Difference between revisions of "Part:BBa K2558212"
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<partinfo>BBa_K2558212 short</partinfo> | <partinfo>BBa_K2558212 short</partinfo> | ||
| − | This construct is composed of constantly expressed luxR, and lux pR-HS (https://parts.igem.org/Part:BBa_K2558001) controlled sfGFP as our reporter. We aim to use this construct to help us test lux pR system and AHL induction efficiency. We designed this device along with K2558211, which is the same except for the different properties of | + | This construct is composed of constantly expressed luxR, and lux pR-HS (https://parts.igem.org/Part:BBa_K2558001) controlled sfGFP as our reporter. We aim to use this construct to help us test lux pR system and AHL induction efficiency. We designed this device along with K2558211, which is the same except for the different properties of the lux pR and the lux pR-HS promotor. |
| + | |||
===Usage and Biology=== | ===Usage and Biology=== | ||
| − | With the hope to find an optimal promotor for our NEON system, we designed 9 mutations on sites | + | With the hope to find an optimal promotor for our NEON system, we designed 9 mutations on sites -35, -36, -37 near the luxR binding site and tested another on -10 site that TUST 2017 reported to show decreased leakage. We conducted experiments to evaluate these lux pR mutants’ reaction to AHL stimulation and their leakage level. The test devices we designed include a constantly expressed luxR and a lux pR (or mutant) driven sfGFP (like BBa_K2558211 with original lux pR promotor, and BBa_K2558212 with lux pR-HS promotor). |
| + | |||
===Results=== | ===Results=== | ||
| − | We conducted the experiment first | + | We conducted the experiment first with 9 mutations on sites -35, -36, -37 near the luxR binding and another on -10 site that TUST 2017 reported to show decreased leakage. We transferred the plasmids with lux pR driven sfGFP into ''E. coli'' DH5α. In theory, AHL can induce gene expression by activating lux pR promotor. We measured the value of Fluorescence/OD without AHL stimulation by microplate reader to show the leakages of different lux pR mutants, as lux pR promotor is not supposed to be activated without AHL. Meanwhile, we also regard the value of Fluorescence/OD with 10^-10 M AHL stimulation to observe the sensitivity and expression intensity of different lux pR mutants. Experiment data is shown in the figures below. (Figure.1) |
| − | + | <div><ul> <li style="display: inline-block;"> [[File:T--Tsinghua-LuxpRPromoter&MutsLeakage&AHLStimulation.png|thumb|none|600px|'''Figure.1. Leakage and 10^-10 mM AHL stimulation of lux pR promotor and its mutations.''' The fluorescence strengths and OD values are measured by microplate reader respectively at 510 nm and 600 nm wavelength. Plasmids with lux pR promotor and its mutants are transferred into ''E.coli'' DH5α. '''A''' The bacteria were treated without AHL inducing. High (Fluorescence/OD) ratio indicates strong leakage of promotor. Among all the strains, lux pR promotor has the strongest leakage and the largest error bar as well. '''B''' The bacteria were treated with 10-10 mM AHL induction. High (Fluorescence/OD) ratio indicates high expression intensity. Mutation 5 has almost the same expression intensity as the wild type lux pR promotor. | |
| + | ]] </li> | ||
| + | It is observed that high expression intensity is accompanied by high level of leakage in lux pR promotors. Wild type lux pR represented with black strand in the figures has the highest level of both leakage and intensity. The next three are Mutant 5 (G-36T), Mutant 6 (G-36C), Mutant 9 (T-35G). Mutant 5 has almost the same intensity as wild type, but the leakage is significantly smaller. Mutant 6 and Mutant 9 have a little bit less leakage and medium intensity. We also did the experiment with 10^-9 M and 10^-8 M AHL, all of the promotors show high expression levels and therefore unable to compare. (Data not shown) | ||
