfat, I. et al. Engineered E. coli Nissle 1917 for the delivery of matrix-tethered therapeutic domains to the gut. Nat Commun 10, 5580 (2019).. | + | [2] Praveschotinunt, P., Duraj-Thatte, A.M., Gelfat, I. et al. Engineered E. coli Nissle 1917 for the delivery of matrix-tethered therapeutic domains to the gut. Nat Commun 10, 5580 (2019).<br/> |
| + | [3] La Manna, S., Di Natale, C., Florio, D., & Marasco, D. (2018). Peptides as Therapeutic Agents for Inflammatory-Related Diseases. International journal of molecular sciences, 19(9), 2714.<br/> | ||
| + | [4] Li, M. C., & He, S. H. (2004). IL-10 and its related cytokines for treatment of inflammatory bowel disease. World journal of gastroenterology, 10(5), 620–625. <br/> | ||
| + | [5] Shukla, P.K., Meena, A.S., Rao, V. et al. Human Defensin-5 Blocks Ethanol and Colitis-Induced Dysbiosis, Tight Junction Disruption and Inflammation in Mouse Intestine. Sci Rep 8, 16241 (2018).<br/> | ||
| + | [6] Duan, L., Rao, X., Braunstein, Z., Toomey, A. C., & Zhong, J. (2017). Role of Incretin Axis in Inflammatory Bowel Disease. Frontiers in immunology, 8, 1734.<br/> | ||
| + | [7] Zhu, Y. , Jie, Z. , Yi, F. , Chen, L. , Zhang, L. , & Fei, Y. , et al. (2018). Control of intestinal inflammation, colitis-associated tumorigenesis, and macrophage polarization by fibrinogen-like protein 2. Frontiers in Immunology, 9, 87-.<br/> | ||
| + | [8] Guidi, L., Mocci, G., Marzo, M., & Rutella, S. (2008). Treatment of Crohn's disease with colony-stimulating factors: An overview. Therapeutics and clinical risk management, 4(5), 927–934. <br/> | ||
| + | [9] Vanz, A. L. , Renard, G. , Palma, M. S. , Chies, J. M. , Dalmora, S. L. , & Basso, L. A. , et al. (2008). Human granulocyte colony stimulating factor (hg-csf): cloning, overexpression, purification and characterization. Microbial Cell Factories, 7(1), 1-12.<br/> | ||
| + | [10] Malekian, R., Jahanian-Najafabadi, A., Moazen, F., Ghavimi, R., Mohammadi, E., & Akbari, V. (2019). High-yield Production of Granulocyte-macrophage Colony-stimulating Factor in E. coli BL21 (DE3) By an Auto-induction Strategy. Iranian journal of pharmaceutical research : IJPR, 18(1), 469–478.<br/> | ||
| + | [11] Koeninger, L. , Armbruster, N. S. , Brinch, K. S. , Kjaerulf, S. , & Wehkamp, J. . (2020). Human β-defensin 2 mediated immune modulation as treatment for experimental colitis. Frontiers in Immunology, 11, 93.<br/> | ||
| + | |||
<!-- Uncomment this to enable Functional Parameter display | <!-- Uncomment this to enable Functional Parameter display | ||
Latest revision as of 21:06, 21 October 2021
TFF1
Sequence and Features
- 10COMPATIBLE WITH RFC[10]
- 12COMPATIBLE WITH RFC[12]
- 21COMPATIBLE WITH RFC[21]
- 23COMPATIBLE WITH RFC[23]
- 25COMPATIBLE WITH RFC[25]
- 1000INCOMPATIBLE WITH RFC[1000]Illegal BsaI.rc site found at 13
Profile
Name: TFF1
Base Pairs: 183bp
Origin: Homo sapiens
Properties: One of human cytokine from The trefoil factor (TFF) family secreted by mucus-producing cells.
Usage and Biology
In order to heal the intestinal tract damage, one of notable symptoms of IBD, we adopted a special therapy expressing the therapeutic proteins controllably by E.coli Nissle 1917 (EcN) in situ. The design is based on a ternary system: sensor - secretion peptide - therapeutic proteins.
TFF1 is one of the candidate therapeutic proteins we screened out to treat IBD, which is the effector element in the ternary system. TFFs facilitate a significant role not only in mucosal repair but also in protecting mucous epithelia from a variety of insults in the gastrointestinal tract. The potential mechanisms to treat IBD involves anti-apoptotic properties, migration and invasion, angiogenesis, and interaction with mucins.
Design and Construction
According to literature research we chose 10 candidate proteins for IBD treatment.
