Team:SJTU-BioX-Shanghai/Project/project2.3

From 2012.igem.org

(Difference between revisions)
(→Membrane Accelerator - PAH degradation & DBT desulfurization)
(→Membrane Accelerator - PAH degradation & DBT desulfurization)
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To accelerate desulfurization of Dibenzothiophene (DBT)  
To accelerate desulfurization of Dibenzothiophene (DBT)  
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To show the superiority of membrane scaffold in organizing enzymes in two dimensional pattern  
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To show the superiority of membrane scaffold in organizing enzymes into two dimensional pattern  
*'''Achievements'''
*'''Achievements'''
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===Background===
===Background===
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Polycyclic aromatic hydrocarbons (PAHs), which consist of two or more fused aromatic rings, are widespread in the environment and persist for a very long time. Some PAHs are toxic, mutagenic and carcinogenic and therefore are health hazards. Efforts have been made to screen bacteria strains that could degrade PAH. Moreover, many researchers focused on studying the mechanism of PAH biodegradation. But the rate of natural biodegradation is relatively slow. Team SJTU-BioX-Shanghai is trying to build a Membrane Accelerator to speed up biodegradation rate of PAH biodegradation process. Naphthalene degradation pathway in Pseudomonas species is well studied and thus recruited in our project to build Membrane Accelerator for PAH biodegradation.
+
Polycyclic aromatic hydrocarbons (PAHs), which consist of two or more fused aromatic rings, are widespread in the environment and persist for a very long time. Some PAHs are toxic, mutagenic and carcinogenic and therefore are health hazards. Efforts have been made to screen bacteria strains that could degrade PAH. Moreover, many researchers focused on studying the mechanism of PAH biodegradation. But the rate of natural biodegradation is relatively slow. We are trying to build a Membrane Accelerator to speed up proceeding rate of PAH biodegradation process. Naphthalene degradation pathway in ''Pseudomonas'' species is well studied and thus recruited in our project to build PAH-degrading ''Membrane Accelerator''. This is the very first time that scaffold system has been applied in accelerating Biodegradation pathway.
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=== Degradation Pathway===
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== Degradation Pathway==
We recruited naphthalene degradation pathway in ''Pseudomonas'' species, which has been well characterized. Six crucial enzymes are involved in naphthalene degradation pathway.
We recruited naphthalene degradation pathway in ''Pseudomonas'' species, which has been well characterized. Six crucial enzymes are involved in naphthalene degradation pathway.
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In the first catabolic step, an oxygen molecule is introduced at the 1,2-position of the aromatic nucleus to produce cis-1,2-dihydroxy-1,2-dihydronaphthalene by naphthalene dihydrodiol dioxygenase(NahA). cis-1,2-Dihydroxy-1,2-dihydronaphthalene is then dehydrogenated to 1,2-dihydroxynaphthalene by cis-naphthalene dihydrodiol dehydrogenase(NahB). 1,2-Dihydroxynaphthalene is cleaved by 1,2-dihydroxynaphthalene dioxygenase(NahC), and the resulting ring-cleavage product spontaneously cyclizes to form 2-hydroxy-2H-chromene-2-carboxylic acid. Enzymatic reactions by an isomerase(NahD) and a hydratase-aldolase(NahE) result in the production of salicylaldehyde, which is then transformed to salicylate by salicyladehyde dehydrogenase(NahF).
