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Team:Peking/DataPage/Parts
From 2013.igem.org
Parts
XylS Main Page-BBa_K1031911 XylS is a σ70-dependent transcriptional factor that activates Pm promoter when benzoate acid or its derivative is present. It is used to build a XylS biosensor circuit. Adaptor for this biosensor will improve the performance of XylS in detection. Visit Wiki
HbpR Main Page-BBa_K1031300 HbpR is a σ54-dependent transcriptional factor, which activates PC promoter in the presence of 2-hydroxybiphenol or 2-aminobiphenol. We built a HbpR biosensor circuit and fine-tuned its performance in E.coli. Visit Wiki
NahF Main Page-BBa_K1031620 NahF is the salicylaldehyde dehydrogenase to convert salicylaldehyde into salicylic acid (salicylate) using NAD+. We tested NahF in E.coli and showed that the NahF works as an Adaptor for the NahR biosensor NahR, significantly improving the performance and range of detection. Visit Wiki
Hybrid Promoter Main Page-BBa_K1031021 The hybrid promoter was constructed for Band-pass Filter. The reporter sfGFP was controlled by both the activator and the inhibitor at the same time. We tested this hybrid promoter and built a model to describe its performance. Visit Wiki
NahR Main Page-BBa_K1031610 Pre-existing Part: Main Page-BBa_J61051 BBa_K1031610 is upgraded from original part BBa_J61051. NahR is a transcription factor mined from Pseudomonas putida which binds to nah and sal promoters to activate transcription in response to the inducer salicylate. We constructed a Psal/NahR biosensor circuit using sfGFP as reporter gene and systematically characterized its performance . Adaptor of this biosensor not only improves the detection efficiency but also expands the detection profile. Visit Wiki
Parts for Biosensors
DmpR
BBa_K1031221,
BBa_K1031222,
BBa_K1031223 and
BBa_K1031224 are the DmpR biosensors using different RBS preceding sfGFP.
BBa_K1031211 is the DmpR transcriptional factor under a constitutive promoter.
HbpR
BBa_K1031300 is the coding sequence of HbpR with terminators.
BBa_K1031301 and
BBa_K1031302 are HbpR biosensors using different RBS preceding sfGFP.
BBa_K1031311 is the HbpR transcriptional factor under a constitutive promoter.
HcaR BBa_K1031410 is the coding sequence of HcaR with terminators. BBa_K1031441, BBa_K1031442, BBa_K1031443 and BBa_K1031444 are HcaR transcriptional factors with different constitutive promoters (Pc). BBa_K1031420, BBa_K1031421 and BBa_K1031422 are HcaR biosensors using different RBS preceding sfGFP.
CapR BBa_K1031100 is the coding sequence of CapR transcriptional factor. BBa_K1031111 and BBa_K1031112 are CapR transcriptional factors under different constitutive promoters (Pc). BBa_K1031113 and BBa_K1031114 are reporters with different RBS for the CapR biosensor.
HpaR BBa_K1031510 is the coding sequence of HpaR transcriptional factor. BBa_K1031520 and BBa_K1031521 are reporters with different RBS for the HpaR biosensor.
NahR BBa_K1031610 is the NahR biosensor circuit.
PaaX BBa_K1031710 is the coding sequence of PaaX with terminators. BBa_K1031742, BBa_K1031743 and BBa_K1031744 are PaaX transcriptional factors under different constitutive promoters (Pc).
XylS BBa_K1031911 is the coding sequence of XylS transcriptional factor with terminators. BBa_K1031912, BBa_K1031913, BBa_K1031916 and BBa_K1031917 are XylS transcriptional factors under different constitutive promoters (Pc). BBa_K1031941 is the reporter for the XylS biosensor.
XylR BBa_K1031803 BBa_K1031804 is the XylR biosensor library using different RBS.
Parts for Adaptors
NahF
BBa_K1031620 is the coding sequence of the enzyme NahF with terminators.
BBa_K1031621,
BBa_K1031622,
BBa_K1031623,
BBa_K1031624 and
BBa_K1031625 are coding sequences of enzyme NahF under different Pc.
XylC
BBa_K1031931 is the coding sequence of enzyme XylC under Pc.
XylB
BBa_K1031922 and
BBa_K1031923 are coding sequences of enzyme XylB under different Pc.
Parts for Band-Pass Filter
BBa_K1031021 is the hybrid promoter which can be activated and inhibited at the same time by two different transcriptional factors. BBa_K1031011 is the ϕR73δ activator used in the Band-pass Filter. BBa_K1031017 is the coding sequence of activator ϕR73δ under Pc. BBa_K1031018 is the coding sequence of activator ϕR73δ under Promoter pSal. BBa_K1031019 is the coding sequence of activator ϕR73δ Regulated by the biosensor NahR. Each of BBa_K1031013, BBa_K1031014, BBa_K1031015 and BBa_K1031016 is the coding sequence of cI with different RBS and pSal as its promoter, which is a crucial component for the Band-pass Filter.
Figure 1. The aromatics spectrum showing the aromatics-sensing profiles of our individual biosensors. Each color segment in the central spectrum represents the detection profile of a biosensor. Structural formulas highlighted in color stand for the aromatic compounds that can be detected by our biosensors. The "plug" icon stands for Adaptors, enzymes that convert the undetectable compounds into the detectable compounds, thus to reinforce the detection capacity of some biosensors. Click Here for the summary of the aromatics spectrum and aromatics-sensing profiles of individual biosensors. Visit Our Wiki
Figure 2. Linear fitting of the data obtained from the orthogonality assay showing the orthogonality between the 4 representative biosensors. The experiments and data processing were performed as described in Fig. 2 and Fig. 3.The black dashed line denotes slope=1 as the reference line. These fittings showed the orthogonality between biosensors, (a, b) XylS and NahR; (c, d) XylS and HbpR; (e, f) NahR and HbpR, (g, h) XylS and DmpR, (i, j) NahR and DmpR, and (k, l) HbpR and DmpR. The experiment data, linear fitting curves of biosensor, and cognate inducers are in different colors: XylS in red, NahR in green, HbpR in orange and DmpR in dark cyan. (For more details, please Click Here)
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