Revision as of 17:53, 10 October 2016

Results

Characterization of the K1372001 biobrick from the 2014 "This is not a lemon" Paris Saclay project

As a part of the characterization of a previous existing Biobrick Part, we have chosen the BBa_K13372001 biobrick from the Paris Saclay 2014 project “This is not a lemon”. It was designed to mimic the ripening of a lemon in E. coli by a salycilate-inducible expression of a suppressor tRNA. The Paris Saclay 2014 team chose to use chromoproteins to express these colours in E. coli. Chromoproteins are reflective proteins that contain a pigmented prosthetic group and do not need to be excited to be seen. They fused a yellow chromoprotein with a blue one in order to display a green color. This construction is referred as the green fusion chromoprotein. In order to make the bacteria ripe like a real lemon, they decided to take advantage of the fusion protein’s design by using a translational suppression system. They added an amber codon (stop codon) within the linker separating the yellow and the blue chromoproteins genes. Therefore, the suppressor tRNA will suppress amber codon allowing the translation of the green fusion chromoprotein in presence of salicylate. Conversely, the down regulation of the suppressor tRNA in absence of salicylate will allow bacteria switch from green to yellow, thus simulating the ripening of a real lemon. This system is referred to as the colour switch system.

summary of the lemon ripening project

The tRNA used is the supD suppressor tRNA. It has been placed under control of a salicylate inducible promoter Psal. Its role is to suppress the introduced amber codon. The nahR gene encodes a transcriptional regulator that is induced by salicylate and thus binds nah or Psal promoters. In presence of high salicylate concentration in the agar media, supD will be expressed and so the green fusion chromoprotein: bacteria will display a green color. However, as bacteria grow into agar, less salicylate will remain available into the media. Thus, the decrease of the nahR-salicylate complex amount within bacteria will lead to supD downregulation through time. In turn, decrease of supD amount will result in less codon readthrough and so less translation of the green fusion protein and more translation of the yellow chromoprotein. As a result, bacteria will gradually change from green to yellow.

explanatory diagram of the lemon ripening

In order to characterize the biobrick, the color switch system (K1372001) was tested on three different constructions:

“TAA”: LacZ and Luc coding sequences in the same open reading frame, separated with an ochre stop codon.
“TQ”: LacZ and Luc coding sequences in the same open reading frame.
“TAG”: LacZ and Luc coding sequences in the same open reading frame, separated with an amber stop codon.

Each condition was tested under three different salicylate concentrations. In order to achieve that, both measurements of Beta-Galactosidase and Luciferase activities were performed on bacteria cultures.

The experiment was conducted on three sets of cultures of bacteria: Remarque : attention on doit parler du plasmide contenant K1372001 + on a pas dit avant pour pcl qui s’appelle d’ailleurs pcl99

“TAA”: BL21|K1372001 and pcl_TAA
“TQ”: BL21|K1372001 and pcl_Tq
“TAG”: BL21|K1372001 and pcl_TAG

Each of those sets of culture were incubated with three different salicylate concentrations: 0, 30µM and 1mM.

Each construction (TAA, TQ or TAG) was tested on 3 different clones (clones 1, 2 or 3), with 3 different salicylate concentrations (0, 30µM or 1mM), with in addition a negative control sample.

Pcl_TAA construction contains two TAA stop codon within the green fusion chromoprotein linker. This codon is not recognized by the supD suppressor t-RNA, thus no blue fluorescence is expected. pcl_Tq construction does not contain any stop codon, thus the green fusion chromoprotein construction should entirely been transcripted and emit both yellow and blue fluorescence. pcl_TAG contains the TAG codon recognized by supD suppressor t-RNA. Thus the transcription and the blue fluorescence of AeBlue should be inducible by salicylate. The luciferase luminescence is expected to vary depending to the different constructions conditions and to salicylate concentrations, instead of the Beta Galactosidase activity, which will remain constant. Thus luciferase data were normalized with those from Beta Galactosidase and our results are expressed as the Luciferase/Beta-Galactosidase activity. This ratio is then independent of the level of transcription, initiation or mRNA stability.

