Difference between revisions of "Part:BBa K2922000"
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<partinfo>BBa_K2922000 short</partinfo>
 
<partinfo>BBa_K2922000 short</partinfo>
  
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This part contains the sequence for the protein beta-glucosidase with protein yebF fused to its N-terminus by GS linker. It can achieve the secretion of Beta-glucosidase with the function of yebF protein.
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This part contains the sequence for the protein Beta-glucosidase with protein YebF fused to its N-terminus by GS linker. It can achieve the secretion of Beta-glucosidase with the function of YebF protein.
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===Biology===
 
===Biology===
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BBa_K2922000 is a composite of ''bgl1A'' (<partinfo>BBa_K2564000</partinfo>) with ''yebF''(<partinfo>BBa_K1659003</partinfo>), a protein reported to be naturally secreted into the extracellular medium by E.coli BL21:
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BBa_K2922000 is a composite of Bgl1A (<partinfo>BBa_K2564000</partinfo>) with YebF (<partinfo>BBa_K1659003</partinfo>), a protein reported to be naturally secreted into the extracellular medium by ''E.coli'' BL21:
  
  
 
'''1. Bgl1A'''
 
'''1. Bgl1A'''
  
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Cellulose is a polymer composed of beta-1,4-linked glucosyl residues. Cellulases (Endoglucanases), cellobiosidases (Exoglucanases), and Beta-glucosidases are required by organisms (some fungi, bacteria) that can consume it. These enzymes are powerful tools for degradation of plant cell walls by pathogens and other organisms consuming plant biomass.  
+
Cellulose is a polymer composed of Beta-1,4-linked glucosyl residues. Cellulases (Endoglucanases), Cellobiosidases (Exoglucanases), and Beta-glucosidases are required by organisms (some fungi, bacteria) that can consume it. These enzymes are powerful tools for degradation of plant cell walls by pathogens and other organisms consuming plant biomass.  
  
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Beta-glucosidase is an 53 kDa enzyme that catalyzes the hydrolysis of the glycosidic bonds to terminal non-reducing residues in beta-D-glucosides and oligosaccharides, with release of glucose.<ref>M. Cox, D. Nelson, Lehninger Principles of Biochemistry.  (2000), vol. 5. New York: Worth Publishers. pp. 306–308.</ref>
+
Beta-glucosidase is a 53 kDa enzyme that catalyzes the hydrolysis of the glycosidic bonds to terminal non-reducing residues in Beta-D-glucosides and oligosaccharides, with release of glucose.<ref>M. Cox, D. Nelson, Lehninger Principles of Biochemistry.  (2000), vol. 5. New York: Worth Publishers. pp. 306–308.</ref>
  
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Depending on the organism cellobiose may be cleaved extracellularly by β-glucosidases (cellobiases) and imported as glucose, or imported directly and cleaved in the cytoplasm. Import generally occurs through phosphotransferase transport systems.<ref>R. M. Weiner et al., Complete genome sequence of the complex carbohydrate-degrading marine bacterium, Saccharophagus degradans strain 2-40 T. 4, e1000087 (2008).</ref>
+
Depending on the organism cellobiose may be cleaved extracellularly by Beta-glucosidases (Cellobiases) and imported as glucose, or imported directly and cleaved in the cytoplasm. Import generally occurs through phosphotransferase transport systems.<ref>R. M. Weiner et al., Complete genome sequence of the complex carbohydrate-degrading marine bacterium, Saccharophagus degradans strain 2-40 T. 4, e1000087 (2008).</ref>
  
  
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YebF is a 13 kDa protein of unknown function that is perhaps the only protein that has been conclusively documented to be secreted into the extracellular medium by a laboratory ''E. coli'' strain. At the N-terminus, YebF has a 2.2 kDa sec-leader sequence which mediates its translocation through the bacterial inner membrane via the Sec pathway, and is cleaved upon translocation into the periplasm to give the 10.8 kDa "mature" form.  
 
YebF is a 13 kDa protein of unknown function that is perhaps the only protein that has been conclusively documented to be secreted into the extracellular medium by a laboratory ''E. coli'' strain. At the N-terminus, YebF has a 2.2 kDa sec-leader sequence which mediates its translocation through the bacterial inner membrane via the Sec pathway, and is cleaved upon translocation into the periplasm to give the 10.8 kDa "mature" form.  
  
