Difference between revisions of "Part:BBa K4593002"

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<partinfo>BBa_K4593002 short</partinfo>
 
<partinfo>BBa_K4593002 short</partinfo>
  
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This part is the coding sequence of endolysin ClyC
  
 
===Usage and Biology===
 
===Usage and Biology===
  
CylC is an endolysin that specifically lyse S.aureus. It is composed of two domains: a EAD domain that facilitates the enzymatic breakdown of peptidoglycan; a CBD domain that recognizes cell surface ligands and attracts the enzyme to its substrate [1].  
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CylC is an endolysin that specifically targets S. aureus. It is composed of two domains: a Cell Binding Domain (CBD) that recognizes cell surface ligands and attracts the enzyme to its substrate; and an Enzymatically Active Domain (EAD) that breaks down cell-wall peptidoglycan[1].
  
 
===Team:BNDS-China 2023===
 
===Team:BNDS-China 2023===
  
Our project intend to develop a set of efficient method of lysing S.aureus. In our project, ClyC is one of the tested endolysin that has the potent bactericidal capability.
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Our project intends to develop a set of efficient methods for detecting and lysing S. aureus. ClyC is one of the tested endolysins that has a potent bactericidal capability and is applied in the lysing experiment in our project.
To express ClyC, this part was cloned into pET-28a and transformed into E. coli BL21 (ED3).  
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====Characterization of lytic activity when expressed in E.coli====
 
====Characterization of lytic activity when expressed in E.coli====
  
To characterize the lytic efficiency of ClyC,we designed plasmid pET28a(+)_ClyC (assembled by Genscript) (Fig.1), which allows ClyC to be expressd under the presence of IPTG.
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To characterize the lytic efficiency of ClyC, we designed plasmid pET28a(+)_ClyC (assembled by Genscript) (Fig.1), which allows ClyC to be expressed under the presence of IPTG.
 
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<p style="text-align:center;"><img src="https://static.igem.wiki/teams/4593/wiki/result/clyc-map.png" width="700" height="auto"/>
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</figure>
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====Examining protein length and purity using SDS-PAGE====
 
====Examining protein length and purity using SDS-PAGE====
  
After ClyC is purified using nickel bead columns, the protein length and purity is confirmed by SDS-PAGE and stained with Coomassie Brilliant Blue.
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After ClyC is purified using nickel bead columns, the protein length and purity are confirmed by SDS-PAGE and stained with Coomassie Brilliant Blue.
 
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<figure>
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<p style="text-align:center;"><img src="https://static.igem.wiki/teams/4593/wiki/result/clyc.png" width="300" height="auto"/>
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Figure 2. SDS-PAGE Result of ClyC Purification
 
Figure 2. SDS-PAGE Result of ClyC Purification
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====Examining lysing ability using spectrophotometer====
 
====Examining lysing ability using spectrophotometer====
  
To examine the sterilizing effect of varying ClyC endolysin concentrations over time, S. aureus was cultured overnight, diluted in TSB medium, and centrifuged once the OD600 reached 1.0. The cells were resuspended in reaction buffer and divided into five groups in sterilized tubes. Different concentrations of ClyC solution were added to each tube, with OD600 readings taken at 0, 15, 35, and 60 minutes post-addition, each measurement repeated thrice. The results underscore the strong bactericidal action of endolysin ClyC.
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To examine the sterilizing effect of varying ClyC endolysin concentrations over time, S. aureus was cultured overnight, diluted in TSB medium, and centrifuged once the OD600 reached 1.0. The cells were resuspended in reaction buffer and divided into five groups in sterilized tubes. Different concentrations of ClyC solution were added to each tube, with OD600 readings taken at 0, 15, 35, and 60 minutes post-addition, each measurement repeated thrice.
 
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<figure>
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<p style="text-align:center;"><img src="https://static.igem.wiki/teams/4593/wiki/result/figure-13.png" width="700" height="auto"/>
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</figcaption>
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</figure>
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</html>
  
 
Figure 3. OD 600 of S. aureus under different concentrations of ClyC with respect to time (error bars are too small to be visible)
 
Figure 3. OD 600 of S. aureus under different concentrations of ClyC with respect to time (error bars are too small to be visible)
  
======Examining lysing ability using chromogenic plates======
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The data highlights the potent bactericidal capability of endolysin ClyC. Over time, there's a noticeable decrease in the OD600 readings, signaling the dwindling of the S. aureus population. Interestingly, the bacterial reduction was more rapid at the 0.8uM concentration than at the 2uM and 0.2uM concentrations. This intriguing outcome could be attributed to the zero-salt environment required by the endolysin [1]. Also, the OD 600 of the mixture exhibits a significant growth just after the endolysin is added even though the resuspended bacteria in each tube are almost homogeneous, which is not explainable. Nonetheless, by the 60-minute mark, all three concentrations substantially curtailed the bacterial numbers, which successfully proved in the lytic activity.
  
