Team:UCSF/Project/Conjugation/Data

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<font face="arial" size = "5"><b><center>Conjugation: DATA</font></b> </center> <br>
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<font face="calibri" size = "5"><b><center>CRISPRi Conjugation - Experiments and Results</font></b> </center> <br>
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<FONT COLOR="#008000"><u>Confirming Conjugation:</FONT COLOR="#008000"></u><br>
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For conjugation to occur, the bacterial strain that passes the plasmid must have the genes necessary to build the conjugative apparatus (a pilus) between the cells. This is normally carried on a large plasmid, called the F plasmid, that itself is transferred during the conjugation. Because of its large size, it is not amenable to many cloning strategies. We instead chose a bacterial strain with the conjugative genes integrated into the chromosome, strain S17-1, and a small conjugative plasmid containing the origin sequence for conjugative transfer, pARO190. We were able to then clone in sequences for dCas9 and a guideRNA for the target of our knockdown – RFP.
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<b><FONT COLOR="#008000">Summary: We have successfully constructed a specific gene repression system using CRISPRi that can be efficiently transmitted between cells via conjugation. </FONT COLOR="#008000"></font></b></center>
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<FONT COLOR="#008000"><u>Confirming Conjugation:</FONT COLOR="#008000"></u><br><br>
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For conjugation to occur, the bacterial strain that passes the plasmid must have the genes necessary to build the conjugative apparatus (a pilus) between the cells. This is normally carried on a large plasmid, called the F plasmid, that itself is transferred during conjugation, but due to its large size, it is not amenable to many cloning strategies. To combat this, we chose a bacterial strain (S17-1) that has the conjugative genes integrated into the chromosome, and a small conjugative plasmid containing the origin sequence for conjugative transfer, pARO190. We were then able to clone in sequences for dCas9 and a guideRNA for the target of our knockdown – RFP.
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We first needed to confirm that conjugation was possible in our experimental setup. Briefly, we co-cultured the donor strain (spectinomycin resistance) containing our empty pARO190 plasmid (carbenicillin resistance) with a recipient strain in which we integrated both RFP  and chloramphenicol resistance into the chromosome (JM109-RFP).  At certain time points, we took a sample of the co-cultures and selected for only those cells that were both recipient strains (chloramphenicol) and now had the antibiotic resistance from the conjugative plasmid (carbenicillin).  These we called “transconjugates”.  On average, we obtained a conjugation efficiency of 37%.
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We first needed to confirm that conjugation was possible in our experimental setup. To test this, we co-cultured the donor strain (spectinomycin resistance) containing our empty pARO190 plasmid (carbenicillin resistance) with our target strain, which has RFP  and chloramphenicol resistance intergrated into its chromosome (JM109-RFP).  At certain time points, we took a sample of the co-cultures and selected for target strain cells that have received the conjugative plasmid, which we call “transconjugates”.   
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<font face="arial" size = "2"> Figure 2: Effect of co-culture time on the efficiency of conjugation. Donor and recipient cells were diluted and mixed together so that the initial OD600 value of each co-culture were 0.05 and then co-cultured in EZ-rich media for 2 hours, 5 hours, and 8 hours, respectively, under 180 rpm shaking in a 37 ℃ shaker. The final cell density was measured by plating on LB agar plates containing Spectinomycin, Chloramphenicol, and Carbenicillin + Chloramphenicol, for the selection of donor, recipient, and transconjugants (recipient received the conjugation plasmid) respectively. The conjugation rate (transconjugants/recipient * 100%) for each experiment was 0.45%, 0.23% and 0.44%, respectively.  
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<font face="calibri" size = "2"> Figure 2: Effect of co-culture time on the efficiency of conjugation. Donor and target cells were diluted and mixed together so that the initial OD600 value of each co-culture was 0.05, and co-cultured in EZ-rich media at 37 ℃ under 180rpm shaking  for 2 hours, 5 hours, and 8 hours, respectively. Final cell densities were measured by plating on LB agar plates containing Spectinomycin, Chloramphenicol, and Carbenicillin + Chloramphenicol, for the selection of donor, target, and transconjugants respectively. The conjugation rate (transconjugants/target * 100%) for each experiment was 0.45%, 0.23% and 0.44%, respectively.
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<FONT COLOR="#008000"><u>Knock-down of RFP with CRISPRi:</FONT COLOR="#008000"></u><br>
<FONT COLOR="#008000"><u>Knock-down of RFP with CRISPRi:</FONT COLOR="#008000"></u><br>
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<br>Next, we confirmed that the CRISPR system we designed could repress RFP expression in our recipient strain. Using direct transformation of our engineered conjugative plasmid pARO190 containing both dCas9 and a guideRNA for RFP, we measured the fluorescence output of RFP after induction of the conjugative plasmid. We were able to observe significant knock-down of RFP expression in the cell containing our CRISPR system.
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<br>Next, we needed to confirm that the CRISPRi system we designed could sufficiently repress RFP expression in our target strain. By directly transforming our engineered conjugative plasmid (which contains our CRISPRi system) into our target cells, we were able to measure RFP fluorescence after induction of the conjugative plasmid. We were able to observe significant knock-down of RFP expression in the cell containing our CRISPRi system.