In the first catabolic step, an oxygen molecule is introduced at the 1,2-position of the aromatic nucleus to produce cis-1,2-dihydroxy-1,2-dihydronaphthalene by naphthalene dihydrodiol dioxygenase(NahA). cis-1,2-Dihydroxy-1,2-dihydronaphthalene is then dehydrogenated to 1,2-dihydroxynaphthalene by cis-naphthalene dihydrodiol dehydrogenase(NahB). 1,2-Dihydroxynaphthalene is cleaved by 1,2-dihydroxynaphthalene dioxygenase(NahC), and the resulting ring-cleavage product spontaneously cyclizes to form 2-hydroxy-2H-chromene-2-carboxylic acid. Enzymatic reactions by an isomerase(NahD) and a hydratase-aldolase(NahE) result in the production of salicylaldehyde, which is then transformed to salicylate by salicyladehyde dehydrogenase(NahF).
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=== Design===
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=== Design of Experiment===
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To test whether Membrane Accelerator could accelerate naphthalene biodegradation pathway, we are trying to link six enzymes in this pathway to orderly organized membrane anchor and expressed them in ''E.coli''. ''E.coli'' expressing the same type and amount of cytoplasmic enzymes is set as control group.
+
To test whether Membrane Accelerator could accelerate naphthalene biodegradation pathway, we are trying to link six crucial enzymes (NahA, B, C, D and E) to orderly organized membrane anchors and expressed them in ''E.coli''. ''E.coli'' expressing the same type and amount of cytoplasmic enzymes is set as control group.
[[File:12SJTU_PAHconstruction.png|thumb|600px|center|Demonstration of Membrane Accelerator designed for speeding naphthalene biodegradation process]]
[[File:12SJTU_PAHconstruction.png|thumb|600px|center|Demonstration of Membrane Accelerator designed for speeding naphthalene biodegradation process]]
==Biodesulfurization of Dibenzothiophene (DBT) ==
==Biodesulfurization of Dibenzothiophene (DBT) ==
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===Background===
===Background===
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We found that many iGEM teams wanted to express enzymes of biodegradation pathway in ''E.coli''. However, it doesn't have significant superiority compared to traditional strain screening. The power of synthetic biology is not fully demonstrated here.  
+
We found that many iGEM teams wanted to express enzymes of biodegradation pathway in ''E.coli''. However, it doesn't have significant superiority compared to traditional strain screening strategy. The power of synthetic biology is not fully demonstrated here.  
We got inspired by project of 2012 iGEM team Calgary. One of their goals is to achieve desulfuration of dibenzothiophene in ''E.coli''. To improve the system, we aimed to link those enzymes to orderly organized membrane anchors, which would enhance desulfurization pathway remarkably.  
We got inspired by project of 2012 iGEM team Calgary. One of their goals is to achieve desulfuration of dibenzothiophene in ''E.coli''. To improve the system, we aimed to link those enzymes to orderly organized membrane anchors, which would enhance desulfurization pathway remarkably.  
Sulfur in crude oil could contribute to global warming, acid rain, and various health issues. Biodesulfurization of fossil fuel could help upgrade the quality of fossil fuel and thus the whole environment.
Sulfur in crude oil could contribute to global warming, acid rain, and various health issues. Biodesulfurization of fossil fuel could help upgrade the quality of fossil fuel and thus the whole environment.
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For more information, click [https://2012.igem.org/Team:Calgary/Project/OSCAR/Desulfurization  Wiki of team Calgary]
For more information, click [https://2012.igem.org/Team:Calgary/Project/OSCAR/Desulfurization  Wiki of team Calgary]
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=== Design===
+
=== Design of Experiment===
We are trying to link DszA, DszB, DszC and DszD to orderly organized membrane anchor to accelerate Desulfurization process in ''E.coli''. Due to decreased distance between those enzymes, the proceeding speed could increase sharply.
We are trying to link DszA, DszB, DszC and DszD to orderly organized membrane anchor to accelerate Desulfurization process in ''E.coli''. Due to decreased distance between those enzymes, the proceeding speed could increase sharply.

