jiang y, lee a, chen j, ruta v, cadene m, chait bt, et al...
TRANSCRIPT
![Page 1: Jiang Y, Lee A, Chen J, Ruta V, Cadene M, Chait BT, et al ...2013.igem.org/files/presentation/Hong_Kong_CUHK_Championship.pdfPDZ Domain PDZ Ligand + - + + Polyproline Periplasm Inner](https://reader030.vdocuments.mx/reader030/viewer/2022041122/5d0d161288c993ed388b4e1d/html5/thumbnails/1.jpg)
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2
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Jiang Y, Lee A, Chen J, Ruta V, Cadene M, Chait BT, et al. X-ray structure of a voltage-dependent K+ channel. Nature. 2003 05/01;423(6935):33-41. 3
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PDZ Domain PDZ Ligand
+
-
+ + +
Periplasm
Inner Membrane
Cytosol
Voltage Sensor Peptide
Polyproline Linkers
(GGGGS)3 Linkers
Effectors
+ + + (GGGGS)3 Linkers
Effectors
4
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PDZ Domain PDZ Ligand
+
-
+ + +
Periplasm
Inner Membrane
Cytosol
Voltage Sensor Peptide
Polyproline Linkers
(GGGGS)3 Linkers
Effectors
+ + + (GGGGS)3 Linkers
Effectors
5
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+
-
Periplasm
Inner Membrane
Cytosol
6
+ + +
+ + +
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+
-
7
+ + +
+ + +
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8
+
-
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We have made:
• BBa_K1092006: Voltage Sensor Peptide
Voltage Sensor Peptide RBS
9
180bp
Voltage Sensor Peptide
![Page 10: Jiang Y, Lee A, Chen J, Ruta V, Cadene M, Chait BT, et al ...2013.igem.org/files/presentation/Hong_Kong_CUHK_Championship.pdfPDZ Domain PDZ Ligand + - + + Polyproline Periplasm Inner](https://reader030.vdocuments.mx/reader030/viewer/2022041122/5d0d161288c993ed388b4e1d/html5/thumbnails/10.jpg)
We have made:
• BBa_K1092008:
ssDsbA-PDZ Domain-Voltage Sensor Peptide
• BBa_K1092024:
T7-RBS-ssDsbA-PDZ Domain-VS-RFP C terminus
10
Voltage Sensor Peptide PDZ Domain
Voltage Sensor Peptide PDZ Domain RFP C terminus RBS
![Page 11: Jiang Y, Lee A, Chen J, Ruta V, Cadene M, Chait BT, et al ...2013.igem.org/files/presentation/Hong_Kong_CUHK_Championship.pdfPDZ Domain PDZ Ligand + - + + Polyproline Periplasm Inner](https://reader030.vdocuments.mx/reader030/viewer/2022041122/5d0d161288c993ed388b4e1d/html5/thumbnails/11.jpg)
11
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12
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Acenaphthene Pyrene
Acenaphthylene Fluorene
Anthracene Benzo[a]pyrene
13
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• Found in car exhaust, tar, cooking fume...
Pictures from http://chemistry.about.com/od/factsstructures/ig/Chemical-Structures---B/Benzo-a-pyrene.htm
Benzo[a]pyrene (BaP)
14
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• Benzo[a]pyrene Diol Epoxide
(Carcinogenic!)
Human Body
Pictures from http://en.wikipedia.org/wiki/Benzo(a)pyrene 15
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• Enzymes: Laccase and dioxygenase
– Inspired by a fungal pathway[1]
1. Hadibarata T, Kristanti RA. Identification of metabolites from benzo[a]pyrene oxidation by ligninolytic enzymes of Polyporus sp. S133. J Environ Manage. 2012 11/30;111(0):115-9.
Laccase
Catechol 1,2-Dioxygenase
Benzo[a]pyrene BaP-1,6-quinone 1-Hydroxy-2-naphthoic acid
Dangerous Safe
16
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• BBa_K1092005
– T7 – RBS – Laccase
Laccase RBS
pSB1C3
Laccase (1542bp)
Plasmid Restriction Digestion Gel Photo
1.5kbp
1kbp 750bp
500bp
250bp
100bp
Laccase
Benzo[a]pyrene BaP-1,6-Quinone
17
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• BBa_K1092003
– T7 – RBS - Dioxygenase
Catechol 1,2-Dioxygeanse RBS
pSB1C3
Dioxygen-ase
(936bp)
Plasmid Restriction Digestion Gel Photo
1kbp 750bp
500bp
250bp
100bp
Catechol 1,2- Dioxygenase
BaP-1,6-Quinone 1-Hydroxy-2-naphthoic acid
18
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WT
T7-Laccase
0.00
0.05
0.10
0.15
0.20
**
OD
398
Control T7 – Laccase
OD
38
9 V
alu
e [1
]
n = 3 p ≤ 0.01
1. Method from: Ramesh A, Archibong AE, Niaz MS. Ovarian susceptibility to benzo[a]pyrene: tissue burden of metabolites and DNA adducts in F-344 rats. Journal of Toxicology and Environmental Health, Part A. 2010 10/28; 2013/10;73(23):1611-25. 19
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0 40 80 1200.0
0.1
0.2
0.3EV
T7-Dioxygenase
Time / min
No
rmali
zed
OD
298
n = 3 p ≤ 0.05
1. Method from: Huang Y, Xun R, Chen G, Xun L. Maintenance role of a glutathionyl-hydroquinone lyase (PcpF) in pentachlorophenol degradation by Sphingobium chlorophenolicum ATCC 39723. Journal of Bacteriology. 2008 December 01;190(23):7595-600.