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<font face="arial" size = "2"> Figure 3: The efficiency of CRISPRi system measured by directly transforming the conjugative plasmid that contains CRISPRi system (sgRNA and dCas9 protein) for RFP into JM109 strain that has RFP inserted into its chromosome (JM109-RFP). The dCas9 protein of the repression system was under control of a pTET promoter and the sgRNA of the system was under control of a constitutively expressed promoter. Positive control was direct transformation of conjugative plasmid backbone (pARO190 without sgRNA and dCas9) into JM109-RFP and negative control was direct transformation of conjugative plasmid that contains CRISPR/Cas repression system (sgRNA and dCas9 protein) for RFP into JM109 strain without any fluorescent markers. RFP levels were measured by flow cytometry and error bars showed standard deviation calculated on the basis of technical replicates.
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<font face="calibri" size = "2"> Figure 3: The efficiency of our CRISPRi system was measured by directly transforming the conjugative plasmid that contains our CRISPRi system (gRNA and dCas9 protein) into our recipient cells (JM109 with RFP inserted into its genome). The dCas9 protein is under the control of a pTET promoter and the gRNA is under the control of a constitutive promoter. The positive control is a direct transformation of the conjugative plasmid backbone (pARO190 without gRNA and dCas9) into our recipient cells. RFP fluorescence is measured via plate reader and error bars show standard deviation calculated on the basis of technical replicates.
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<font face="arial" size = "2"> Figure 4: The dose-response curve for the CRISPRi system. JM109-RFP was transformed directly with the conjugative plasmid containing the CRISPRi system (sgRNA and dCas9 protein) for RFP. The dCas9 protein of the repression system was under control of a pTET promoter and the sgRNA of the system was under control of a constitutively expressed promoter. RFP levels were measured under different aTc concentrations (0, 0.625, 1, 6.25, 9.375, 12.5, 18.75, 25, 37.5, 50, 250, 500 ng/mL aTc). Positive control was direct transformation of conjugative plasmid backbone (pARO190 without sgRNA and dCas9) into JM109-RFP, and negative control was directly transform of conjugative plasmid that contains CRISPR/Cas repression system (sgRNA and dCas9 protein) for RFP into JM109 strain without any fluorescent markers. RFP levels were measured by flow cytometry and error bars showed standard deviation calculated on the basis of technical replicates.
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<font face="calibri" size = "2"> Figure 4: Figure 4: The dose-response curve for our CRISPRi (dCas9 and gRNA) system. The conjugative plasmid containing our CRISPRi system was directly transformed into our target strain (JM109-RFP) and RFP fluorescence was measured under different aTc concentrations (0, 0.625, 1, 6.25, 9.375, 12.5, 18.75, 25, 37.5, 50, 250, 500 ng/mL aTc). Our positive control was a direct transformation of the conjugative plasmid backbone (pARO190 without gRNA and dCas9) into our target strain, and our negative control was directly transform of conjugative plasmid that contains CRISPR/Cas repression system (gRNA and dCas9 protein) for RFP into JM109 strain without any fluorescent markers. RFP fluorescence was measured via flow cytometry and error bars show standard deviation calculated on the basis of technical replicates.
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<FONT COLOR="#008000"><u>Conjugation of the CRISPRi System into Target Cells:</FONT COLOR="#008000"></u>
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<FONT COLOR="#008000"><u>Conjugation of the CRISPRi System into Target Cells:</FONT COLOR="#008000"></u><br>
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<br>With both the delivery system and the CRISPR repression functional in our assay, we moved to test both pieces together and induce knock-down of a specific gene by transferring specific instructions from one cell to another via conjugation.
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<br>After demonstrating that our delivery (conjugation) and repression systems (CRISPRi system) are both functional in our assays, we moved on to test whether or not we can do both. That is, if it is possible to induce knock-down of a specific gene by transferring specific instructions from one cell to another via conjugation.  
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<br><br>We co-cultured our donor strain containing the CRISPRi system with the JM-109 recipient strain for eight hours. The cultures were diluted and selected for transconjugates by antibiotic resistance (cam and carb) and then induced with aTc to express dCas9 on the conjugative plasmid. Using FACS, we measured the RFP output post-conjugation at various time points post-induction.
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<br><br>We co-cultured our donor strain containing the CRISPRi system with the JM-109 target strain for eight hours. The cultures were then diluted and selected for transconjugates by antibiotic resistance (cam and carb) and then induced with aTc to express dCas9 on the conjugative plasmid. Using FACS, we measured the RFP output post-conjugation at various time points post-induction.