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Export from periplasm into the extracellular space takes places via the Omp pathway, whereby the electropositive dynamic region of YebF electrostatically helps load YebF onto the OmpF/OmpC porins at their electronegative periplasmic face, and after which the disordered N-terminal region of YebF gets threaded through the OmpF lumen. YebF has been used successfully to mediate the secretion of recombinant proteins.<ref>https://parts.igem.org/wiki/index.php?title=Part:BBa_K1659003#Biology</ref>
+
Export from periplasm into the extracellular space takes place via the Omp pathway, whereby the electropositive dynamic region of YebF electrostatically helps load YebF onto the OmpF/OmpC porins at their electronegative periplasmic face, and after which the disordered N-terminal region of YebF gets threaded through the OmpF lumen. YebF has been used successfully to mediate the secretion of recombinant proteins.<ref>https://parts.igem.org/wiki/index.php?title=Part:BBa_K1659003#Biology</ref>
 
<html>
 
<html>
 
     <figure>
 
     <figure>
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===Usage===
 
===Usage===
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In order to let yebF help secrete our cellulase out of the ''E. coli'' membrane, we fused the cellulase gene fragment with yebF gene fragment at the N-terminal by Overlap Extension Polymerase Chain Reaction(OE-PCR), and inserted a flexible GS Linker (GGGGS). PCR product was identified by agarose gel electrophoresis (Fig.1)
+
In order to let YebF help secrete Cellulase out of the ''E. coli'' membrane, we fused the Cellulase gene fragment with YebF gene fragment at the N-terminal by Overlap Extension Polymerase Chain Reaction(OE-PCR), and inserted a flexible GS Linker (GGGGS). PCR product was identified by agarose gel electrophoresis (Fig.1)
  
 
<html>
 
<html>
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     </figure>
 
     </figure>
 
</html>
 
</html>
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:'''Fig. 1''' Agarose Gel Electrophoresis of yebF-bgl1A (<partinfo>BBa_K2922000</partinfo>)OE-PCR product. Lane M: Marker. The PCR product in the second step, it showed a signal band at about 1800 bp.
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:'''Fig. 1''' Agarose Gel Electrophoresis of ''yebF-bgl1A'' (<partinfo>BBa_K2922000</partinfo>)OE-PCR product. Lane M: Marker. The PCR product in the second step, it showed a signal band at about 1800 bp.
  
  
 
===Characterization===
 
===Characterization===
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These parts were insert into the expression vectors with T7 and RBS (<partinfo>BBa_K525998</partinfo>) by restriction sites ''Eco''R I and ''Pst'' I. Then transformed the expression vectors into ''E. coli'' DH5α, and the correct construction of this recombinant plasmid was confirmed by chloramphenicol, colony PCR and plasmid sequencing.
+
These parts were inserted into the expression vectors with T7 and RBS (<partinfo>BBa_K525998</partinfo>). Then transformed the expression vectors into ''E. coli'' DH5α, and the correct construction of this recombinant plasmid was confirmed by chloramphenicol, colony PCR and plasmid sequencing.
  
 
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'''1. SDS-PAGE'''
 
'''1. SDS-PAGE'''
  
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We transformed the constructed plasmid into ''E. coli'' BL21 (DE3). After confirmed by the same method, the positive clones were cultivated and induced to express by IPTG. The supernatant of culture medium was obtained by centrifugation. And we gain the total protein by ultrasonic crushing. The lysate was then centrifuged and the supernatant was electrophoresed on a sodium dodecyl sulfate (SDS)-12% (wt/ol) polyacrylamide gel, followed by Silver staining. (Fig. 2)
+
We transformed the constructed plasmid into ''E. coli'' BL21 (DE3). The positive clones were cultivated and induced to express by IPTG. The supernatant of culture medium was obtained by centrifugation. And we gain the total protein by ultrasonic crushing. The lysate was then centrifuged and the supernatant was electrophoresed on a sodium dodecyl sulfate (SDS)-12% (wt/ol) polyacrylamide gel, followed by Silver staining. (Fig. 2)
  
