Difference between revisions of "Part:BBa K4195105"
 
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Encoding the siRNA sequence which can silence the ompA gene in ''E. coli'' BL21(DE3). Use <partinfo>BBa_I0500</partinfo> to silence the ompA gene in ''E. coli'' BL21(DE3).
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Encoding the siRNA sequence which can silence the ''ompA'' gene in ''E. coli'' BL21(DE3). Use <partinfo>BBa_I0500</partinfo> to silence the ''ompA'' gene in ''E. coli'' BL21(DE3).
  
  
 
===Biology===
 
===Biology===
  
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In ''E. coli'', the omp system is precisely regulated. OmpA, an OM porin containing a PG interaction motif, adds noncovalent stability to the envelop of Gram-negative bacteria(''1''). The high stability of envelop is obviously disadvantageous for OMV massive secretion. In order to avoid the effects of endogenous ompA, we need a way to silence this gene. RNAi was used to silence it.
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In ''E. coli'', the omp system is precisely regulated. OmpA, an OM porin containing a PG interaction motif, adds noncovalent stability to the envelop of Gram-negative bacteria(''1''). The high stability of envelop is obviously disadvantageous for OMV massive secretion. In order to avoid the effects of endogenous ''ompA'', 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 ompA 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 ''ompA'' 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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[[File:T--XMU-China--fig.1 siRNA for OmpA circuit.png|300px]]
 
[[File:T--XMU-China--fig.1 siRNA for OmpA circuit.png|300px]]
  
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'''Fig. 1 Gene circuit of ompA RNAi sequence.'''
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'''Fig. 1 Gene circuit of <i>ompA</i> RNAi sequence.'''
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===Characterization===
 
===Characterization===
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====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 K4195105).
 
When we were building this circuit, colony PCR was used to certify the plasmid was correct. We got the target fragment-1890bp (lane K4195105).
  
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'''Fig. 2 The result of colony PCR. Plasmid pSB1C3.'''
 
'''Fig. 2 The result of colony PCR. Plasmid pSB1C3.'''
  
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====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. We can draw the conclusion that the composite part <partinfo>BBa_K4195105</partinfo> can’t achieve 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. We can draw the conclusion that the composite part <partinfo>BBa_K4195105</partinfo> can’t achieve 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 08:00, 13 October 2022


I0500-OmpA 5'UTR-OmpA 0.88-hfq binding sequence-B0015


Encoding the siRNA sequence which can silence the ompA gene in E. coli BL21(DE3). Use BBa_I0500 to silence the ompA gene in E. coli BL21(DE3).


Biology

In E. coli, the omp system is precisely regulated. OmpA, an OM porin containing a PG interaction motif, adds noncovalent stability to the envelop of Gram-negative bacteria(1). The high stability of envelop is obviously disadvantageous for OMV massive secretion. In order to avoid the effects of endogenous ompA, 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 ompA 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-ompA 0.88-hfq binding sequence) and the double terminator (BBa_B0015) on the expression vector pSB1C3 to get the composite part BBa_K4195105 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.

T--XMU-China--fig.1 siRNA for OmpA circuit.png

Fig. 1 Gene circuit of ompA 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 K4195105).

T--XMU-China--fig.2 BBa K4195105 colony PCR BL21(DE3).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. We can draw the conclusion that the composite part BBa_K4195105 can’t achieve hypervesiculation ability compared with control group.

T--XMU-China--fig. 3NC vs OmpA 0.88-OMV secretion.png

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


Assembly Compatibility:
  • 10
    COMPATIBLE WITH RFC[10]
  • 12
    INCOMPATIBLE WITH RFC[12]
    Illegal NheI site found at 1205
  • 21
    INCOMPATIBLE WITH RFC[21]
    Illegal BamHI site found at 1144
    Illegal XhoI site found at 1434
  • 23
    COMPATIBLE WITH RFC[23]
  • 25
    INCOMPATIBLE WITH RFC[25]
    Illegal AgeI site found at 979
  • 1000
    INCOMPATIBLE WITH RFC[1000]
    Illegal SapI site found at 961