Difference between revisions of "Part:BBa K4005006"
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| − | <partinfo> | + | <partinfo>BBa_K4005006 short</partinfo> |
| − | <partinfo> | + | <partinfo>BBa_K4005006 SequenceAndFeatures</partinfo> |
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| − | === Usage and Biology | + | |
| − | Angiogenin (Angiogenin, ANG) belongs to the secreted ribonuclease superfamily, and was originally discovered to be an angiogenic factor derived from human tumors. Subsequent studies have shown that ANG is also present in normal human tissues and body fluids. ANG increases the transcription of ribosomal RNA (rRNA) in the nucleus, while vascular endothelial growth factor (VEGF) and fibroblast growth factor-2 (FGF-2) activate mTOR and S6 kinase pathways to promote protein synthesis. Therefore, ANG can cooperate with VEGF and FGF-2 to promote protein synthesis in endothelial cells. In addition, ANG is necessary for endothelial cell proliferation. In addition to promoting angiogenesis, ANG is also involved in many other physiological and pathological processes, such as neuroprotection, inflammation, and tumorigenesis. Loss of function mutations in the ANG gene have been found in both amyotrophic lateral sclerosis (ALS) and Parkinson's disease (PD). | + | |
| − | + | == Profile == | |
| + | == BBa_K4005006 == | ||
| + | === Name: pro-rANG-His-ter === | ||
| + | === Base Pairs: 675 bp === | ||
| + | === Origin: human，synthetic === | ||
| + | === Properties: A coding sequence for Angiogenin. === | ||
| + | |||
| + | == Usage and Biology == | ||
| + | Angiogenin (Angiogenin, ANG) belongs to the secreted ribonuclease superfamily, and was originally discovered to be an angiogenic factor derived from human tumors. Subsequent studies have shown that ANG is also present in normal human tissues and body fluids. ANG increases the transcription of ribosomal RNA (rRNA) in the nucleus, while vascular endothelial growth factor (VEGF) and fibroblast growth factor-2 (FGF-2) activate mTOR and S6 kinase pathways to promote protein synthesis. Therefore, ANG can cooperate with VEGF and FGF-2 to promote protein synthesis in endothelial cells. In addition, ANG is necessary for endothelial cell proliferation. In addition to promoting angiogenesis, ANG is also involved in many other physiological and pathological processes, such as neuroprotection, inflammation, and tumorigenesis. Loss of function mutations in the ANG gene have been found in both amyotrophic lateral sclerosis (ALS) and Parkinson's disease (PD). | ||
== Construct design == | == Construct design == | ||
[[File:T--Shanghai Metro Utd--BBa K4005001-figure1.png|500px|thumb|center|Figure 1. The rANG protein expression box..]] | [[File:T--Shanghai Metro Utd--BBa K4005001-figure1.png|500px|thumb|center|Figure 1. The rANG protein expression box..]] | ||
The profiles of every basic part are as follows: | The profiles of every basic part are as follows: | ||
| − | |||
=== BBa_K4005000=== | === BBa_K4005000=== | ||
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===BBa_K4005003=== | ===BBa_K4005003=== | ||
Name: 6His | Name: 6His | ||
| + | |||
Base Pairs: 18bp | Base Pairs: 18bp | ||
| + | |||
Origin: synthetic | Origin: synthetic | ||
| + | |||
Properties: Polyhistidine tag | Properties: Polyhistidine tag | ||
| Line 43: | Line 48: | ||
===BBa_K4005001=== | ===BBa_K4005001=== | ||
Name: P7 | Name: P7 | ||
| + | |||
Base Pairs: 19bp | Base Pairs: 19bp | ||
| + | |||
Origin: T7 phage, genome | Origin: T7 phage, genome | ||
| + | |||
Properties: A promoter for initiation of the transcription. | Properties: A promoter for initiation of the transcription. | ||
=== BBa_K4030002 === | === BBa_K4030002 === | ||
Name: TT | Name: TT | ||
| + | |||
Base Pairs: 140bp | Base Pairs: 140bp | ||
| + | |||
Origin: Escherichia coli | Origin: Escherichia coli | ||
| + | |||
Properties: Transcription terminator | Properties: Transcription terminator | ||
