Difference between revisions of "Part:BBa K4181014"

Revision as of 08:53, 12 October 2022 (view source) JunzhiYan (Talk | contribs) ← Older edit		Latest revision as of 10:31, 12 October 2022 (view source) JunzhiYan (Talk | contribs) (→‎Usage and Biology)
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−	===Usage and Biology===	+	===Biology===
−	<p>cotB and cotE proteins are both innate proteins of B.subtilis which will express when sporulation is induced. They help organize the outer spore surface and therefore can be chosen as the anchoring proteins used in the spore display system, fused with exogeneous proteins to display them on the spore surface. Firstly, since cotB and cotE proteins are bacteriophage surface proteins of Bacillus subtilis and their coding genes are available in their genome, we extracted the genome of Bacillus subtilis strain WB800N, and then used this genome as a template to PCR the gene sequences corresponding to cotE and cotB proteins from the genome. With the design of PCR primers, we added the cotE to the homologous arm of the pHT01 plasmid sequence.A RBS sequence was added to the 5' end of the cotE gene sequence, and the stop codon was removed at its 3' end and the linker sequence was added; the homologous arm of the tyrosinase coding sequence and the RBS sequence were added to the 5' end of the cotB gene sequence, and the stop codon was removed at its 3' end. The stop codon was removed at the 3' end and the FLAG tag was added. </p>	+	<p>The melanin-binding-peptide 4B4 is an oligopeptide with only 10 amino acids, and according to the procedures mentioned above, we had added the flag-tag to it for verification. As another peptide on the spore surface, we chose the immunofluorescence assay similar to the ones done on tyrosinase. Anti-flag antibody coupled with PE-CY7 was used and we observe the results both from phase contract/ fluorescecnce microscopy and the flow cytometer. The excitation light is at 562nm and the emitted light is 770nm, so theoritically, red dots could be recognized if there were 4B4 expression on the surface. The microscope we used only got the excitation wave length for RFP, which is 532nm. Given that there must be a error band for the real wave length, we determined to have a try using 532nm light as the excitation light of CY7. The results of immunofluorescence is as below.</p>
−	[[File:2022-SJTU-Biox-Shanghai-1.png|500px]]<br>	+
		+	[[File:2022-SJTU-Biox-Shanghai-1.png|500px|center]]<br>
	'''Figure 1.'''  Electrophoresis results after PCR of cotE and the first PCR electrophoresis results of cotB. The picture indicates a positive result.<br>		'''Figure 1.'''  Electrophoresis results after PCR of cotE and the first PCR electrophoresis results of cotB. The picture indicates a positive result.<br>
	<p>Next, PCR the cotB gene sequence again, and add 4B4 melanin-binding peptide and the stop codon to the 3' end of this sequence by designing your primers for this PCR.</p>		<p>Next, PCR the cotB gene sequence again, and add 4B4 melanin-binding peptide and the stop codon to the 3' end of this sequence by designing your primers for this PCR.</p>
−	[[File:2022-SJTU-Biox-Shanghai-2.png|500px|]]<br>	+	<p style="text-align: center;">
		+	[[File:2022-SJTU-Biox-Shanghai-2.png|500px|center]]<br>
	'''Figure 2.''' Electrophoresis results of cotB after the second PCR and Dsup-encoded gene after PCR. The picture indicates a positive result.<br>		'''Figure 2.''' Electrophoresis results of cotB after the second PCR and Dsup-encoded gene after PCR. The picture indicates a positive result.<br>
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	<partinfo>BBa_K4181014 SequenceAndFeatures</partinfo>		<partinfo>BBa_K4181014 SequenceAndFeatures</partinfo>
		+	===Characterization===
		+	cotE and cotB proteins are closely related to tyrosinase activity.Tyrosinase and the melanin-binding-peptide were the next to be demonstrated because of their display on the spore surface, and the process of sporulation has been mentioned above. Because there was his-tag linking with our tyrosinase protein, we decided to use immunofluorescence to detect it. The following is the result of our immunofluorescence test:</p>
		+	<p style="text-align: center;">
		+	[[File:2022-SJTU-Biox-Shanghai-3.png|500px|center]]<br>
		+	'''Figure 3.'''  Immunofluorescence assay on tyrosinase anchoring on the spore surface. Groups: Samples containing plasmid with IPTG induced; Samples containing plasmid without IPTG induced; WB800N wildtype. <br>
		+	.
		+	===Flow Cytometry===
		+	FCM was also conducted by similar procedures and the results are as below:</p>
		+	[[File:2022-SJTU-Biox-Shanghai-4.png|500px|center]]<br>
		+	<p align="center">'''Figure 4.'''  Results of flow cytometry for the detection of tyrosinase. <br></p>
		+	<p>From the results, compared with the control group, samples with IPTG-induced plasmids showed more positive signals, whilst nearly no signals had been detected in the negative controls, suggesting a similar results as the immunofluoresecnce results. However, the peak of positive signals is just by the side of the negative peak, indicating a weak fluorescence intensity. From the result of FCM, it is more obvious that the total expression proportion of the target protein is relatively low. After discussion, we thought this was caused by several reasons. Firstly, during the growth and propagation of B.subtilis, the plasmid may be lost and thus no proteins can be generated. Secondly, as we could observe a large amount of spores under the phase-contract microscopy, it reminded us that we added IPTG for induction at the time when the OD of becteria was ranging from 0.6-0.8. This concentration was before the log-growth phase so that the bacteria would still propogate after IPTG induction. With the mother cells absorbing IPTG, less IPTG is left for daughter cells so that the bacteria produced by binary fissions later could not exposed to suffient amount of IPTG. Of course, as it can be indicated by fig20, B.subtilis would go through a quick propagation after transferred into sporulation medium, the concentration of ITPG at that stage of experiment could went even lower since no extra IPTG was added given its negative effects on the bacteria. Therefore, the concentration might be too low to induce the later produced bacteria generating proteins. Thirdly, we thought this might be caused by competitions between endogeneous cot proteins and the ones we introduced by exogeneous plasmid. As it is mentioned in our design, we cloned cotB and cotE proteins directly form the bacterial genome. So, there’re intrinsic prioteins to express under the regulation of sporulation signals naturally and thus compete with our exogeneous proteins to occupy the space on the spores’ outer surface. According to our results from Western blot, the expression level of our target priteins was not so much. In this regard, an unclear competitive advantage of exogeneous introduced proteins over the endogeneous ones might lead to the low anchoring rate of target proteins displayed in the outer surface. Generally, these results suggested we had successfully induced the expression and anchoring of tyrosinase on the spore surface. And there was notable expression disparity between the bacteria with IPTG-induced plasmid and the bacteria with no IPTG-induced plasmid and the wildtype.</p>
	<!-- Uncomment this to enable Functional Parameter display		<!-- Uncomment this to enable Functional Parameter display
	===Functional Parameters===		===Functional Parameters===
	<partinfo>BBa_K4181014 parameters</partinfo>		<partinfo>BBa_K4181014 parameters</partinfo>
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Latest revision as of 10:31, 12 October 2022

