Difference between revisions of "Part:BBa K4195105"

Revision as of 21:51, 10 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.

Fig. 1 Gene circuit of ompA RNAi sequence.

Characterization

When we were building this circuit, colony PCR was used to certify the plasmid was correct. We got the target fragment-1890bp (lane K4195105).

Fig. 2 The result of colony PCR. Plasmid pSB1C3.

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.

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

@@ Line 3: / Line 3: @@
 <partinfo>BBa_K4195105 short</partinfo>
-none
-<!-- Add more about the biology of this part here
+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).
-===Usage and Biology===
+===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 (<partinfo>BBa_I0500</partinfo>), the part (OmpA 5'UTR-ompA 0.88-hfq binding sequence) and the double terminator (<partinfo>BBa_B0015</partinfo>) on the expression vector pSB1C3 to get the composite part <partinfo>BBa_K4195105</partinfo> 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.
+[[File:T--XMU-China--fig.1 siRNA for OmpA circuit.png|300px]]
+'''Fig. 1 Gene circuit of ompA RNAi sequence.'''
+===Characterization===
+When we were building this circuit, colony PCR was used to certify the plasmid was correct. We got the target fragment-1890bp (lane K4195105).
+[[File:T--XMU-China--fig.2 BBa K4195105 colony PCR BL21(DE3).png|300px]]
+'''Fig. 2 The result of colony PCR. Plasmid pSB1C3.'''
+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.
+[[File:T--XMU-China--fig. 3NC vs OmpA 0.88-OMV secretion.png|300px]]
+'''Fig. 3 Normalized protein concentration and OD<sub>600</sub> of experimental and control group.'''
+===Reference===
+. C. Schwechheimer, C. J. Sullivan, M. J. Kuehn, Envelope control of outer membrane vesicle production in Gram-negative bacteria. ''Biochemistry'' '''52''', 3031-3040 (2013).
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