Difference between revisions of "Part:BBa K1031300"

Revision as of 03:47, 25 September 2013

HbpR-Terminator

Overview

HbpR (For more details:http://2013.igem.org/Team:Peking/Project/BioSensors/HbpR) is 54-dependent transcriptional factor belonging to NtrC family of prokaryotic transcriptional activators. It shares a high homology to members of the XylR/DmpR subclass. HbpR was found in Pseudomonas azelaica. which can use 2-hydroxybiphenyl (2-HBP) and 2, 2’-dihydroxybiphenyl as sole carbon and energy sources through enzymes encoded by hbpCAD functioning in meta-cleavage pathway.

Metabolic Operon

Fig.1 Operon and pathway of HboR(a) Operon of HbpR. Orange rectangle shows hbpR gene. Blue and green rectangles show hbpCA and hbpD genes controled by PC and PD respectively. The orange rectangle show hbpR gene which encodes HbpR protein. When exposed to effector 2-hydroxybiphenyl, HbpR will activate PC and PD. (b) Pathway for the primary metabolism of 2-hydroxybiphenyl and 2-propylphenol in P. azelaica HBP1. The enzymes for each step are also indicated.

Protein Domains

Fig.2 Four domains of HbpR protein. A domain is sensing domain, conformation change may happen with inducer's binding. B domain is a linker. C domain contains an AAA ATPase motif. It has the capacity to hydrolyze ATP and to interact with sigma54 RNA polymerase. D domain binds to DNA via a typical helix-turn-helix motif.

Inducible Promoter Structure

Fig.3 Regions containing the binding sites for HbpR (UAS) are shown within boxes in the sequence. Sequence numbers refer to the locations of the transcriptional start sites of hbpC and hbpD. HbpR binds to UAS C-1 and UAS C-2. The 32-bp space between the centers of UASs C-1 and C-2 is critical for cooperative interactions. 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 hbpC promoter is still inducible with 2-HBP, albeit at a lower level. The presence of UAS pair C-3/C-4 mediated a higher promoter activity for transcription of hbpR.

Sequence and Features

Assembly Compatibility:

10
COMPATIBLE WITH RFC[10]
12
COMPATIBLE WITH RFC[12]
21
INCOMPATIBLE WITH RFC[21]
Illegal XhoI site found at 1673
23
COMPATIBLE WITH RFC[23]
25
COMPATIBLE WITH RFC[25]
1000
INCOMPATIBLE WITH RFC[1000]
Illegal SapI.rc site found at 387

Characterization of Biosensor

Construction and Tuning

We used PCR to get hbpR gene from bacterial strain and inducible promoter Pc' was synthesized by Genscript Company. The gene hbpR was controlled by a constitutive promoter Pc on plasmid pSB4K5. Another plasmid pUC57 containing Pc'-RBS-sfGFP was double transformed with pSB4K5 to construct HbpR biosensor. To tune its performance, Pc constitutive promoter library and RBS library for reporter were constructed.(Fig. 4)

Fig.4 Construction of the HbpR biosensor and improvements of its performance. (a) Structure of plasmids for hbpR gene and the reporter gene sfGFP. There is a library for the constitutive promoter before HbpR and the RBS before sfGFP respectively, both of which function to fine-tune the expression level of HbpR. (b) Induction ratio of HbpR controlled by promoters with different expression intensity. The effectors 2-HBP and 2-ABP are plotted in different colors. Data were collected via Microplate Reader. (c) Induction ratio of HbpR when exposed to a series of concentration of 2-ABP. The reporter system includes Pc-RBS-sfGFP. Three lines represent sfGFP controlled by different RBS. Fluorescence intensity of sfGFP is detected and calculated to plot induction ratio. (d) Induction ratio of HbpR when exposed to a series of concentration of 2-HBP.

On-Off Detection

Fig. 5. On-Off test results for sensor strain 114-32 HbpR. (a) On/off response of strain HbpR to 78 aromatic compounds. (For the full name of the compounds, CLICK HERE(hyperlink is needed here)). The strain showed induction ratio more than 10 folds when exposed to 2-HBP and 2-ABP. (B) The detection range of sensor strain HbpR is profiled in yellow at the aromatics spectrum. The structure formula of typical inducer 2-HBP and 2-ABP is showed near its chemical formula.

Dose-response Curve

Fig. 6. Dose response curves for the induction effect of 2-HBP and 2-ABP to the best-performed HbpR sensor strain (BBa_J23114-HbpR and Pc-BBa_B0032-sfGFP).