 
<html>
 
<html>
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     </figure>
 
     </figure>
 
</html>
 
</html>
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:'''Fig. 2''' SDS-PAGE analysis of E. coli BL21 (DE3) by Sliver staining. YebF-bgl1A: protein of E. coli BL21 (DE3) carrying T7-RBS-yebF-bgl1A (<partinfo>BBa_K2922006</partinfo>), target bands can be seen in both cells and the medium at 63.4 kDa; Control: protein of E. coli BL21 (DE3) carrying T7 and RBS (<partinfo>BBa_K525998</partinfo>).
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:'''Fig. 2''' SDS-PAGE analysis of ''E. coli'' BL21 (DE3) by Sliver staining. YebF-bgl1A: protein of ''E. coli'' BL21 (DE3) carrying T7-RBS-yebF-bgl1A (<partinfo>BBa_K2922006</partinfo>), target bands can be seen in both cells and the medium at 63.4 kDa; Control: protein of E. coli BL21 (DE3) carrying T7 and RBS (<partinfo>BBa_K525998</partinfo>).
  
  
 
'''2. HPLC'''
 
'''2. HPLC'''
  
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We use HPLC to verify the activity of bgl1A. First of all, we used the different concentrations of glucose solution and cellobiose solution to make SWC (Standard Working Curve) of HPLC.  
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We use HPLC to verify the activity of Bgl1A. First of all, we used the different concentrations of glucose solution and cellobiose solution to make SWC (Standard Working Curve) of HPLC.  
  
 
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Then mix the crude enzyme solution with cellobiose, incubate under the condition of 37°C, 200 rpm using a shaking incubator for reaction. Take out one tube of reaction system into boiling water bath for 8 minutes to stop the reaction when and after interval time since reaction started. And then carry out HPLC on the sample.  
+
Then mix the crude enzyme solution with cellobiose, incubate under the condition of 37°C, 200 rpm using a shaking incubator for reaction. Take out one tube of reaction system into boiling water bath for 8 minutes to stop the reaction after interval time since reaction started. And then carry out HPLC on the sample.  
  
 
<html>
 
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:'''Fig. 4''' The results of HPLC. (A): T7-RBS-yebF-bgl1A supernatant; (B): T7-RBS-yebF-bgl1A broken supernatant  
 
:'''Fig. 4''' The results of HPLC. (A): T7-RBS-yebF-bgl1A supernatant; (B): T7-RBS-yebF-bgl1A broken supernatant  
  
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Result of the broken supernatant and supernatant of medium cultures with PT7-RBS-yebF-bgl1A part shows that D-cellobiose got consumed with extension of reaction time and more D-glucose obtained. Bgl1A could degrade D-cellobiose into D-glucose.
+
Result of the broken supernatant and supernatant of medium cultures with T7-RBS-yebF-bgl1A part shows that D-cellobiose got consumed with extension of reaction time and more D-glucose obtained. Bgl1A could degrade D-cellobiose into D-glucose.
  
  

Revision as of 10:05, 20 October 2019


Beta-D-glucosidase fused at N-terminal with YebF secretion protein

This part contains the sequence for the protein Beta-glucosidase with protein YebF fused to its N-terminus by GS linker. It can achieve the secretion of Beta-glucosidase with the function of YebF protein.

Biology

BBa_K2922000 is a composite of Bgl1A (BBa_K2564000) with YebF (BBa_K1659003), a protein reported to be naturally secreted into the extracellular medium by E.coli BL21:


1. Bgl1A

Cellulose is a polymer composed of Beta-1,4-linked glucosyl residues. Cellulases (Endoglucanases), Cellobiosidases (Exoglucanases), and Beta-glucosidases are required by organisms (some fungi, bacteria) that can consume it. These enzymes are powerful tools for degradation of plant cell walls by pathogens and other organisms consuming plant biomass.