For a broader analysis, four S. aureus groups were diluted 200-fold and plated on chromogenic agar after 120 minutes of lysing. A 0.5uM concentration was chosen for its representativeness in evaluating ClyC endolysin's efficiency. The colony density post-overnight incubation aligns with the OD600 results, reaffirming the study's successful execution in this aspect
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====Examining lysing ability using chromogenic plates====
  
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For further confirmation, four S. aureus groups were diluted 200-fold and plated on chromogenic agar after 120 minutes of lysing. A 0.5uM concentration was chosen for its representativeness in evaluating ClyC's efficiency. The colony density post-overnight incubation aligns with the OD600 results, reaffirming the study's successful execution in this aspect.
  
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<html>
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<figure>
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<p style="text-align:center;"><img src="https://static.igem.wiki/teams/4593/wiki/result/clyc-pic.jpg" width="700" height="auto"/>
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</figcaption>
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</figure>
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</html>
  
 
Figure 4. Overnight S.aureus chromogenic plate of S.aureus treated with different endolysin ClyC concentrations for 120 min.  
 
Figure 4. Overnight S.aureus chromogenic plate of S.aureus treated with different endolysin ClyC concentrations for 120 min.  
A) water      B) elution buffer   C) 2uM ClyC     D) 0.5uM ClyC
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A) water
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B) elution buffer  
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C) 2uM ClyC
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D) 0.5uM ClyC
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<span class='h3bb'>Sequence and Features</span>
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<partinfo>BBa_K4593002 SequenceAndFeatures</partinfo>
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<!-- Uncomment this to enable Functional Parameter display
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===Functional Parameters===
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<partinfo>BBa_K4593002 parameters</partinfo>
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Latest revision as of 14:19, 12 October 2023


ClyC

This part is the coding sequence of endolysin ClyC

Usage and Biology

CylC is an endolysin that specifically targets S. aureus. It is composed of two domains: a Cell Binding Domain (CBD) that recognizes cell surface ligands and attracts the enzyme to its substrate; and an Enzymatically Active Domain (EAD) that breaks down cell-wall peptidoglycan[1].

Team:BNDS-China 2023

Our project intends to develop a set of efficient methods for detecting and lysing S. aureus. ClyC is one of the tested endolysins that has a potent bactericidal capability and is applied in the lysing experiment in our project.

Characterization of lytic activity when expressed in E.coli

To characterize the lytic efficiency of ClyC, we designed plasmid pET28a(+)_ClyC (assembled by Genscript) (Fig.1), which allows ClyC to be expressed under the presence of IPTG.


Fig. 1 The plasmid map of pET28a(+)_ClyC product

Examining protein length and purity using SDS-PAGE

After ClyC is purified using nickel bead columns, the protein length and purity are confirmed by SDS-PAGE and stained with Coomassie Brilliant Blue.

Figure 2. SDS-PAGE Result of ClyC Purification

The protein eluted displays prominent bands at about 35 kDa in both lanes, showing consistency with the calculated molecular mass (34.6 kDa). Interestingly, the final wash also shows a high purity of ClyC, suggesting that the reserved sample remains in high concentration even after the washing steps.

Examining lysing ability using spectrophotometer

To examine the sterilizing effect of varying ClyC endolysin concentrations over time, S. aureus was cultured overnight, diluted in TSB medium, and centrifuged once the OD600 reached 1.0. The cells were resuspended in reaction buffer and divided into five groups in sterilized tubes. Different concentrations of ClyC solution were added to each tube, with OD600 readings taken at 0, 15, 35, and 60 minutes post-addition, each measurement repeated thrice.

Figure 3. OD 600 of S. aureus under different concentrations of ClyC with respect to time (error bars are too small to be visible)

The data highlights the potent bactericidal capability of endolysin ClyC. Over time, there's a noticeable decrease in the OD600 readings, signaling the dwindling of the S. aureus population. Interestingly, the bacterial reduction was more rapid at the 0.8uM concentration than at the 2uM and 0.2uM concentrations. This intriguing outcome could be attributed to the zero-salt environment required by the endolysin [1]. Also, the OD 600 of the mixture exhibits a significant growth just after the endolysin is added even though the resuspended bacteria in each tube are almost homogeneous, which is not explainable. Nonetheless, by the 60-minute mark, all three concentrations substantially curtailed the bacterial numbers, which successfully proved in the lytic activity.

Examining lysing ability using chromogenic plates

For further confirmation, four S. aureus groups were diluted 200-fold and plated on chromogenic agar after 120 minutes of lysing. A 0.5uM concentration was chosen for its representativeness in evaluating ClyC's efficiency. The colony density post-overnight incubation aligns with the OD600 results, reaffirming the study's successful execution in this aspect.

Figure 4. Overnight S.aureus chromogenic plate of S.aureus treated with different endolysin ClyC concentrations for 120 min.

A) water

B) elution buffer

C) 2uM ClyC

D) 0.5uM ClyC


Sequence and Features


Assembly Compatibility:
  • 10
    COMPATIBLE WITH RFC[10]
  • 12
    COMPATIBLE WITH RFC[12]
  • 21
    COMPATIBLE WITH RFC[21]
  • 23
    COMPATIBLE WITH RFC[23]
  • 25
    INCOMPATIBLE WITH RFC[25]
    Illegal NgoMIV site found at 681
    Illegal AgeI site found at 550
  • 1000
    COMPATIBLE WITH RFC[1000]