cotE protein DNA sequence

We added a Linker sequence to the end of the cotE protein sequence to facilitate the production of cotE with a further binding peptide to function with the cotB protein.

Biology

The melanin-binding-peptide 4B4 is an oligopeptide with only 10 amino acids, and according to the procedures mentioned above, we had added the flag-tag to it for verification. As another peptide on the spore surface, we chose the immunofluorescence assay similar to the ones done on tyrosinase. Anti-flag antibody coupled with PE-CY7 was used and we observe the results both from phase contract/ fluorescecnce microscopy and the flow cytometer. The excitation light is at 562nm and the emitted light is 770nm, so theoritically, red dots could be recognized if there were 4B4 expression on the surface. The microscope we used only got the excitation wave length for RFP, which is 532nm. Given that there must be a error band for the real wave length, we determined to have a try using 532nm light as the excitation light of CY7. The results of immunofluorescence is as below.

Figure 1. Electrophoresis results after PCR of cotE and the first PCR electrophoresis results of cotB. The picture indicates a positive result.

Next, PCR the cotB gene sequence again, and add 4B4 melanin-binding peptide and the stop codon to the 3' end of this sequence by designing your primers for this PCR.

Figure 2. Electrophoresis results of cotB after the second PCR and Dsup-encoded gene after PCR. The picture indicates a positive result.
Sequence and Features

Characterization

cotE and cotB proteins are closely related to tyrosinase activity.Tyrosinase and the melanin-binding-peptide were the next to be demonstrated because of their display on the spore surface, and the process of sporulation has been mentioned above. Because there was his-tag linking with our tyrosinase protein, we decided to use immunofluorescence to detect it. The following is the result of our immunofluorescence test:

Figure 3. Immunofluorescence assay on tyrosinase anchoring on the spore surface. Groups: Samples containing plasmid with IPTG induced; Samples containing plasmid without IPTG induced; WB800N wildtype.
.

Flow Cytometry

FCM was also conducted by similar procedures and the results are as below:

Figure 4. Results of flow cytometry for the detection of tyrosinase.

From the results, compared with the control group, samples with IPTG-induced plasmids showed more positive signals, whilst nearly no signals had been detected in the negative controls, suggesting a similar results as the immunofluoresecnce results. However, the peak of positive signals is just by the side of the negative peak, indicating a weak fluorescence intensity. From the result of FCM, it is more obvious that the total expression proportion of the target protein is relatively low. After discussion, we thought this was caused by several reasons. Firstly, during the growth and propagation of B.subtilis, the plasmid may be lost and thus no proteins can be generated. Secondly, as we could observe a large amount of spores under the phase-contract microscopy, it reminded us that we added IPTG for induction at the time when the OD of becteria was ranging from 0.6-0.8. This concentration was before the log-growth phase so that the bacteria would still propogate after IPTG induction. With the mother cells absorbing IPTG, less IPTG is left for daughter cells so that the bacteria produced by binary fissions later could not exposed to suffient amount of IPTG. Of course, as it can be indicated by fig20, B.subtilis would go through a quick propagation after transferred into sporulation medium, the concentration of ITPG at that stage of experiment could went even lower since no extra IPTG was added given its negative effects on the bacteria. Therefore, the concentration might be too low to induce the later produced bacteria generating proteins. Thirdly, we thought this might be caused by competitions between endogeneous cot proteins and the ones we introduced by exogeneous plasmid. As it is mentioned in our design, we cloned cotB and cotE proteins directly form the bacterial genome. So, there’re intrinsic prioteins to express under the regulation of sporulation signals naturally and thus compete with our exogeneous proteins to occupy the space on the spores’ outer surface. According to our results from Western blot, the expression level of our target priteins was not so much. In this regard, an unclear competitive advantage of exogeneous introduced proteins over the endogeneous ones might lead to the low anchoring rate of target proteins displayed in the outer surface. Generally, these results suggested we had successfully induced the expression and anchoring of tyrosinase on the spore surface. And there was notable expression disparity between the bacteria with IPTG-induced plasmid and the bacteria with no IPTG-induced plasmid and the wildtype.