| − | <li style="display: inline-block;"> [[File:T--Tsinghua-LuxpRMut5&10PromotersLeakage&AHLStimulation.png|thumb|none|600px|'''Figure.2. Leakage and AHL stimulation of of lux pR Mutant 5 and Mutant 10.''' The fluorescence strengths and OD values are measured by microplate reader at 510 nm and 600 nm wavelength. A Plasmid with lux pR Mutant 5 is transferred into E.coli DH5α. The bacteria | + | <li style="display: inline-block;"> [[File:T--Tsinghua-LuxpRMut5&10PromotersLeakage&AHLStimulation.png|thumb|none|600px|'''Figure.2. Leakage and AHL stimulation of of lux pR Mutant 5 and Mutant 10.''' The fluorescence strengths and OD values are measured by microplate reader respectively at 510 nm and 600 nm wavelength. '''A''' Plasmid with lux pR Mutant 5 is transferred into ''E.coli'' DH5α. The bacteria were treated without or with 10^-10 mM, 10^-9 mM and 10^-8 mM AHL inducing. '''B''' Plasmid with lux pR Mutant 10 is transferred into ''E.coli'' DH5α. The bacteria were treated without or with 10^-10 mM, 10^-9 mM and 10^-8 mM AHL inducing.]] </li> |
| − | <li style="display: inline-block;"> [[File:T--Tsinghua-LuxpRWT&Mut5&10&HSLeakage&AHLStimulation.png|thumb|none|600px|'''Figure.3. Leakage and 10-10 mM AHL stimulation of of lux pR | + | <li style="display: inline-block;"> [[File:T--Tsinghua-LuxpRWT&Mut5&10&HSLeakage&AHLStimulation.png|thumb|none|600px|'''Figure.3. Leakage and 10^-10 mM AHL stimulation of of lux pR promotor WT, Mutant 5, Mutant 10 and HS.''' The fluorescence strengths and OD values are measured by microplate reader respectively at 510 nm and 600 nm wavelength. Plasmids with lux pR promotor WT, Mutant 5 and Mutant 10 are transferred into ''E.coli'' DH5α. '''A''' The bacteria were treated without AHL inducing. High (Fluorescence/OD) ratio indicates strong leakage of promotor. '''B''' The bacteria were treated with 10^-10 mM AHL induction. High (Fluorescence/OD) ratio indicates high expression intensity.]] |
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| − | + | ||
| − | We repeated AHL stimulation test on Mutant 5 and Mutant 10 (Figure.2) and decided to combine the two mutations together to form a new | + | We repeated AHL stimulation test on Mutant 5 and Mutant 10 (Figure.2) and decided to combine the two mutations together to form a new promotor with high intensity and small leakage. We named it lux pR-HS. We tested lux pR-HS under the same conditions. We can see that the lux pR-HS has similar leakage to Mutant 10, while it has much higher expression intensity. (Figure.3) The statistics of relative induction and leakage intensity of the 10 Mutants and lux pR-HS are shown in Table.1 |
<li style="display: inline-block;"> [[File:T--Tsinghua-ResultsOfLuxpRMutationAnalysis.png|thumb|none|500px|'''Table.1. Results of lux pR mutation analysis.''']] | <li style="display: inline-block;"> [[File:T--Tsinghua-ResultsOfLuxpRMutationAnalysis.png|thumb|none|500px|'''Table.1. Results of lux pR mutation analysis.''']] | ||
| − | As for why | + | As for why some mutations on -35 to -37 sites would decrease the leakage of lux pR without severely influencing the expression level, we have some hypotheses and explanations. It is reported that -35 to -37 sites are last three bases of lux box which is upstream of the lux promotor and bound specifically by luxR, one of regulatory protein involved in lux expression system.[1] G-36T mutation has less influence than other mutation on sites -35 to -37, which is same to our result. Besides, G-36T is not involved in the two regions of nucleotides -52 to -50 and -39 to -37 which directly contacted with luxR protein. Therefore, this single substitution of nucleotide would decrease the leakage of lux promotor without influencing the expression level too much.[2] |
| + | |||
===Protocol=== | ===Protocol=== | ||
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# two Pick a single colony by a sterile tip from each of the LB plates for all the experimental and control groups. Add the colony into 5ml LB medium with ampicillin at 100 ng/µl. Incubate for 6-8 h at 37℃ in a shaker. | # two Pick a single colony by a sterile tip from each of the LB plates for all the experimental and control groups. Add the colony into 5ml LB medium with ampicillin at 100 ng/µl. Incubate for 6-8 h at 37℃ in a shaker. | ||