[1]
20
Control
T7-Dioxygenase
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• Repressor: QsrR
– Quinone-mediated transcriptional repressor[1]
1. Ji Q, Zhang L, Jones MB, Sun F, Deng X, Liang H, et al. Molecular mechanism of quinone signaling mediated through S-quinonization of a YodB family repressor QsrR. Proceedings of the National Academy of Sciences. 2013 March 26;110(13):5010-5.
Cy
s-5
QsrR
QsrR Binding Site Downstream Genes (Regulated by QsrR)
Quinone
Cy
s-5
QsrR
mRNA
21
BaP-1,6-quinone
![Page 22: Jiang Y, Lee A, Chen J, Ruta V, Cadene M, Chait BT, et al ...2013.igem.org/files/presentation/Hong_Kong_CUHK_Championship.pdfPDZ Domain PDZ Ligand + - + + Polyproline Periplasm Inner](https://reader030.vdocuments.mx/reader030/viewer/2022041122/5d0d161288c993ed388b4e1d/html5/thumbnails/22.jpg)
• Biobricks
– BBa_K1092001: T7–RBS–QsrR
– BBa_K1092014: Constitutive Promoter (BBa_J23100)–RBS–QsrR Bind Site–Dioxygenase
Catechol 1,2-Dioxygenase
QsrR Binding Site
RBS
QsrR RBS
pSB1C3
QsrR (339bp)
Plasmid Restriction Digestion Gel Photo
1kbp
750bp
500bp
250bp
100bp
22
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QsrR Binding Site RBS PDZ
Domain Voltage Sensor
Peptide Dioxygenase
23
RBS PDZ Ligand
Voltage Sensor Peptide
Laccase
Laccase
Catechol 1,2-Dioxygenase
Benzo[a]pyrene BaP-1,6-quinone 1-Hydroxy-2-naphthoic acid
![Page 24: Jiang Y, Lee A, Chen J, Ruta V, Cadene M, Chait BT, et al ...2013.igem.org/files/presentation/Hong_Kong_CUHK_Championship.pdfPDZ Domain PDZ Ligand + - + + Polyproline Periplasm Inner](https://reader030.vdocuments.mx/reader030/viewer/2022041122/5d0d161288c993ed388b4e1d/html5/thumbnails/24.jpg)
+
-
Arai R, Ueda H, Kitayama A, Kamiya N, Nagamune T. Design of the linkers which effectively separate domains of a bifunctional fusion protein. Protein Engineering. 2001 August 01;14(8):529-32. 24
+ + +
+ + +
Laccase Dioxygenase
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Arai R, Ueda H, Kitayama A, Kamiya N, Nagamune T. Design of the linkers which effectively separate domains of a bifunctional fusion protein. Protein Engineering. 2001 August 01;14(8):529-32. 25
+
-
Laccase Dioxygenase
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BBa_K1092000 QsrR
BBa_K1092001 T7-RBS-QsrR
BBa_K1092002 Dioxygenase
BBa_K1092003 T7-RBS-Dioxygenase
BBa_K1092004 Laccase
BBa_K1092005 T7-RBS-Laccase
BBa_K1092006 Voltage Sensor Peptide
BBa_K1092007 ssDsbA-PDZ Ligand-Voltage Sensor Peptide
BBa_K1092008 ssDsbA-PDZ Domain-Voltage Sensor Peptide
BBa_K1092013 T7-RBS-Voltage Sensor Peptide
BBa_K1092014 T7-QsrR Binding Site-RBS-Dioxygenase
BBa_K1092024 pSB1C3-T7-RBS-ssDsbA-PDZ Domain-Voltage Switch-RFP C terminus
BBa_K1092105 RFP N terminus
BBa_K1092106 RFP C terminus 26
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QsrR Binding Site RBS PDZ
Domain Voltage Sensor
Peptide Dioxygenase
RBS PDZ Ligand
Voltage Sensor Peptide
Laccase
27
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28
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• Biomolecular Fluorescent Complementation (BiFC).
• Fluorescent proteins were splited at loop regions at DNA level, and coexpressed. A few fluorescent signals are found.
• Fluorescent signals are enhanced when linked to interacting proteins pair.
• Used widely to study protein-protein interaction.
• No documented reversible BiFC up until now.