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<font face="arial" size = "2"> Figures 5 and 6: The effectiveness of CRISPRi system transferred through conjugation from donor to recipient strain. Donor (S17-1) strain contain conjugative plasmid (sgRNA and dCas9 on pARO190 plasmid backbone) and a positive control donor strain (S17-1 strains contain only pARO190 backbone) were co-cultured with recipient strain (JM109 with RFP inserted into chromosome) for 8 hours, then diluted 100 times and start induction in new EZ-rich media. 500 ng/mL aTc were supplemented to induce the production of dCas9 protein of the CRISPRi system. Different antibiotic marker were used (Carbenicillin + Chloramphenicol, and Chloramphenicol) for the selection of recipient cells with and without conjugation. The histogram displayed RFP fluorescence for each sample measured by flow cytometry.
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<font face="calibri" size = "2"> Figure 5: The effectiveness of our CRISPRi system transferred via conjugation from donor to target strain. Our donor (S17-1) strain, which contains our conjugative plasmid (gRNA and dCas9 on pARO190 plasmid backbone) and a positive control donor strain (S17-1 containing only pARO190 backbone) were co-cultured separately with our target strain (JM109 with RFP inserted into its chromosome) for 8 hours. The co-cultures were then diluted 100 times and inducted with 500ng/mL aTc in new EZ-rich media. Different antibiotic markers were used (Carbenicillin + Chloramphenicol, and Chloramphenicol) to select for target cells with and without the conjugative plasmid. The histograms show RFP fluorescence for each sample, which was measured via flow cytometry.
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<font face="arial" size = "2"> Figures 7 and 8: The effectiveness of CRISPRi system transferred through conjugation from donor to recipient strain. Donor (S17-1) strain contain conjugative plasmid (sgRNA and dCas9 on pARO190 plasmid backbone) and a positive control donor strain (S17-1 strains contain only pARO190 backbone) were co-cultured with recipient strain (JM109 with RFP inserted into chromosome) for 8 hours, then diluted 100 times and start induction in new EZ-rich media. 500 ng/mL aTc were supplemented to induce the production of dCas9 protein of the CRISPRi system. Different antibiotic marker were used (Carbenicillin + Chloramphenicol, and Chloramphenicol) for the selection of recipient cells with and without conjugation. RFP fluorescence were measured by flow cytometry and error bars showed standard deviation calculated on the basis of technical replicates.
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<font face="calibri" size = "2"> Figure 6: The effectiveness of our CRISPRi system transferred via conjugation from donor to target strain. Our donor (S17-1) strain, which contains our conjugative plasmid (gRNA and dCas9 on pARO190 plasmid backbone) and a positive control donor strain (S17-1 containing only pARO190 backbone) were co-cultured separately with our target strain (JM109 with RFP inserted into its chromosome) for 8 hours. The co-cultures were then diluted 100 times and inducted with 500ng/mL aTc in new EZ-rich media. Different antibiotic markers were used (Carbenicillin + Chloramphenicol, and Chloramphenicol) to select for target cells with and without the conjugative plasmid. RFP fluorescence was measured via flow cytometry and error bars show standard deviation calculated on the basis of technical replicates.
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After conjugation and transfer of the conjugative plasmid, we see shifts in the populations of RFP expressing cells in those strains with our CRISPRi system compared to control. Our data in the second trial seem to suggest that the dCas9 expression is somewhat leaky behind our pTET promoter, showing low levels of expression without induction. Since our guideRNA is constitutively produced, this results in a small amount of specific targeting, and therefore RPF repression, without induction. It also appears as if overexpression of the dCas9 protein could be somewhat toxic to the cells, so we are currently working to modify the promoter to achieve more tight regulation of dCas9 expression. </font></div>
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After the transfer of the conjugative plasmid, there is a decrease in RFP expression in strains that have received the CRISPRi system compared to the control (pARO190 backbone), which shows no significant change. Our data in the second trial seem to suggest that dCas9 expression is somewhat leaky behind our pTET promoter, for there is expression of dCas9 without induction. Since our guideRNA is constitutively expressed, this results in a small amount of specific targeting, and therefore RFP repression, without induction. It also appears that overexpression of the dCas9 protein could be somewhat toxic to the cells, so we are currently working on modifying the promoter to achieve a tighter regulation of dCas9 expression. </font></div>
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<FONT COLOR="#008000"><u>Specificity of targeting through CRISPRi Conjugation</FONT COLOR="#008000"></u><br><br>
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To test the specificity of our system, we obtained a strain of E. coli (kindly provided by Stanley Qi, UCSF) containing both RFP and GFP integrated into its chromosome. We then conjugated our donor strain with this new recipient strain and measured RFP and GFP fluorescence. As can be seen in the graphs below, RFP fluorescence decreased only when the plasmid containing dCas9 and RFP-gRNA were conjugated. GFP fluorescence was not affected in any of the conditions, showing that the dCas9-gRNA complex transferred into cells via conjugation is highly specific.    </font></div>
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<FONT COLOR="#008000">In summary, we have shown that a specific targeting system using CRISPRi can be efficiently transmitted between cells to achieve repression of select genes. </FONT COLOR="#008000"></font></center>
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<b><FONT COLOR="#008000">We have shown that a specific gene repression system using CRISPRi can be efficiently transmitted between cells by conjugation. </FONT COLOR="#008000"></font></b></center>
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Latest revision as of 02:00, 29 October 2013