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It is an transcription terminator derived from the E.coli rrB rRNA operon | It is an transcription terminator derived from the E.coli rrB rRNA operon | ||
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| − | |||
| − | |||
| − | |||
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| − | [[File:T--Shanghai Metro Utd--BBa K4005004- | + | == Experimental approach == |
| + | pET-28a-rANG which produces ANG protein is shown in Figure 1. | ||
| + | [[File:T--Shanghai Metro Utd--BBa K4005005-figure2.png|500px|thumb|center|Figure 2. Schematic map of pET-28a-rANG plasmid and its construction..]] | ||
| + | [[File:T--Shanghai Metro Utd--BBa K4005004-figure2a.png|500px|thumb|center|Figure 3: the scanning gel electrophoresis map of the plasmid vector after enzyme digestion.]] | ||
| + | [[File:T--Shanghai Metro Utd--BBa K4005004-figure2b.png|500px|thumb|center|Figure 3: the scanning gel electrophoresis map of the plasmid vector after enzyme digestion.]] | ||
| + | As seen in figure 3, lane 1 is the pET-28a without enzyme digestion and lane 2 to 9 is the result for pET-28a after enzyme digestion. The bands of our plasmid vectors after enzyme digestion(5311bp) showed at 5000 bp around which are correct and the bands at 300 bp around were the SUMO fragments that were cut by enzyme digestion. After that, we could further conduct the E. coli transformation. | ||
| + | [[File:T--Shanghai Metro Utd--BBa K4005004-figure3.png|500px|thumb|center|Figure 4: The gel electrophoresis map of PCR.]] | ||
Lane 1 to 6 is the result of PCR. We got rANG band at around 400bp (369bp). Enzyme digestion was conducted and it was linked with digested pET-28a. | Lane 1 to 6 is the result of PCR. We got rANG band at around 400bp (369bp). Enzyme digestion was conducted and it was linked with digested pET-28a. | ||
| − | [[File:T--Shanghai Metro Utd--BBa K4005004-figure4a.png|500px|thumb|center|Figure | + | [[File:T--Shanghai Metro Utd--BBa K4005004-figure4a.png|500px|thumb|center|Figure 5. E. coil having the desired pET28a-rANG.]] |
| − | [[File:T--Shanghai Metro Utd--BBa K4005004-figure4b.png|500px|thumb|center|Figure | + | [[File:T--Shanghai Metro Utd--BBa K4005004-figure4b.png|500px|thumb|center|Figure 5. E. coil having the desired pET28a-rANG.]] |
| − | The plates in Fig. | + | The plates in Fig. 5 (1) showed monoclonals of pET28a-rANG constructs. |
| − | The pET28a-rANG was constructed successfully which has been proved by sequencing as shown in Fig. | + | The pET28a-rANG was constructed successfully which has been proved by sequencing as shown in Fig. 5 (2). |
Recombination E. coli | Recombination E. coli | ||
| − | [[File:T-- | + | [[File:T--Shanghai_Metro_Utd--BBa_K4005004-figure5a.png|500px|thumb|center|Figure 6: the scanning gel electrophoresis map of Colony PCR (the top was before and the bottom was after).]] |
| − | [[File:T-- | + | [[File: T--Shanghai_Metro_Utd--BBa_K4005004-figure5b.png|500px|thumb|center|Figure 6: the scanning gel electrophoresis map of Colony PCR (the top was before and the bottom was after).]] |
| + | |||
Lane NC to XCN6 and lane XCN7 to N6 are the results of colony PCR. We get the band 531bp at 500bp around. It indicates that the obtained recombinant monoclonals were positive monoclonals containing the pET-28a-rANG recombinant plasmid. | Lane NC to XCN6 and lane XCN7 to N6 are the results of colony PCR. We get the band 531bp at 500bp around. It indicates that the obtained recombinant monoclonals were positive monoclonals containing the pET-28a-rANG recombinant plasmid. | ||
| + | == Proof of function == | ||
| + | We did SDS-PAGE assey of protein and have obtained Freeze-dried powder of the ANG protein produced by our engineered Escherichia coli (Figure 7). | ||
| + | [[File:T--Shanghai Metro Utd--BBa K4005001-figure2a.png|500px|thumb|center|Figure 7. SDS-PAGE assey of protein and Freeze-dried powder of the ANG protein..]] | ||
| + | [[File:T--Shanghai Metro Utd--BBa K4005001-figure2b.png|500px|thumb|center|Figure 7. SDS-PAGE assey of protein and Freeze-dried powder of the ANG protein..]] | ||
