Difference between revisions of "Part:BBa K1800002"

(Characterization of TU_Dresden 2019)
(Characterization: TU_Dresden 2019)
 
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== Characterizatio: [https://2019.igem.org/Team:TU_Dresden TU_Dresden 2019] ==
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== Characterization: [https://2019.igem.org/Team:TU_Dresden TU_Dresden 2019] ==
 
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The following characterization assays were done by the Team: [https://2019.igem.org/Team:TU_Dresden TU_Dresden 2019]
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This team adapted this BioBrick to the RCF25 standard. Therefore it had to be uploaded as a separate BioBrick, which can be found here: [https://parts.igem.org/Part:BBa_K3037007 BBa_K3037007]
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The sequences are identical and it is the same BioBrick just in a different standard. The proof that the standard did not influence expression or activity can be found in the characterization.
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Find more information about the RCF25 standard here: [[Help:Assembly_standard_25|Freiburg RFC 25 standard]]
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=== Outline ===
 
=== Outline ===
 
We performed the following characterization experiments:
 
We performed the following characterization experiments:
  
1) Comparison of the growth curve of BioBrick in RFC10 and RFC25. Expression in pOOC97 [https://parts.igem.org/Part:BBa_K3037000 (BBa_K3037000)]
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<b>1)</b> Growth curve of expression in pOCC97 [https://parts.igem.org/Part:BBa_K3037000 (BBa_K3037000)] in <span style="font-style: italic;">E. coli</span> pRARE T7
  
2) Determination of the total protein amount of cleared lysate after expression
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<b>2)</b> Determination of the total protein concentration of cleared lysate after expression
assay of the substrate conversion (TMB) compared to [https://parts.igem.org/Part:BBa_K3037007 (BBa_K3037007)]
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assay of the substrate conversion (TMB) compared to [https://parts.igem.org/Part:BBa_K1800002 (BBa_K1800002)]
  
3) Protein Expression monitoring in SDS-PAGE
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<b>3)</b> Protein Expression monitored via SDS-PAGE
  
4) Determination of the total protein amount of cleared lysate after expression
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<b>4)</b> Activity assay of the substrate conversion TMB compared to [https://parts.igem.org/Part:BBa_K1800002 (BBa_K1800002)]
assay of the substrate conversion (TMB) compared to [https://parts.igem.org/Part:BBa_K3037007 (BBa_K3037007)]
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=== Experiments in Detail ===
 
=== Experiments in Detail ===
  
==== 1) Comparison of the growth curve of BioBrick in RFC10 and RFC25. Expression in pOOC97 [https://parts.igem.org/Part:BBa_K3037000 (BBa_K3037000)] ====
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==== 1) Growth curve of expression in pOCC97 [https://parts.igem.org/Part:BBa_K3037000 (BBa_K3037000)] in <span style="font-style: italic;">E. coli</span> pRARE T7 ====
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The HRP was expressed using the plasmid pOCC97 as a backbone [https://parts.igem.org/Part:BBa_K3037000 (BBa_K3037000)]
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The purpose of this experiment was to show that the <span style="font-style: italic;">Escherichia coli</span> pRARE T7 grows normally after the induction of HRP expression.
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For this, growth of bacteria was monitored by measuring the Optical absorbance at 600 nm during different time points before and after induction with 1 mM IPTG. As shown in the following Figure, the <span style="font-style: italic;">Escherichia coli</span> growth is not affected by the expression of the protein. It shows a normal growth behaviour as expected in a batch culture (Figure 1).
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[[File:T--TU_Dresden--Expression_in_pOCC97_BBa_K3037007.png|center|400px|thumb|none|Figure 1: Growth curve of <span style="font-style: italic;">Escherichia coli</span> before and after expressing HRP. Vector pOCC97 (BBa_K3037000). Induction with 1mM IPTG]]
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==== 2) Determination of the total protein concentration of cleared lysate after expression assay of the substrate conversion (TMB) compared to [https://parts.igem.org/Part:BBa_K1800002  (BBa_K1800002)]  ====
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The purpose of this experiment is to show that the <span style="font-style: italic;">Escherichia coli</span> grows normaly after the induction of the expression of HRP and also there is no difference between the growing of the BioBrick in the RFC10 and the RFC25.
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In order to determine the total protein content of the cleared lysate after the expression the following assay was performed. First, the standard curve was done with the Pierce BCA protein assay kit of Thermo Scientific [https://www.thermofisher.com/order/catalog/product/23225?SID=srch-srp-23225#/23225?SID=srch-srp-23225 (#23225)] (Figure 2).
  