CRISPRi Conjugation - Experiments and Results


Summary: We have successfully constructed a specific gene repression system using CRISPRi that can be efficiently transmitted between cells via conjugation.


Confirming Conjugation:

For conjugation to occur, the bacterial strain that passes the plasmid must have the genes necessary to build the conjugative apparatus (a pilus) between the cells. This is normally carried on a large plasmid, called the F plasmid, that itself is transferred during conjugation, but due to its large size, it is not amenable to many cloning strategies. To combat this, we chose a bacterial strain (S17-1) that has the conjugative genes integrated into the chromosome, and a small conjugative plasmid containing the origin sequence for conjugative transfer, pARO190. We were then able to clone in sequences for dCas9 and a guideRNA for the target of our knockdown – RFP.
We first needed to confirm that conjugation was possible in our experimental setup. To test this, we co-cultured the donor strain (spectinomycin resistance) containing our empty pARO190 plasmid (carbenicillin resistance) with our target strain, which has RFP and chloramphenicol resistance intergrated into its chromosome (JM109-RFP). At certain time points, we took a sample of the co-cultures and selected for target strain cells that have received the conjugative plasmid, which we call “transconjugates”.
Figure 2: Effect of co-culture time on the efficiency of conjugation. Donor and target cells were diluted and mixed together so that the initial OD600 value of each co-culture was 0.05, and co-cultured in EZ-rich media at 37 ℃ under 180rpm shaking for 2 hours, 5 hours, and 8 hours, respectively. Final cell densities were measured by plating on LB agar plates containing Spectinomycin, Chloramphenicol, and Carbenicillin + Chloramphenicol, for the selection of donor, target, and transconjugants respectively. The conjugation rate (transconjugants/target * 100%) for each experiment was 0.45%, 0.23% and 0.44%, respectively.
Knock-down of RFP with CRISPRi:

