Part:BBa_K2448029
Psicose Biosensor pPsiR-PsiR from Sinorhizobium fredii
This part is a Psicose Biosensors based on the PsiR transcription factor from Sinorhizobium fredii (BBa_K2448007) and its associated promoter pPsiR (BBa_K2448013).
Usage and Biology
Biosensors rely on a basic theoretical principle: a certain concentration of a molecule of interest induces the proportional production of an easily detectable output, like fluorescence. Transcription-factor based biosensors allow quick and cheap detection or quantification of various chemical compounds.
Psicose biosensors were the lynchpin of our iGEM project. In order to improve the enzymatic production of psicose, we needed an efficient method to screen large banks of mutants. To address this problem, we designed a collection of specific biosensors able to detect psicose concentration in vivo (BBa_K2448025, BBa_K2448026, BBa_K2448027, BBa_K2448028, BBa_K2448029, BBa_K2448030 an BBa_K2448031). This part is, after BBa_K2448025 and BBa_K2448027, the second best candidate for screening a library of mutants and identify the cells carrying an improved version of our enzyme, the D-Psicose 3-epimerase (Dpe) from Clostridium cellulolyticum (BBa_K2448021).
Features
This biosensor was built using the Universal Biosensing Chassis (BBa_K2448023, BBa_K2448024) which is a composite part that provides an answer to the lack of rapid and reliable building methods for transcription-factor based biosensors.
It is based on the PsiR transcription factor from Sinorhizobium fredii (BBa_K2448007) and its associated promoter pPsiR (BBa_K2448013).
PsiR from Sinorhizobium fredii (BBa_K2448007) is a predicted LacI family transcription factor with high affinity for D-Psicose. This implies that PsiR is potentially capable of binding a consensus sequence in the promoter region and preventing transcription of the regulated promoters in the absence of D-Psicose, in a similar manner to the way LacI does in the absence of allolactose (or the synthetic IPTG).
In this biosensor, we used this Helix-Turn-Helix transcription factor together with the Sinorhizobium fredii pPsiR promoter (BBa_K2448013) which is the promoter region (0.4 kb upstream) of the PsiR gene of Sinorhizobium fredii (NGR_b11520). pPsiR is predicted to be repressed by the PsiR transcription factor (BBa_K2448007) which is inhibited in the presence of D-Psicose. This promoter regulates the expression of mCherry in our biosensor.
The results presented hereafter show that this duo PsiR - pPsiR behaved as predicted under and without induction.
Principle
When pTacI is induced by IPTG, it drives the transcription of the PsiR gene coding for the PsiR protein which is predicted to be a transcription factor able to bind D-Psicose. If D-Psicose is present in the cell, the transcription factor will bind preferentially to it and thus be inactivated. The repression of the related promoter pPsi will be released, enabling the transcription of a fluorescent protein, mCherry. If D-Psicose isn’t present in the cell, PsiR will bind to pPsi, preventing any transcription of mCherry.
Characterization
The detailed protocol is presented in the Experience page.
Optimal measurement time
The characterization of the biosensors allowed us to determine many important parameters. For instance, running the experiment for a long period (almost 23 hours) got us an estimation of the optimal measurement time.
To estimate this duration, we looked at the raw data and observed that it took around 9 hours to get an observable signal for the lowest concentration of inducer. It means that sensitivity threshold and consequently maximum accuracy is reached 9 hours after induction.
Since we wanted to detect and measure D-Psicose concentration between 1 mM and 300 mM, we needed a biosensor able to get maximum accuracy for this range of concentration in a minimal time. Taking into account the raw data, we can estimate that for this biosensor if D-Psicose concentration is above 10 mM, a 5 hour incubation after induction would give relevant results.
Basal expression
The biosensor show a basal expression of 1800 arbitrary units of fluorescence at 23 hour post-induction. This basal activity even without psicose in the media is due to an imbalance between the amount of PsiR transcription factor available and the pPsiR promoter strength. Even when PsiR is produced, the transcription factor can’t totally prevent the transcription from happening.
Dynamic range
Determining the dynamic range of our biosensor will give us an estimate of its sensitivity, its maximum and its potential use. We can observe in figure 2 a perfect foldchange in range of concentrations corresponding to bioproduction range (1 mM to 300 mM psicose), but it tends to saturate at high concentrations.
This gives us two important pieces of information:
- First, the results show that PsiR seems to interact with psicose and therefore behaves as predicted. The same observation applies for the pPsiR promoter which seems tightly regulated by PsiR under psicose induction, behaving also as predicted.
- Second, the dynamic range of this biosensor appears to go from 1 mM to 300 mM psicose.
Figure 2. In vivo characterization of this Psicose Biosensor in E. coli DH5alpha. The graph shows the mCherry measured florescence over psicose concentration in the media. Each data point is the mean of two technical duplicates and of three biological triplicates. Error bars represent standard deviations.
Sequence and Features
- 10COMPATIBLE WITH RFC[10]
- 12COMPATIBLE WITH RFC[12]
- 21INCOMPATIBLE WITH RFC[21]Illegal BamHI site found at 1334
Illegal XhoI site found at 62 - 23COMPATIBLE WITH RFC[23]
- 25INCOMPATIBLE WITH RFC[25]Illegal NgoMIV site found at 1556
Illegal AgeI site found at 791
Illegal AgeI site found at 1124
Illegal AgeI site found at 2348
Illegal AgeI site found at 2460 - 1000COMPATIBLE WITH RFC[1000]
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