For this the development of the culture was monitored by measuring the OD at 600 nm during different time points before and after induction with 1 mM IPTG. As shown in the curve the growing of the bacteria is not affected by the expression of the protein. <span style="font-style: italic;">Escherichia coli</span> show a the normal growth behaviour as expected in a batch culture.
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[[File:T--TU_Dresden--BSA.png|center|400px|thumb|none|Figure 2: Calibration curve with known BSA concentrations in order to determine the concentrations of our samples.]]
  
[[File:T--TU_Dresden--Growing_comparison_HRP_BBa_K1800002.png|center|400px|thumb|none|Growth curve of Expression in pOCC97, BBa_K3037000]]
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Then different cultures of <i>E. coli</i> pRARE T7 transformed with different BioBricks using pOCC97 [https://parts.igem.org/Part:BBa_K3037000 (BBa_K3037000)] as a vector were set. The BioBricks used were:
  
==== 2) Determination of total protein amount of cleared lysate: ====
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* A fusion protein of MBP and HRP [https://parts.igem.org/Part:BBa_K3037008 (BBa_K3037008)]
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* This HRP but in the RFC10 standard [https://parts.igem.org/Part:BBa_K1800002 (BBa_K1800002)]
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* This HRP adapted to the RFC25 standard (BBa_K3037007)
  
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Then a culture of 100 mL <i>E. coli</i> pRARE T7 transformed with the different BioBricks was cultivated until the OD reached 0.5, then the culture was induced with 0.5 mM IPTG and 6 hours after that it was spun down. The pellet was stored at -80 degrees and left overnight. The next day the cells were lysed and the supernatant was taken to measure the protein concentration. The results were compared with the standard curve to calculate the concentration as shown in Figure 3.
  
A culture of 100mL <span style="font-style: italic;">Escherichia coli</span> pRARE T7 transformed with the HRP BioBrick inside pOOC97 [https://parts.igem.org/Part:BBa_K3037000 (BBa_K3037000)], they were cultivated until the OD reach 0.5, then the culture was induced with 0.5 mM IPTG and 6 hours after that it was spin down. The pellet was frezeed at -80 degrees and leaved overnight. The next day the cells were lysate and the supernatand was taken for measure the protein concentration. The standard curve was done with the Pierce BCA protein assat kit of thermo scientific (#23225).
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[[File:T--TU_Dresden--HRP2.png|center|600px|thumb|none|Figure 3: Protein concentration of HRP measured in the cleared lysate of <i>E. coli</i> pRARE T7 carrying the expression backbone pOCC97 (BBa_K3037000) with different inserts. Expression was induced 0.5 mM IPTG]]
  
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==== 3) Protein Expression monitoring in SDS-PAGE: ====
  
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A culture of 100 mL <span style="font-style: italic;">Escherichia coli</span> pRARE T7 were transformed with the HRP BioBrick inside pOCC97 [https://parts.igem.org/Part:BBa_K3037000 (BBa_K3037000),] they were cultivated until the absorbance reached 0.5. Samples before induction were taken. Then the culture was induced with 0.5 mM IPTG,every 30 minutes samples were collected (5 samples), then 3 more each 1 hour. Before making the SDS-PAGE, the samples were adjusted to absorbance of 0.5 to have the same amount of cells in each lane. By doing so, the increase of a specific protein can be observed. The results show the increase of the concentration of the protein in time (Figure 4).
  
<gallery mode="packed", caption="Assay to determine protein amount", widths=400px, heights=200px>
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[[File:T--TU_Dresden--SDS-PAGE_HRP_BBa_K3037007.png|center|500px|thumb|left|Figure 4: SDS-PAGE of the expression of HRP (BBa_K3037007) in the vector pOCC97 (BBa_K3037000). Upper anotations showing the different times of induction in minutes. The protein band is marked with an arrow]]
File:T--TU_Dresden--Standard_curve.png|<span style="color:#0000ff"> ''Calibration curve''  </span> (Protein Amount Assay with known BSA concentration)
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File:T--TU_Dresden--Standard_plot.png|<span style="color:#0000ff">''Values of Total Protein Amounts determined with calibration curve''  </span> (Values corresponding to the curve shown left)
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File:T--TU_Dresden--comparison_HRP_assay.png|<span style="color:#0000ff">''Total Amounts'' </span>  (Total protein amounts obtained by expression)
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File:T--TU_Dresden--Measurements_plot_HRP_assay.png|<span style="color:#0000ff">''Values of Calibration curve''  </span> (Values corresponding to the curve shown left)
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</gallery>
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==== 3) Expression assay: ====
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As it can be seen in the SDS-PAGE, the protein of interest is increasing over time from the point of induction onwards. HRP is marked with a black arrow pointing left.
  
