Difference between revisions of "Part:BBa K3182108"

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<partinfo>BBa_K3182108 short</partinfo>[[File:T--Linkoping_Sweden--sfGFPillustration.jpeg|420px|thumb|right|<b>Figure Y.</b> Mechanism of action]]
 
<partinfo>BBa_K3182108 short</partinfo>[[File:T--Linkoping_Sweden--sfGFPillustration.jpeg|420px|thumb|right|<b>Figure Y.</b> Mechanism of action]]
A cellulose binding domain (CBDcipA) from Clostridium thermocellum Cellulose scaffolding protein (CipA) which can be used to purify or attach proteins to cellulose, this part has a sfGFP fused to the CBDcipA. The part also has a flexible GS-linker (-GGGGSGGGGS-) with a thrombin site (-LVPRGS-, thrombin RS) added at the end, clevage with thrombin will add one glycine and one serine to the N-terminal of the C-terminal fusion protein of the CBDcipA.  
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This part consists of a cellulose binding domain (CBD) from Clostridium thermocellum cellulose scaffolding protein (CipA) with an sfGFP fused,  using a flexible GS-linker (-GGGGSGGGGS-), to the CBDCipA. A thrombin cleavage site (-LVPRGS-) is added to the end of the linker and its breakage will leave a glycine and serine amino acid attached to the N-terminal of the AsPink fusion protein.  
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An internal BamHI recognition sequence (RS) has been added to enable changeable fusion proteins. BamHI was chosen because its RS codes for glycine and serine, fitting it to the end of the thrombin site. It is also cost-effective enzyme and is unaffected by methylated DNA.
Also added a BamHI recognition sequence (BamHI RS) to enable changeable fusion protein to the CBDcipA. BamHI was chosen because its RS codes for one glycine and one serine, fitting it to the end of the thrombin site, BamHI can also be used with methylated DNA. This part has a sfGFP for easy trackable characterization of the CBDcipA.
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This part can be used to track purification, measure CBD binding ability and report breakage of the thrombinsite.
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This part uses an expression system with a T7 promotor (<partinfo>BBa_I719005</partinfo>) as well as a 5'-UTR (<partinfo>BBa_K1758100</partinfo>) region which has been shown to further increase expression in E. coli (<partinfo>BBa_K1758106</partinfo>), ([http://www.ncbi.nlm.nih.gov/pubmed/2676996 Olins et al. 1989]), ([http://www.ncbi.nlm.nih.gov/pubmed/23927491 Takahashi et al. 2013]).
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<h1>Usage and Biology</h1>
 
<h1>Usage and Biology</h1>
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The potential usage of this part can be divided in three part. Measurement of CBD binding ability, tracking of purification and reporter of linker breakage.
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<h2> Measurement of CBD binding ability </h2>
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<h2> Tracking of purification </h2>
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<h2> Reporter of linker breakage </h2>
 
[[File:T--Linkoping_Sweden--cellulosewashillustration.jpeg|420px|thumb|left|<b>Figure X.</b> Basic overlook of cellulose purification.]]
 
[[File:T--Linkoping_Sweden--cellulosewashillustration.jpeg|420px|thumb|left|<b>Figure X.</b> Basic overlook of cellulose purification.]]
 
[[File:T--Linkoping_Sweden--Thrombincontrolphoto.jpg|420px|thumb|right|<b>Figure X.</b> The cellulose bandage (Epiprotect) has been washed in bacterial lysate of the biobrick according to the illustration on the left. This was performed in an Eppendorf tube for 15 min on an end-to-end rotator. After binding the CBD-sfGFP, the bandage was washed three time with 70 % ethanol. The bandage was afterwards incubated over night in thrombin cleavage buffer (left) and in thrombin cleavage buffer+thrombin (right).]]
 
[[File:T--Linkoping_Sweden--Thrombincontrolphoto.jpg|420px|thumb|right|<b>Figure X.</b> The cellulose bandage (Epiprotect) has been washed in bacterial lysate of the biobrick according to the illustration on the left. This was performed in an Eppendorf tube for 15 min on an end-to-end rotator. After binding the CBD-sfGFP, the bandage was washed three time with 70 % ethanol. The bandage was afterwards incubated over night in thrombin cleavage buffer (left) and in thrombin cleavage buffer+thrombin (right).]]