T--Paris Saclay--activity Luc Gal Tq fonction salicylate.PNG

The Tq plasmid does not contain any stop codon between LacZ and Luc. Thus, no matter the salicylate concentration, both Luciferase and Beta Galactosidase activities are supposed to be detected. As expected a high level of Luciferase/bGal activity is observed, but the ratio decreases when salicylate concentration increases. Indeed, both activities of Luciferase and bGal drop from 30µM of salicylate, but luciferase activity was more affected by the salicylate than bGal one. One may hypothesis that salicylate inhibits differently both reporter proteins activities, with a stronger inhibition of luciferase activity. We cannot determine whether this inhibition is due to a physiological consequence onto bacteria metabolism or occures after protein extraction.

In order to read the next results, we calculated a readthrough percentage, by doing a ratio between luciferase/bGal from TAA or TAG constructs and luciferase/bGal from TQ. In this way, we obtain a readthrough percentage.

T--Paris Saclay--activity Luc Gal TAA fonction salicylate.PNG

In TAA condition, regardless of the salicylate concentration, there is no significant Luciferase activity, so the ratio remains very low at any concentrations. We conclude that supD suppressor tRNA is very specific of the TAG codon and has no impact on the TAA stop codon.

T--Paris Saclay--activity Luc Gal TAG fonction salicylate.PNG

In TAG condition we can see an increase of stop codon readthrough activity with the increase of the salicylate concentration. In comparison to the results obtained with the TAA construction, the readthrough level increases similarly to the concentration of salicylate. This indicates that TAG stop codon is efficiently readthrough in presence of supD tRNA, allowing the production of a significant amount of luciferase.

In conclusion, the Psal promoter is fully inducible by salicylate and the suppressor tRNA is functional to suppress the TAG codon. These experiments demonstrate that K1372001biobrick is fully functional.