Beta-glucosidase is a 53 kDa enzyme that catalyzes the hydrolysis of the glycosidic bonds to terminal non-reducing residues in Beta-D-glucosides and oligosaccharides, with release of glucose.[1]

Depending on the organism cellobiose may be cleaved extracellularly by Beta-glucosidases (Cellobiases) and imported as glucose, or imported directly and cleaved in the cytoplasm. Import generally occurs through phosphotransferase transport systems.[2]


2. YebF

YebF is a 13 kDa protein of unknown function that is perhaps the only protein that has been conclusively documented to be secreted into the extracellular medium by a laboratory E. coli strain. At the N-terminus, YebF has a 2.2 kDa sec-leader sequence which mediates its translocation through the bacterial inner membrane via the Sec pathway, and is cleaved upon translocation into the periplasm to give the 10.8 kDa "mature" form.

Export from periplasm into the extracellular space takes place via the Omp pathway, whereby the electropositive dynamic region of YebF electrostatically helps load YebF onto the OmpF/OmpC porins at their electronegative periplasmic face, and after which the disordered N-terminal region of YebF gets threaded through the OmpF lumen. YebF has been used successfully to mediate the secretion of recombinant proteins.[3]


Usage

In order to let YebF help secrete Cellulase out of the E. coli membrane, we fused the Cellulase gene fragment with YebF gene fragment at the N-terminal by Overlap Extension Polymerase Chain Reaction(OE-PCR), and inserted a flexible GS Linker (GGGGS). PCR product was identified by agarose gel electrophoresis (Fig.1)


Fig. 1 Agarose Gel Electrophoresis of yebF-bgl1A (BBa_K2922000)OE-PCR product. Lane M: Marker. The PCR product in the second step, it showed a signal band at about 1800 bp.


Characterization

These parts were inserted into the expression vectors with T7 and RBS (BBa_K525998). Then transformed the expression vectors into E. coli DH5α, and the correct construction of this recombinant plasmid was confirmed by chloramphenicol, colony PCR and plasmid sequencing.



1. SDS-PAGE

We transformed the constructed plasmid into E. coli BL21 (DE3). The positive clones were cultivated and induced to express by IPTG. The supernatant of culture medium was obtained by centrifugation. And we gain the total protein by ultrasonic crushing. The lysate was then centrifuged and the supernatant was electrophoresed on a sodium dodecyl sulfate (SDS)-12% (wt/ol) polyacrylamide gel, followed by Silver staining. (Fig. 2)


Fig. 2 SDS-PAGE analysis of E. coli BL21 (DE3) by Sliver staining. YebF-bgl1A: protein of E. coli BL21 (DE3) carrying T7-RBS-yebF-bgl1A (BBa_K2922006), target bands can be seen in both cells and the medium at 63.4 kDa; Control: protein of E. coli BL21 (DE3) carrying T7 and RBS (BBa_K525998).


2. HPLC

We use HPLC to verify the activity of Bgl1A. First of all, we used the different concentrations of glucose solution and cellobiose solution to make SWC (Standard Working Curve) of HPLC.


Fig. 3 SWC for T7-RBS-yebF-bgl1A, made through the relationship between peak area and concentration.


Then mix the crude enzyme solution with cellobiose, incubate under the condition of 37°C, 200 rpm using a shaking incubator for reaction. Take out one tube of reaction system into boiling water bath for 8 minutes to stop the reaction after interval time since reaction started. And then carry out HPLC on the sample.


Fig. 4 The results of HPLC. (A): T7-RBS-yebF-bgl1A supernatant; (B): T7-RBS-yebF-bgl1A broken supernatant

Result of the broken supernatant and supernatant of medium cultures with T7-RBS-yebF-bgl1A part shows that D-cellobiose got consumed with extension of reaction time and more D-glucose obtained. Bgl1A could degrade D-cellobiose into D-glucose.


Reference

  1. ↑ M. Cox, D. Nelson, Lehninger Principles of Biochemistry. (2000), vol. 5. New York: Worth Publishers. pp. 306–308.
  2. ↑ R. M. Weiner et al., Complete genome sequence of the complex carbohydrate-degrading marine bacterium, Saccharophagus degradans strain 2-40 T. 4, e1000087 (2008).
  3. ↑ https://parts.igem.org/wiki/index.php?title=Part:BBa_K1659003#Biology

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 1591
  • 1000
    COMPATIBLE WITH RFC[1000]