Next, we needed to confirm that the CRISPRi system we designed could sufficiently repress RFP expression in our target strain. By directly transforming our engineered conjugative plasmid (which contains our CRISPRi system) into our target cells, we were able to measure RFP fluorescence after induction of the conjugative plasmid. We were able to observe significant knock-down of RFP expression in the cell containing our CRISPRi system.
Figure 3: The efficiency of our CRISPRi system was measured by directly transforming the conjugative plasmid that contains our CRISPRi system (gRNA and dCas9 protein) into our recipient cells (JM109 with RFP inserted into its genome). The dCas9 protein is under the control of a pTET promoter and the gRNA is under the control of a constitutive promoter. The positive control is a direct transformation of the conjugative plasmid backbone (pARO190 without gRNA and dCas9) into our recipient cells. RFP fluorescence is measured via plate reader and error bars show standard deviation calculated on the basis of technical replicates.
Figure 4: Figure 4: The dose-response curve for our CRISPRi (dCas9 and gRNA) system. The conjugative plasmid containing our CRISPRi system was directly transformed into our target strain (JM109-RFP) and RFP fluorescence was measured under different aTc concentrations (0, 0.625, 1, 6.25, 9.375, 12.5, 18.75, 25, 37.5, 50, 250, 500 ng/mL aTc). Our positive control was a direct transformation of the conjugative plasmid backbone (pARO190 without gRNA and dCas9) into our target strain, and our negative control was directly transform of conjugative plasmid that contains CRISPR/Cas repression system (gRNA and dCas9 protein) for RFP into JM109 strain without any fluorescent markers. RFP fluorescence was measured via flow cytometry and error bars show standard deviation calculated on the basis of technical replicates.
Conjugation of the CRISPRi System into Target Cells:

After demonstrating that our delivery (conjugation) and repression systems (CRISPRi system) are both functional in our assays, we moved on to test whether or not we can do both. That is, if it is possible to induce knock-down of a specific gene by transferring specific instructions from one cell to another via conjugation.

We co-cultured our donor strain containing the CRISPRi system with the JM-109 target strain for eight hours. The cultures were then diluted and selected for transconjugates by antibiotic resistance (cam and carb) and then induced with aTc to express dCas9 on the conjugative plasmid. Using FACS, we measured the RFP output post-conjugation at various time points post-induction.
Figure 5: The effectiveness of our CRISPRi system transferred via conjugation from donor to target strain. Our donor (S17-1) strain, which contains our conjugative plasmid (gRNA and dCas9 on pARO190 plasmid backbone) and a positive control donor strain (S17-1 containing only pARO190 backbone) were co-cultured separately with our target strain (JM109 with RFP inserted into its chromosome) for 8 hours. The co-cultures were then diluted 100 times and inducted with 500ng/mL aTc in new EZ-rich media. Different antibiotic markers were used (Carbenicillin + Chloramphenicol, and Chloramphenicol) to select for target cells with and without the conjugative plasmid. The histograms show RFP fluorescence for each sample, which was measured via flow cytometry.
Figure 6: The effectiveness of our CRISPRi system transferred via conjugation from donor to target strain. Our donor (S17-1) strain, which contains our conjugative plasmid (gRNA and dCas9 on pARO190 plasmid backbone) and a positive control donor strain (S17-1 containing only pARO190 backbone) were co-cultured separately with our target strain (JM109 with RFP inserted into its chromosome) for 8 hours. The co-cultures were then diluted 100 times and inducted with 500ng/mL aTc in new EZ-rich media. Different antibiotic markers were used (Carbenicillin + Chloramphenicol, and Chloramphenicol) to select for target cells with and without the conjugative plasmid. RFP fluorescence was measured via flow cytometry and error bars show standard deviation calculated on the basis of technical replicates.

After the transfer of the conjugative plasmid, there is a decrease in RFP expression in strains that have received the CRISPRi system compared to the control (pARO190 backbone), which shows no significant change. Our data in the second trial seem to suggest that dCas9 expression is somewhat leaky behind our pTET promoter, for there is expression of dCas9 without induction. Since our guideRNA is constitutively expressed, this results in a small amount of specific targeting, and therefore RFP repression, without induction. It also appears that overexpression of the dCas9 protein could be somewhat toxic to the cells, so we are currently working on modifying the promoter to achieve a tighter regulation of dCas9 expression.

Specificity of targeting through CRISPRi Conjugation

To test the specificity of our system, we obtained a strain of E. coli (kindly provided by Stanley Qi, UCSF) containing both RFP and GFP integrated into its chromosome. We then conjugated our donor strain with this new recipient strain and measured RFP and GFP fluorescence. As can be seen in the graphs below, RFP fluorescence decreased only when the plasmid containing dCas9 and RFP-gRNA were conjugated. GFP fluorescence was not affected in any of the conditions, showing that the dCas9-gRNA complex transferred into cells via conjugation is highly specific.

We have shown that a specific gene repression system using CRISPRi can be efficiently transmitted between cells by conjugation.