@@ Line 3: / Line 3: @@
 =Characterization of the K1372001 biobrick from the 2014 "This is not a lemon" Paris Saclay project=
-As a part of the characterization of a previous existing Biobrick Part, we chose the BBa_K13372001 biobrick from the Paris Saclay 2014 project “This is not a lemon”. It was designed to mimic the ripening of a lemon in E.Coli by an inducible expression of a t-RNA suppressor by salycilate.
+As a part of the characterization of a previous existing Biobrick Part, we have chosen the BBa_K13372001 biobrick from the Paris Saclay 2014 project “This is not a lemon”. It was designed to mimic the ripening of a lemon in E. coli by a salycilate-inducible expression of a suppressor tRNA.
-The Paris Saclay 2014 team chose to use chromoproteins to express these colors in E. coli. Chromoproteins are reflective proteins that contain a pigmented prosthetic group and do not need to be excited to be seen. They fused a yellow chromoprotein with a blue one in order to display a green color. This construction is referred as the green fusion chromoprotein. In order to make the bacteria ripe like a real lemon, they decided to take advantage of the fusion protein’s design by using a translational suppression system. They added amber codons within the linker separating the yellow and the blue chromoproteins. Therefore, the suppressor t-RNA will suppress amber codons allowing the translation of the green fusion chromoprotein in presence of salicylate. Conversely, the down regulation of the suppressor t-RNA in absence of salicylate will allow bacteria switch from green to yellow, thus simulating the ripening of a real lemon. This system is referred to as the color switch system.
+The Paris Saclay 2014 team chose to use chromoproteins to express these colours in E. coli. Chromoproteins are reflective proteins that contain a pigmented prosthetic group and do not need to be excited to be seen. They fused a yellow chromoprotein with a blue one in order to display a green color. This construction is referred as the green fusion chromoprotein. In order to make the bacteria ripe like a real lemon, they decided to take advantage of the fusion protein’s design by using a translational suppression system. They added an amber codon (stop codon) within the linker separating the yellow and the blue chromoproteins genes. Therefore, the suppressor tRNA will suppress amber codon allowing the translation of the green fusion chromoprotein in presence of salicylate. Conversely, the down regulation of the suppressor tRNA in absence of salicylate will allow bacteria switch from green to yellow, thus simulating the ripening of a real lemon. This system is referred to as the colour switch system.
 [[File:T--Paris_Saclay--project_2014_1.jpeg.png|400px|thumb|centre|summary of the lemon ripening project]]
-The t-RNA used is the supD suppressor t-RNA. It has been placed under control of a salicylate inducible promoter Psal. Its role is to suppress the introduced amber codon. The nahR gene encodes a transcriptional regulator that is induced by salicylate and thus bind nah or Psal promoters. In presence of high salicylate concentration in the agar media, supD will be expressed and so the green fusion chromoprotein: bacteria will display a green color. However, as bacteria grow into agar, less salicylate will remain available into the media. Thus, the decrease of the nahR-salicylate complex amount within bacteria will lead to supD downregulation through time. In turn, decrease of supD amount will result in less codon readthrough and so less translation of the green fusion protein and more translation of the yellow chromoprotein. As a result, bacteria will gradually change from green to yellow.
+The tRNA used is the supD suppressor tRNA. It has been placed under control of a salicylate inducible promoter Psal. Its role is to suppress the introduced amber codon. The nahR gene encodes a transcriptional regulator that is induced by salicylate and thus binds nah or Psal promoters. In presence of high salicylate concentration in the agar media, supD will be expressed and so the green fusion chromoprotein: bacteria will display a green color. However, as bacteria grow into agar, less salicylate will remain available into the media. Thus, the decrease of the nahR-salicylate complex amount within bacteria will lead to supD downregulation through time. In turn, decrease of supD amount will result in less codon readthrough and so less translation of the green fusion protein and more translation of the yellow chromoprotein. As a result, bacteria will gradually change from green to yellow.
 [[File:T--Paris_Saclay--project_2014_2.jpeg|400px|thumb|centre|explanatory diagram of the lemon ripening]]
 In order to characterize the biobrick, the color switch system (K1372001) was tested on three different constructions:
-* “TAA”: LacZ and Luc genes in the same open reading frame, separated with an ochre codon.
+* “TAA”: LacZ and Luc coding sequences in the same open reading frame, separated with an ochre stop codon.
-* “Qt”: LacZ and Luc genes in the same open reading frame.
+* “TQ”: LacZ and Luc coding sequences in the same open reading frame.
-* “TAG”: LacZ and Luc genes in the same open reading frame, separated with an amber codon.
+* “TAG”: LacZ and Luc coding sequences in the same open reading frame, separated with an amber stop codon.
-Each condition was tested under three different salicylate concentrations. In order to achieve that, both measurements of Beta-Galactosidase activity and of the luminescence resulting from Luciferase activity were made on bacteria cultures.
+Each condition was tested under three different salicylate concentrations. In order to achieve that, both measurements of Beta-Galactosidase and Luciferase activities were performed on bacteria cultures.
 The experiment was conducted on three sets of cultures of bacteria:
 Remarque : attention on doit parler du plasmide contenant K1372001 + on a pas dit avant pour pcl qui s’appelle d’ailleurs pcl99
 * “TAA”: BL21|K1372001 and pcl_TAA
-* “Qt”: BL21|K1372001 and pcl_Tq
+* “TQ”: BL21|K1372001 and pcl_Tq
 * “TAG”: BL21|K1372001 and pcl_TAG
 Each of those sets of culture were incubated with three different salicylate concentrations: 0, 30µM and 1mM.