A culture of 100 mL <span style="font-style: italic;">Escherichia coli</span> pRARE T7 transformed with the HRP BioBrick inside pOOC97 (BBa_K3037000), they were cultivated until the OD600 reach 0.5. Samples before induction were taken. Then the culuture was induced with 0.5 mM IPTG, samples were taken each 30 minutes (5 samples), then 3 more each 1 hour. Before making the SDS-PAGE, the samples were adjusted to OD of 0.5 to have the same amount of cells in each lane. This way the increase in one specific protein can be observed. The results show the increase of the concentration of the protein in time.
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==== 4) Activity assay of the substrate conversion (TMB) compared to BBa_K1800002 ====
  
[[File:T--TU_Dresden--SDS-PAGE_HRP_BBa_K3037007.png|center|500px|thumb|left]]
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The conversion of transparent TMB substrate to blue reaction product was monitored at 370 nm over half an hour with absorption measurements every 60 seconds for the HRP adapted to the RFC10 standard [https://parts.igem.org/Part:BBa_K1800002 (BBa_K1800002)] and to the RFC25 [https://parts.igem.org/Part:BBa_K3037007 (BBa_K3037007)] (Figure 5)
  
As can be seen in the SDS-PAGE the protein of interest is incresing over time from the point of induction onwards. HRP is marked with a black arrow pointing left.
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[[File:Activity Assay HRPs.png|center|400px|thumb|left|Figure 5: Activity assay of HRP in different iGEM standards expressed in pOCC97 (BBa_K3037000) monitored at 370 nm measuring every 60 seconds.]]
  
==== 4) Activity assay of the substrate conversion (TMB) compared to BBa_K3037007 ====
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As it can be seen in the graph, the activity of this BioBrick and the original one from which it was adapted from are not different. This was our expected result, since the sequences are the same and only the prefix and suffix were changed from RCF10 to RCF25.
The conversion of transparent TMB substrate to blue reaction product was monitored at 370 nm over half an hour with absorption measurement every 60 seconds.
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[[File:Activity Assay HRPs.png|center|400px|thumb|left]]
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As can be seen in the graph, the activity of this BioBrick and the original one that it was adapted from are not different. This was to be expected, since the sequences are the same and only the prefix and suffix were changed from RCF10 to RCF25.
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== References ==
 
== References ==

Latest revision as of 23:29, 21 October 2019


Horseradish Peroxidase

Overview

This BioBrick was adapted to the Freiburg RFC25 standard by the Team: TU_Dresden 2019 and their characterization was implemented in this page. Also you can find it here: BBa_K3037007

Description

Class III plant peroxidases catalyze various oxidative reactions in which electrons are transferred to peroxide species, and substrate molecules are oxidized (Krainer, 2015). Peroxidases can be found in most plants and have been proposed to influence various functions related to the degradation of indole-3-acetic acid (IAA) (Lamport, 1986) and cell wall elasticity (Goldberg et al., 1986). Horseradish peroxidases is a peroxidase that has been used exhaustively as a reporter enzyme in diagnostics and histochemistry. In our lab, we designed an HRP part in accordance to RFC 10. HRP in our experiment will serve as a proof of concept for the Agrobacterium tumefaciens mediated transformation of tobacco plants with CBDA synthase. HRP will be inserted into the pORE vector for transformation of A. tumefaciens. The A. tumefaciens will then be used to transform tobacco plants. The tobacco will then produce hairy roots suspended in the culture that contains the HRP part.

Characterization: TU_Dresden 2019

Outline

We performed the following characterization experiments:

1) Growth curve of expression in pOCC97 (BBa_K3037000) in E. coli pRARE T7

2) Determination of the total protein concentration of cleared lysate after expression assay of the substrate conversion (TMB) compared to (BBa_K1800002)

3) Protein Expression monitored via SDS-PAGE

4) Activity assay of the substrate conversion TMB compared to (BBa_K1800002)

Experiments in Detail

1) Growth curve of expression in pOCC97 (BBa_K3037000) in E. coli pRARE T7

The HRP was expressed using the plasmid pOCC97 as a backbone (BBa_K3037000)

The purpose of this experiment was to show that the Escherichia coli pRARE T7 grows normally after the induction of HRP expression.

For this, growth of bacteria was monitored by measuring the Optical absorbance at 600 nm during different time points before and after induction with 1 mM IPTG. As shown in the following Figure, the Escherichia coli growth is not affected by the expression of the protein. It shows a normal growth behaviour as expected in a batch culture (Figure 1).