Revision as of 10:20, 26 October 2012

Membrane Accelerator - PAH degradation & DBT desulfurization

  • State of the art

Natural biodegradation is a very slow process but indispensible in environment restoration. Previous synthetic scaffold system has been used to accelerate biosynthetic pathway. This year, iGEM team SJTU-BioX-Shanghai is trying for the first time to recruit scaffold system to accelerate biodegradation pathway. It offered a new direction in the application of synthetic scaffold system.

  • Aims

To testify the feasibility of Membrane Accelerator in Biodegradation Pathway

To accelerate degradation of Polycyclic Aromatic Hydrocarbon (PAH)

To accelerate desulfurization of Dibenzothiophene (DBT)

To show the superiority of membrane scaffold in organizing enzymes into two dimensional pattern

  • Achievements

We proposed a novel concept to apply scaffold system in facilitating biodegradation pathway

We selected two well-studied biodegradation pathways, which could potentially benefit environment restoration

Biodegradation of Polycyclic Aromatic Hydrocarbon (PAH)

Background

Polycyclic aromatic hydrocarbons (PAHs), which consist of two or more fused aromatic rings, are widespread in the environment and persist for a very long time. Some PAHs are toxic, mutagenic and carcinogenic and therefore are health hazards. Efforts have been made to screen bacteria strains that could degrade PAH. Moreover, many researchers focused on studying the mechanism of PAH biodegradation. But the rate of natural biodegradation is relatively slow. We are trying to build a Membrane Accelerator to speed up proceeding rate of PAH biodegradation process. Naphthalene degradation pathway in Pseudomonas species is well studied and thus recruited in our project to build PAH-degrading Membrane Accelerator. This is the very first time that scaffold system has been applied in accelerating Biodegradation pathway.

Degradation Pathway

We recruited naphthalene degradation pathway in Pseudomonas species, which has been well characterized. Six crucial enzymes are involved in naphthalene degradation pathway.

Demonstration of naphthalene degradation pathway in Pseudomonas species

In the first catabolic step, an oxygen molecule is introduced at the 1,2-position of the aromatic nucleus to produce cis-1,2-dihydroxy-1,2-dihydronaphthalene by naphthalene dihydrodiol dioxygenase(NahA). cis-1,2-Dihydroxy-1,2-dihydronaphthalene is then dehydrogenated to 1,2-dihydroxynaphthalene by cis-naphthalene dihydrodiol dehydrogenase(NahB). 1,2-Dihydroxynaphthalene is cleaved by 1,2-dihydroxynaphthalene dioxygenase(NahC), and the resulting ring-cleavage product spontaneously cyclizes to form 2-hydroxy-2H-chromene-2-carboxylic acid. Enzymatic reactions by an isomerase(NahD) and a hydratase-aldolase(NahE) result in the production of salicylaldehyde, which is then transformed to salicylate by salicyladehyde dehydrogenase(NahF).

Design of Experiment

To test whether Membrane Accelerator could accelerate naphthalene biodegradation pathway, we are trying to link six crucial enzymes (NahA, B, C, D and E) to orderly organized membrane anchors and expressed them in E.coli. E.coli expressing the same type and amount of cytoplasmic enzymes is set as control group.

Demonstration of Membrane Accelerator designed for speeding naphthalene biodegradation process

Biodesulfurization of Dibenzothiophene (DBT)

Background

We found that many iGEM teams wanted to express enzymes of biodegradation pathway in E.coli. However, it doesn't have significant superiority compared to traditional strain screening strategy. The power of synthetic biology is not fully demonstrated here. We got inspired by project of 2012 iGEM team Calgary. One of their goals is to achieve desulfuration of dibenzothiophene in E.coli. To improve the system, we aimed to link those enzymes to orderly organized membrane anchors, which would enhance desulfurization pathway remarkably. Sulfur in crude oil could contribute to global warming, acid rain, and various health issues. Biodesulfurization of fossil fuel could help upgrade the quality of fossil fuel and thus the whole environment.

Desulfurization Pathway

Four enzymes are involved in Desulfurization pathway. Dibenzothiophene monooxygenase (DszC) is responsible for converting DBT to DBT-sulfoxide and finally to DBT-sulfone (DBTO2). DBT-sulfone monooxygenase (DszA) then carries out the next step in the pathway, producing 2-hydroxybiphenyl-2-sulfinic acid (HBPS). HBPS is then converted to the final product by HBPS desulfinase (DszB), producing 2-HBP. The sulfur is released from the hydrocarbon in the form of sulfite. Oxidoreductase (DszD) uses NADH to recycle the FMNH2, allowing the whole reaction to proceed.

The 4S Desulfurization Pathway, showing the desulfurization of the model compound DBT by DszA, DszB, DszC, and DszD. Credits to 2012 iGEM team Calgary

For more information, click Wiki of team Calgary

Design of Experiment

We are trying to link DszA, DszB, DszC and DszD to orderly organized membrane anchor to accelerate Desulfurization process in E.coli. Due to decreased distance between those enzymes, the proceeding speed could increase sharply.


Reference

1.Habe, H. and T. Omori (2003). "Genetics of polycyclic aromatic hydrocarbon metabolism in diverse aerobic bacteria." Bioscience, biotechnology, and biochemistry 67(2): 225-243.



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