-Each construction (TAA, Tq or TAG) was tested on 3 different clones (clones 1, 2 or 3), with 3 different salicylate concentrations (0, 30µM or 1mM), with in addition a negative control sample.
+Each construction (TAA, TQ or TAG) was tested on 3 different clones (clones 1, 2 or 3), with 3 different salicylate concentrations (0, 30µM or 1mM), with in addition a negative control sample.
 Pcl_TAA construction contains two TAA stop codon within the green fusion chromoprotein linker. This codon is not recognized by the supD suppressor t-RNA, thus no blue fluorescence is expected.
 pcl_Tq construction does not contain any stop codon, thus the green fusion chromoprotein construction should entirely been transcripted and emit both yellow and blue fluorescence.
 pcl_TAG contains the TAG codon recognized by supD suppressor t-RNA. Thus the transcription and the blue fluorescence of AeBlue should be inducible by salicylate.
-The luciferase luminescence is expected to vary depending to the different constructions conditions and to salicylate concentrations, instead of the Beta Galactosidase activity which will remain constant. Thus luciferase data were normalized with those from Beta Galactosidase and our results are expressed as the Luciferase/Beta-Galactosidase activity.
+The luciferase luminescence is expected to vary depending to the different constructions conditions and to salicylate concentrations, instead of the Beta Galactosidase activity, which will remain constant. Thus luciferase data were normalized with those from Beta Galactosidase and our results are expressed as the Luciferase/Beta-Galactosidase activity. This ratio is then independent of the level of transcription, initiation or mRNA stability.
 [[File:T--Paris_Saclay--activity_Luc_Gal_Tq_fonction_salicylate.PNG|400px|thumb|centre|]]
-In the Tq conditions, the plasmid does not contain any stop codon between LacZ and Luc. Thus, no matter the salicylate concentration, the Luciferase activity is supposed to be highly detected, and the ratio luciferase/bGal should be superior to 1.
+The Tq plasmid does not contain any stop codon between LacZ and Luc. Thus, no matter the salicylate concentration, both Luciferase and Beta Galactosidase activities are supposed to be detected.
-As expected a very high level of Luciferase/bGal activity is observed, but a decrease is noticed with the rise of salicylate. Indeed, both activity of Luciferase and bGal drop from 30µM of salicylate. It is obvious that salicylate has an impact on our protein’s activities tested.
+As expected a high level of Luciferase/bGal activity is observed, but the ratio decreases when salicylate concentration increases. Indeed, both activities of Luciferase and bGal drop from 30µM of salicylate, but luciferase activity was more affected by the salicylate than bGal one.
-We can make the hypothesis that the salicylate has a direct or indirect influence on the metabolism of bacteria, and thus could reduce the synthesis of protein, whose luciferase and beta-galactosidase.
+One may hypothesis that salicylate inhibits differently both reporter proteins activities, with a stronger inhibition of luciferase activity. We cannot determine whether this inhibition is due to a physiological consequence onto bacteria metabolism or occures after protein extraction.
-In order to read the next results, we will evaluate the levels of activity in TAA and TAG constructions in comparison to those in Tq, and express it in percentage.
+In order to read the next results, we calculated a readthrough percentage, by doing a ratio between luciferase/bGal from TAA or TAG constructs and luciferase/bGal from TQ. In this way, we obtain a readthrough percentage.
 [[File:T--Paris_Saclay--activity_Luc_Gal_TAA_fonction_salicylate.PNG|400px|thumb|centre|]]
-In the TAA conditions, regardless of the salicylate concentration, there is no significant activity of Luciferase/Beta-Galactosidase.
+In TAA condition, regardless of the salicylate concentration, there is no significant Luciferase activity, so the ratio remains very low at any concentrations.
-Those results indicate that bacteria with part K1321001 and the TAA green protein fusion are unable to emit blue fluorescence due to the luciferase activity.
+We conclude that supD suppressor tRNA is very specific of the TAG codon and has no impact on the TAA stop codon.
-The stop codon TAA does not seem to be recognized by the supD tRNA suppressor, and
 [[File:T--Paris_Saclay--activity_Luc_Gal_TAG_fonction_salicylate.PNG|400px|thumb|centre|]]
-In TAG condition we can see a rising of the luciferase/bGal activity with the increase of the salicylate concentration.
+In TAG condition we can see an increase of stop codon readthrough activity with the increase of the salicylate concentration.
+In comparison to the results obtained with the TAA construction, the readthrough level increases similarly to the concentration of salicylate.
+This indicates that TAG stop codon is efficiently readthrough in presence of supD tRNA, allowing the production of a significant amount of luciferase.
-In comparison to the results obtained with the TAA construction, the luciferase fluorescence activity is way higher for each salicylate condition. Thus this luminescence is specific to the amber codon. This proves the good transcription and translation of the Luc gene, in consequence to a high TAG read-through in presence of supD.
+In conclusion, the Psal promoter is fully inducible by salicylate and the suppressor tRNA is functional to suppress the TAG codon. These experiments demonstrate that K1372001biobrick is fully functional.
-The suppressor RNAt supD is specific to amber codon, and cannot ensure the transcription of Luc in presence of the ochre codon.
-In addition, the luciferase/bGal activity sharply rises from 30µM of salicylate in the TAG construction, but stays null for TAA. Thereby the variations of salicylate concentration are responsible of the increased production of supD specific to the TAA codon.
 {{Team:Paris_Saclay/project_footer}}

Difference between revisions of "Team:Paris Saclay/Results"

Revision as of 17:53, 10 October 2016

Results

Characterization of the K1372001 biobrick from the 2014 "This is not a lemon" Paris Saclay project