Difference between revisions of "Part:BBa K4195106"
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| − | Encoding the siRNA sequence which can silence the lpp gene in ''E. coli'' BL21(DE3). Use <partinfo>BBa_I0500</partinfo> to silence the ompA gene in ''E. coli'' BL21(DE3). | + | Encoding the siRNA sequence which can silence the ''lpp'' gene in ''E. coli'' BL21(DE3). Use <partinfo>BBa_I0500</partinfo> to silence the ''ompA'' gene in ''E. coli'' BL21(DE3). |
===Biology=== | ===Biology=== | ||
| − | In ''E. coli'', Lpp is an abundant lipoprotein which can covalently cross-links the OM and PG, providing structural envelop integrity and stability(''1''). The high stability of envelop is obviously disadvantageous for OMV massive secretion. In order to avoid the effects of endogenous lpp, we need a way to silence this gene. RNAi was used to silence it. | + | In ''E. coli'', Lpp is an abundant lipoprotein which can covalently cross-links the OM and PG, providing structural envelop integrity and stability(''1''). The high stability of envelop is obviously disadvantageous for OMV massive secretion. In order to avoid the effects of endogenous <i>lpp</i>, we need a way to silence this gene. RNAi was used to silence it. |
RNAi design can use TACE system. In the TACE system, a gene loop for transferring the DNA sequence corresponding to the siRNA, where the GGA Cassette can be replaced by the sequence encoding the siRNA according to the GGA assembly standard. OmpA 5’-UTR can protect siRNA from degradation, and hfq binding sequence can improve the binding efficiency of siRNA and target mRNA. | RNAi design can use TACE system. In the TACE system, a gene loop for transferring the DNA sequence corresponding to the siRNA, where the GGA Cassette can be replaced by the sequence encoding the siRNA according to the GGA assembly standard. OmpA 5’-UTR can protect siRNA from degradation, and hfq binding sequence can improve the binding efficiency of siRNA and target mRNA. | ||
| − | Using the siRNA design software provided by Team: Bielefeld-CeBiTec in iGEM 2018: siRCon, the siRNA sequence design for endogenous lpp in ''E. coli'' BL21(DE3) was used for RNAi. The number 0.88 means the silence probability (up to 1.0). | + | Using the siRNA design software provided by Team: Bielefeld-CeBiTec in iGEM 2018: siRCon, the siRNA sequence design for endogenous ''lpp'' in ''E. coli'' BL21(DE3) was used for RNAi. The number 0.88 means the silence probability (up to 1.0). |
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===Usage=== | ===Usage=== | ||
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[[File:T--XMU-China--fig. 1siRNA for Lpp circuit.png|300px]] | [[File:T--XMU-China--fig. 1siRNA for Lpp circuit.png|300px]] | ||
| − | '''Fig. 1 Gene circuit of lpp RNAi sequence.''' | + | '''Fig. 1 Gene circuit of <i>lpp</i> RNAi sequence.''' |
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===Characterization=== | ===Characterization=== | ||
| − | + | ====1. Agarose gel electrophoresis (AGE)==== | |
When we were building this circuit, colony PCR was used to certify the plasmid was correct. We got the target fragment-1890bp (lane K4195106). | When we were building this circuit, colony PCR was used to certify the plasmid was correct. We got the target fragment-1890bp (lane K4195106). | ||
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'''Fig. 2 The result of colony PCR. Plasmid pSB1C3.''' | '''Fig. 2 The result of colony PCR. Plasmid pSB1C3.''' | ||
| − | + | ====2. Hypervesiculation ability==== | |
Then, the colony with the corrected sequence was cultivated to verify its hypervesiculation ability. We purified and quantitated the OMV of experimental and control group, whose gene circuit only contains the promoter <partinfo>BBa_I0500</partinfo>. The experimental result is shown on Fig. 3. Observing the difference of OD<sub>600</sub> between two groups, we can guess that bacterial membrane structure’s stability decreases in experimental group and draw the conclusion that the composite part <partinfo>BBa_K4195106</partinfo> has the hypervesiculation ability compared with control group. | Then, the colony with the corrected sequence was cultivated to verify its hypervesiculation ability. We purified and quantitated the OMV of experimental and control group, whose gene circuit only contains the promoter <partinfo>BBa_I0500</partinfo>. The experimental result is shown on Fig. 3. Observing the difference of OD<sub>600</sub> between two groups, we can guess that bacterial membrane structure’s stability decreases in experimental group and draw the conclusion that the composite part <partinfo>BBa_K4195106</partinfo> has the hypervesiculation ability compared with control group. | ||
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'''Fig. 3 Normalized protein concentration and OD<sub>600</sub> of experimental and control group.''' | '''Fig. 3 Normalized protein concentration and OD<sub>600</sub> of experimental and control group.''' | ||
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===Reference=== | ===Reference=== | ||
Latest revision as of 08:02, 13 October 2022
I0500-OmpA 5'UTR-Lpp 0.88-hfq binding sequence-B0015
Encoding the siRNA sequence which can silence the lpp gene in E. coli BL21(DE3). Use BBa_I0500 to silence the ompA gene in E. coli BL21(DE3).