Kodama, Y. & Hu, C.-D. BioTechniques. 53, 285–98 (2012). 29
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Promoter RBS PDZ domain PDZ ligand Voltage
sensor peptide
Voltage sensor peptide
RFP-N terminus RFP-C terminus
Terminator
1 s 1 s 1 s
30
- +
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• BiFC
• Target protein to the corresponding membrane (e.g. ER, Golgi)
• The system works on its own base on the native membrane potential
31
RBS PDZ domain PDZ ligand Voltage sensor peptide
Voltage sensor peptide
RFP-N terminus RFP-C terminus
Terminator
Promoter
Signaling peptide
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Adapted from: Huang, L. J. et al. The Journal of cell biology 145, 951–9 (1999).
33
+
+
-
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Voltage Switch
Reversible BiFC
DegradeCellular Content
Bacterial Screen
Biosafety Control
Study Protein
Complements
Much More
34
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35
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Others* = Australia, Austria, Belgium, Canada, China, Denmark, England, Finland, France, Germany, Hong Kong, India, Indonesia, South Korea, Malaysia, Mexico, Russia, Singapore, South Africa, Taiwan, Thailand, The Netherlands, Ukraine, USA, Vietnam 36
CUHK
Human Practice
International
Macau
(60 students)
Lab Workshop
Synthetic Biology Talk
Survey
Others*
(110 students)
Survey
Local
High School
(135+234students)
Lab Workshop
Synthetic Biology Talk
Survey
Open Day
Undergraduate Students
(110 students)
Poster Exhibition
Survey
![Page 37: Jiang Y, Lee A, Chen J, Ruta V, Cadene M, Chait BT, et al ...2013.igem.org/files/presentation/Hong_Kong_CUHK_Championship.pdfPDZ Domain PDZ Ligand + - + + Polyproline Periplasm Inner](https://reader030.vdocuments.mx/reader030/viewer/2022041122/5d0d161288c993ed388b4e1d/html5/thumbnails/37.jpg)
37
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Interesting 30%
Useful 31%
Interesting and Useful
23%
Neither good or bad 11%
Dangerous 5%
38
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0%
10%
20%
30%
40%
50%
60%
70%
iGEMonly
SyntheticBiology
only
Both Neither
Pe
rce
nta
ge
of
Re
spo
nd
en
ts
High School Students (Hong Kong) High School Students (Macau)
University Students (Hong Kong) University Students (International)
39
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3.71 3.84
0
1
2
3
4
5
Believers Non Believers
3.37 3.62
0
1
2
3
4
5
Believers Non Believers
Me
an
De
gre
e o
f A
cce
pta
bil
ity
40
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41
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iGEM only 11%
Synthetic Biology
9%
Both 66%
Neither 14%
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Yes 95%
No 5%
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• Comics convey message about iGEM and synthetic biology well
• Views on synthetic biology directly relates to religion’s view
• Many agree that synthetic biology will be an integral part of knowledge-based economy
• Future Plan: – Wider outreach and full detailed comics in English
and Chinese languages
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• Research Group of Prof. CHAN King Ming
• Research Group of Prof. CHAN Ting Fung
• Research Group of Prof. NGO Chi Ki, Jacky
• Prof. KONG Siu Kai • Prof. GE Wei • Prof. JIANG Liwen • Jacky Loo • Qin Hao • Sunny • Nelson So
• School of Life Sciences, CUHK • School of Biomedical
Engineering, CUHK • University Safety Office,
CUHK • Shanghai Jiao Tong
University
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Hadibarata T, Kristanti RA. Identification of metabolites from benzo[a]pyrene oxidation by ligninolytic enzymes of Polyporus sp. S133. J Environ Manage. 2012 11/30;111(0):115-9.
Huang Y, Xun R, Chen G, Xun L. Maintenance role of a glutathionyl-hydroquinone lyase (PcpF) in pentachlorophenol degradation by Sphingobium chlorophenolicum ATCC 39723. Journal of Bacteriology. 2008 December 01;190(23):7595-600.
Ji Q, Zhang L, Jones MB, Sun F, Deng X, Liang H, et al. Molecular mechanism of quinone signaling mediated through S-quinonization of a YodB family repressor QsrR. Proceedings of the National Academy of Sciences. 2013 March 26;110(13):5010-5.
Jiang Y, Lee A, Chen J, Ruta V, Cadene M, Chait BT, et al. X-ray structure of a voltage-dependent K+ channel. Nature. 2003 05/01;423(6935):33-41.
Kodama Y and Hu CD. Bimolecular fluorescence complementation (BiFC): A 5-year update and future perspectives. BioTechniques. 2012 November; 53(5): 285-298.
Ramesh A, Archibong AE, Niaz MS. Ovarian susceptibility to benzo[a]pyrene: tissue burden of metabolites and DNA adducts in F-344 rats. Journal of Toxicology and Environmental Health, Part A. 2010 10/28; 2013/10;73(23):1611-25.
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