Orthogonality

Sensor	Host	Main Inducers
XylS	Pseudomonas putida	BzO 2-MeBzO 3-MeBzO 2,3-MeBzO 3,4-MeBzO
NahR	Pseudomonas putida	4-MeSaA 4-C1SaA 5-C1SaA SaA Aspirin
DmpR	Pseudomonas sp.600	Phl 2-MePhl 3-MePhl 4-MePhl 2-ClPhl
HbpR	Pseudomonas azelaica	o-Phenylphenol 2,6'-DiHydroxybiphenol

we have confirmed the orthogonality among inducers of different biosensors, which is one of the main features we expect for our aromatics-sensing toolkit. Our s

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 <partinfo>BBa_K1031300 short</partinfo>
-Introduction
+=='''Overview'''==
 HbpR (For more details:http://2013.igem.org/Team:Peking/Project/BioSensors/HbpR) is 54-dependent transcriptional factor belonging to NtrC family of prokaryotic transcriptional activators. It shares a high homology to members of the XylR/DmpR subclass. HbpR was found in Pseudomonas azelaica. which can use 2-hydroxybiphenyl (2-HBP) and 2, 2’-dihydroxybiphenyl as sole carbon and energy sources through enzymes encoded by hbpCAD functioning in meta-cleavage pathway.
 <html>
 <p><b>Metabolic Operon</b></p>
-<img src="https://static.igem.org/mediawiki/igem.org/0/03/HbpR_Figure1_2013Peking_WH.png", width=400px; left=100px/>
+<img src="https://static.igem.org/mediawiki/2013/3/36/Peking2013_HbpR_Overview.png" style="width:800px;margin-left:60px"  ></a>
-<img  style="position:relative; left:50px" src="https://static.igem.org/mediawiki/igem.org/7/7b/HbpR_Figure2_2013Peking_WH.png", width=400px;/>
-<p  style="position:relative; top:-80px "><b>Fig. 1a.</b> Operon of hbpR. Orange rectangle shows hbpR gene. Blue and green rectangles show hbpCA and hbpD genes controled by PC and PD respectively. The orange rectangle show hbpR gene which encodes HbpR protein. When exposed to effector 2-hydroxybiphenyl, HbpR will activate PC and PD. </br>
+<p style="text-align:center"><b>Fig.1</b> Operon and pathway of HboR(a) Operon of HbpR. Orange rectangle shows hbpR gene. Blue and green rectangles show hbpCA and hbpD genes controled by PC and PD respectively. The orange rectangle show hbpR gene which encodes HbpR protein. When exposed to effector 2-hydroxybiphenyl, HbpR will activate PC and PD. (b) Pathway for the primary metabolism of 2-hydroxybiphenyl and 2-propylphenol in<i> P. azelaica</i> HBP1. The enzymes for each step are also indicated.
- <b>Fig. 1b.</b> Pathway for the primary metabolism of 2-hydroxybiphenyl and 2-propylphenol in<i> P. azelaica</i> HBP1. The enzymes for each step are also indicated.
+<p>
-<p><b>Protein Domains</b></p>
+<b>Protein Domains</b></p>
+<br/>
 <img src="https://static.igem.org/mediawiki/igem.org/9/94/HbpR_Figure3_2013Peking_WH.png", width=400px;/>
-<p style="position:absolute; top: 600px; left: 450px;"><b>Fig. 2</b> Four domains of HbpR protein. A domain is sensing domain, conformation change may happen with inducer's binding. B domain is a linker. C domain contains an AAA ATPase motif. It has the capacity to hydrolyze ATP and to interact with sigma54 RNA polymerase. D domain binds to DNA via a typical helix-turn-helix motif.
+<p style="position:absolute; top: 700px; left: 450px;"><b>Fig.2</b> Four domains of HbpR protein. A domain is sensing domain, conformation change may happen with inducer's binding. B domain is a linker. C domain contains an AAA ATPase motif. It has the capacity to hydrolyze ATP and to interact with sigma54 RNA polymerase. D domain binds to DNA via a typical helix-turn-helix motif.
 </p>
@@ Line 19: / Line 21: @@
 <img style="position:relative; top:-130px; left:0px;" src="https://static.igem.org/mediawiki/igem.org/7/7b/HbpR_Figure4_2013Peking_WH.png", width=400px;/>
-<p id="FigureHbpR3"style="position:absolute; top:800px; left:450px; height:300px;">
+<p id="FigureHbpR3"style="position:absolute; top:900px; left:450px; height:300px;">
-<B>Fig. 3.</B> Regions containing the binding sites for HbpR (UAS) are shown within boxes in the sequence. Sequence numbers refer to the locations of the transcriptional start sites of hbpC and hbpD. HbpR binds to UAS C-1 and UAS C-2. The 32-bp space between the centers of UASs C-1 and C-2 is critical for cooperative interactions. 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 hbpC promoter is still inducible with 2-HBP, albeit at a lower level. The presence of UAS pair C-3/C-4 mediated a higher promoter activity for transcription of hbpR.
