Difference between revisions of "Part:BBa K1031302"

Revision as of 11:01, 25 September 2013

Pc-B0032-sfGFP-Terminator (HbpR)

Structure

HbpR is the activator of two promoters, Pc and Pd, they are σ-54 dependent. HbpR binds to UAS C-1 and UAS C-2 on Pc, UAS D-1 and D-2 on Pd. The 32-bp space between the centers of UASs C-1 and C-2 is critical for cooperative interactions. However, when the UASs C-1/C-2 are deleted and UASs C-3/C-4 are placed in an appropriate position with respect to the promoter region, the Pc promoter is still inducible with 2-HBP, albeit at a lower level. It shows that the presence of UAS pair C-3/C-4 mediated a higher promoter activity for transcription of hbpR(Fig 1 a, b)

Fig 1 The sequences preceding hbpC and hbpD promoter contains the binding sites for HbpR (UAS). The UASs are boxed in red. (a) HbpR binding sites on Pc promoter, there are 4 UASs responsible for binding with HbpR. (b) HbpR binding sites on Pd promoter, there are 2 UASs for binding with HbpR.

Sequence and Features

Assembly Compatibility:

10
COMPATIBLE WITH RFC[10]
12
COMPATIBLE WITH RFC[12]
21
COMPATIBLE WITH RFC[21]
23
COMPATIBLE WITH RFC[23]
25
COMPATIBLE WITH RFC[25]
1000
INCOMPATIBLE WITH RFC[1000]
Illegal SapI.rc site found at 266

Construction and data

K1031301 is composed of three elements, the inducible promoter Pc, RBS (Ribosome Binding Site) B0031[1], and reporter gene sfGFP. (Fig 2)

Fig 2 Construction of reporter circuit. The orange arrow represents Pc promoter for HbpR. The green oval stands for RBS B0031. sfGFP coding sequence is shown with dark blue, while terminator B0015[2] is in dark red.

We created a library for the RBS of sfGFP, including B0031, B0032 and B0034. Dose response curve were tested at the presence of 2-ABP and 2-HBP respectively. Experiment results showed that for inducers 2-ABP and 2-HBP, RBS B0032 had a superior performance compared with BBa_B0031 and BBa_B0034(Fig 3 a, b)

Fig 3 (a) Dose response curve of HbpR when exposed to 2-ABP at the concentration of 0.5µM, 1µM, 5µM, 10µM, 50µM, 100µM respectively. The reporter circuit consists of Pc promoter, RBS B0031, and reporter gene sfGFP. The curve with medium orange represents the circuit with B0031. Three lines represent circuit adopting different RBS. Fluorescence intensity of sfGFP is detected and calculated to plot induction ratio. (b) Dose response curve of HbpR when exposed to 2-HBP at the concentration of 0.5µM, 1µM, 5µM, 10µM, 50µM, 100µM respectively.

@@ Line 2: / Line 2: @@
 <partinfo>BBa_K1031302 short</partinfo>
-Ph-32-sfGFP-TT is a reporter for HbpR biosensor. Ph is a promoter which induced by HbpR when exposed to 2-hydroxybiphenyl and 2-aminobiphenl. BBa_B0032 is the RBS in this reporter. The reporter gene is superfold GFP followed by part BBa_B0015.
+<!-- -->
+== '''Structure''' ==
+HbpR is the activator of two promoters, Pc and Pd, they are σ-54 dependent. HbpR binds to UAS C-1 and UAS C-2 on Pc, UAS D-1 and D-2 on Pd. The 32-bp space between the centers of UASs C-1 and C-2 is critical for cooperative interactions. However, when the UASs C-1/C-2 are deleted and UASs C-3/C-4 are placed in an appropriate position with respect to the promoter region, the Pc promoter is still inducible with 2-HBP, albeit at a lower level. It shows that the presence of UAS pair C-3/C-4 mediated a higher promoter activity for transcription of hbpR('''Fig 1 a, b''')
+<html>
+<img src="https://static.igem.org/mediawiki/igem.org/a/a3/HbpR_Figure4_2013Peking_WH1.png", width=700px; />
+</html>
+'''Fig 1'''  The sequences preceding hbpC and hbpD promoter contains the binding sites for HbpR (UAS). The UASs are boxed in red. ('''a''') HbpR binding sites on ''Pc'' promoter, there are 4 UASs responsible for binding with HbpR. ('''b''') HbpR binding sites on ''Pd'' promoter, there are 2 UASs for binding with HbpR.
+== '''Sequence and Features''' ==
-<!-- Add more about the biology of this part here
-===Usage and Biology===
 <!-- -->
 <span class='h3bb'>Sequence and Features</span>
 <partinfo>BBa_K1031302 SequenceAndFeatures</partinfo>
+== '''Construction and data''' ==
+K1031301 is composed of three elements, the inducible promoter ''Pc'', RBS (Ribosome Binding Site) B0031[https://parts.igem.org/Part:BBa_B0031], and reporter gene sfGFP.   ('''Fig 2''')
+<html>
+<img src="https://static.igem.org/mediawiki/igem.org/3/3f/Peking2013_part_31-Pc_HbpR.png", width=400px; />
+</html>
+'''Fig 2''' Construction of reporter circuit. The orange arrow represents ''Pc'' promoter for HbpR. The green oval stands for RBS B0031. sfGFP coding sequence is shown with dark blue, while terminator B0015[https://parts.igem.org/Part:BBa_B0015] is in dark red.
+We created a library for the RBS of sfGFP, including B0031, B0032 and B0034. Dose response curve were tested at the presence of 2-ABP and 2-HBP respectively. Experiment results showed that for inducers 2-ABP and 2-HBP, RBS B0032 had a superior performance compared with BBa_B0031 and BBa_B0034('''Fig 3 a, b''')
+<html>
+<img src="https://static.igem.org/mediawiki/igem.org/thumb/3/39/Peking2013_part_RBS_library_HbpR.png/800px-Peking2013_part_RBS_library_HbpR.png", width=850px; />
+</html>
+'''Fig 3''' ('''a''') Dose response curve of HbpR when exposed to 2-ABP at the concentration of 0.5µM, 1µM, 5µM, 10µM, 50µM, 100µM respectively. The reporter circuit consists of Pc promoter, RBS B0031, and reporter gene sfGFP. The curve with medium orange represents the circuit with B0031. Three lines represent circuit adopting different RBS. Fluorescence intensity of sfGFP is detected and calculated to plot induction ratio. ('''b''') Dose response curve of HbpR when exposed to 2-HBP at the concentration of 0.5µM, 1µM, 5µM, 10µM, 50µM, 100µM respectively.
 <!-- Uncomment this to enable Functional Parameter display
 ===Functional Parameters===
-<partinfo>BBa_K1031302 parameters</partinfo>
+<partinfo>BBa_K1031301
-<!-- -->