| + | The activity of recombinant ANG protein was determined by the RNA degradation assay. The result indicated that ANG protein possesses ribonuclease activity as we expected. | ||
| + | |||
| + | [[File:T--Shanghai Metro Utd--BBa K4005005-figure8.png|500px|thumb|center|Figure 8. RNA degradation by ANG..]] | ||
| + | |||
| + | |||
| + | == Improvement of an existing part == | ||
| + | |||
| + | |||
| + | [[File:T--Shanghai Metro Utd--BBa K4005004-figure9.png|500px|thumb|center|Figure 9. The blast results about the DNA sequence of our new part BBa_K4005006 and the old part BBa_K3523005..]] | ||
| + | Compared to the old part BBa_K3523005, composite part T7 pro-His-SOD-His-T7 ter, we design a new part BBa_K4005006, which replaced the SOD gene sequence fragment with rANG gene fragment. According to literature reports, heparan sulphate proteoglycans (HSPGs) are required for ANG to enter cells. HSPGs are linear anionic glycosaminoglycan (GAG) chains covalently linked to the core protein, composed of disaccharide repeating units of uronic acid and glucosamine, and the glucosamine residues 3-OH, 6-OH and -NH And the 2-OH of uronic acid is replaced by a sulfate group. HSPGs exist on the plasma membrane of all animals and are the main component of the extracellular matrix. Factors such as size, location, degree of sulfation, and uronic acid in different cells, tissues, and developmental stages contribute to the structural diversity of heparan sulphate (HS). This structural diversity is the basis for HSPGs to perform multiple functions. In previous research, our laboratory constructed a library of HS mutant mouse lung endothelial cells by knocking out key genes in the HS biosynthesis process. In this study, we prokaryotic expression and purification of recombinant ANG protein, using heparin and heparin derivatives and HS mutant mouse lung endothelial cell library to perform enzyme-linked immunosorbent assay and flow cytometry experiments to explore the interaction between ANG and HS The specificity and clarify its structure-activity relationship. | ||
| + | |||
| + | == Future plan == | ||
| + | In future applications, the product we get may have two directions of develop, but all in the clinical medicine aspect. One is to directly invent a new drug with the protein product of this gene and the other one is to explore its pharmacology regarding the relevant diseases which could be used to develop more new drugs. | ||
| + | |||
| + | The first kind of drug may have an effect on adjusting the nerve system, treating diseases like inflammation and the further developed drugs may be a possible treatment of some present incurable diseases such as PD and tumor. However, the overuse of ANG will also overpromote the generation of endothelial cells and vessels and may even cause cancer in some situations, so the correct usage of this drug shall be also necessary for being studied. | ||
| + | |||
| + | Market Survey | ||
| + | According to relevant data, among the 65-year-olds, one in ten people are Parkinson's disease patients; among the 85-year-olds, the number of people who have Parkinson's disease reaches 30%-50%. The research progress and molecular biological characteristics of Angiopoietin and its related proteins are reviewed. So far, four kinds of Angiopoietin and some isoforms or variants of Angiopoietin have been discovered. These proteins have a common structure: a signal peptide related to secretion at the amino terminus, a helix-like domain that mediates homo-oligomers, and a fibrinogen-like domain that mediates ligand activity at the carboxyl terminus. | ||
| + | |||
| + | Marketing Plan | ||
| + | The theory we have resulted in a unique product (but not medicine), which will be studied and researched by staff members in the collaborated pharmaceutical company), and the final medical products will be entirely produced and owned by the partner company. The outcome of our company remains with unknown effects on medicine. However, the result will be owned by our target group (pharmaceutical company). | ||