# three Measure OD600 of the culture medium with photometer. Dilute the culture medium until OD600 reaches 0.6. | # three Measure OD600 of the culture medium with photometer. Dilute the culture medium until OD600 reaches 0.6. | ||
| − | # four Add 100 µl bacteria culture medium into a sterile 96-well plate. Add AHL to final concentrations of 0, 10-10,10-9,10-8 M. Fresh LB medium serves as blank control. Positive control is colony constantly expressing sfGFP and negative control is colony without sfGFP expression. Place the 96-well plate into an automatic microplate reader. Incubate at 16℃ overnight and | + | # four Add 100 µl bacteria culture medium into a sterile 96-well plate. Add AHL to final concentrations of 0, 10^-10,10^-9,10^-8 M. Fresh LB medium serves as blank control. Positive control is colony constantly expressing sfGFP and negative control is colony without sfGFP expression. Place the 96-well plate into an automatic microplate reader. Incubate at 16℃ overnight and measure the fluorometric value at 510 nm and OD600 of each well every 30 minutes. |
| − | # five Each group | + | # five Each group should be repeated for at least 3 times. |
| − | + | ||
===Reference=== | ===Reference=== | ||
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<br/>[2] Zeng, Weiqian, et al. "Rational design of an ultrasensitive quorum-sensing switch." Acs Synthetic Biology 6.8(2017). | <br/>[2] Zeng, Weiqian, et al. "Rational design of an ultrasensitive quorum-sensing switch." Acs Synthetic Biology 6.8(2017). | ||
| − | < | + | <br/> |
| − | + | ===Sequence and Features=== | |
<partinfo>BBa_K2558212 SequenceAndFeatures</partinfo> | <partinfo>BBa_K2558212 SequenceAndFeatures</partinfo> | ||
Latest revision as of 16:12, 17 October 2018
lux pR-HS test device
This construct is composed of constantly expressed luxR, and lux pR-HS (https://parts.igem.org/Part:BBa_K2558001) controlled sfGFP as our reporter. We aim to use this construct to help us test lux pR system and AHL induction efficiency. We designed this device along with K2558211, which is the same except for the different properties of the lux pR and the lux pR-HS promotor.
Usage and Biology
With the hope to find an optimal promotor for our NEON system, we designed 9 mutations on sites -35, -36, -37 near the luxR binding site and tested another on -10 site that TUST 2017 reported to show decreased leakage. We conducted experiments to evaluate these lux pR mutants’ reaction to AHL stimulation and their leakage level. The test devices we designed include a constantly expressed luxR and a lux pR (or mutant) driven sfGFP (like BBa_K2558211 with original lux pR promotor, and BBa_K2558212 with lux pR-HS promotor).
Results
We conducted the experiment first with 9 mutations on sites -35, -36, -37 near the luxR binding and another on -10 site that TUST 2017 reported to show decreased leakage. We transferred the plasmids with lux pR driven sfGFP into E. coli DH5α. In theory, AHL can induce gene expression by activating lux pR promotor. We measured the value of Fluorescence/OD without AHL stimulation by microplate reader to show the leakages of different lux pR mutants, as lux pR promotor is not supposed to be activated without AHL. Meanwhile, we also regard the value of Fluorescence/OD with 10^-10 M AHL stimulation to observe the sensitivity and expression intensity of different lux pR mutants. Experiment data is shown in the figures below. (Figure.1)
-
Figure.1. Leakage and 10^-10 mM AHL stimulation of lux pR promotor and its mutations. The fluorescence strengths and OD values are measured by microplate reader respectively at 510 nm and 600 nm wavelength. Plasmids with lux pR promotor and its mutants are transferred into E.coli DH5α. A The bacteria were treated without AHL inducing. High (Fluorescence/OD) ratio indicates strong leakage of promotor. Among all the strains, lux pR promotor has the strongest leakage and the largest error bar as well. B The bacteria were treated with 10-10 mM AHL induction. High (Fluorescence/OD) ratio indicates high expression intensity. Mutation 5 has almost the same expression intensity as the wild type lux pR promotor. -