+<B>Fig.3</B> Regions containing the binding sites for HbpR (UAS) are shown within boxes in the sequence. Sequence numbers refer to the locations of the transcriptional start sites of hbpC and hbpD. HbpR binds to UAS C-1 and UAS C-2. The 32-bp space between the centers of UASs C-1 and C-2 is critical for cooperative interactions. 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 hbpC promoter is still inducible with 2-HBP, albeit at a lower level. The presence of UAS pair C-3/C-4 mediated a higher promoter activity for transcription of hbpR.
 </p>
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 <span class='h3bb'>Sequence and Features</span>
 <partinfo>BBa_K1031300 SequenceAndFeatures</partinfo>
+=='''Characterization of Biosensor'''==
 <html>
 <p><b>Construction and Tuning</b></p>
@@ Line 42: / Line 47: @@
 <img id="FigurePic5" src=" https://static.igem.org/mediawiki/igem.org/e/ee/HbpR_Figure5_2013Peking_WH.png ", width=800px/>
 <p style="position:relative">
-<B>Fig. 4.</B> Construction of the HbpR biosensor and improvements of its performance. (a) Structure of plasmids for hbpR gene and the reporter gene sfGFP. There is a library for the constitutive promoter before HbpR and the RBS before sfGFP respectively, both of which function to fine-tune the expression level of HbpR. (b) Induction ratio of HbpR controlled by promoters with different expression intensity. The effectors 2-HBP and 2-ABP are plotted in different colors. Data were collected via Microplate Reader. (c) Induction ratio of HbpR when exposed to a series of concentration of 2-ABP. The reporter system includes Pc-RBS-sfGFP. Three lines represent sfGFP controlled by different RBS. Fluorescence intensity of sfGFP is detected and calculated to plot induction ratio. (d) Induction ratio of HbpR when exposed to a series of concentration of 2-HBP.
+<B>Fig.4</B> Construction of the HbpR biosensor and improvements of its performance. (a) Structure of plasmids for hbpR gene and the reporter gene sfGFP. There is a library for the constitutive promoter before HbpR and the RBS before sfGFP respectively, both of which function to fine-tune the expression level of HbpR. (b) Induction ratio of HbpR controlled by promoters with different expression intensity. The effectors 2-HBP and 2-ABP are plotted in different colors. Data were collected via Microplate Reader. (c) Induction ratio of HbpR when exposed to a series of concentration of 2-ABP. The reporter system includes Pc-RBS-sfGFP. Three lines represent sfGFP controlled by different RBS. Fluorescence intensity of sfGFP is detected and calculated to plot induction ratio. (d) Induction ratio of HbpR when exposed to a series of concentration of 2-HBP.
 </p>
 <p><b>On-Off Detection</b></p>
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 </html>
-== Orthogonality ==
+== '''Orthogonality''' ==
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 <p style="position: relative; top: -100px;">
-we have confirmed the orthogonality among inducers of different biosensors, which is one of the main features we expect for our aromatics-sensing toolkit. Our sensors are well suited to multicomponent analysis.
+we have confirmed the orthogonality among inducers of different biosensors, which is one of the main features we expect for our aromatics-sensing toolkit. Our s
-</br>
-</p>
-</html>
-'''Related Parts:'''
-XylS: https://parts.igem.org/Part:BBa_K1031911   Wiki: http://2013.igem.org/Team:Peking/Project/BioSensors/XylS
-NahR: https://parts.igem.org/Part:BBa_K1031610 Wiki: http://2013.igem.org/Team:Peking/Project/BioSensors/NahR
-HbpR: https://parts.igem.org/Part:BBa_K1031300 Wiki: http://2013.igem.org/Team:Peking/Project/BioSensors/HbpR
-DmpR: http://2013.igem.org/Team:Peking/Project/BioSensors/DmpR
-Orthoganaility between inducer A (originally detected by biosensor I) and B (originally detected by biosensor II) were tested in the following manner (Fig. 1). To test the effect of inducer B upon the dose-response curve of inducer A obtained by biosensor I:
-(1) Fluorescence intensity of biosensor I elicited by inducer A of concentration gradient was measured as standard results''' (Fig. 1a, Lane 1)''';
-(2) And fluorescence intensity of biosensor I induced by inducer A of concentration gradient in the presence of a certain concentration of inducer B was measured (Fig. 1a, Lane 2 and 3) and compared with the standard results.