| + | |||
| + | We will market our product using many different ways. For example, online surveys, email marketing, mobile marketing, and social media marketing are considered the cheapest among all types of marketing. Since we are a brand new company, we do not have many budgets available for us, so we would consider the ways I listed above first. Once we have more budget allowed, we might try other ways of marketing our product. For example, printed marketing materials, such as brochures, flyers, business cards, etc. We can also try trade shows and other marketing that cost some money. | ||
| + | |||
| + | Challenges | ||
| + | During the experimental work, the main challenges were the plasmid DNA extraction and the protein purification process. One aspect of the difficulty is the continuous low concentration of plasmid DNA when we first extracted them. But as we navigate through and become more familiar with the long process, we successfully extracted with an ideal concentration. | ||
| + | |||
| + | Moreover, heterologous overexpression often results in low expression levels and inactive protein due to insufficient membrane insertion and folding or lack of post-translational modifications. And over-expression of membrane proteins can be toxic to the cell. Nevertheless, eventually, we obtained the freeze-dried protein powder. But with no doubt, we will further solidify this part of the work. | ||
| + | |||
| + | Before our product come into a real application, there are still some concerns regarding our Angiogenin protein. We need to conduct more experiments and tests to further ensure its purity, stability and biological activity. In addition, we would further focus on the yield issues, storage conditions and how to use our products to determine the dose of curing some present incurable diseases. | ||
| − | + | == Reference == | |
| − | + | === World Health Organization Estimated Deaths 2012. http://www.who.int/entity/healthinfo/global_burden_disease/GHE_Deaths_2012_country.xls?ua=1 === | |
| − | http://www.who.int/entity/healthinfo/global_burden_disease/GHE_Deaths_2012_country.xls?ua=1 | + | === Biography.com Editors. (2017, April 28). Muhammad Ali. Biography. https://www.biography.com/athlete/muhammad-ali === |
| − | ==== Biography.com Editors. (2017, April 28). Muhammad Ali. Biography. https://www.biography.com/athlete/muhammad-ali | + | === Parkinson disease: MedlinePlus genetics. (n.d.). MedlinePlus-Health Information from the National Library of Medicine. https://medlineplus.gov/genetics/condition/parkinson-disease/ === |
| − | + | === Zhang J, et al. Nucleic Acids Res. 2002 Mar 1;30(5):1169-75 === | |
| − | https://medlineplus.gov/genetics/condition/parkinson-disease/ | + | === https://www.ncbi.nlm.nih.gov/Structure/pdb/5EOP === |
| − | ==== Zhang J, et al. Nucleic Acids Res. 2002 Mar 1;30(5):1169-75 | + | === Sheng J, et al. Acta Biochim Biophys Sin (Shanghai). 2016 May;48(5):399-410. doi: 10.1093/abbs/gmv131. === |
| − | https://www.ncbi.nlm.nih.gov/Structure/pdb/5EOP | + | === Aparicio-Erriu IM, et al. Front Neurosci. 2012 Nov 19;6:167. doi: 10.3389/fnins.2012.00167. === |
| − | ==== Sheng J, et al. Acta Biochim Biophys Sin (Shanghai). 2016 May;48(5):399-410. doi: 10.1093/abbs/gmv131. | + | === Wang YN, et al. Cancer Cell. 2018 Apr 9;33(4):752-769.e8. doi: 10.1016/j.ccell.2018.02.012. === |
| − | + | ||
| − | + | ||
Latest revision as of 11:54, 21 October 2021
pro-rANG-His-ter
- 10INCOMPATIBLE WITH RFC[10]Illegal XbaI site found at 47
- 12INCOMPATIBLE WITH RFC[12]Illegal NotI site found at 529
- 21INCOMPATIBLE WITH RFC[21]Illegal XhoI site found at 538
- 23INCOMPATIBLE WITH RFC[23]Illegal XbaI site found at 47
- 25INCOMPATIBLE WITH RFC[25]Illegal XbaI site found at 47
- 1000COMPATIBLE WITH RFC[1000]
Profile
BBa_K4005006
Name: pro-rANG-His-ter
Base Pairs: 675 bp
Origin: human，synthetic
Properties: A coding sequence for Angiogenin.