Biology
In E. coli, Lpp is an abundant lipoprotein which can covalently cross-links the OM and PG, providing structural envelop integrity and stability(1). The high stability of envelop is obviously disadvantageous for OMV massive secretion. In order to avoid the effects of endogenous lpp, we need a way to silence this gene. RNAi was used to silence it.
RNAi design can use TACE system. In the TACE system, a gene loop for transferring the DNA sequence corresponding to the siRNA, where the GGA Cassette can be replaced by the sequence encoding the siRNA according to the GGA assembly standard. OmpA 5’-UTR can protect siRNA from degradation, and hfq binding sequence can improve the binding efficiency of siRNA and target mRNA.
Using the siRNA design software provided by Team: Bielefeld-CeBiTec in iGEM 2018: siRCon, the siRNA sequence design for endogenous lpp in E. coli BL21(DE3) was used for RNAi. The number 0.88 means the silence probability (up to 1.0).
Usage
We assembled the inducible promoter (BBa_I0500), the part (OmpA 5'UTR-lpp 0.88-hfq binding sequence) and the double terminator (BBa_B0015) on the expression vector pSB1C3 to get the composite part BBa_K4195106 by standard assembly (Fig. 1). Then the ligation mixture was transformed into E. coli DH5α & E. coli BL21(DE3), and the positive transformants were confirmed by chloramphenicol, colony PCR and sequencing.
Fig. 1 Gene circuit of lpp RNAi sequence.
Characterization
1. Agarose gel electrophoresis (AGE)
When we were building this circuit, colony PCR was used to certify the plasmid was correct. We got the target fragment-1890bp (lane K4195106).
.png)
Fig. 2 The result of colony PCR. Plasmid pSB1C3.
2. Hypervesiculation ability
Then, the colony with the corrected sequence was cultivated to verify its hypervesiculation ability. We purified and quantitated the OMV of experimental and control group, whose gene circuit only contains the promoter BBa_I0500. The experimental result is shown on Fig. 3. Observing the difference of OD600 between two groups, we can guess that bacterial membrane structure’s stability decreases in experimental group and draw the conclusion that the composite part BBa_K4195106 has the hypervesiculation ability compared with control group.
Fig. 3 Normalized protein concentration and OD600 of experimental and control group.
Reference
1. C. Schwechheimer, C. J. Sullivan, M. J. Kuehn, Envelope control of outer membrane vesicle production in Gram-negative bacteria. Biochemistry 52, 3031-3040 (2013).
Sequence and Features
- 10COMPATIBLE WITH RFC[10]
- 12INCOMPATIBLE WITH RFC[12]Illegal NheI site found at 1205
- 21INCOMPATIBLE WITH RFC[21]Illegal BamHI site found at 1144
Illegal XhoI site found at 1434 - 23COMPATIBLE WITH RFC[23]
- 25INCOMPATIBLE WITH RFC[25]Illegal AgeI site found at 979
- 1000INCOMPATIBLE WITH RFC[1000]Illegal SapI site found at 961