Difference between revisions of "Part:BBa K2922007"
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This part contains the sequence for the protein endoglucanase A with protein YebF fused to its N-terminus by GS Linker. We use T7 promoter and RBS related to achieve the high level secretion of Endoglucanase A with the function of YebF protein. | This part contains the sequence for the protein endoglucanase A with protein YebF fused to its N-terminus by GS Linker. We use T7 promoter and RBS related to achieve the high level secretion of Endoglucanase A with the function of YebF protein. | ||
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===Biology=== | ===Biology=== | ||
| − | BBa_K2922007 is a composite of | + | BBa_K2922007 is a composite of CenA(<partinfo>BBa_K118023</partinfo>) with YebF(<partinfo>BBa_K1659003</partinfo>) expressed in T7-RBS (<partinfo>BBa_K525998</partinfo>) system with the related protein reported to be naturally secreted into the extracellular medium by ''E.coli'' BL21: |
'''1. Endoglucanase A''' | '''1. Endoglucanase A''' | ||
| − | Cellulose is a polymer composed of | + | 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. |
| − | Cellulases ( | + | |
| − | 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. | + | |
| − | Bacterium ''Cellulomonas fimi'' uses 3 | + | Bacterium ''Cellulomonas fimi'' uses 3 Endoglucanases (including CenA, accession M15823) and an Exoglucanase in the degradation of cellulose into cellobiose, before using Beta-glucosidase to catalyse the conversion of cellobiose to D-glucose. |
'''2. YebF''' | '''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 | + | 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 |
<ref>https://parts.igem.org/wiki/index.php?title=Part:BBa_K1659003#Biology</ref>. | <ref>https://parts.igem.org/wiki/index.php?title=Part:BBa_K1659003#Biology</ref>. | ||
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<html> | <html> | ||
<figure> | <figure> | ||
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===Usage=== | ===Usage=== | ||
| − | In order to secrete our | + | In order to secrete our Cellulases out of the ''E. coli'' membrane, we fused the Cellulase gene fragments with ''yebF'' gene fragment at the N-terminal using a flexible GS linker (GGGGS) by overlap extension polymerase chain reaction (OE-PCR). PCR product was purified by agarose gel electrophoresis (Fig. 1). |
<html> | <html> | ||
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===Characterization=== | ===Characterization=== | ||
| − | These parts were insert into the expression vectors with T7 and RBS (<partinfo>BBa_K525998</partinfo>) | + | These parts were insert into the expression vectors with T7 and RBS (<partinfo>BBa_K525998</partinfo>). Then the ligation mixture was transformed into ''E. coli'' DH5α, and the correct recombinant one was confirmed by chloramphenicol, colony PCR and sequencing. |
<html> | <html> | ||
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'''1. SDS-PAGE''' | '''1. SDS-PAGE''' | ||
| − | The constructed plasmid was transformed into ''E. coli'' BL21 (DE3). Positive clones that were selected by chloramphenicol preliminarily and then by colony PCR, while finally confirmed by sequencing were cultivated and induced by IPTG | + | The constructed plasmid was transformed into ''E. coli'' BL21 (DE3). Positive clones that were selected by chloramphenicol preliminarily and then by colony PCR, while finally confirmed by sequencing were cultivated and induced by IPTG. The supernatant of culture, namely '''''sup''''', was obtained by centrifugation. And the total protein was gained by ultrasonication. The lysate underwent centrifugation and its supernatant, namely '''broken ''sup''''', was electrophoresed on a sodium dodecyl sulfate (SDS)-12% (wt/vol) polyacrylamide gel, followed by Coomassie blue staining (Fig. 2) |
<html> | <html> | ||
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</figure> | </figure> | ||
</html> | </html> | ||
| − | :'''Fig.2''' SDS-PAGE analysis of ''E. coli'' BL21 (DE3) by Sliver staining. YebF- | + | :'''Fig.2''' SDS-PAGE analysis of ''E. coli'' BL21 (DE3) by Sliver staining. YebF-CenA: protein of ''E. coli'' BL21 (DE3) carrying T7-RBS-yebF-cenA (<partinfo>BBa_K2922007</partinfo>), target bands can be seen in the medium at 60 kDa; Control: protein of ''E. coli'' BL21 (DE3) carrying T7 and RBS (<partinfo>BBa_K525998</partinfo>). |
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Zones with the broken ''sup'' and ''sup'' of YebF-CenA added showed due to the hydrolysis of CMC (carboxymethyl cellulose) whereas the blank control didn't show any clearance zones. The obvious difference showed that the broken ''sup'' and ''sup'' of YebF-CenA had enzymatic activity. This was to say that the enzyme, YebF-CenA, which was expressed successfully, had a certain level of enzymatic activity to hydrolyze cellulose. Besides, what the results showed was in accordance with the results of SDS-PAGE (Fig. 2) as well. | Zones with the broken ''sup'' and ''sup'' of YebF-CenA added showed due to the hydrolysis of CMC (carboxymethyl cellulose) whereas the blank control didn't show any clearance zones. The obvious difference showed that the broken ''sup'' and ''sup'' of YebF-CenA had enzymatic activity. This was to say that the enzyme, YebF-CenA, which was expressed successfully, had a certain level of enzymatic activity to hydrolyze cellulose. Besides, what the results showed was in accordance with the results of SDS-PAGE (Fig. 2) as well. | ||
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===References=== | ===References=== | ||
<references/> | <references/> | ||
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Revision as of 10:43, 20 October 2019
Expression system of YebF-CenA coding YebF-Endoglucanase A with T7 promoter
This part contains the sequence for the protein endoglucanase A with protein YebF fused to its N-terminus by GS Linker. We use T7 promoter and RBS related to achieve the high level secretion of Endoglucanase A with the function of YebF protein.