Usage and Biology
Angiogenin (Angiogenin, ANG) belongs to the secreted ribonuclease superfamily, and was originally discovered to be an angiogenic factor derived from human tumors. Subsequent studies have shown that ANG is also present in normal human tissues and body fluids. ANG increases the transcription of ribosomal RNA (rRNA) in the nucleus, while vascular endothelial growth factor (VEGF) and fibroblast growth factor-2 (FGF-2) activate mTOR and S6 kinase pathways to promote protein synthesis. Therefore, ANG can cooperate with VEGF and FGF-2 to promote protein synthesis in endothelial cells. In addition, ANG is necessary for endothelial cell proliferation. In addition to promoting angiogenesis, ANG is also involved in many other physiological and pathological processes, such as neuroprotection, inflammation, and tumorigenesis. Loss of function mutations in the ANG gene have been found in both amyotrophic lateral sclerosis (ALS) and Parkinson's disease (PD).
Construct design
The profiles of every basic part are as follows:
BBa_K4005000
Name: rANG
Base Pairs: 375bp
Origin: Homo sapiens (Human)
Properties: A coding sequence for Angiogenin.
Usage and Biology
ANG is necessary for the proliferation of endothelial cells, and mutations in the loss of function of the ANG gene are likely to be important causes of cardiovascular diseases such as amyotrophic lateral sclerosis (ALS) and Parkinson's disease (PD)
BBa_K4005003
Name: 6His
Base Pairs: 18bp
Origin: synthetic
Properties: Polyhistidine tag
Usage and Biology
It is an polyhistidine tag, which is used in the purification of recombinant proteins
BBa_K4005001
Name: P7
Base Pairs: 19bp
Origin: T7 phage, genome
Properties: A promoter for initiation of the transcription.
BBa_K4030002
Name: TT
Base Pairs: 140bp
Origin: Escherichia coli
Properties: Transcription terminator
Usage and Biology
It is an transcription terminator derived from the E.coli rrB rRNA operon
Experimental approach
pET-28a-rANG which produces ANG protein is shown in Figure 1.
As seen in figure 3, lane 1 is the pET-28a without enzyme digestion and lane 2 to 9 is the result for pET-28a after enzyme digestion. The bands of our plasmid vectors after enzyme digestion(5311bp) showed at 5000 bp around which are correct and the bands at 300 bp around were the SUMO fragments that were cut by enzyme digestion. After that, we could further conduct the E. coli transformation.
Lane 1 to 6 is the result of PCR. We got rANG band at around 400bp (369bp). Enzyme digestion was conducted and it was linked with digested pET-28a.
The plates in Fig. 5 (1) showed monoclonals of pET28a-rANG constructs. The pET28a-rANG was constructed successfully which has been proved by sequencing as shown in Fig. 5 (2).
Recombination E. coli
Lane NC to XCN6 and lane XCN7 to N6 are the results of colony PCR. We get the band 531bp at 500bp around. It indicates that the obtained recombinant monoclonals were positive monoclonals containing the pET-28a-rANG recombinant plasmid.
Proof of function
We did SDS-PAGE assey of protein and have obtained Freeze-dried powder of the ANG protein produced by our engineered Escherichia coli (Figure 7).
The activity of recombinant ANG protein was determined by the RNA degradation assay. The result indicated that ANG protein possesses ribonuclease activity as we expected.