Figure 1: Growth curve of Escherichia coli before and after expressing HRP. Vector pOCC97 (BBa_K3037000). Induction with 1mM IPTG

2) Determination of the total protein concentration of cleared lysate after expression assay of the substrate conversion (TMB) compared to (BBa_K1800002)

In order to determine the total protein content of the cleared lysate after the expression the following assay was performed. First, the standard curve was done with the Pierce BCA protein assay kit of Thermo Scientific (#23225) (Figure 2).

Figure 2: Calibration curve with known BSA concentrations in order to determine the concentrations of our samples.

Then different cultures of E. coli pRARE T7 transformed with different BioBricks using pOCC97 (BBa_K3037000) as a vector were set. The BioBricks used were:

  • A fusion protein of MBP and HRP (BBa_K3037008)
  • This HRP but in the RFC10 standard (BBa_K1800002)
  • This HRP adapted to the RFC25 standard (BBa_K3037007)

Then a culture of 100 mL E. coli pRARE T7 transformed with the different BioBricks was cultivated until the OD reached 0.5, then the culture was induced with 0.5 mM IPTG and 6 hours after that it was spun down. The pellet was stored at -80 degrees and left overnight. The next day the cells were lysed and the supernatant was taken to measure the protein concentration. The results were compared with the standard curve to calculate the concentration as shown in Figure 3.

Figure 3: Protein concentration of HRP measured in the cleared lysate of E. coli pRARE T7 carrying the expression backbone pOCC97 (BBa_K3037000) with different inserts. Expression was induced 0.5 mM IPTG

3) Protein Expression monitoring in SDS-PAGE:

A culture of 100 mL Escherichia coli pRARE T7 were transformed with the HRP BioBrick inside pOCC97 (BBa_K3037000), they were cultivated until the absorbance reached 0.5. Samples before induction were taken. Then the culture was induced with 0.5 mM IPTG,every 30 minutes samples were collected (5 samples), then 3 more each 1 hour. Before making the SDS-PAGE, the samples were adjusted to absorbance of 0.5 to have the same amount of cells in each lane. By doing so, the increase of a specific protein can be observed. The results show the increase of the concentration of the protein in time (Figure 4).

Figure 4: SDS-PAGE of the expression of HRP (BBa_K3037007) in the vector pOCC97 (BBa_K3037000). Upper anotations showing the different times of induction in minutes. The protein band is marked with an arrow

As it can be seen in the SDS-PAGE, the protein of interest is increasing over time from the point of induction onwards. HRP is marked with a black arrow pointing left.

4) Activity assay of the substrate conversion (TMB) compared to BBa_K1800002

The conversion of transparent TMB substrate to blue reaction product was monitored at 370 nm over half an hour with absorption measurements every 60 seconds for the HRP adapted to the RFC10 standard (BBa_K1800002) and to the RFC25 (BBa_K3037007) (Figure 5)

Figure 5: Activity assay of HRP in different iGEM standards expressed in pOCC97 (BBa_K3037000) monitored at 370 nm measuring every 60 seconds.

As it can be seen in the graph, the activity of this BioBrick and the original one from which it was adapted from are not different. This was our expected result, since the sequences are the same and only the prefix and suffix were changed from RCF10 to RCF25.

References

Krainer, F. W., & Glieder, A. (2015). An updated view on horseradish peroxidases: recombinant production and biotechnological applications. Applied microbiology and biotechnology, 99(4), 1611-1625.

Lamport, D.T.A. 1986. Roles for peroxidase in cell wall genesis, p. 199-208. In: H. Greppin, C. Penel, and T. Gasper (eds.). Molecular and physiological aspects of plant peroxidase. Univ. of Geneva Press, Switzerland.

Lamport, D.T.A. 1986. Roles for peroxidase in cell wall genesis, p. 199-208. In: H. Greppin, C. Penel, and T. Gasper (eds.). Goldberg, R., A. Imberty, M. Liberman, and R. Prat. 1986. Relationships between peroxidase activities and cell wall plasticity, p. 209-220. In: H. Greppin, C. Penel, and T. Gasper (eds.). Molecular and physiological aspects of plant peroxidase. Univ. of Geneva Press, Switzerland.



Sequence and Features


Assembly Compatibility:
  • 10
    COMPATIBLE WITH RFC[10]
  • 12
    INCOMPATIBLE WITH RFC[12]
    Illegal NheI site found at 154
  • 21
    INCOMPATIBLE WITH RFC[21]
    Illegal BglII site found at 396
    Illegal XhoI site found at 480
  • 23
    COMPATIBLE WITH RFC[23]
  • 25
    COMPATIBLE WITH RFC[25]
  • 1000
    COMPATIBLE WITH RFC[1000]