Biology
BBa_K2922007 is a composite of CenA(BBa_K118023) with YebF(BBa_K1659003) expressed in T7-RBS (BBa_K525998) system with the related protein reported to be naturally secreted into the extracellular medium by E.coli BL21:
1. Endoglucanase A
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.
Bacterium Cellulomonas fimi uses 3 Endoglucanases (including CenA, accession M15823) and an Exoglucanase in the degradation of cellulose into cellobiose, before using Beta-glucosidase to catalyse the conversion of cellobiose to D-glucose.
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 [1].
Usage
In order to secrete our Cellulases out of the E. coli membrane, we fused the Cellulase gene fragments with yebF gene fragment at the N-terminal using a flexible GS linker (GGGGS) by overlap extension polymerase chain reaction (OE-PCR). PCR product was purified by agarose gel electrophoresis (Fig. 1).
- Fig.1 Agarose Gel Electrophoresis of yebF-cenA OE-PCR product. Lane M: Marker.
Characterization
These parts were insert into the expression vectors with T7 and RBS (BBa_K525998). Then the ligation mixture was transformed into E. coli DH5α, and the correct recombinant one was confirmed by chloramphenicol, colony PCR and sequencing.
1. SDS-PAGE
The constructed plasmid was transformed into E. coli BL21 (DE3). Positive clones that were selected by chloramphenicol preliminarily and then by colony PCR, while finally confirmed by sequencing were cultivated and induced by IPTG. The supernatant of culture, namely sup, was obtained by centrifugation. And the total protein was gained by ultrasonication. The lysate underwent centrifugation and its supernatant, namely broken sup, was electrophoresed on a sodium dodecyl sulfate (SDS)-12% (wt/vol) polyacrylamide gel, followed by Coomassie blue staining (Fig. 2)
- Fig.2 SDS-PAGE analysis of E. coli BL21 (DE3) by Sliver staining. YebF-CenA: protein of E. coli BL21 (DE3) carrying T7-RBS-yebF-cenA (BBa_K2922007), target bands can be seen in the medium at 60 kDa; Control: protein of E. coli BL21 (DE3) carrying T7 and RBS (BBa_K525998).
2. Congo Red Assay
Congo Red assay was utilized to qualitatively test the enzymatic activity of CenA in the form of crude enzyme, and this method was from iGEM18-UESTC-China, who had a nice collaboration with us this year. As Congo Red only binds to long chain polysaccharides but not short chain, the short chain therefore are washed off during staining procedure resulting in halo formation [2]. The results are shown in Fig. 3.
- Fig.3 Activity determination of YebF-CenA using Congo Red assay. Left: T7-RBS-yebF-cenA medium supernatant and control (LB liquid medium). Right: T7-RBS-yebF-cenA broken supernatant and control (PBS).
Zones with the broken sup and sup of YebF-CenA added showed due to the hydrolysis of CMC (carboxymethyl cellulose) whereas the blank control didn't show any clearance zones. The obvious difference showed that the broken sup and sup of YebF-CenA had enzymatic activity. This was to say that the enzyme, YebF-CenA, which was expressed successfully, had a certain level of enzymatic activity to hydrolyze cellulose. Besides, what the results showed was in accordance with the results of SDS-PAGE (Fig. 2) as well.
References
- ↑ https://parts.igem.org/wiki/index.php?title=Part:BBa_K1659003#Biology
- ↑ S. S. J. U. o. E. Lakhundi, Synthetic biology approach to cellulose degradation. (2012).