Improvement of an existing part
Compared to the old part BBa_K3523005, composite part T7 pro-His-SOD-His-T7 ter, we design a new part BBa_K4005006, which replaced the SOD gene sequence fragment with rANG gene fragment. According to literature reports, heparan sulphate proteoglycans (HSPGs) are required for ANG to enter cells. HSPGs are linear anionic glycosaminoglycan (GAG) chains covalently linked to the core protein, composed of disaccharide repeating units of uronic acid and glucosamine, and the glucosamine residues 3-OH, 6-OH and -NH And the 2-OH of uronic acid is replaced by a sulfate group. HSPGs exist on the plasma membrane of all animals and are the main component of the extracellular matrix. Factors such as size, location, degree of sulfation, and uronic acid in different cells, tissues, and developmental stages contribute to the structural diversity of heparan sulphate (HS). This structural diversity is the basis for HSPGs to perform multiple functions. In previous research, our laboratory constructed a library of HS mutant mouse lung endothelial cells by knocking out key genes in the HS biosynthesis process. In this study, we prokaryotic expression and purification of recombinant ANG protein, using heparin and heparin derivatives and HS mutant mouse lung endothelial cell library to perform enzyme-linked immunosorbent assay and flow cytometry experiments to explore the interaction between ANG and HS The specificity and clarify its structure-activity relationship.
Future plan
In future applications, the product we get may have two directions of develop, but all in the clinical medicine aspect. One is to directly invent a new drug with the protein product of this gene and the other one is to explore its pharmacology regarding the relevant diseases which could be used to develop more new drugs.
The first kind of drug may have an effect on adjusting the nerve system, treating diseases like inflammation and the further developed drugs may be a possible treatment of some present incurable diseases such as PD and tumor. However, the overuse of ANG will also overpromote the generation of endothelial cells and vessels and may even cause cancer in some situations, so the correct usage of this drug shall be also necessary for being studied.
Market Survey According to relevant data, among the 65-year-olds, one in ten people are Parkinson's disease patients; among the 85-year-olds, the number of people who have Parkinson's disease reaches 30%-50%. The research progress and molecular biological characteristics of Angiopoietin and its related proteins are reviewed. So far, four kinds of Angiopoietin and some isoforms or variants of Angiopoietin have been discovered. These proteins have a common structure: a signal peptide related to secretion at the amino terminus, a helix-like domain that mediates homo-oligomers, and a fibrinogen-like domain that mediates ligand activity at the carboxyl terminus.
Marketing Plan The theory we have resulted in a unique product (but not medicine), which will be studied and researched by staff members in the collaborated pharmaceutical company), and the final medical products will be entirely produced and owned by the partner company. The outcome of our company remains with unknown effects on medicine. However, the result will be owned by our target group (pharmaceutical company).
We will market our product using many different ways. For example, online surveys, email marketing, mobile marketing, and social media marketing are considered the cheapest among all types of marketing. Since we are a brand new company, we do not have many budgets available for us, so we would consider the ways I listed above first. Once we have more budget allowed, we might try other ways of marketing our product. For example, printed marketing materials, such as brochures, flyers, business cards, etc. We can also try trade shows and other marketing that cost some money.
Challenges During the experimental work, the main challenges were the plasmid DNA extraction and the protein purification process. One aspect of the difficulty is the continuous low concentration of plasmid DNA when we first extracted them. But as we navigate through and become more familiar with the long process, we successfully extracted with an ideal concentration.
Moreover, heterologous overexpression often results in low expression levels and inactive protein due to insufficient membrane insertion and folding or lack of post-translational modifications. And over-expression of membrane proteins can be toxic to the cell. Nevertheless, eventually, we obtained the freeze-dried protein powder. But with no doubt, we will further solidify this part of the work.
Before our product come into a real application, there are still some concerns regarding our Angiogenin protein. We need to conduct more experiments and tests to further ensure its purity, stability and biological activity. In addition, we would further focus on the yield issues, storage conditions and how to use our products to determine the dose of curing some present incurable diseases.