-The effect of inducer A upon the dose-response curve of inducer B obtained by biosensor II was tested vice versa '''(Fig. 1b)'''.
-https://static.igem.org/mediawiki/igem.org/4/45/Peking2013_MAFigure1.jpg
-'''Fig. 1.''' Orthogonality test assay for inducer A (detected by biosensor I) and inducer B (detected by biosensor II). (a) Biosensor I was added into the test assay. Different mixtures of inducers were added into lane 1, 2, and 3 respectively as listed above. Effect of inducer B upon the dose-response curve of inducer A was tested by comparing the fluorescence intensity of biosensor I among lane 1 ,2, and 3. (b) Biosensor II was added into the test assay. Different mixtures of inducers were added into lane 1, 2, and 3 respectively as listed above. Effect of inducer A upon the dose-response curve of inducer B was tested by comparing the fluorescence intensity of biosensor II among lane 1 ,2, and 3.
-We managed to demonstrate the orthogonality among inducers of different biosensors in a more quantitative and visible way. If inducer A and B were orthogonal, the fluorescence intensity should be identical no matter with or without the irrelevant inducer B. That is to say, the ideal experimental points should be aligned in a line whose slope is one.
-The orithogonality of inducers of XylS, NahR, HbpR and DmpR biosensors have been carefully confirmed using the test assay introduced above '''(Fig. 2)'''. The experimental points were processed by linear fitting and the slopes of the fitting curves were compared with 1. The closer the slope was to 1, the more orthogonal the inducers were. The results showed that inducers of biosensor XylS and NahR '''(Fig. 2a, b)''', XylS and HbpR''' (Fig. 2c, d)''', NahR and HbpR '''(Fig. 2e, f)''', XylS and DmpR '''(Fig. 2g, h)''', NahR and DmpR '''(Fig. 2i, j)''', and HbpR and DmpR '''(Fig. 2k, l)''' are all highly orthogonal, which is summarized in '''Fig. 2.'''
-https://static.igem.org/mediawiki/igem.org/c/c7/Peking2013_Figure3ab.jpg
-https://static.igem.org/mediawiki/igem.org/9/96/Peking2013_MAFigure3cd.jpg
-https://static.igem.org/mediawiki/igem.org/4/44/Peking2013_MAFigureef.jpg
-'''Fig. 2.''' Experimental points and the linear fitting curves of the orthogonality test. The black dashed lines are with the slopes of 1, showing as the reference line. The slopes of the experimental fitting curves were showed in the upside portion of the figure, all of them were around 1. These data showed the orthogonality among inducers of 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 experimental points and linear fitting curves of biosensor and its inducers are marked in different colors: XylS in red, NahR in green, HbpR in orange and DmpR in dark cyan.
-== Reference: ==
-[1] Jaspers, M. C., Suske, W. A., Schmid, A., Goslings, D. A., Kohler, H. P. E., & van der Meer, J. R. HbpR, a new member of the XylR/DmpR subclass within the NtrC family of bacterial transcriptional activators, regulates expression of 2-hydroxybiphenyl metabolism in Pseudomonas azelaica HBP1. Journal of bacteriology, (2000).182(2), 405-417.
-[2] Neuwald AF, Aravind L, Spouge JL, Koonin EV AAA+: A class of chaperone-like ATPases associated with the assembly, operation, and disassembly of protein complexes. Genome Res (1999)9: 27–43
-[3] Pe´rez-Martı´n J, de Lorenzo. VATP binding to the s54-dependent activator XylR triggers a protein multimerization cycle catalyzed by UAS DNA. Cell (1996) 86: 331–339
-[4] Jaspers, M. C., Sturme, M., & van der Meer, J. R. Unusual location of two nearby pairs of upstream activating sequences for HbpR, the main regulatory protein for the 2-hydroxybiphenyl degradation pathway of ‘Pseudomonas azelaica’HBP1. Microbiology, (2001).147(8), 2183-2194.
-[5] Jaspers, M. C., Suske, W. A., Schmid, A., Goslings, D. A., Kohler, H. P. E., & van der Meer, J. R.. HbpR, a new member of the XylR/DmpR subclass within the NtrC family of bacterial transcriptional activators, regulates expression of 2-hydroxybiphenyl metabolism in Pseudomonas azelaica HBP1. Journal of bacteriology, (2000)182(2), 405-417.
-[6] Jaspers, M. C., Sturme, M., & van der Meer, J. R. Unusual location of two nearby pairs of upstream activating sequences for HbpR, the main regulatory protein for the 2-hydroxybiphenyl degradation pathway of ‘Pseudomonas azelaica’HBP1. Microbiology, (2001). 147(8), 2183-2194.