Revision as of 14:58, 14 August 2019

Sequence and Features


Assembly Compatibility:
  • 10
    COMPATIBLE WITH RFC[10]
  • 12
    COMPATIBLE WITH RFC[12]
  • 21
    INCOMPATIBLE WITH RFC[21]
    Illegal BamHI site found at 580
  • 23
    COMPATIBLE WITH RFC[23]
  • 25
    COMPATIBLE WITH RFC[25]
  • 1000
    INCOMPATIBLE WITH RFC[1000]
    Illegal SapI.rc site found at 598


Introduction

pT7-CBDcipA-sfGFP
Figure Y. Mechanism of action

This part consists of a cellulose binding domain (CBD) from Clostridium thermocellum cellulose scaffolding protein (CipA) with an sfGFP fused, using a flexible GS-linker (-GGGGSGGGGS-), to the CBDCipA. A thrombin cleavage site (-LVPRGS-) is added to the end of the linker and its breakage will leave a glycine and serine amino acid attached to the N-terminal of the AsPink fusion protein.

An internal BamHI recognition sequence (RS) has been added to enable changeable fusion proteins. BamHI was chosen because its RS codes for glycine and serine, fitting it to the end of the thrombin site. It is also cost-effective enzyme and is unaffected by methylated DNA.

This part can be used to track purification, measure CBD binding ability and report breakage of the thrombinsite.

This part uses an expression system with a T7 promotor (BBa_I719005) as well as a 5'-UTR (BBa_K1758100) region which has been shown to further increase expression in E. coli (BBa_K1758106), (Olins et al. 1989), (Takahashi et al. 2013).








CBDcipA and sfGFP 3D structure

Figure Y. Crystal structure of CBDcipA with a resolution of 1.75 Å which were solved by Tormo et al. 1989. PDB code 1NBC. In red from the left, W118, R112, D56, H57 and Y67, thought to be the surface which interacts strongly with cellulose.
Figure Y. Crystal structure of sfGFP with a resolution of 1.4 Å which were solved by Pédelacq et al. 2006. PDB code 2B3P. In red the chromophore can be seen. Excitation wavelength: 485 nm, emission wavelength: 510 nm


























Expression system

The part has a very strong expression with a T7 promotor (BBa_I719005) as well as a 5'-UTR (BBa_K1758100) region which has been shown to further increase expression in E. coli (BBa_K1758106), (Olins et al. 1989), (Takahashi et al. 2013). Both this part and the part were sfGFP was changed for AsPink (BBa_K3182000) showed great expression.

Figure B. Benchling screenshot of the expression system. This expression system leads to a high expression and therefore protein yield.

Usage and Biology

The potential usage of this part can be divided in three part. Measurement of CBD binding ability, tracking of purification and reporter of linker breakage.

Measurement of CBD binding ability

Tracking of purification

Reporter of linker breakage

Figure X. Basic overlook of cellulose purification.
Figure X. The cellulose bandage (Epiprotect) has been washed in bacterial lysate of the biobrick according to the illustration on the left. This was performed in an Eppendorf tube for 15 min on an end-to-end rotator. After binding the CBD-sfGFP, the bandage was washed three time with 70 % ethanol. The bandage was afterwards incubated over night in thrombin cleavage buffer (left) and in thrombin cleavage buffer+thrombin (right).












Figure Y. Crystal structure of sfGFP with a resolution of 1.4 Å which were solved by Pédelacq et al. 2006. PDB code 2B3P. In red the chromophore can be seen. Excitation wavelength: 485 nm, emission wavelength: 510 nm












T--Linkoping Sweden--CBD-sfGFPbind.png T--Linkoping Sweden--CBD-sfGFPstorodl4.jpeg T--Linkoping Sweden--CBD-sfGFPrör4.jpeg Figure Z Picture 1: Binding studies of the CBDcipA-sfGFP bound to bacterial cellulose. Washed three times with either 70 % ethanol, PBS or deionized water. Picture 2: Induced culture after 16 hours. E. coli BL21 (DE3) cells were grown in prescence of 25 ug/mL chlorampenicol until an OD600 of 0.8 at 37 degrees Celsius, and later induced with 0.5 mM IPTG. The induced culture were then incubated in 16 degrees Celsius for 16 hours. Picture 3: Left: CBDcipA-sfGFP bound to bacterial cellulose in form of a thin film, right: bacterial cellulose reference. Binding of CBDcipA-sfGFP was done the same way as the pictures below.



T--Linkoping Sweden--CBD-sfGFPrör1.jpeg T--Linkoping Sweden--CBD-sfGFPrör2.jpeg T--Linkoping Sweden--CBD-sfGFPrör3.jpeg

Figure A Picture 1: Lysate containing CBDcipA-sfGFP with bacterial cellulose before incubation. Picture 2: Lysate bound to bacterial cellulose after incubation in room temperature for 30 minutes on an end-to-end rotator. Picture 3: Bacterial cellulose after incubation with 70 % ethanol in room temperature for 30 minutes on an end-to-end rotator. All pictures were taken on a UV-table for better visualization of the result.