Table 1. List of candidate therapeutic proteins
| Part Name | Element Name | Reference |
|---|---|---|
| BBa_K3924000 BBa_K3924001 BBa_K3924002 |
TFF1/2/3 | [1][2] |
| BBa_K3924003 | Chromofungin(CHR) | [3] |
| BBa_K3924004 | IL10 | [4] |
| BBa_K3924005 | Defensin-5(HD5) | [5] |
| BBa_K3924006 | GLP2 | [6] |
| BBa_K3924007 | Fgl2 | [7] |
| BBa_K3924008 | SOCS1-KIR | [3] |
| BBa_K3924009 | tkip | [3] |
| BBa_K3924037 | G-CSF | [8][9] |
| BBa_K3924038 | GM-CSF | [8][10] |
| BBa_K3924039 | Beta-defensin 4A(hBD2) | [11] |
The sequence of TFF1 is acquired from Gene database (Gene ID: 7031). The sequences were synthesized on pMV plasmids by biological companies and cloned into pEGFP & RGP-TMAR plasmids by ourselves for the following experiments. PCR technique and HiFi assembly method were frequently utilized. Eventually, we have successfully constructed the plasmids RGP-csgA-TFF1 as the best carrier of our treatment protein. The plasmids were amplified inside E. coli DH5α and imported into E. coli Nissle through electrotransformation. The protein expression of the TFF1 was tested using SDS-PAGE and western blot.
Functional Verification
All of these proteins are worth studying, but we only chose a few proteins as a proof of concept in our actual wet lab experiments because of the time limit and the high expense of gene synthesis.
For all candidate therapeutic proteins we did codon analysis with our own software tool.(Fig 3)
As for TFF1, the result of codon preference is shown in Fig 4.
Reference
[1] Aamann, L., Vestergaard, E. M., & Grønbæk, H. (2014). Trefoil factors in inflammatory bowel disease. World journal of gastroenterology, 20(12), 3223–3230.
[2] Praveschotinunt, P., Duraj-Thatte, A.M., Gelfat, I. et al. Engineered E. coli Nissle 1917 for the delivery of matrix-tethered therapeutic domains to the gut. Nat Commun 10, 5580 (2019).
[3] La Manna, S., Di Natale, C., Florio, D., & Marasco, D. (2018). Peptides as Therapeutic Agents for Inflammatory-Related Diseases. International journal of molecular sciences, 19(9), 2714.
[4] Li, M. C., & He, S. H. (2004). IL-10 and its related cytokines for treatment of inflammatory bowel disease. World journal of gastroenterology, 10(5), 620–625.
[5] Shukla, P.K., Meena, A.S., Rao, V. et al. Human Defensin-5 Blocks Ethanol and Colitis-Induced Dysbiosis, Tight Junction Disruption and Inflammation in Mouse Intestine. Sci Rep 8, 16241 (2018).
[6] Duan, L., Rao, X., Braunstein, Z., Toomey, A. C., & Zhong, J. (2017). Role of Incretin Axis in Inflammatory Bowel Disease. Frontiers in immunology, 8, 1734.
[7] Zhu, Y. , Jie, Z. , Yi, F. , Chen, L. , Zhang, L. , & Fei, Y. , et al. (2018). Control of intestinal inflammation, colitis-associated tumorigenesis, and macrophage polarization by fibrinogen-like protein 2. Frontiers in Immunology, 9, 87-.
[8] Guidi, L., Mocci, G., Marzo, M., & Rutella, S. (2008). Treatment of Crohn's disease with colony-stimulating factors: An overview. Therapeutics and clinical risk management, 4(5), 927–934.
[9] Vanz, A. L. , Renard, G. , Palma, M. S. , Chies, J. M. , Dalmora, S. L. , & Basso, L. A. , et al. (2008). Human granulocyte colony stimulating factor (hg-csf): cloning, overexpression, purification and characterization. Microbial Cell Factories, 7(1), 1-12.
[10] Malekian, R., Jahanian-Najafabadi, A., Moazen, F., Ghavimi, R., Mohammadi, E., & Akbari, V. (2019). High-yield Production of Granulocyte-macrophage Colony-stimulating Factor in E. coli BL21 (DE3) By an Auto-induction Strategy. Iranian journal of pharmaceutical research : IJPR, 18(1), 469–478.
[11] Koeninger, L. , Armbruster, N. S. , Brinch, K. S. , Kjaerulf, S. , & Wehkamp, J. . (2020). Human β-defensin 2 mediated immune modulation as treatment for experimental colitis. Frontiers in Immunology, 11, 93.