Figure.2. Leakage and AHL stimulation of of lux pR Mutant 5 and Mutant 10. The fluorescence strengths and OD values are measured by microplate reader respectively at 510 nm and 600 nm wavelength. A Plasmid with lux pR Mutant 5 is transferred into E.coli DH5α. The bacteria were treated without or with 10^-10 mM, 10^-9 mM and 10^-8 mM AHL inducing. B Plasmid with lux pR Mutant 10 is transferred into E.coli DH5α. The bacteria were treated without or with 10^-10 mM, 10^-9 mM and 10^-8 mM AHL inducing. -
Figure.3. Leakage and 10^-10 mM AHL stimulation of of lux pR promotor WT, Mutant 5, Mutant 10 and HS. The fluorescence strengths and OD values are measured by microplate reader respectively at 510 nm and 600 nm wavelength. Plasmids with lux pR promotor WT, Mutant 5 and Mutant 10 are transferred into E.coli DH5α. A The bacteria were treated without AHL inducing. High (Fluorescence/OD) ratio indicates strong leakage of promotor. B The bacteria were treated with 10^-10 mM AHL induction. High (Fluorescence/OD) ratio indicates high expression intensity.We repeated AHL stimulation test on Mutant 5 and Mutant 10 (Figure.2) and decided to combine the two mutations together to form a new promotor with high intensity and small leakage. We named it lux pR-HS. We tested lux pR-HS under the same conditions. We can see that the lux pR-HS has similar leakage to Mutant 10, while it has much higher expression intensity. (Figure.3) The statistics of relative induction and leakage intensity of the 10 Mutants and lux pR-HS are shown in Table.1
-
As for why some mutations on -35 to -37 sites would decrease the leakage of lux pR without severely influencing the expression level, we have some hypotheses and explanations. It is reported that -35 to -37 sites are last three bases of lux box which is upstream of the lux promotor and bound specifically by luxR, one of regulatory protein involved in lux expression system.[1] G-36T mutation has less influence than other mutation on sites -35 to -37, which is same to our result. Besides, G-36T is not involved in the two regions of nucleotides -52 to -50 and -39 to -37 which directly contacted with luxR protein. Therefore, this single substitution of nucleotide would decrease the leakage of lux promotor without influencing the expression level too much.[2]
Protocol
- one Transform the plasmids into E. coli DH5α.
- two Pick a single colony by a sterile tip from each of the LB plates for all the experimental and control groups. Add the colony into 5ml LB medium with ampicillin at 100 ng/µl. Incubate for 6-8 h at 37℃ in a shaker.
- three Measure OD600 of the culture medium with photometer. Dilute the culture medium until OD600 reaches 0.6.
- four Add 100 µl bacteria culture medium into a sterile 96-well plate. Add AHL to final concentrations of 0, 10^-10,10^-9,10^-8 M. Fresh LB medium serves as blank control. Positive control is colony constantly expressing sfGFP and negative control is colony without sfGFP expression. Place the 96-well plate into an automatic microplate reader. Incubate at 16℃ overnight and measure the fluorometric value at 510 nm and OD600 of each well every 30 minutes.
- five Each group should be repeated for at least 3 times.
Reference
[1] Antunes, L. C., et al. "A mutational analysis defines Vibrio fischeri LuxR binding sites." Journal of Bacteriology 190.13(2008):4392-4397.
[2] Zeng, Weiqian, et al. "Rational design of an ultrasensitive quorum-sensing switch." Acs Synthetic Biology 6.8(2017).
Sequence and Features
Assembly Compatibility:- 10COMPATIBLE WITH RFC[10]
- 12INCOMPATIBLE WITH RFC[12]Illegal NheI site found at 1074
Illegal NheI site found at 1097 - 21COMPATIBLE WITH RFC[21]
- 23COMPATIBLE WITH RFC[23]
- 25COMPATIBLE WITH RFC[25]
- 1000INCOMPATIBLE WITH RFC[1000]Illegal SapI.rc site found at 177
It is observed that high expression intensity is accompanied by high level of leakage in lux pR promotors. Wild type lux pR represented with black strand in the figures has the highest level of both leakage and intensity. The next three are Mutant 5 (G-36T), Mutant 6 (G-36C), Mutant 9 (T-35G). Mutant 5 has almost the same intensity as wild type, but the leakage is significantly smaller. Mutant 6 and Mutant 9 have a little bit less leakage and medium intensity. We also did the experiment with 10^-9 M and 10^-8 M AHL, all of the promotors show high expression levels and therefore unable to compare. (Data not shown)
